# HG changeset patch
# User artbio
# Date 1555267424 14400
# Node ID 376fae7c9f32562be1d6e2aa1b8c6d5d5946e6bd
# Parent  07aa8f928d4b477d6920c54530e24f0905c058ba
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 32eba59fa52705ae74fd9fe65f6f55be783bfc74

diff -r 07aa8f928d4b -r 376fae7c9f32 small_rna_maps.py
--- a/small_rna_maps.py	Wed Apr 10 06:38:33 2019 -0400
+++ b/small_rna_maps.py	Sun Apr 14 14:43:44 2019 -0400
@@ -11,9 +11,9 @@
     the_parser.add_argument('--inputs', dest='inputs', required=True,
                             nargs='+', help='list of input BAM files')
     the_parser.add_argument('--minsize', dest='minsize', type=int,
-                            default=0, help='minimal size of reads')
+                            default=19, help='minimal size of reads')
     the_parser.add_argument('--maxsize', dest='maxsize', type=int,
-                            default=10000, help='maximal size of reads')
+                            default=29, help='maximal size of reads')
     the_parser.add_argument('--cluster', dest='cluster', type=int,
                             default=0, help='clustering distance')
     the_parser.add_argument('--sample_names', dest='sample_names',
@@ -63,12 +63,11 @@
         self.bam_object = pysam.AlignmentFile(bam_file, 'rb')
         self.chromosomes = dict(zip(self.bam_object.references,
                                 self.bam_object.lengths))
-        self.map_dict = self.create_map(self.bam_object, self.minsize,
-                                        self.maxsize, self.nostrand)
+        self.map_dict = self.create_map(self.bam_object, self.nostrand)
         if self.cluster:
             self.map_dict = self.tile_map(self.map_dict, self.cluster)
 
-    def create_map(self, bam_object, minsize, maxsize, nostrand=False):
+    def create_map(self, bam_object, nostrand=False):
         '''
         Returns a map_dictionary {(chromosome,read_position,polarity):
                                                     [read_length, ...]}
@@ -294,16 +293,12 @@
         out is an *open* file handler
         '''
         for chrom in sorted(sizedic):
-            sizes = sizedic[chrom]['F'].keys()
-            sizes.extend(sizedic[chrom]['R'].keys())
+            sizes = range(self.minsize, self.maxsize+1)
             strandness = defaultdict(int)
             sizeness = defaultdict(int)
             for polarity in sizedic[chrom]:
-                for size in range(min(sizes), max(sizes)+1):
-                    try:
-                        strandness[polarity] += sizedic[chrom][polarity][size]
-                    except KeyError:
-                        pass
+                for size in sizes:
+                    strandness[polarity] += sizedic[chrom][polarity][size]
                     sizeness[size] += sizedic[chrom][polarity][size]
             Strandbias = strandness['F'] + strandness['R']
             if Strandbias:
@@ -318,7 +313,7 @@
                 else:
                     sizeness[size] = 0
             for polarity in sorted(sizedic[chrom]):
-                for size in range(min(sizes), max(sizes)+1):
+                for size in sizes:
                     try:
                         line = [self.sample_name, chrom, polarity, size,
                                 sizedic[chrom][polarity][size],
diff -r 07aa8f928d4b -r 376fae7c9f32 small_rna_maps.xml
--- a/small_rna_maps.xml	Wed Apr 10 06:38:33 2019 -0400
+++ b/small_rna_maps.xml	Sun Apr 14 14:43:44 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="small_rna_maps" name="small_rna_maps" version="2.13.0">
+<tool id="small_rna_maps" name="small_rna_maps" version="2.13.1">
   <description></description>
   <requirements>
         <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
@@ -81,9 +81,9 @@
     <param name="normalization" type="text" label="Enter a size/normalization factor."
         help="Enter normalisation factors separated by space eg [0.75 1.23 1.1], no normalization if no values" value="1"/>
     <param name="minsize" type="integer" label="Minimal size of reads for inclusion in analysis"
-           value="0" help="default value: 0" />
+           value="19" help="default value: 19" />
     <param name="maxsize" type="integer" label="Maximal size of reads for inclusion in analysis"
-           value="10000" help="default value: 10000" />
+           value="29" help="default value: 29" />
     <conditional name="plots_options">
         <param name="plots_options_selector" type="select" display="radio" label="Plot Options">
             <option value="one_plot">Just one plot per chromosome</option>
@@ -164,8 +164,6 @@
         <test> <!-- 0 -->
             <param name="inputs" value="input1.bam,input_new2.bam" ftype="bam" />
             <param name="normalization" value="1 2" />
-            <param name="minsize" value="0" />
-            <param name="maxsize" value="10000" />
             <param name="plots_options_selector" value="one_plot" />
             <param name="first_plot" value="Counts" />
             <output file="input1_input2new_norm_1_2_counts.tab" name="output_tab" />
@@ -174,8 +172,6 @@
         <test> <!-- 1 -->
             <param name="inputs" value="input1.bam" ftype="bam" />
             <param name="normalization" value="1.0" />
-            <param name="minsize" value="0" />
-            <param name="maxsize" value="10000" />
             <param name="ylimits" value="yes" />
             <param name="ymin" value="-5" />
             <param name="ymax" value="5" />
@@ -187,8 +183,6 @@
         <test> <!-- 2 -->
             <param name="inputs" value="input1.bam" ftype="bam" />
             <param name="normalization" value="1.0" />
-            <param name="minsize" value="0" />
-            <param name="maxsize" value="10000" />
             <param name="plots_options_selector" value="cluster" />
             <param name="first_plot" value="Counts" />
             <param name="cluster" value="5" />
@@ -201,8 +195,6 @@
         <test> <!-- 3 -->
             <param name="inputs" value="input1.bam" ftype="bam" />
             <param name="normalization" value="1.0" />
-            <param name="minsize" value="0" />
-            <param name="maxsize" value="10000" />
             <param name="plots_options_selector" value="cluster" />
             <param name="first_plot" value="Counts" />
             <param name="cluster" value="5" />
@@ -215,8 +207,6 @@
         <test> <!-- 4 -->
             <param name="inputs" value="input1.bam" ftype="bam" />
             <param name="normalization" value="1.0" />
-            <param name="minsize" value="0" />
-            <param name="maxsize" value="10000" />
             <param name="plots_options_selector" value="cluster" />
             <param name="first_plot" value="Counts" />
             <param name="cluster" value="5" />
@@ -229,8 +219,6 @@
         <test> <!-- 5 -->
             <param name="inputs" value="input1.bam" ftype="bam" />
             <param name="normalization" value="1.0" />
-            <param name="minsize" value="0" />
-            <param name="maxsize" value="10000" />
             <param name="plots_options_selector" value="cluster" />
             <param name="first_plot" value="Counts" />
             <param name="cluster" value="5" />
@@ -245,8 +233,6 @@
         <test> <!-- 6 -->
             <param name="inputs" value="input1.bam" ftype="bam" />
             <param name="normalization" value="1.0" />
-            <param name="minsize" value="0" />
-            <param name="maxsize" value="10000" />
             <param name="plots_options_selector" value="cluster" />
             <param name="first_plot" value="Counts" />
             <param name="cluster" value="5" />
@@ -261,8 +247,6 @@
         <test> <!-- 7 -->
             <param name="inputs" value="input1.bam" ftype="bam" />
             <param name="normalization" value="1.0" />
-            <param name="minsize" value="20" />
-            <param name="maxsize" value="30" />
             <param name="plots_options_selector" value="one_plot" />
             <param name="first_plot" value="Size" />
             <output file="input1_min20_max30_size.tab" name="output_tab" />
@@ -271,8 +255,6 @@
         <test> <!-- 8 -->
             <param name="inputs" value="input1.bam" ftype="bam" />
             <param name="normalization" value="1.0" />
-            <param name="minsize" value="0" />
-            <param name="maxsize" value="10000" />
             <param name="plots_options_selector" value="one_plot" />
             <param name="first_plot" value="Mean" />
             <output file="input1_mean.tab" name="output_tab" />
@@ -281,8 +263,6 @@
         <test> <!-- 9 -->
             <param name="inputs" value="input1.bam" ftype="bam" />
             <param name="normalization" value="1.0" />
-            <param name="minsize" value="0" />
-            <param name="maxsize" value="10000" />
             <param name="plots_options_selector" value="one_plot" />
             <param name="first_plot" value="Median" />
             <output file="input1_median.tab" name="output_tab" />
@@ -291,8 +271,6 @@
         <test> <!-- 10 -->
             <param name="inputs" value="input1.bam,input2.bam" ftype="bam" />
             <param name="normalization" value="1.0 2.0" />
-            <param name="minsize" value="0" />
-            <param name="maxsize" value="10000" />
             <param name="plots_options_selector" value="one_plot" />
             <param name="first_plot" value="Counts" />
             <output file="input1_input2_norm_1_2_counts.tab" name="output_tab" />
@@ -301,8 +279,6 @@
         <test> <!-- 11 -->
             <param name="inputs" value="input1.bam,input2.bam" ftype="bam" />
             <param name="normalization" value="1.0 1.0" />
-            <param name="minsize" value="0" />
-            <param name="maxsize" value="10000" />
             <param name="ylimits" value="yes" />
             <param name="ymin" value="-5" />
             <param name="ymax" value="5" />
@@ -316,8 +292,6 @@
         <test> <!-- 12 -->
             <param name="inputs" value="input_single_chr.bam,input_single_chr.bam,input_single_chr.bam,input_single_chr.bam,input_single_chr.bam,input_single_chr.bam" ftype="bam" />
             <param name="normalization" value="1.0 1.0 1.0 1.0 1.0 1.0" />
-            <param name="minsize" value="0" />
-            <param name="maxsize" value="10000" />
             <param name="plots_options_selector" value="one_plot" />
             <param name="first_plot" value="Coverage" />
             <output file="input_single_chr_x_6_single_plot_coverage.tab" name="output_tab" />
@@ -326,8 +300,6 @@
         <test> <!-- 13 -->
             <param name="inputs" value="input1.bam,input2.bam" ftype="bam" />
             <param name="normalization" value="1.0 1.0" />
-            <param name="minsize" value="0" />
-            <param name="maxsize" value="10000" />
             <param name="plots_options_selector" value="global" />
             <param name="mergestrands" value="nomerge" />
             <param name="first_plot" value="Size" />
@@ -337,8 +309,6 @@
         <test> <!-- 14 -->
             <param name="inputs" value="input1.bam,input2.bam" ftype="bam" />
             <param name="normalization" value="1.0 1.0" />
-            <param name="minsize" value="0" />
-            <param name="maxsize" value="10000" />
             <param name="plots_options_selector" value="global" />
             <param name="mergestrands" value="merge" />
             <param name="first_plot" value="Size" />
diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/bed1.bed
--- a/test-data/bed1.bed	Wed Apr 10 06:38:33 2019 -0400
+++ b/test-data/bed1.bed	Sun Apr 14 14:43:44 2019 -0400
@@ -1,84 +1,55 @@
-FBtr0070001	0	17	cluster_1	1	+	0.0588235294118
-FBtr0070001	6	33	cluster_2	14	+	0.518518518519
-FBtr0070001	26	53	cluster_3	42	+	1.55555555556
-FBtr0070533	0	15	cluster_4	1	+	0.0666666666667
-FBtr0070533	11	55	cluster_5	23	+	0.522727272727
-FBtr0070603	0	62	cluster_6	68	+	1.09677419355
-FBtr0070603	50	71	cluster_7	2	+	0.0952380952381
-FBtr0070604	0	15	cluster_8	1	+	0.0666666666667
-FBtr0070604	17	40	cluster_9	2	+	0.0869565217391
-FBtr0070604	29	53	cluster_10	36	+	1.5
-FBtr0070604	56	71	cluster_11	1	+	0.0666666666667
-FBtr0070911	14	35	cluster_12	1	+	0.047619047619
-FBtr0070911	37	52	cluster_13	1	+	0.0666666666667
-FBtr0078490	12	32	cluster_14	4	+	0.2
-FBtr0078490	24	50	cluster_15	3	+	0.115384615385
-FBtr0078490	37	55	cluster_16	1	+	0.0555555555556
-FBtr0078580	0	47	cluster_17	1102	+	23.4468085106
-FBtr0078580	51	68	cluster_18	2	+	0.117647058824
-FBtr0078790	0	19	cluster_19	1	+	0.0526315789474
-FBtr0078790	16	32	cluster_20	2	+	0.125
-FBtr0078790	32	55	cluster_21	1	+	0.0434782608696
-FBtr0078790	41	71	cluster_22	9	+	0.3
-FBtr0078790	54	69	cluster_23	1	-	0.0666666666667
-FBtr0079064	0	23	cluster_24	2	+	0.0869565217391
-FBtr0079064	32	47	cluster_25	1	+	0.0666666666667
-FBtr0079064	51	68	cluster_26	1	+	0.0588235294118
-FBtr0079090	0	28	cluster_27	2	+	0.0714285714286
-FBtr0079090	25	49	cluster_28	1	+	0.0416666666667
-FBtr0079090	32	48	cluster_29	1	+	0.0625
-FBtr0079090	52	70	cluster_30	1	+	0.0555555555556
-FBtr0079090	35	56	cluster_31	1	-	0.047619047619
-FBtr0079338	11	31	cluster_32	5	+	0.25
-FBtr0079338	24	40	cluster_33	1	+	0.0625
-FBtr0079338	41	63	cluster_34	10	+	0.454545454545
-FBtr0079528	0	38	cluster_35	97	+	2.55263157895
-FBtr0079528	27	43	cluster_36	1	+	0.0625
-FBtr0079528	34	54	cluster_37	3	+	0.15
-FBtr0079528	50	65	cluster_38	5	+	0.333333333333
-FBtr0079596	0	33	cluster_39	148	+	4.48484848485
-FBtr0079596	52	73	cluster_40	4	+	0.190476190476
-FBtr0079677	0	23	cluster_41	2	+	0.0869565217391
-FBtr0079677	51	70	cluster_42	2	+	0.105263157895
-FBtr0079690	0	15	cluster_43	1	+	0.0666666666667
-FBtr0079690	21	51	cluster_44	2	+	0.0666666666667
-FBtr0079690	32	49	cluster_45	2	+	0.117647058824
-FBtr0079692	0	23	cluster_46	3	+	0.130434782609
-FBtr0079692	17	35	cluster_47	1	+	0.0555555555556
-FBtr0079692	24	41	cluster_48	1	+	0.0588235294118
-FBtr0079692	31	51	cluster_49	1	+	0.05
-FBtr0079693	0	24	cluster_50	5	+	0.208333333333
-FBtr0079693	24	47	cluster_51	1	+	0.0434782608696
-FBtr0079694	0	25	cluster_52	5	+	0.2
-FBtr0079694	17	36	cluster_53	1	+	0.0526315789474
-FBtr0079694	51	68	cluster_54	1	+	0.0588235294118
-FBtr0079702	0	15	cluster_55	1	+	0.0666666666667
-FBtr0079702	18	36	cluster_56	2	+	0.111111111111
-FBtr0079702	55	70	cluster_57	1	+	0.0666666666667
-FBtr0079728	0	17	cluster_58	2	+	0.117647058824
-FBtr0079728	7	27	cluster_59	1	+	0.05
-FBtr0079728	18	42	cluster_60	1	+	0.0416666666667
-FBtr0079728	32	49	cluster_61	3	+	0.176470588235
-FBtr0079728	55	70	cluster_62	1	+	0.0666666666667
-FBtr0079729	0	15	cluster_63	1	+	0.0666666666667
-FBtr0079729	12	34	cluster_64	1	+	0.0454545454545
-FBtr0079729	51	72	cluster_65	2	+	0.0952380952381
-FBtr0079752	0	24	cluster_66	2	+	0.0833333333333
-FBtr0079752	6	27	cluster_67	2	+	0.0952380952381
-FBtr0079752	32	49	cluster_68	2	+	0.117647058824
-FBtr0079752	51	71	cluster_69	2	+	0.1
-FBtr0079820	44	74	cluster_70	13	+	0.433333333333
-FBtr0080609	0	44	cluster_71	60	+	1.36363636364
-FBtr0080609	41	62	cluster_72	1	+	0.047619047619
-FBtr0080609	50	66	cluster_73	2	+	0.125
-FBtr0080644	0	27	cluster_74	6	+	0.222222222222
-FBtr0080646	0	27	cluster_75	3	+	0.111111111111
-FBtr0080647	0	27	cluster_76	10	+	0.37037037037
-FBtr0080660	0	27	cluster_77	7	+	0.259259259259
-FBtr0080663	0	34	cluster_78	102	+	3.0
-FBtr0080663	25	43	cluster_79	1	+	0.0555555555556
-FBtr0080663	31	47	cluster_80	2	+	0.125
-FBtr0080663	49	70	cluster_81	10	+	0.47619047619
-FBtr0080664	0	35	cluster_82	108	+	3.08571428571
-FBtr0080664	27	52	cluster_83	9	+	0.36
-FBtr0080664	49	71	cluster_84	11	+	0.5
+FBtr0070001	6	39	cluster_1	12	+	0.363636363636
+FBtr0070001	26	53	cluster_2	42	+	1.55555555556
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+FBtr0070533	27	55	cluster_4	7	+	0.25
+FBtr0070603	0	23	cluster_5	2	+	0.0869565217391
+FBtr0070603	11	53	cluster_6	35	+	0.833333333333
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+FBtr0070604	17	40	cluster_8	2	+	0.0869565217391
+FBtr0070604	30	53	cluster_9	34	+	1.47826086957
+FBtr0070911	14	35	cluster_10	1	+	0.047619047619
+FBtr0078490	27	50	cluster_11	1	+	0.0434782608696
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+FBtr0078790	51	71	cluster_16	1	+	0.05
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+FBtr0079090	0	28	cluster_18	1	+	0.0357142857143
+FBtr0079090	25	49	cluster_19	1	+	0.0416666666667
+FBtr0079090	35	56	cluster_20	1	-	0.047619047619
+FBtr0079338	12	31	cluster_21	1	+	0.0526315789474
+FBtr0079338	41	63	cluster_22	9	+	0.409090909091
+FBtr0079528	0	38	cluster_23	77	+	2.02631578947
+FBtr0079528	35	55	cluster_24	1	+	0.05
+FBtr0079596	0	24	cluster_25	50	+	2.08333333333
+FBtr0079596	12	33	cluster_26	1	+	0.047619047619
+FBtr0079596	52	73	cluster_27	3	+	0.142857142857
+FBtr0079677	0	23	cluster_28	2	+	0.0869565217391
+FBtr0079677	51	70	cluster_29	1	+	0.0526315789474
+FBtr0079690	26	51	cluster_30	1	+	0.04
+FBtr0079692	0	23	cluster_31	2	+	0.0869565217391
+FBtr0079692	31	51	cluster_32	1	+	0.05
+FBtr0079693	0	24	cluster_33	1	+	0.0416666666667
+FBtr0079693	24	47	cluster_34	1	+	0.0434782608696
+FBtr0079694	0	25	cluster_35	3	+	0.12
+FBtr0079694	17	36	cluster_36	1	+	0.0526315789474
+FBtr0079728	7	27	cluster_37	1	+	0.05
+FBtr0079728	18	42	cluster_38	1	+	0.0416666666667
+FBtr0079729	12	34	cluster_39	1	+	0.0454545454545
+FBtr0079752	0	24	cluster_40	1	+	0.0416666666667
+FBtr0079752	6	26	cluster_41	1	+	0.05
+FBtr0079752	51	71	cluster_42	2	+	0.1
+FBtr0079820	44	74	cluster_43	6	+	0.2
+FBtr0080609	0	23	cluster_44	17	+	0.739130434783
+FBtr0080609	11	44	cluster_45	6	+	0.181818181818
+FBtr0080609	41	62	cluster_46	1	+	0.047619047619
+FBtr0080644	0	27	cluster_47	2	+	0.0740740740741
+FBtr0080646	0	27	cluster_48	2	+	0.0740740740741
+FBtr0080647	0	27	cluster_49	2	+	0.0740740740741
+FBtr0080660	0	27	cluster_50	6	+	0.222222222222
+FBtr0080663	0	27	cluster_51	69	+	2.55555555556
+FBtr0080663	13	32	cluster_52	2	+	0.105263157895
+FBtr0080663	50	70	cluster_53	1	+	0.05
+FBtr0080664	0	35	cluster_54	78	+	2.22857142857
+FBtr0080664	32	56	cluster_55	2	+	0.0833333333333
diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/bed2.bed
--- a/test-data/bed2.bed	Wed Apr 10 06:38:33 2019 -0400
+++ b/test-data/bed2.bed	Sun Apr 14 14:43:44 2019 -0400
@@ -1,83 +1,55 @@
-FBtr0070001	0	17	cluster_1	1	.	0.0588235294118
-FBtr0070001	6	33	cluster_2	14	.	0.518518518519
-FBtr0070001	26	53	cluster_3	42	.	1.55555555556
-FBtr0070533	0	15	cluster_4	1	.	0.0666666666667
-FBtr0070533	11	55	cluster_5	23	.	0.522727272727
-FBtr0070603	0	62	cluster_6	68	.	1.09677419355
-FBtr0070603	50	71	cluster_7	2	.	0.0952380952381
-FBtr0070604	0	15	cluster_8	1	.	0.0666666666667
-FBtr0070604	17	40	cluster_9	2	.	0.0869565217391
-FBtr0070604	29	53	cluster_10	36	.	1.5
-FBtr0070604	56	71	cluster_11	1	.	0.0666666666667
-FBtr0070911	14	35	cluster_12	1	.	0.047619047619
-FBtr0070911	37	52	cluster_13	1	.	0.0666666666667
-FBtr0078490	12	32	cluster_14	4	.	0.2
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-FBtr0078580	0	47	cluster_17	1102	.	23.4468085106
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-FBtr0078790	0	19	cluster_19	1	.	0.0526315789474
-FBtr0078790	16	32	cluster_20	2	.	0.125
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-FBtr0078790	41	71	cluster_22	9	.	0.3
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-FBtr0079596	52	73	cluster_39	4	.	0.190476190476
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-FBtr0079729	51	72	cluster_64	2	.	0.0952380952381
-FBtr0079752	0	24	cluster_65	2	.	0.0833333333333
-FBtr0079752	6	27	cluster_66	2	.	0.0952380952381
-FBtr0079752	32	49	cluster_67	2	.	0.117647058824
-FBtr0079752	51	71	cluster_68	2	.	0.1
-FBtr0079820	44	74	cluster_69	13	.	0.433333333333
-FBtr0080609	0	44	cluster_70	60	.	1.36363636364
-FBtr0080609	41	62	cluster_71	1	.	0.047619047619
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-FBtr0080646	0	27	cluster_74	3	.	0.111111111111
-FBtr0080647	0	27	cluster_75	10	.	0.37037037037
-FBtr0080660	0	27	cluster_76	7	.	0.259259259259
-FBtr0080663	0	34	cluster_77	102	.	3.0
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-FBtr0080663	31	47	cluster_79	2	.	0.125
-FBtr0080663	49	70	cluster_80	10	.	0.47619047619
-FBtr0080664	0	35	cluster_81	108	.	3.08571428571
-FBtr0080664	27	52	cluster_82	9	.	0.36
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+FBtr0079728	7	27	cluster_37	1	.	0.05
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+FBtr0079729	12	34	cluster_39	1	.	0.0454545454545
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+FBtr0080609	0	23	cluster_44	17	.	0.739130434783
+FBtr0080609	11	44	cluster_45	6	.	0.181818181818
+FBtr0080609	41	62	cluster_46	1	.	0.047619047619
+FBtr0080644	0	27	cluster_47	2	.	0.0740740740741
+FBtr0080646	0	27	cluster_48	2	.	0.0740740740741
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+FBtr0080660	0	27	cluster_50	6	.	0.222222222222
+FBtr0080663	0	27	cluster_51	69	.	2.55555555556
+FBtr0080663	13	32	cluster_52	2	.	0.105263157895
+FBtr0080663	50	70	cluster_53	1	.	0.05
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+FBtr0080664	32	56	cluster_55	2	.	0.0833333333333
diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/bed3.bed
--- a/test-data/bed3.bed	Wed Apr 10 06:38:33 2019 -0400
+++ b/test-data/bed3.bed	Sun Apr 14 14:43:44 2019 -0400
@@ -1,84 +1,55 @@
-FBtr0070001	0	17	cluster_1	1	+	0.0588235294118
-FBtr0070001	6	33	cluster_2	14	+	0.518518518519
-FBtr0070001	26	53	cluster_3	42	+	1.55555555556
-FBtr0070533	0	15	cluster_4	1	+	0.0666666666667
-FBtr0070533	11	55	cluster_5	23	+	0.522727272727
-FBtr0070603	0	62	cluster_6	68	+	1.09677419355
-FBtr0070603	50	71	cluster_7	2	+	0.0952380952381
-FBtr0070604	0	15	cluster_8	1	+	0.0666666666667
-FBtr0070604	17	40	cluster_9	2	+	0.0869565217391
-FBtr0070604	29	53	cluster_10	36	+	1.5
-FBtr0070604	56	71	cluster_11	1	+	0.0666666666667
-FBtr0070911	14	35	cluster_12	1	+	0.047619047619
-FBtr0070911	37	52	cluster_13	1	+	0.0666666666667
-FBtr0078490	12	32	cluster_14	4	+	0.2
-FBtr0078490	24	50	cluster_15	3	+	0.115384615385
-FBtr0078490	37	55	cluster_16	1	+	0.0555555555556
-FBtr0078580	0	47	cluster_17	1102	+	23.4468085106
-FBtr0078580	51	68	cluster_18	2	+	0.117647058824
-FBtr0078790	0	19	cluster_19	1	+	0.0526315789474
-FBtr0078790	16	32	cluster_20	2	+	0.125
-FBtr0078790	32	55	cluster_21	1	+	0.0434782608696
-FBtr0078790	41	71	cluster_22	9	+	0.3
-FBtr0078790	54	69	cluster_23	1	-	0.0666666666667
-FBtr0079064	0	23	cluster_24	2	+	0.0869565217391
-FBtr0079064	32	47	cluster_25	1	+	0.0666666666667
-FBtr0079064	51	68	cluster_26	1	+	0.0588235294118
-FBtr0079090	0	28	cluster_27	2	+	0.0714285714286
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-FBtr0079090	32	48	cluster_29	1	+	0.0625
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-FBtr0079677	51	70	cluster_42	2	+	0.105263157895
-FBtr0079690	0	15	cluster_43	1	+	0.0666666666667
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-FBtr0079692	17	35	cluster_47	1	+	0.0555555555556
-FBtr0079692	24	41	cluster_48	1	+	0.0588235294118
-FBtr0079692	31	51	cluster_49	1	+	0.05
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-FBtr0079702	0	15	cluster_55	1	+	0.0666666666667
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-FBtr0079752	6	27	cluster_67	2	+	0.0952380952381
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-FBtr0079752	51	71	cluster_69	2	+	0.1
-FBtr0079820	44	74	cluster_70	13	+	0.433333333333
-FBtr0080609	0	44	cluster_71	60	+	1.36363636364
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-FBtr0080663	0	34	cluster_78	102	+	3.0
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+FBtr0079752	51	71	cluster_42	2	+	0.1
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+FBtr0080660	0	27	cluster_50	6	+	0.222222222222
+FBtr0080663	0	27	cluster_51	69	+	2.55555555556
+FBtr0080663	13	32	cluster_52	2	+	0.105263157895
+FBtr0080663	50	70	cluster_53	1	+	0.05
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+FBtr0080664	32	56	cluster_55	2	+	0.0833333333333
diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/bed4.bed
--- a/test-data/bed4.bed	Wed Apr 10 06:38:33 2019 -0400
+++ b/test-data/bed4.bed	Sun Apr 14 14:43:44 2019 -0400
@@ -1,9 +1,7 @@
 FBtr0070001	26	53	cluster_1	42	+	1.55555555556
-FBtr0070603	0	62	cluster_2	68	+	1.09677419355
-FBtr0070604	29	53	cluster_3	36	+	1.5
-FBtr0078580	0	47	cluster_4	1102	+	23.4468085106
-FBtr0079528	0	38	cluster_5	97	+	2.55263157895
-FBtr0079596	0	33	cluster_6	148	+	4.48484848485
-FBtr0080609	0	44	cluster_7	60	+	1.36363636364
-FBtr0080663	0	34	cluster_8	102	+	3.0
-FBtr0080664	0	35	cluster_9	108	+	3.08571428571
+FBtr0070604	30	53	cluster_2	34	+	1.47826086957
+FBtr0078580	0	52	cluster_3	452	+	8.69230769231
+FBtr0079528	0	38	cluster_4	77	+	2.02631578947
+FBtr0079596	0	24	cluster_5	50	+	2.08333333333
+FBtr0080663	0	27	cluster_6	69	+	2.55555555556
+FBtr0080664	0	35	cluster_7	78	+	2.22857142857
diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/bed5.bed
--- a/test-data/bed5.bed	Wed Apr 10 06:38:33 2019 -0400
+++ b/test-data/bed5.bed	Sun Apr 14 14:43:44 2019 -0400
@@ -1,15 +1,10 @@
-FBtr0070001	6	33	cluster_1	14	.	0.518518518519
-FBtr0070001	26	53	cluster_2	42	.	1.55555555556
-FBtr0070533	11	55	cluster_3	23	.	0.522727272727
-FBtr0070603	0	62	cluster_4	68	.	1.09677419355
-FBtr0070604	29	53	cluster_5	36	.	1.5
-FBtr0078580	0	47	cluster_6	1102	.	23.4468085106
-FBtr0079338	41	63	cluster_7	10	.	0.454545454545
-FBtr0079528	0	38	cluster_8	97	.	2.55263157895
-FBtr0079596	0	33	cluster_9	148	.	4.48484848485
-FBtr0079820	44	74	cluster_10	13	.	0.433333333333
-FBtr0080609	0	44	cluster_11	60	.	1.36363636364
-FBtr0080663	0	34	cluster_12	102	.	3.0
-FBtr0080663	49	70	cluster_13	10	.	0.47619047619
-FBtr0080664	0	35	cluster_14	108	.	3.08571428571
-FBtr0080664	49	71	cluster_15	11	.	0.5
+FBtr0070001	26	53	cluster_1	42	.	1.55555555556
+FBtr0070603	11	53	cluster_2	35	.	0.833333333333
+FBtr0070604	30	53	cluster_3	34	.	1.47826086957
+FBtr0078580	0	52	cluster_4	452	.	8.69230769231
+FBtr0079338	41	63	cluster_5	9	.	0.409090909091
+FBtr0079528	0	38	cluster_6	77	.	2.02631578947
+FBtr0079596	0	24	cluster_7	50	.	2.08333333333
+FBtr0080609	0	23	cluster_8	17	.	0.739130434783
+FBtr0080663	0	27	cluster_9	69	.	2.55555555556
+FBtr0080664	0	35	cluster_10	78	.	2.22857142857
diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/clustering.pdf
Binary file test-data/clustering.pdf has changed
diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/clustering.tab
--- a/test-data/clustering.tab	Wed Apr 10 06:38:33 2019 -0400
+++ b/test-data/clustering.tab	Sun Apr 14 14:43:44 2019 -0400
@@ -1,119 +1,97 @@
 Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts	Start-End	Cluster Size	density
-input1.bam	FBtr0070001	72	1	F	1	1-17	17	0.0588235294118
-input1.bam	FBtr0070001	72	12	F	14	7-33	27	0.518518518519
+input1.bam	FBtr0070001	72	1	F	0	1-1	1	0.0
+input1.bam	FBtr0070001	72	12	F	12	7-39	33	0.363636363636
 input1.bam	FBtr0070001	72	30	F	42	27-53	27	1.55555555556
 input1.bam	FBtr0070001	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0070533	72	1	F	1	1-15	15	0.0666666666667
-input1.bam	FBtr0070533	72	25	F	23	12-55	44	0.522727272727
+input1.bam	FBtr0070533	72	1	F	0	1-1	1	0.0
+input1.bam	FBtr0070533	72	20	F	7	19-41	23	0.304347826087
+input1.bam	FBtr0070533	72	32	F	7	28-55	28	0.25
 input1.bam	FBtr0070533	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0070603	72	21	F	68	1-62	62	1.09677419355
-input1.bam	FBtr0070603	72	53	F	2	51-71	21	0.0952380952381
+input1.bam	FBtr0070603	72	2	F	2	1-23	23	0.0869565217391
+input1.bam	FBtr0070603	72	23	F	35	12-53	42	0.833333333333
+input1.bam	FBtr0070603	72	42	F	1	42-62	21	0.047619047619
 input1.bam	FBtr0070603	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0070604	72	1	F	1	1-15	15	0.0666666666667
+input1.bam	FBtr0070604	72	1	F	0	1-1	1	0.0
 input1.bam	FBtr0070604	72	20	F	2	18-40	23	0.0869565217391
-input1.bam	FBtr0070604	72	31	F	36	30-53	24	1.5
-input1.bam	FBtr0070604	72	57	F	1	57-71	15	0.0666666666667
+input1.bam	FBtr0070604	72	31	F	34	31-53	23	1.47826086957
 input1.bam	FBtr0070604	72	72	F	0	72-72	1	0.0
 input1.bam	FBtr0070911	73	1	F	0	1-1	1	0.0
 input1.bam	FBtr0070911	73	15	F	1	15-35	21	0.047619047619
-input1.bam	FBtr0070911	73	38	F	1	38-52	15	0.0666666666667
 input1.bam	FBtr0070911	73	73	F	0	73-73	1	0.0
 input1.bam	FBtr0078490	72	1	F	0	1-1	1	0.0
-input1.bam	FBtr0078490	72	15	F	4	13-32	20	0.2
-input1.bam	FBtr0078490	72	26	F	3	25-50	26	0.115384615385
-input1.bam	FBtr0078490	72	38	F	1	38-55	18	0.0555555555556
+input1.bam	FBtr0078490	72	28	F	1	28-50	23	0.0434782608696
 input1.bam	FBtr0078490	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0078580	72	16	F	1102	1-47	47	23.4468085106
-input1.bam	FBtr0078580	72	52	F	2	52-68	17	0.117647058824
+input1.bam	FBtr0078580	72	13	F	452	1-52	52	8.69230769231
 input1.bam	FBtr0078580	72	72	F	0	72-72	1	0.0
 input1.bam	FBtr0078790	73	1	F	1	1-19	19	0.0526315789474
-input1.bam	FBtr0078790	73	17	F	2	17-32	16	0.125
 input1.bam	FBtr0078790	73	33	F	1	33-55	23	0.0434782608696
-input1.bam	FBtr0078790	73	47	F	9	42-71	30	0.3
-input1.bam	FBtr0078790	73	69	R	1	55-69	15	0.0666666666667
+input1.bam	FBtr0078790	73	43	F	4	42-63	22	0.181818181818
+input1.bam	FBtr0078790	73	52	F	1	52-71	20	0.05
 input1.bam	FBtr0078790	73	73	F	0	73-73	1	0.0
-input1.bam	FBtr0079064	72	2	F	2	1-23	23	0.0869565217391
-input1.bam	FBtr0079064	72	33	F	1	33-47	15	0.0666666666667
-input1.bam	FBtr0079064	72	52	F	1	52-68	17	0.0588235294118
+input1.bam	FBtr0079064	72	2	F	1	1-23	23	0.0434782608696
 input1.bam	FBtr0079064	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0079090	72	1	F	2	1-28	28	0.0714285714286
+input1.bam	FBtr0079090	72	1	F	1	1-28	28	0.0357142857143
 input1.bam	FBtr0079090	72	26	F	1	26-49	24	0.0416666666667
-input1.bam	FBtr0079090	72	33	F	1	33-48	16	0.0625
-input1.bam	FBtr0079090	72	53	F	1	53-70	18	0.0555555555556
 input1.bam	FBtr0079090	72	56	R	1	36-56	21	0.047619047619
 input1.bam	FBtr0079090	72	72	F	0	72-72	1	0.0
 input1.bam	FBtr0079338	73	1	F	0	1-1	1	0.0
-input1.bam	FBtr0079338	73	14	F	5	12-31	20	0.25
-input1.bam	FBtr0079338	73	25	F	1	25-40	16	0.0625
-input1.bam	FBtr0079338	73	44	F	10	42-63	22	0.454545454545
+input1.bam	FBtr0079338	73	13	F	1	13-31	19	0.0526315789474
+input1.bam	FBtr0079338	73	42	F	9	42-63	22	0.409090909091
 input1.bam	FBtr0079338	73	73	F	0	73-73	1	0.0
-input1.bam	FBtr0079528	71	9	F	97	1-38	38	2.55263157895
-input1.bam	FBtr0079528	71	28	F	1	28-43	16	0.0625
-input1.bam	FBtr0079528	71	36	F	3	35-54	20	0.15
-input1.bam	FBtr0079528	71	51	F	5	51-65	15	0.333333333333
+input1.bam	FBtr0079528	71	9	F	77	1-38	38	2.02631578947
+input1.bam	FBtr0079528	71	36	F	1	36-55	20	0.05
 input1.bam	FBtr0079528	71	71	F	0	71-71	1	0.0
-input1.bam	FBtr0079596	73	10	F	148	1-33	33	4.48484848485
-input1.bam	FBtr0079596	73	53	F	4	53-73	21	0.190476190476
+input1.bam	FBtr0079596	73	3	F	50	1-24	24	2.08333333333
+input1.bam	FBtr0079596	73	13	F	1	13-33	21	0.047619047619
+input1.bam	FBtr0079596	73	53	F	3	53-73	21	0.142857142857
 input1.bam	FBtr0079596	73	73	F	0	73-73	1	0.0
 input1.bam	FBtr0079677	72	3	F	2	1-23	23	0.0869565217391
-input1.bam	FBtr0079677	72	52	F	2	52-70	19	0.105263157895
+input1.bam	FBtr0079677	72	52	F	1	52-70	19	0.0526315789474
 input1.bam	FBtr0079677	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0079690	72	1	F	1	1-15	15	0.0666666666667
-input1.bam	FBtr0079690	72	24	F	2	22-51	30	0.0666666666667
-input1.bam	FBtr0079690	72	33	F	2	33-49	17	0.117647058824
+input1.bam	FBtr0079690	72	1	F	0	1-1	1	0.0
+input1.bam	FBtr0079690	72	27	F	1	27-51	25	0.04
 input1.bam	FBtr0079690	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0079692	73	1	F	3	1-23	23	0.130434782609
-input1.bam	FBtr0079692	73	18	F	1	18-35	18	0.0555555555556
-input1.bam	FBtr0079692	73	25	F	1	25-41	17	0.0588235294118
+input1.bam	FBtr0079692	73	1	F	2	1-23	23	0.0869565217391
 input1.bam	FBtr0079692	73	32	F	1	32-51	20	0.05
 input1.bam	FBtr0079692	73	73	F	0	73-73	1	0.0
-input1.bam	FBtr0079693	72	1	F	5	1-24	24	0.208333333333
+input1.bam	FBtr0079693	72	1	F	1	1-24	24	0.0416666666667
 input1.bam	FBtr0079693	72	25	F	1	25-47	23	0.0434782608696
 input1.bam	FBtr0079693	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0079694	72	1	F	5	1-25	25	0.2
+input1.bam	FBtr0079694	72	1	F	3	1-25	25	0.12
 input1.bam	FBtr0079694	72	18	F	1	18-36	19	0.0526315789474
-input1.bam	FBtr0079694	72	52	F	1	52-68	17	0.0588235294118
 input1.bam	FBtr0079694	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0079702	72	1	F	1	1-15	15	0.0666666666667
-input1.bam	FBtr0079702	72	19	F	2	19-36	18	0.111111111111
-input1.bam	FBtr0079702	72	56	F	1	56-70	15	0.0666666666667
+input1.bam	FBtr0079702	72	1	F	0	1-1	1	0.0
 input1.bam	FBtr0079702	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0079728	72	1	F	2	1-17	17	0.117647058824
+input1.bam	FBtr0079728	72	1	F	0	1-1	1	0.0
 input1.bam	FBtr0079728	72	8	F	1	8-27	20	0.05
 input1.bam	FBtr0079728	72	19	F	1	19-42	24	0.0416666666667
-input1.bam	FBtr0079728	72	33	F	3	33-49	17	0.176470588235
-input1.bam	FBtr0079728	72	56	F	1	56-70	15	0.0666666666667
 input1.bam	FBtr0079728	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0079729	72	1	F	1	1-15	15	0.0666666666667
+input1.bam	FBtr0079729	72	1	F	0	1-1	1	0.0
 input1.bam	FBtr0079729	72	13	F	1	13-34	22	0.0454545454545
-input1.bam	FBtr0079729	72	54	F	2	52-72	21	0.0952380952381
 input1.bam	FBtr0079729	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0079752	72	1	F	2	1-24	24	0.0833333333333
-input1.bam	FBtr0079752	72	9	F	2	7-27	21	0.0952380952381
-input1.bam	FBtr0079752	72	33	F	2	33-49	17	0.117647058824
+input1.bam	FBtr0079752	72	1	F	1	1-24	24	0.0416666666667
+input1.bam	FBtr0079752	72	7	F	1	7-26	20	0.05
 input1.bam	FBtr0079752	72	52	F	2	52-71	20	0.1
 input1.bam	FBtr0079752	72	72	F	0	72-72	1	0.0
 input1.bam	FBtr0079820	74	1	F	0	1-1	1	0.0
-input1.bam	FBtr0079820	74	50	F	13	45-74	30	0.433333333333
+input1.bam	FBtr0079820	74	50	F	6	45-74	30	0.2
 input1.bam	FBtr0079820	74	74	F	0	74-74	1	0.0
-input1.bam	FBtr0080609	72	10	F	60	1-44	44	1.36363636364
+input1.bam	FBtr0080609	72	3	F	17	1-23	23	0.739130434783
+input1.bam	FBtr0080609	72	16	F	6	12-44	33	0.181818181818
 input1.bam	FBtr0080609	72	42	F	1	42-62	21	0.047619047619
-input1.bam	FBtr0080609	72	51	F	2	51-66	16	0.125
 input1.bam	FBtr0080609	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0080644	72	6	F	6	1-27	27	0.222222222222
+input1.bam	FBtr0080644	72	2	F	2	1-27	27	0.0740740740741
 input1.bam	FBtr0080644	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0080646	72	4	F	3	1-27	27	0.111111111111
+input1.bam	FBtr0080646	72	4	F	2	1-27	27	0.0740740740741
 input1.bam	FBtr0080646	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0080647	72	6	F	10	1-27	27	0.37037037037
+input1.bam	FBtr0080647	72	4	F	2	1-27	27	0.0740740740741
 input1.bam	FBtr0080647	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0080660	72	4	F	7	1-27	27	0.259259259259
+input1.bam	FBtr0080660	72	4	F	6	1-27	27	0.222222222222
 input1.bam	FBtr0080660	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0080663	71	9	F	102	1-34	34	3.0
-input1.bam	FBtr0080663	71	26	F	1	26-43	18	0.0555555555556
-input1.bam	FBtr0080663	71	32	F	2	32-47	16	0.125
-input1.bam	FBtr0080663	71	50	F	10	50-70	21	0.47619047619
+input1.bam	FBtr0080663	71	4	F	69	1-27	27	2.55555555556
+input1.bam	FBtr0080663	71	14	F	2	14-32	19	0.105263157895
+input1.bam	FBtr0080663	71	51	F	1	51-70	20	0.05
 input1.bam	FBtr0080663	71	71	F	0	71-71	1	0.0
-input1.bam	FBtr0080664	71	11	F	108	1-35	35	3.08571428571
-input1.bam	FBtr0080664	71	33	F	9	28-52	25	0.36
-input1.bam	FBtr0080664	71	53	F	11	50-71	22	0.5
+input1.bam	FBtr0080664	71	9	F	78	1-35	35	2.22857142857
+input1.bam	FBtr0080664	71	34	F	2	33-56	24	0.0833333333333
 input1.bam	FBtr0080664	71	71	F	0	71-71	1	0.0
diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/clustering_unstranded.pdf
Binary file test-data/clustering_unstranded.pdf has changed
diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/clustering_unstranded.tab
--- a/test-data/clustering_unstranded.tab	Wed Apr 10 06:38:33 2019 -0400
+++ b/test-data/clustering_unstranded.tab	Sun Apr 14 14:43:44 2019 -0400
@@ -1,117 +1,97 @@
 Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts	Start-End	Cluster Size	density
-input1.bam	FBtr0070001	72	1	F	1	1-17	17	0.0588235294118
-input1.bam	FBtr0070001	72	12	F	14	7-33	27	0.518518518519
+input1.bam	FBtr0070001	72	1	F	0	1-1	1	0.0
+input1.bam	FBtr0070001	72	12	F	12	7-39	33	0.363636363636
 input1.bam	FBtr0070001	72	30	F	42	27-53	27	1.55555555556
 input1.bam	FBtr0070001	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0070533	72	1	F	1	1-15	15	0.0666666666667
-input1.bam	FBtr0070533	72	25	F	23	12-55	44	0.522727272727
+input1.bam	FBtr0070533	72	1	F	0	1-1	1	0.0
+input1.bam	FBtr0070533	72	20	F	7	19-41	23	0.304347826087
+input1.bam	FBtr0070533	72	32	F	7	28-55	28	0.25
 input1.bam	FBtr0070533	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0070603	72	21	F	68	1-62	62	1.09677419355
-input1.bam	FBtr0070603	72	53	F	2	51-71	21	0.0952380952381
+input1.bam	FBtr0070603	72	2	F	2	1-23	23	0.0869565217391
+input1.bam	FBtr0070603	72	23	F	35	12-53	42	0.833333333333
+input1.bam	FBtr0070603	72	42	F	1	42-62	21	0.047619047619
 input1.bam	FBtr0070603	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0070604	72	1	F	1	1-15	15	0.0666666666667
+input1.bam	FBtr0070604	72	1	F	0	1-1	1	0.0
 input1.bam	FBtr0070604	72	20	F	2	18-40	23	0.0869565217391
-input1.bam	FBtr0070604	72	31	F	36	30-53	24	1.5
-input1.bam	FBtr0070604	72	57	F	1	57-71	15	0.0666666666667
+input1.bam	FBtr0070604	72	31	F	34	31-53	23	1.47826086957
 input1.bam	FBtr0070604	72	72	F	0	72-72	1	0.0
 input1.bam	FBtr0070911	73	1	F	0	1-1	1	0.0
 input1.bam	FBtr0070911	73	15	F	1	15-35	21	0.047619047619
-input1.bam	FBtr0070911	73	38	F	1	38-52	15	0.0666666666667
 input1.bam	FBtr0070911	73	73	F	0	73-73	1	0.0
 input1.bam	FBtr0078490	72	1	F	0	1-1	1	0.0
-input1.bam	FBtr0078490	72	15	F	4	13-32	20	0.2
-input1.bam	FBtr0078490	72	26	F	3	25-50	26	0.115384615385
-input1.bam	FBtr0078490	72	38	F	1	38-55	18	0.0555555555556
+input1.bam	FBtr0078490	72	28	F	1	28-50	23	0.0434782608696
 input1.bam	FBtr0078490	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0078580	72	16	F	1102	1-47	47	23.4468085106
-input1.bam	FBtr0078580	72	52	F	2	52-68	17	0.117647058824
+input1.bam	FBtr0078580	72	13	F	452	1-52	52	8.69230769231
 input1.bam	FBtr0078580	72	72	F	0	72-72	1	0.0
 input1.bam	FBtr0078790	73	1	F	1	1-19	19	0.0526315789474
-input1.bam	FBtr0078790	73	17	F	2	17-32	16	0.125
 input1.bam	FBtr0078790	73	33	F	1	33-55	23	0.0434782608696
-input1.bam	FBtr0078790	73	47	F	9	42-71	30	0.3
-input1.bam	FBtr0078790	73	71	F	1	69-73	5	0.2
-input1.bam	FBtr0079064	72	2	F	2	1-23	23	0.0869565217391
-input1.bam	FBtr0079064	72	33	F	1	33-47	15	0.0666666666667
-input1.bam	FBtr0079064	72	52	F	1	52-68	17	0.0588235294118
+input1.bam	FBtr0078790	73	43	F	4	42-63	22	0.181818181818
+input1.bam	FBtr0078790	73	52	F	1	52-71	20	0.05
+input1.bam	FBtr0078790	73	73	F	0	73-73	1	0.0
+input1.bam	FBtr0079064	72	2	F	1	1-23	23	0.0434782608696
 input1.bam	FBtr0079064	72	72	F	0	72-72	1	0.0
-input1.bam	FBtr0079090	72	1	F	2	1-28	28	0.0714285714286
+input1.bam	FBtr0079090	72	1	F	1	1-28	28	0.0357142857143
 input1.bam	FBtr0079090	72	26	F	1	26-49	24	0.0416666666667
-input1.bam	FBtr0079090	72	33	F	1	33-48	16	0.0625
-input1.bam	FBtr0079090	72	54	F	2	53-76	24	0.0833333333333
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diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/global_merge.pdf
Binary file test-data/global_merge.pdf has changed
diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/global_merge.tab
--- a/test-data/global_merge.tab	Wed Apr 10 06:38:33 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1045 +0,0 @@
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diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/global_nomerge.pdf
Binary file test-data/global_nomerge.pdf has changed
diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/global_nomerge.tab
--- a/test-data/global_nomerge.tab	Wed Apr 10 06:38:33 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1045 +0,0 @@
-Dataset	Chromosome	Polarity	Size	Counts
-input1.bam	FBtr0070001	F	16	2
-input1.bam	FBtr0070001	F	17	1
-input1.bam	FBtr0070001	F	18	0
-input1.bam	FBtr0070001	F	19	1
-input1.bam	FBtr0070001	F	20	4
-input1.bam	FBtr0070001	F	21	4
-input1.bam	FBtr0070001	F	22	29
-input1.bam	FBtr0070001	F	23	15
-input1.bam	FBtr0070001	F	24	1
-input1.bam	FBtr0070001	R	16	0
-input1.bam	FBtr0070001	R	17	0
-input1.bam	FBtr0070001	R	18	0
-input1.bam	FBtr0070001	R	19	0
-input1.bam	FBtr0070001	R	20	0
-input1.bam	FBtr0070001	R	21	0
-input1.bam	FBtr0070001	R	22	0
-input1.bam	FBtr0070001	R	23	0
-input1.bam	FBtr0070001	R	24	0
-input1.bam	FBtr0070533	F	15	2
-input1.bam	FBtr0070533	F	16	1
-input1.bam	FBtr0070533	F	17	1
-input1.bam	FBtr0070533	F	18	6
-input1.bam	FBtr0070533	F	19	3
-input1.bam	FBtr0070533	F	20	2
-input1.bam	FBtr0070533	F	21	2
-input1.bam	FBtr0070533	F	22	4
-input1.bam	FBtr0070533	F	23	2
-input1.bam	FBtr0070533	F	24	0
-input1.bam	FBtr0070533	F	25	1
-input1.bam	FBtr0070533	R	15	0
-input1.bam	FBtr0070533	R	16	0
-input1.bam	FBtr0070533	R	17	0
-input1.bam	FBtr0070533	R	18	0
-input1.bam	FBtr0070533	R	19	0
-input1.bam	FBtr0070533	R	20	0
-input1.bam	FBtr0070533	R	21	0
-input1.bam	FBtr0070533	R	22	0
-input1.bam	FBtr0070533	R	23	0
-input1.bam	FBtr0070533	R	24	0
-input1.bam	FBtr0070533	R	25	0
-input1.bam	FBtr0070603	F	15	9
-input1.bam	FBtr0070603	F	16	6
-input1.bam	FBtr0070603	F	17	10
-input1.bam	FBtr0070603	F	18	7
-input1.bam	FBtr0070603	F	19	1
-input1.bam	FBtr0070603	F	20	6
-input1.bam	FBtr0070603	F	21	3
-input1.bam	FBtr0070603	F	22	3
-input1.bam	FBtr0070603	F	23	10
-input1.bam	FBtr0070603	F	24	2
-input1.bam	FBtr0070603	F	25	5
-input1.bam	FBtr0070603	F	26	5
-input1.bam	FBtr0070603	F	27	3
-input1.bam	FBtr0070603	R	15	0
-input1.bam	FBtr0070603	R	16	0
-input1.bam	FBtr0070603	R	17	0
-input1.bam	FBtr0070603	R	18	0
-input1.bam	FBtr0070603	R	19	0
-input1.bam	FBtr0070603	R	20	0
-input1.bam	FBtr0070603	R	21	0
-input1.bam	FBtr0070603	R	22	0
-input1.bam	FBtr0070603	R	23	0
-input1.bam	FBtr0070603	R	24	0
-input1.bam	FBtr0070603	R	25	0
-input1.bam	FBtr0070603	R	26	0
-input1.bam	FBtr0070603	R	27	0
-input1.bam	FBtr0070604	F	15	2
-input1.bam	FBtr0070604	F	16	0
-input1.bam	FBtr0070604	F	17	0
-input1.bam	FBtr0070604	F	18	2
-input1.bam	FBtr0070604	F	19	2
-input1.bam	FBtr0070604	F	20	0
-input1.bam	FBtr0070604	F	21	1
-input1.bam	FBtr0070604	F	22	23
-input1.bam	FBtr0070604	F	23	10
-input1.bam	FBtr0070604	R	15	0
-input1.bam	FBtr0070604	R	16	0
-input1.bam	FBtr0070604	R	17	0
-input1.bam	FBtr0070604	R	18	0
-input1.bam	FBtr0070604	R	19	0
-input1.bam	FBtr0070604	R	20	0
-input1.bam	FBtr0070604	R	21	0
-input1.bam	FBtr0070604	R	22	0
-input1.bam	FBtr0070604	R	23	0
-input1.bam	FBtr0070911	F	15	1
-input1.bam	FBtr0070911	F	16	0
-input1.bam	FBtr0070911	F	17	0
-input1.bam	FBtr0070911	F	18	0
-input1.bam	FBtr0070911	F	19	0
-input1.bam	FBtr0070911	F	20	0
-input1.bam	FBtr0070911	F	21	1
-input1.bam	FBtr0070911	R	15	0
-input1.bam	FBtr0070911	R	16	0
-input1.bam	FBtr0070911	R	17	0
-input1.bam	FBtr0070911	R	18	0
-input1.bam	FBtr0070911	R	19	0
-input1.bam	FBtr0070911	R	20	0
-input1.bam	FBtr0070911	R	21	0
-input1.bam	FBtr0078490	F	15	3
-input1.bam	FBtr0078490	F	16	3
-input1.bam	FBtr0078490	F	17	0
-input1.bam	FBtr0078490	F	18	1
-input1.bam	FBtr0078490	F	19	0
-input1.bam	FBtr0078490	F	20	0
-input1.bam	FBtr0078490	F	21	0
-input1.bam	FBtr0078490	F	22	0
-input1.bam	FBtr0078490	F	23	1
-input1.bam	FBtr0078490	R	15	0
-input1.bam	FBtr0078490	R	16	0
-input1.bam	FBtr0078490	R	17	0
-input1.bam	FBtr0078490	R	18	0
-input1.bam	FBtr0078490	R	19	0
-input1.bam	FBtr0078490	R	20	0
-input1.bam	FBtr0078490	R	21	0
-input1.bam	FBtr0078490	R	22	0
-input1.bam	FBtr0078490	R	23	0
-input1.bam	FBtr0078580	F	15	592
-input1.bam	FBtr0078580	F	16	20
-input1.bam	FBtr0078580	F	17	31
-input1.bam	FBtr0078580	F	18	9
-input1.bam	FBtr0078580	F	19	8
-input1.bam	FBtr0078580	F	20	9
-input1.bam	FBtr0078580	F	21	5
-input1.bam	FBtr0078580	F	22	13
-input1.bam	FBtr0078580	F	23	5
-input1.bam	FBtr0078580	F	24	180
-input1.bam	FBtr0078580	F	25	212
-input1.bam	FBtr0078580	F	26	1
-input1.bam	FBtr0078580	F	27	2
-input1.bam	FBtr0078580	F	28	17
-input1.bam	FBtr0078580	R	15	0
-input1.bam	FBtr0078580	R	16	0
-input1.bam	FBtr0078580	R	17	0
-input1.bam	FBtr0078580	R	18	0
-input1.bam	FBtr0078580	R	19	0
-input1.bam	FBtr0078580	R	20	0
-input1.bam	FBtr0078580	R	21	0
-input1.bam	FBtr0078580	R	22	0
-input1.bam	FBtr0078580	R	23	0
-input1.bam	FBtr0078580	R	24	0
-input1.bam	FBtr0078580	R	25	0
-input1.bam	FBtr0078580	R	26	0
-input1.bam	FBtr0078580	R	27	0
-input1.bam	FBtr0078580	R	28	0
-input1.bam	FBtr0078790	F	15	2
-input1.bam	FBtr0078790	F	16	2
-input1.bam	FBtr0078790	F	17	1
-input1.bam	FBtr0078790	F	18	1
-input1.bam	FBtr0078790	F	19	2
-input1.bam	FBtr0078790	F	20	2
-input1.bam	FBtr0078790	F	21	0
-input1.bam	FBtr0078790	F	22	2
-input1.bam	FBtr0078790	F	23	1
-input1.bam	FBtr0078790	R	15	1
-input1.bam	FBtr0078790	R	16	0
-input1.bam	FBtr0078790	R	17	0
-input1.bam	FBtr0078790	R	18	0
-input1.bam	FBtr0078790	R	19	0
-input1.bam	FBtr0078790	R	20	0
-input1.bam	FBtr0078790	R	21	0
-input1.bam	FBtr0078790	R	22	0
-input1.bam	FBtr0078790	R	23	0
-input1.bam	FBtr0079064	F	15	2
-input1.bam	FBtr0079064	F	16	0
-input1.bam	FBtr0079064	F	17	1
-input1.bam	FBtr0079064	F	18	0
-input1.bam	FBtr0079064	F	19	0
-input1.bam	FBtr0079064	F	20	0
-input1.bam	FBtr0079064	F	21	1
-input1.bam	FBtr0079064	R	15	0
-input1.bam	FBtr0079064	R	16	0
-input1.bam	FBtr0079064	R	17	0
-input1.bam	FBtr0079064	R	18	0
-input1.bam	FBtr0079064	R	19	0
-input1.bam	FBtr0079064	R	20	0
-input1.bam	FBtr0079064	R	21	0
-input1.bam	FBtr0079090	F	15	1
-input1.bam	FBtr0079090	F	16	1
-input1.bam	FBtr0079090	F	17	0
-input1.bam	FBtr0079090	F	18	1
-input1.bam	FBtr0079090	F	19	0
-input1.bam	FBtr0079090	F	20	0
-input1.bam	FBtr0079090	F	21	0
-input1.bam	FBtr0079090	F	22	0
-input1.bam	FBtr0079090	F	23	0
-input1.bam	FBtr0079090	F	24	1
-input1.bam	FBtr0079090	F	25	0
-input1.bam	FBtr0079090	F	26	0
-input1.bam	FBtr0079090	F	27	0
-input1.bam	FBtr0079090	F	28	1
-input1.bam	FBtr0079090	R	15	0
-input1.bam	FBtr0079090	R	16	0
-input1.bam	FBtr0079090	R	17	0
-input1.bam	FBtr0079090	R	18	0
-input1.bam	FBtr0079090	R	19	0
-input1.bam	FBtr0079090	R	20	0
-input1.bam	FBtr0079090	R	21	1
-input1.bam	FBtr0079090	R	22	0
-input1.bam	FBtr0079090	R	23	0
-input1.bam	FBtr0079090	R	24	0
-input1.bam	FBtr0079090	R	25	0
-input1.bam	FBtr0079090	R	26	0
-input1.bam	FBtr0079090	R	27	0
-input1.bam	FBtr0079090	R	28	0
-input1.bam	FBtr0079338	F	15	2
-input1.bam	FBtr0079338	F	16	2
-input1.bam	FBtr0079338	F	17	1
-input1.bam	FBtr0079338	F	18	1
-input1.bam	FBtr0079338	F	19	1
-input1.bam	FBtr0079338	F	20	0
-input1.bam	FBtr0079338	F	21	3
-input1.bam	FBtr0079338	F	22	6
-input1.bam	FBtr0079338	R	15	0
-input1.bam	FBtr0079338	R	16	0
-input1.bam	FBtr0079338	R	17	0
-input1.bam	FBtr0079338	R	18	0
-input1.bam	FBtr0079338	R	19	0
-input1.bam	FBtr0079338	R	20	0
-input1.bam	FBtr0079338	R	21	0
-input1.bam	FBtr0079338	R	22	0
-input1.bam	FBtr0079528	F	15	12
-input1.bam	FBtr0079528	F	16	11
-input1.bam	FBtr0079528	F	17	0
-input1.bam	FBtr0079528	F	18	5
-input1.bam	FBtr0079528	F	19	4
-input1.bam	FBtr0079528	F	20	12
-input1.bam	FBtr0079528	F	21	3
-input1.bam	FBtr0079528	F	22	2
-input1.bam	FBtr0079528	F	23	3
-input1.bam	FBtr0079528	F	24	36
-input1.bam	FBtr0079528	F	25	8
-input1.bam	FBtr0079528	F	26	5
-input1.bam	FBtr0079528	F	27	2
-input1.bam	FBtr0079528	F	28	2
-input1.bam	FBtr0079528	F	29	1
-input1.bam	FBtr0079528	R	15	0
-input1.bam	FBtr0079528	R	16	0
-input1.bam	FBtr0079528	R	17	0
-input1.bam	FBtr0079528	R	18	0
-input1.bam	FBtr0079528	R	19	0
-input1.bam	FBtr0079528	R	20	0
-input1.bam	FBtr0079528	R	21	0
-input1.bam	FBtr0079528	R	22	0
-input1.bam	FBtr0079528	R	23	0
-input1.bam	FBtr0079528	R	24	0
-input1.bam	FBtr0079528	R	25	0
-input1.bam	FBtr0079528	R	26	0
-input1.bam	FBtr0079528	R	27	0
-input1.bam	FBtr0079528	R	28	0
-input1.bam	FBtr0079528	R	29	0
-input1.bam	FBtr0079596	F	15	43
-input1.bam	FBtr0079596	F	16	34
-input1.bam	FBtr0079596	F	17	16
-input1.bam	FBtr0079596	F	18	5
-input1.bam	FBtr0079596	F	19	10
-input1.bam	FBtr0079596	F	20	13
-input1.bam	FBtr0079596	F	21	3
-input1.bam	FBtr0079596	F	22	16
-input1.bam	FBtr0079596	F	23	8
-input1.bam	FBtr0079596	F	24	0
-input1.bam	FBtr0079596	F	25	0
-input1.bam	FBtr0079596	F	26	3
-input1.bam	FBtr0079596	F	27	1
-input1.bam	FBtr0079596	R	15	0
-input1.bam	FBtr0079596	R	16	0
-input1.bam	FBtr0079596	R	17	0
-input1.bam	FBtr0079596	R	18	0
-input1.bam	FBtr0079596	R	19	0
-input1.bam	FBtr0079596	R	20	0
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-input1.bam	FBtr0079596	R	23	0
-input1.bam	FBtr0079596	R	24	0
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-input1.bam	FBtr0079596	R	26	0
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-input1.bam	FBtr0079677	F	20	0
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-input1.bam	FBtr0079690	F	15	3
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-input1.bam	FBtr0079690	R	15	0
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-input2.bam	FBtr0079596	F	15	31
-input2.bam	FBtr0079596	F	16	21
-input2.bam	FBtr0079596	F	17	18
-input2.bam	FBtr0079596	F	18	79
-input2.bam	FBtr0079596	F	19	48
-input2.bam	FBtr0079596	F	20	49
-input2.bam	FBtr0079596	F	21	40
-input2.bam	FBtr0079596	F	22	26
-input2.bam	FBtr0079596	F	23	2
-input2.bam	FBtr0079596	F	24	1
-input2.bam	FBtr0079596	R	15	0
-input2.bam	FBtr0079596	R	16	0
-input2.bam	FBtr0079596	R	17	0
-input2.bam	FBtr0079596	R	18	0
-input2.bam	FBtr0079596	R	19	0
-input2.bam	FBtr0079596	R	20	0
-input2.bam	FBtr0079596	R	21	1
-input2.bam	FBtr0079596	R	22	0
-input2.bam	FBtr0079596	R	23	0
-input2.bam	FBtr0079596	R	24	0
-input2.bam	FBtr0079677	F	15	2
-input2.bam	FBtr0079677	F	16	1
-input2.bam	FBtr0079677	F	17	2
-input2.bam	FBtr0079677	F	18	0
-input2.bam	FBtr0079677	F	19	1
-input2.bam	FBtr0079677	F	20	1
-input2.bam	FBtr0079677	R	15	0
-input2.bam	FBtr0079677	R	16	0
-input2.bam	FBtr0079677	R	17	0
-input2.bam	FBtr0079677	R	18	0
-input2.bam	FBtr0079677	R	19	0
-input2.bam	FBtr0079677	R	20	0
-input2.bam	FBtr0079690	F	15	1
-input2.bam	FBtr0079690	F	16	1
-input2.bam	FBtr0079690	F	17	0
-input2.bam	FBtr0079690	F	18	0
-input2.bam	FBtr0079690	F	19	0
-input2.bam	FBtr0079690	F	20	2
-input2.bam	FBtr0079690	F	21	1
-input2.bam	FBtr0079690	R	15	0
-input2.bam	FBtr0079690	R	16	0
-input2.bam	FBtr0079690	R	17	0
-input2.bam	FBtr0079690	R	18	0
-input2.bam	FBtr0079690	R	19	0
-input2.bam	FBtr0079690	R	20	0
-input2.bam	FBtr0079690	R	21	0
-input2.bam	FBtr0079692	F	15	1
-input2.bam	FBtr0079692	F	16	0
-input2.bam	FBtr0079692	F	17	0
-input2.bam	FBtr0079692	F	18	1
-input2.bam	FBtr0079692	F	19	0
-input2.bam	FBtr0079692	F	20	0
-input2.bam	FBtr0079692	F	21	1
-input2.bam	FBtr0079692	F	22	1
-input2.bam	FBtr0079692	R	15	0
-input2.bam	FBtr0079692	R	16	0
-input2.bam	FBtr0079692	R	17	0
-input2.bam	FBtr0079692	R	18	0
-input2.bam	FBtr0079692	R	19	0
-input2.bam	FBtr0079692	R	20	0
-input2.bam	FBtr0079692	R	21	0
-input2.bam	FBtr0079692	R	22	0
-input2.bam	FBtr0079693	F	15	4
-input2.bam	FBtr0079693	F	16	2
-input2.bam	FBtr0079693	F	17	0
-input2.bam	FBtr0079693	F	18	1
-input2.bam	FBtr0079693	F	19	0
-input2.bam	FBtr0079693	F	20	2
-input2.bam	FBtr0079693	R	15	0
-input2.bam	FBtr0079693	R	16	0
-input2.bam	FBtr0079693	R	17	0
-input2.bam	FBtr0079693	R	18	0
-input2.bam	FBtr0079693	R	19	0
-input2.bam	FBtr0079693	R	20	0
-input2.bam	FBtr0079694	F	15	2
-input2.bam	FBtr0079694	F	16	0
-input2.bam	FBtr0079694	F	17	1
-input2.bam	FBtr0079694	F	18	2
-input2.bam	FBtr0079694	F	19	1
-input2.bam	FBtr0079694	R	15	0
-input2.bam	FBtr0079694	R	16	0
-input2.bam	FBtr0079694	R	17	0
-input2.bam	FBtr0079694	R	18	0
-input2.bam	FBtr0079694	R	19	0
-input2.bam	FBtr0079702	F	15	2
-input2.bam	FBtr0079702	F	16	0
-input2.bam	FBtr0079702	F	17	1
-input2.bam	FBtr0079702	F	18	1
-input2.bam	FBtr0079702	R	15	0
-input2.bam	FBtr0079702	R	16	0
-input2.bam	FBtr0079702	R	17	0
-input2.bam	FBtr0079702	R	18	0
-input2.bam	FBtr0079728	F	15	3
-input2.bam	FBtr0079728	F	16	1
-input2.bam	FBtr0079728	F	17	1
-input2.bam	FBtr0079728	F	18	1
-input2.bam	FBtr0079728	R	15	0
-input2.bam	FBtr0079728	R	16	0
-input2.bam	FBtr0079728	R	17	0
-input2.bam	FBtr0079728	R	18	0
-input2.bam	FBtr0079729	F	15	1
-input2.bam	FBtr0079729	F	16	2
-input2.bam	FBtr0079729	F	17	1
-input2.bam	FBtr0079729	R	15	0
-input2.bam	FBtr0079729	R	16	0
-input2.bam	FBtr0079729	R	17	0
-input2.bam	FBtr0079752	F	17	1
-input2.bam	FBtr0079752	F	18	0
-input2.bam	FBtr0079752	F	19	0
-input2.bam	FBtr0079752	F	20	0
-input2.bam	FBtr0079752	F	21	0
-input2.bam	FBtr0079752	F	22	0
-input2.bam	FBtr0079752	F	23	0
-input2.bam	FBtr0079752	F	24	1
-input2.bam	FBtr0079752	R	17	0
-input2.bam	FBtr0079752	R	18	0
-input2.bam	FBtr0079752	R	19	0
-input2.bam	FBtr0079752	R	20	0
-input2.bam	FBtr0079752	R	21	0
-input2.bam	FBtr0079752	R	22	0
-input2.bam	FBtr0079752	R	23	0
-input2.bam	FBtr0079752	R	24	0
-input2.bam	FBtr0079820	F	15	27
-input2.bam	FBtr0079820	F	16	10
-input2.bam	FBtr0079820	F	17	7
-input2.bam	FBtr0079820	F	18	8
-input2.bam	FBtr0079820	F	19	25
-input2.bam	FBtr0079820	F	20	24
-input2.bam	FBtr0079820	F	21	7
-input2.bam	FBtr0079820	F	22	1
-input2.bam	FBtr0079820	R	15	0
-input2.bam	FBtr0079820	R	16	0
-input2.bam	FBtr0079820	R	17	0
-input2.bam	FBtr0079820	R	18	0
-input2.bam	FBtr0079820	R	19	0
-input2.bam	FBtr0079820	R	20	0
-input2.bam	FBtr0079820	R	21	0
-input2.bam	FBtr0079820	R	22	0
-input2.bam	FBtr0080609	F	17	2
-input2.bam	FBtr0080609	F	18	1
-input2.bam	FBtr0080609	F	19	2
-input2.bam	FBtr0080609	F	20	0
-input2.bam	FBtr0080609	F	21	0
-input2.bam	FBtr0080609	F	22	1
-input2.bam	FBtr0080609	F	23	1
-input2.bam	FBtr0080609	F	24	0
-input2.bam	FBtr0080609	F	25	1
-input2.bam	FBtr0080609	R	17	0
-input2.bam	FBtr0080609	R	18	0
-input2.bam	FBtr0080609	R	19	0
-input2.bam	FBtr0080609	R	20	0
-input2.bam	FBtr0080609	R	21	0
-input2.bam	FBtr0080609	R	22	0
-input2.bam	FBtr0080609	R	23	0
-input2.bam	FBtr0080609	R	24	0
-input2.bam	FBtr0080609	R	25	0
-input2.bam	FBtr0080644	F	15	8
-input2.bam	FBtr0080644	R	15	0
-input2.bam	FBtr0080646	F	15	10
-input2.bam	FBtr0080646	F	16	1
-input2.bam	FBtr0080646	F	17	0
-input2.bam	FBtr0080646	F	18	0
-input2.bam	FBtr0080646	F	19	0
-input2.bam	FBtr0080646	F	20	0
-input2.bam	FBtr0080646	F	21	1
-input2.bam	FBtr0080646	R	15	0
-input2.bam	FBtr0080646	R	16	0
-input2.bam	FBtr0080646	R	17	0
-input2.bam	FBtr0080646	R	18	0
-input2.bam	FBtr0080646	R	19	0
-input2.bam	FBtr0080646	R	20	0
-input2.bam	FBtr0080646	R	21	0
-input2.bam	FBtr0080647	F	15	9
-input2.bam	FBtr0080647	F	16	2
-input2.bam	FBtr0080647	F	17	0
-input2.bam	FBtr0080647	F	18	1
-input2.bam	FBtr0080647	R	15	0
-input2.bam	FBtr0080647	R	16	0
-input2.bam	FBtr0080647	R	17	0
-input2.bam	FBtr0080647	R	18	0
-input2.bam	FBtr0080660	F	15	11
-input2.bam	FBtr0080660	R	15	0
-input2.bam	FBtr0080663	F	15	26
-input2.bam	FBtr0080663	F	16	14
-input2.bam	FBtr0080663	F	17	14
-input2.bam	FBtr0080663	F	18	26
-input2.bam	FBtr0080663	F	19	9
-input2.bam	FBtr0080663	F	20	7
-input2.bam	FBtr0080663	F	21	4
-input2.bam	FBtr0080663	F	22	5
-input2.bam	FBtr0080663	F	23	0
-input2.bam	FBtr0080663	F	24	1
-input2.bam	FBtr0080663	R	15	0
-input2.bam	FBtr0080663	R	16	0
-input2.bam	FBtr0080663	R	17	0
-input2.bam	FBtr0080663	R	18	0
-input2.bam	FBtr0080663	R	19	0
-input2.bam	FBtr0080663	R	20	0
-input2.bam	FBtr0080663	R	21	0
-input2.bam	FBtr0080663	R	22	0
-input2.bam	FBtr0080663	R	23	0
-input2.bam	FBtr0080663	R	24	0
-input2.bam	FBtr0080664	F	15	165
-input2.bam	FBtr0080664	F	16	59
-input2.bam	FBtr0080664	F	17	20
-input2.bam	FBtr0080664	F	18	75
-input2.bam	FBtr0080664	F	19	24
-input2.bam	FBtr0080664	F	20	21
-input2.bam	FBtr0080664	F	21	8
-input2.bam	FBtr0080664	F	22	4
-input2.bam	FBtr0080664	F	23	4
-input2.bam	FBtr0080664	F	24	0
-input2.bam	FBtr0080664	F	25	3
-input2.bam	FBtr0080664	F	26	4
-input2.bam	FBtr0080664	R	15	0
-input2.bam	FBtr0080664	R	16	0
-input2.bam	FBtr0080664	R	17	0
-input2.bam	FBtr0080664	R	18	0
-input2.bam	FBtr0080664	R	19	0
-input2.bam	FBtr0080664	R	20	0
-input2.bam	FBtr0080664	R	21	0
-input2.bam	FBtr0080664	R	22	1
-input2.bam	FBtr0080664	R	23	1
-input2.bam	FBtr0080664	R	24	0
-input2.bam	FBtr0080664	R	25	0
-input2.bam	FBtr0080664	R	26	0
diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/input1__single_plot_mean.pdf
Binary file test-data/input1__single_plot_mean.pdf has changed
diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/input1_cluster5_counts.tab
--- a/test-data/input1_cluster5_counts.tab	Wed Apr 10 06:38:33 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,132 +0,0 @@
-Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts
-input1.bam	FBtr0070001	72	1	F	1
-input1.bam	FBtr0070001	72	12	F	14
-input1.bam	FBtr0070001	72	30	F	42
-input1.bam	FBtr0070001	72	72	F	0
-input1.bam	FBtr0070533	72	1	F	1
-input1.bam	FBtr0070533	72	25	F	23
-input1.bam	FBtr0070533	72	72	F	0
-input1.bam	FBtr0070603	72	1	F	0
-input1.bam	FBtr0070603	72	21	F	68
-input1.bam	FBtr0070603	72	53	F	2
-input1.bam	FBtr0070603	72	72	F	0
-input1.bam	FBtr0070604	72	1	F	1
-input1.bam	FBtr0070604	72	20	F	2
-input1.bam	FBtr0070604	72	31	F	36
-input1.bam	FBtr0070604	72	57	F	1
-input1.bam	FBtr0070604	72	72	F	0
-input1.bam	FBtr0070911	73	1	F	0
-input1.bam	FBtr0070911	73	15	F	1
-input1.bam	FBtr0070911	73	38	F	1
-input1.bam	FBtr0070911	73	73	F	0
-input1.bam	FBtr0078490	72	1	F	0
-input1.bam	FBtr0078490	72	15	F	4
-input1.bam	FBtr0078490	72	26	F	3
-input1.bam	FBtr0078490	72	38	F	1
-input1.bam	FBtr0078490	72	72	F	0
-input1.bam	FBtr0078580	72	1	F	0
-input1.bam	FBtr0078580	72	16	F	1102
-input1.bam	FBtr0078580	72	52	F	2
-input1.bam	FBtr0078580	72	72	F	0
-input1.bam	FBtr0078790	73	1	F	1
-input1.bam	FBtr0078790	73	17	F	2
-input1.bam	FBtr0078790	73	33	F	1
-input1.bam	FBtr0078790	73	47	F	9
-input1.bam	FBtr0078790	73	69	R	1
-input1.bam	FBtr0078790	73	73	F	0
-input1.bam	FBtr0079064	72	1	F	0
-input1.bam	FBtr0079064	72	2	F	2
-input1.bam	FBtr0079064	72	33	F	1
-input1.bam	FBtr0079064	72	52	F	1
-input1.bam	FBtr0079064	72	72	F	0
-input1.bam	FBtr0079090	72	1	F	2
-input1.bam	FBtr0079090	72	26	F	1
-input1.bam	FBtr0079090	72	33	F	1
-input1.bam	FBtr0079090	72	53	F	1
-input1.bam	FBtr0079090	72	56	R	1
-input1.bam	FBtr0079090	72	72	F	0
-input1.bam	FBtr0079338	73	1	F	0
-input1.bam	FBtr0079338	73	14	F	5
-input1.bam	FBtr0079338	73	25	F	1
-input1.bam	FBtr0079338	73	44	F	10
-input1.bam	FBtr0079338	73	73	F	0
-input1.bam	FBtr0079528	71	1	F	0
-input1.bam	FBtr0079528	71	9	F	97
-input1.bam	FBtr0079528	71	28	F	1
-input1.bam	FBtr0079528	71	36	F	3
-input1.bam	FBtr0079528	71	51	F	5
-input1.bam	FBtr0079528	71	71	F	0
-input1.bam	FBtr0079596	73	1	F	0
-input1.bam	FBtr0079596	73	10	F	148
-input1.bam	FBtr0079596	73	53	F	4
-input1.bam	FBtr0079596	73	73	F	0
-input1.bam	FBtr0079677	72	1	F	0
-input1.bam	FBtr0079677	72	3	F	2
-input1.bam	FBtr0079677	72	52	F	2
-input1.bam	FBtr0079677	72	72	F	0
-input1.bam	FBtr0079690	72	1	F	1
-input1.bam	FBtr0079690	72	24	F	2
-input1.bam	FBtr0079690	72	33	F	2
-input1.bam	FBtr0079690	72	72	F	0
-input1.bam	FBtr0079692	73	1	F	3
-input1.bam	FBtr0079692	73	18	F	1
-input1.bam	FBtr0079692	73	25	F	1
-input1.bam	FBtr0079692	73	32	F	1
-input1.bam	FBtr0079692	73	73	F	0
-input1.bam	FBtr0079693	72	1	F	5
-input1.bam	FBtr0079693	72	25	F	1
-input1.bam	FBtr0079693	72	72	F	0
-input1.bam	FBtr0079694	72	1	F	5
-input1.bam	FBtr0079694	72	18	F	1
-input1.bam	FBtr0079694	72	52	F	1
-input1.bam	FBtr0079694	72	72	F	0
-input1.bam	FBtr0079702	72	1	F	1
-input1.bam	FBtr0079702	72	19	F	2
-input1.bam	FBtr0079702	72	56	F	1
-input1.bam	FBtr0079702	72	72	F	0
-input1.bam	FBtr0079728	72	1	F	2
-input1.bam	FBtr0079728	72	8	F	1
-input1.bam	FBtr0079728	72	19	F	1
-input1.bam	FBtr0079728	72	33	F	3
-input1.bam	FBtr0079728	72	56	F	1
-input1.bam	FBtr0079728	72	72	F	0
-input1.bam	FBtr0079729	72	1	F	1
-input1.bam	FBtr0079729	72	13	F	1
-input1.bam	FBtr0079729	72	54	F	2
-input1.bam	FBtr0079729	72	72	F	0
-input1.bam	FBtr0079752	72	1	F	2
-input1.bam	FBtr0079752	72	9	F	2
-input1.bam	FBtr0079752	72	33	F	2
-input1.bam	FBtr0079752	72	52	F	2
-input1.bam	FBtr0079752	72	72	F	0
-input1.bam	FBtr0079820	74	1	F	0
-input1.bam	FBtr0079820	74	50	F	13
-input1.bam	FBtr0079820	74	74	F	0
-input1.bam	FBtr0080609	72	1	F	0
-input1.bam	FBtr0080609	72	10	F	60
-input1.bam	FBtr0080609	72	42	F	1
-input1.bam	FBtr0080609	72	51	F	2
-input1.bam	FBtr0080609	72	72	F	0
-input1.bam	FBtr0080644	72	1	F	0
-input1.bam	FBtr0080644	72	6	F	6
-input1.bam	FBtr0080644	72	72	F	0
-input1.bam	FBtr0080646	72	1	F	0
-input1.bam	FBtr0080646	72	4	F	3
-input1.bam	FBtr0080646	72	72	F	0
-input1.bam	FBtr0080647	72	1	F	0
-input1.bam	FBtr0080647	72	6	F	10
-input1.bam	FBtr0080647	72	72	F	0
-input1.bam	FBtr0080660	72	1	F	0
-input1.bam	FBtr0080660	72	4	F	7
-input1.bam	FBtr0080660	72	72	F	0
-input1.bam	FBtr0080663	71	1	F	0
-input1.bam	FBtr0080663	71	9	F	102
-input1.bam	FBtr0080663	71	26	F	1
-input1.bam	FBtr0080663	71	32	F	2
-input1.bam	FBtr0080663	71	50	F	10
-input1.bam	FBtr0080663	71	71	F	0
-input1.bam	FBtr0080664	71	1	F	0
-input1.bam	FBtr0080664	71	11	F	108
-input1.bam	FBtr0080664	71	33	F	9
-input1.bam	FBtr0080664	71	53	F	11
-input1.bam	FBtr0080664	71	71	F	0
diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/input1_counts.tab
--- a/test-data/input1_counts.tab	Wed Apr 10 06:38:33 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,300 +0,0 @@
-Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts
-input1.bam	FBtr0070001	72	1	F	1
-input1.bam	FBtr0070001	72	7	F	6
-input1.bam	FBtr0070001	72	8	F	3
-input1.bam	FBtr0070001	72	11	F	2
-input1.bam	FBtr0070001	72	16	F	1
-input1.bam	FBtr0070001	72	17	F	1
-input1.bam	FBtr0070001	72	18	F	1
-input1.bam	FBtr0070001	72	27	F	2
-input1.bam	FBtr0070001	72	30	F	1
-input1.bam	FBtr0070001	72	31	F	11
-input1.bam	FBtr0070001	72	32	F	27
-input1.bam	FBtr0070001	72	34	F	1
-input1.bam	FBtr0070001	72	72	F	0
-input1.bam	FBtr0070533	72	1	F	1
-input1.bam	FBtr0070533	72	12	F	2
-input1.bam	FBtr0070533	72	15	F	1
-input1.bam	FBtr0070533	72	19	F	5
-input1.bam	FBtr0070533	72	20	F	1
-input1.bam	FBtr0070533	72	21	F	1
-input1.bam	FBtr0070533	72	22	F	1
-input1.bam	FBtr0070533	72	25	F	1
-input1.bam	FBtr0070533	72	26	F	1
-input1.bam	FBtr0070533	72	28	F	1
-input1.bam	FBtr0070533	72	32	F	4
-input1.bam	FBtr0070533	72	35	F	1
-input1.bam	FBtr0070533	72	37	F	2
-input1.bam	FBtr0070533	72	38	F	2
-input1.bam	FBtr0070533	72	72	F	0
-input1.bam	FBtr0070603	72	1	F	2
-input1.bam	FBtr0070603	72	3	F	1
-input1.bam	FBtr0070603	72	4	F	1
-input1.bam	FBtr0070603	72	6	F	1
-input1.bam	FBtr0070603	72	7	F	7
-input1.bam	FBtr0070603	72	8	F	4
-input1.bam	FBtr0070603	72	9	F	7
-input1.bam	FBtr0070603	72	12	F	2
-input1.bam	FBtr0070603	72	13	F	1
-input1.bam	FBtr0070603	72	15	F	2
-input1.bam	FBtr0070603	72	16	F	2
-input1.bam	FBtr0070603	72	17	F	3
-input1.bam	FBtr0070603	72	18	F	1
-input1.bam	FBtr0070603	72	19	F	9
-input1.bam	FBtr0070603	72	20	F	3
-input1.bam	FBtr0070603	72	21	F	1
-input1.bam	FBtr0070603	72	22	F	3
-input1.bam	FBtr0070603	72	24	F	2
-input1.bam	FBtr0070603	72	25	F	1
-input1.bam	FBtr0070603	72	26	F	6
-input1.bam	FBtr0070603	72	27	F	3
-input1.bam	FBtr0070603	72	32	F	1
-input1.bam	FBtr0070603	72	34	F	3
-input1.bam	FBtr0070603	72	38	F	1
-input1.bam	FBtr0070603	72	42	F	1
-input1.bam	FBtr0070603	72	51	F	1
-input1.bam	FBtr0070603	72	56	F	1
-input1.bam	FBtr0070603	72	72	F	0
-input1.bam	FBtr0070604	72	1	F	1
-input1.bam	FBtr0070604	72	18	F	1
-input1.bam	FBtr0070604	72	22	F	1
-input1.bam	FBtr0070604	72	30	F	2
-input1.bam	FBtr0070604	72	31	F	10
-input1.bam	FBtr0070604	72	32	F	24
-input1.bam	FBtr0070604	72	57	F	1
-input1.bam	FBtr0070604	72	72	F	0
-input1.bam	FBtr0070911	73	1	F	0
-input1.bam	FBtr0070911	73	15	F	1
-input1.bam	FBtr0070911	73	38	F	1
-input1.bam	FBtr0070911	73	73	F	0
-input1.bam	FBtr0078490	72	1	F	0
-input1.bam	FBtr0078490	72	13	F	2
-input1.bam	FBtr0078490	72	17	F	1
-input1.bam	FBtr0078490	72	18	F	1
-input1.bam	FBtr0078490	72	25	F	1
-input1.bam	FBtr0078490	72	28	F	2
-input1.bam	FBtr0078490	72	38	F	1
-input1.bam	FBtr0078490	72	72	F	0
-input1.bam	FBtr0078580	72	1	F	1041
-input1.bam	FBtr0078580	72	3	F	3
-input1.bam	FBtr0078580	72	4	F	4
-input1.bam	FBtr0078580	72	5	F	5
-input1.bam	FBtr0078580	72	6	F	4
-input1.bam	FBtr0078580	72	7	F	1
-input1.bam	FBtr0078580	72	8	F	2
-input1.bam	FBtr0078580	72	11	F	1
-input1.bam	FBtr0078580	72	12	F	13
-input1.bam	FBtr0078580	72	14	F	7
-input1.bam	FBtr0078580	72	15	F	1
-input1.bam	FBtr0078580	72	16	F	4
-input1.bam	FBtr0078580	72	17	F	1
-input1.bam	FBtr0078580	72	19	F	1
-input1.bam	FBtr0078580	72	20	F	2
-input1.bam	FBtr0078580	72	21	F	5
-input1.bam	FBtr0078580	72	24	F	3
-input1.bam	FBtr0078580	72	25	F	2
-input1.bam	FBtr0078580	72	29	F	1
-input1.bam	FBtr0078580	72	31	F	1
-input1.bam	FBtr0078580	72	52	F	2
-input1.bam	FBtr0078580	72	72	F	0
-input1.bam	FBtr0078790	73	1	F	1
-input1.bam	FBtr0078790	73	17	F	2
-input1.bam	FBtr0078790	73	33	F	1
-input1.bam	FBtr0078790	73	42	F	4
-input1.bam	FBtr0078790	73	44	F	2
-input1.bam	FBtr0078790	73	46	F	1
-input1.bam	FBtr0078790	73	47	F	1
-input1.bam	FBtr0078790	73	52	F	1
-input1.bam	FBtr0078790	73	69	R	1
-input1.bam	FBtr0078790	73	73	F	0
-input1.bam	FBtr0079064	72	1	F	1
-input1.bam	FBtr0079064	72	3	F	1
-input1.bam	FBtr0079064	72	33	F	1
-input1.bam	FBtr0079064	72	52	F	1
-input1.bam	FBtr0079064	72	72	F	0
-input1.bam	FBtr0079090	72	1	F	2
-input1.bam	FBtr0079090	72	26	F	1
-input1.bam	FBtr0079090	72	33	F	1
-input1.bam	FBtr0079090	72	53	F	1
-input1.bam	FBtr0079090	72	56	R	1
-input1.bam	FBtr0079090	72	72	F	0
-input1.bam	FBtr0079338	73	1	F	0
-input1.bam	FBtr0079338	73	12	F	1
-input1.bam	FBtr0079338	73	13	F	2
-input1.bam	FBtr0079338	73	14	F	1
-input1.bam	FBtr0079338	73	17	F	1
-input1.bam	FBtr0079338	73	25	F	1
-input1.bam	FBtr0079338	73	42	F	8
-input1.bam	FBtr0079338	73	43	F	1
-input1.bam	FBtr0079338	73	46	F	1
-input1.bam	FBtr0079338	73	73	F	0
-input1.bam	FBtr0079528	71	1	F	19
-input1.bam	FBtr0079528	71	3	F	55
-input1.bam	FBtr0079528	71	4	F	2
-input1.bam	FBtr0079528	71	8	F	4
-input1.bam	FBtr0079528	71	10	F	1
-input1.bam	FBtr0079528	71	11	F	2
-input1.bam	FBtr0079528	71	13	F	1
-input1.bam	FBtr0079528	71	14	F	4
-input1.bam	FBtr0079528	71	16	F	1
-input1.bam	FBtr0079528	71	17	F	4
-input1.bam	FBtr0079528	71	18	F	4
-input1.bam	FBtr0079528	71	28	F	1
-input1.bam	FBtr0079528	71	35	F	1
-input1.bam	FBtr0079528	71	36	F	1
-input1.bam	FBtr0079528	71	37	F	1
-input1.bam	FBtr0079528	71	51	F	5
-input1.bam	FBtr0079528	71	71	F	0
-input1.bam	FBtr0079596	73	1	F	13
-input1.bam	FBtr0079596	73	3	F	13
-input1.bam	FBtr0079596	73	4	F	31
-input1.bam	FBtr0079596	73	5	F	2
-input1.bam	FBtr0079596	73	6	F	11
-input1.bam	FBtr0079596	73	8	F	9
-input1.bam	FBtr0079596	73	9	F	12
-input1.bam	FBtr0079596	73	10	F	3
-input1.bam	FBtr0079596	73	11	F	19
-input1.bam	FBtr0079596	73	12	F	1
-input1.bam	FBtr0079596	73	13	F	20
-input1.bam	FBtr0079596	73	14	F	6
-input1.bam	FBtr0079596	73	15	F	1
-input1.bam	FBtr0079596	73	16	F	3
-input1.bam	FBtr0079596	73	17	F	2
-input1.bam	FBtr0079596	73	18	F	1
-input1.bam	FBtr0079596	73	19	F	1
-input1.bam	FBtr0079596	73	53	F	2
-input1.bam	FBtr0079596	73	54	F	2
-input1.bam	FBtr0079596	73	73	F	0
-input1.bam	FBtr0079677	72	1	F	1
-input1.bam	FBtr0079677	72	5	F	1
-input1.bam	FBtr0079677	72	52	F	1
-input1.bam	FBtr0079677	72	53	F	1
-input1.bam	FBtr0079677	72	72	F	0
-input1.bam	FBtr0079690	72	1	F	1
-input1.bam	FBtr0079690	72	22	F	1
-input1.bam	FBtr0079690	72	27	F	1
-input1.bam	FBtr0079690	72	33	F	2
-input1.bam	FBtr0079690	72	72	F	0
-input1.bam	FBtr0079692	73	1	F	3
-input1.bam	FBtr0079692	73	18	F	1
-input1.bam	FBtr0079692	73	25	F	1
-input1.bam	FBtr0079692	73	32	F	1
-input1.bam	FBtr0079692	73	73	F	0
-input1.bam	FBtr0079693	72	1	F	5
-input1.bam	FBtr0079693	72	25	F	1
-input1.bam	FBtr0079693	72	72	F	0
-input1.bam	FBtr0079694	72	1	F	5
-input1.bam	FBtr0079694	72	18	F	1
-input1.bam	FBtr0079694	72	52	F	1
-input1.bam	FBtr0079694	72	72	F	0
-input1.bam	FBtr0079702	72	1	F	1
-input1.bam	FBtr0079702	72	19	F	2
-input1.bam	FBtr0079702	72	56	F	1
-input1.bam	FBtr0079702	72	72	F	0
-input1.bam	FBtr0079728	72	1	F	2
-input1.bam	FBtr0079728	72	8	F	1
-input1.bam	FBtr0079728	72	19	F	1
-input1.bam	FBtr0079728	72	33	F	3
-input1.bam	FBtr0079728	72	56	F	1
-input1.bam	FBtr0079728	72	72	F	0
-input1.bam	FBtr0079729	72	1	F	1
-input1.bam	FBtr0079729	72	13	F	1
-input1.bam	FBtr0079729	72	52	F	1
-input1.bam	FBtr0079729	72	57	F	1
-input1.bam	FBtr0079729	72	72	F	0
-input1.bam	FBtr0079752	72	1	F	2
-input1.bam	FBtr0079752	72	7	F	1
-input1.bam	FBtr0079752	72	12	F	1
-input1.bam	FBtr0079752	72	33	F	2
-input1.bam	FBtr0079752	72	52	F	2
-input1.bam	FBtr0079752	72	72	F	0
-input1.bam	FBtr0079820	74	1	F	0
-input1.bam	FBtr0079820	74	45	F	1
-input1.bam	FBtr0079820	74	46	F	2
-input1.bam	FBtr0079820	74	48	F	1
-input1.bam	FBtr0079820	74	49	F	1
-input1.bam	FBtr0079820	74	51	F	1
-input1.bam	FBtr0079820	74	54	F	4
-input1.bam	FBtr0079820	74	55	F	1
-input1.bam	FBtr0079820	74	56	F	2
-input1.bam	FBtr0079820	74	74	F	0
-input1.bam	FBtr0080609	72	1	F	13
-input1.bam	FBtr0080609	72	3	F	2
-input1.bam	FBtr0080609	72	4	F	10
-input1.bam	FBtr0080609	72	5	F	2
-input1.bam	FBtr0080609	72	7	F	19
-input1.bam	FBtr0080609	72	8	F	4
-input1.bam	FBtr0080609	72	9	F	3
-input1.bam	FBtr0080609	72	12	F	1
-input1.bam	FBtr0080609	72	15	F	1
-input1.bam	FBtr0080609	72	16	F	1
-input1.bam	FBtr0080609	72	17	F	2
-input1.bam	FBtr0080609	72	19	F	1
-input1.bam	FBtr0080609	72	20	F	1
-input1.bam	FBtr0080609	72	42	F	1
-input1.bam	FBtr0080609	72	51	F	1
-input1.bam	FBtr0080609	72	52	F	1
-input1.bam	FBtr0080609	72	72	F	0
-input1.bam	FBtr0080644	72	1	F	1
-input1.bam	FBtr0080644	72	4	F	2
-input1.bam	FBtr0080644	72	7	F	1
-input1.bam	FBtr0080644	72	12	F	2
-input1.bam	FBtr0080644	72	72	F	0
-input1.bam	FBtr0080646	72	1	F	1
-input1.bam	FBtr0080646	72	6	F	1
-input1.bam	FBtr0080646	72	7	F	1
-input1.bam	FBtr0080646	72	72	F	0
-input1.bam	FBtr0080647	72	1	F	3
-input1.bam	FBtr0080647	72	3	F	1
-input1.bam	FBtr0080647	72	6	F	2
-input1.bam	FBtr0080647	72	8	F	1
-input1.bam	FBtr0080647	72	11	F	2
-input1.bam	FBtr0080647	72	12	F	1
-input1.bam	FBtr0080647	72	72	F	0
-input1.bam	FBtr0080660	72	1	F	0
-input1.bam	FBtr0080660	72	4	F	4
-input1.bam	FBtr0080660	72	7	F	3
-input1.bam	FBtr0080660	72	72	F	0
-input1.bam	FBtr0080663	71	1	F	22
-input1.bam	FBtr0080663	71	3	F	56
-input1.bam	FBtr0080663	71	4	F	4
-input1.bam	FBtr0080663	71	7	F	1
-input1.bam	FBtr0080663	71	8	F	4
-input1.bam	FBtr0080663	71	12	F	2
-input1.bam	FBtr0080663	71	14	F	2
-input1.bam	FBtr0080663	71	15	F	1
-input1.bam	FBtr0080663	71	16	F	3
-input1.bam	FBtr0080663	71	17	F	7
-input1.bam	FBtr0080663	71	26	F	1
-input1.bam	FBtr0080663	71	32	F	2
-input1.bam	FBtr0080663	71	50	F	1
-input1.bam	FBtr0080663	71	51	F	9
-input1.bam	FBtr0080663	71	71	F	0
-input1.bam	FBtr0080664	71	1	F	16
-input1.bam	FBtr0080664	71	3	F	56
-input1.bam	FBtr0080664	71	4	F	4
-input1.bam	FBtr0080664	71	6	F	1
-input1.bam	FBtr0080664	71	7	F	1
-input1.bam	FBtr0080664	71	8	F	4
-input1.bam	FBtr0080664	71	9	F	1
-input1.bam	FBtr0080664	71	11	F	3
-input1.bam	FBtr0080664	71	12	F	3
-input1.bam	FBtr0080664	71	13	F	2
-input1.bam	FBtr0080664	71	14	F	3
-input1.bam	FBtr0080664	71	16	F	2
-input1.bam	FBtr0080664	71	17	F	10
-input1.bam	FBtr0080664	71	18	F	1
-input1.bam	FBtr0080664	71	21	F	1
-input1.bam	FBtr0080664	71	28	F	2
-input1.bam	FBtr0080664	71	32	F	1
-input1.bam	FBtr0080664	71	33	F	1
-input1.bam	FBtr0080664	71	34	F	1
-input1.bam	FBtr0080664	71	35	F	1
-input1.bam	FBtr0080664	71	36	F	1
-input1.bam	FBtr0080664	71	37	F	1
-input1.bam	FBtr0080664	71	38	F	1
-input1.bam	FBtr0080664	71	50	F	2
-input1.bam	FBtr0080664	71	51	F	7
-input1.bam	FBtr0080664	71	52	F	1
-input1.bam	FBtr0080664	71	56	F	1
-input1.bam	FBtr0080664	71	71	F	0
diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/input1_counts_yminneg5_5.tab
--- a/test-data/input1_counts_yminneg5_5.tab	Wed Apr 10 06:38:33 2019 -0400
+++ b/test-data/input1_counts_yminneg5_5.tab	Sun Apr 14 14:43:44 2019 -0400
@@ -1,300 +1,190 @@
 Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts
-input1.bam	FBtr0070001	72	1	F	1
-input1.bam	FBtr0070001	72	7	F	6
+input1.bam	FBtr0070001	72	1	F	0
+input1.bam	FBtr0070001	72	7	F	5
 input1.bam	FBtr0070001	72	8	F	3
 input1.bam	FBtr0070001	72	11	F	2
 input1.bam	FBtr0070001	72	16	F	1
 input1.bam	FBtr0070001	72	17	F	1
-input1.bam	FBtr0070001	72	18	F	1
 input1.bam	FBtr0070001	72	27	F	2
 input1.bam	FBtr0070001	72	30	F	1
 input1.bam	FBtr0070001	72	31	F	11
 input1.bam	FBtr0070001	72	32	F	27
 input1.bam	FBtr0070001	72	34	F	1
 input1.bam	FBtr0070001	72	72	F	0
-input1.bam	FBtr0070533	72	1	F	1
-input1.bam	FBtr0070533	72	12	F	2
-input1.bam	FBtr0070533	72	15	F	1
+input1.bam	FBtr0070533	72	1	F	0
 input1.bam	FBtr0070533	72	19	F	5
 input1.bam	FBtr0070533	72	20	F	1
-input1.bam	FBtr0070533	72	21	F	1
 input1.bam	FBtr0070533	72	22	F	1
-input1.bam	FBtr0070533	72	25	F	1
-input1.bam	FBtr0070533	72	26	F	1
 input1.bam	FBtr0070533	72	28	F	1
-input1.bam	FBtr0070533	72	32	F	4
+input1.bam	FBtr0070533	72	32	F	3
 input1.bam	FBtr0070533	72	35	F	1
 input1.bam	FBtr0070533	72	37	F	2
-input1.bam	FBtr0070533	72	38	F	2
 input1.bam	FBtr0070533	72	72	F	0
-input1.bam	FBtr0070603	72	1	F	2
+input1.bam	FBtr0070603	72	1	F	0
 input1.bam	FBtr0070603	72	3	F	1
 input1.bam	FBtr0070603	72	4	F	1
-input1.bam	FBtr0070603	72	6	F	1
-input1.bam	FBtr0070603	72	7	F	7
-input1.bam	FBtr0070603	72	8	F	4
-input1.bam	FBtr0070603	72	9	F	7
-input1.bam	FBtr0070603	72	12	F	2
+input1.bam	FBtr0070603	72	12	F	1
 input1.bam	FBtr0070603	72	13	F	1
-input1.bam	FBtr0070603	72	15	F	2
-input1.bam	FBtr0070603	72	16	F	2
+input1.bam	FBtr0070603	72	15	F	1
+input1.bam	FBtr0070603	72	16	F	1
 input1.bam	FBtr0070603	72	17	F	3
-input1.bam	FBtr0070603	72	18	F	1
-input1.bam	FBtr0070603	72	19	F	9
-input1.bam	FBtr0070603	72	20	F	3
+input1.bam	FBtr0070603	72	19	F	8
+input1.bam	FBtr0070603	72	20	F	2
 input1.bam	FBtr0070603	72	21	F	1
 input1.bam	FBtr0070603	72	22	F	3
-input1.bam	FBtr0070603	72	24	F	2
+input1.bam	FBtr0070603	72	24	F	1
 input1.bam	FBtr0070603	72	25	F	1
 input1.bam	FBtr0070603	72	26	F	6
 input1.bam	FBtr0070603	72	27	F	3
 input1.bam	FBtr0070603	72	32	F	1
-input1.bam	FBtr0070603	72	34	F	3
-input1.bam	FBtr0070603	72	38	F	1
+input1.bam	FBtr0070603	72	34	F	2
 input1.bam	FBtr0070603	72	42	F	1
-input1.bam	FBtr0070603	72	51	F	1
-input1.bam	FBtr0070603	72	56	F	1
 input1.bam	FBtr0070603	72	72	F	0
-input1.bam	FBtr0070604	72	1	F	1
+input1.bam	FBtr0070604	72	1	F	0
 input1.bam	FBtr0070604	72	18	F	1
 input1.bam	FBtr0070604	72	22	F	1
-input1.bam	FBtr0070604	72	30	F	2
 input1.bam	FBtr0070604	72	31	F	10
 input1.bam	FBtr0070604	72	32	F	24
-input1.bam	FBtr0070604	72	57	F	1
 input1.bam	FBtr0070604	72	72	F	0
 input1.bam	FBtr0070911	73	1	F	0
 input1.bam	FBtr0070911	73	15	F	1
-input1.bam	FBtr0070911	73	38	F	1
 input1.bam	FBtr0070911	73	73	F	0
 input1.bam	FBtr0078490	72	1	F	0
-input1.bam	FBtr0078490	72	13	F	2
-input1.bam	FBtr0078490	72	17	F	1
-input1.bam	FBtr0078490	72	18	F	1
-input1.bam	FBtr0078490	72	25	F	1
-input1.bam	FBtr0078490	72	28	F	2
-input1.bam	FBtr0078490	72	38	F	1
+input1.bam	FBtr0078490	72	28	F	1
 input1.bam	FBtr0078490	72	72	F	0
-input1.bam	FBtr0078580	72	1	F	1041
+input1.bam	FBtr0078580	72	1	F	420
 input1.bam	FBtr0078580	72	3	F	3
 input1.bam	FBtr0078580	72	4	F	4
 input1.bam	FBtr0078580	72	5	F	5
-input1.bam	FBtr0078580	72	6	F	4
+input1.bam	FBtr0078580	72	6	F	2
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-input1.bam	FBtr0080664	71	11	F	3
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-input1.bam	FBtr0080664	71	14	F	3
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-input1.bam	FBtr0080664	71	17	F	10
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-input1.bam	FBtr0080664	71	28	F	2
-input1.bam	FBtr0080664	71	32	F	1
+input1.bam	FBtr0080664	71	14	F	1
+input1.bam	FBtr0080664	71	17	F	1
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-input1.bam	FBtr0080664	71	34	F	1
-input1.bam	FBtr0080664	71	35	F	1
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-input1.bam	FBtr0080664	71	37	F	1
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-input1.bam	FBtr0080664	71	52	F	1
-input1.bam	FBtr0080664	71	56	F	1
 input1.bam	FBtr0080664	71	71	F	0
diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/input1_coverage.tab
--- a/test-data/input1_coverage.tab	Wed Apr 10 06:38:33 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1603 +0,0 @@
-Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Coverage
-input1.bam	FBtr0070001	72	1	F	1
-input1.bam	FBtr0070001	72	2	F	1
-input1.bam	FBtr0070001	72	3	F	1
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-input1.bam	FBtr0070001	72	8	F	10
-input1.bam	FBtr0070001	72	9	F	10
-input1.bam	FBtr0070001	72	10	F	10
-input1.bam	FBtr0070001	72	11	F	12
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-input1.bam	FBtr0070001	72	13	F	12
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-input1.bam	FBtr0070001	72	15	F	12
-input1.bam	FBtr0070001	72	16	F	13
-input1.bam	FBtr0070001	72	17	F	14
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-input1.bam	FBtr0070001	72	28	F	11
-input1.bam	FBtr0070001	72	29	F	8
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-input1.bam	FBtr0070001	72	32	F	44
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-input1.bam	FBtr0070533	72	30	F	11
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-input1.bam	FBtr0070533	72	32	F	15
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-input1.bam	FBtr0070533	72	72	F	0
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-input1.bam	FBtr0079752	72	46	F	2
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-input1.bam	FBtr0079752	72	53	F	2
-input1.bam	FBtr0079752	72	54	F	2
-input1.bam	FBtr0079752	72	55	F	2
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-input1.bam	FBtr0079820	74	48	F	4
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-input1.bam	FBtr0079820	74	50	F	5
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-input1.bam	FBtr0079820	74	58	F	13
-input1.bam	FBtr0079820	74	59	F	13
-input1.bam	FBtr0079820	74	60	F	13
-input1.bam	FBtr0079820	74	61	F	13
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-input1.bam	FBtr0080609	72	1	F	13
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-input1.bam	FBtr0080609	72	3	F	15
-input1.bam	FBtr0080609	72	4	F	25
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-input1.bam	FBtr0080609	72	6	F	27
-input1.bam	FBtr0080609	72	7	F	46
-input1.bam	FBtr0080609	72	8	F	50
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-input1.bam	FBtr0080609	72	18	F	57
-input1.bam	FBtr0080609	72	19	F	49
-input1.bam	FBtr0080609	72	20	F	50
-input1.bam	FBtr0080609	72	21	F	50
-input1.bam	FBtr0080609	72	22	F	49
-input1.bam	FBtr0080609	72	23	F	49
-input1.bam	FBtr0080609	72	24	F	8
-input1.bam	FBtr0080609	72	25	F	7
-input1.bam	FBtr0080609	72	26	F	7
-input1.bam	FBtr0080609	72	27	F	7
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-input1.bam	FBtr0080609	72	30	F	7
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-input1.bam	FBtr0080609	72	36	F	4
-input1.bam	FBtr0080609	72	37	F	4
-input1.bam	FBtr0080609	72	38	F	4
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-input1.bam	FBtr0080609	72	41	F	2
-input1.bam	FBtr0080609	72	42	F	3
-input1.bam	FBtr0080609	72	43	F	3
-input1.bam	FBtr0080609	72	44	F	3
-input1.bam	FBtr0080609	72	45	F	1
-input1.bam	FBtr0080609	72	46	F	1
-input1.bam	FBtr0080609	72	47	F	1
-input1.bam	FBtr0080609	72	48	F	1
-input1.bam	FBtr0080609	72	49	F	1
-input1.bam	FBtr0080609	72	50	F	1
-input1.bam	FBtr0080609	72	51	F	2
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-input1.bam	FBtr0080609	72	53	F	3
-input1.bam	FBtr0080609	72	54	F	3
-input1.bam	FBtr0080609	72	55	F	3
-input1.bam	FBtr0080609	72	56	F	3
-input1.bam	FBtr0080609	72	57	F	3
-input1.bam	FBtr0080609	72	58	F	3
-input1.bam	FBtr0080609	72	59	F	3
-input1.bam	FBtr0080609	72	60	F	3
-input1.bam	FBtr0080609	72	61	F	3
-input1.bam	FBtr0080609	72	62	F	3
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-input1.bam	FBtr0080609	72	64	F	2
-input1.bam	FBtr0080609	72	65	F	2
-input1.bam	FBtr0080609	72	66	F	2
-input1.bam	FBtr0080609	72	67	F	1
-input1.bam	FBtr0080609	72	68	F	1
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-input1.bam	FBtr0080644	72	1	F	1
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-input1.bam	FBtr0080644	72	3	F	1
-input1.bam	FBtr0080644	72	4	F	3
-input1.bam	FBtr0080644	72	5	F	3
-input1.bam	FBtr0080644	72	6	F	3
-input1.bam	FBtr0080644	72	7	F	4
-input1.bam	FBtr0080644	72	8	F	4
-input1.bam	FBtr0080644	72	9	F	4
-input1.bam	FBtr0080644	72	10	F	4
-input1.bam	FBtr0080644	72	11	F	4
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-input1.bam	FBtr0080644	72	26	F	4
-input1.bam	FBtr0080644	72	27	F	4
-input1.bam	FBtr0080644	72	72	F	0
-input1.bam	FBtr0080646	72	1	F	1
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-input1.bam	FBtr0080646	72	4	F	1
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-input1.bam	FBtr0080646	72	6	F	2
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-input1.bam	FBtr0080646	72	17	F	2
-input1.bam	FBtr0080646	72	18	F	2
-input1.bam	FBtr0080646	72	19	F	2
-input1.bam	FBtr0080646	72	20	F	2
-input1.bam	FBtr0080646	72	21	F	2
-input1.bam	FBtr0080646	72	22	F	2
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-input1.bam	FBtr0080646	72	24	F	2
-input1.bam	FBtr0080646	72	25	F	2
-input1.bam	FBtr0080646	72	26	F	2
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-input1.bam	FBtr0080647	72	1	F	3
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-input1.bam	FBtr0080647	72	3	F	4
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-input1.bam	FBtr0080647	72	5	F	4
-input1.bam	FBtr0080647	72	6	F	6
-input1.bam	FBtr0080647	72	7	F	6
-input1.bam	FBtr0080647	72	8	F	7
-input1.bam	FBtr0080647	72	9	F	7
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-input1.bam	FBtr0080647	72	13	F	10
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-input1.bam	FBtr0080647	72	22	F	5
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-input1.bam	FBtr0080647	72	24	F	5
-input1.bam	FBtr0080647	72	25	F	5
-input1.bam	FBtr0080647	72	26	F	5
-input1.bam	FBtr0080647	72	27	F	5
-input1.bam	FBtr0080647	72	72	F	0
-input1.bam	FBtr0080660	72	1	F	0
-input1.bam	FBtr0080660	72	4	F	4
-input1.bam	FBtr0080660	72	5	F	4
-input1.bam	FBtr0080660	72	6	F	4
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-input1.bam	FBtr0080660	72	8	F	7
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-input1.bam	FBtr0080660	72	12	F	7
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-input1.bam	FBtr0080660	72	14	F	7
-input1.bam	FBtr0080660	72	15	F	7
-input1.bam	FBtr0080660	72	16	F	7
-input1.bam	FBtr0080660	72	17	F	7
-input1.bam	FBtr0080660	72	18	F	7
-input1.bam	FBtr0080660	72	19	F	7
-input1.bam	FBtr0080660	72	20	F	7
-input1.bam	FBtr0080660	72	21	F	7
-input1.bam	FBtr0080660	72	22	F	7
-input1.bam	FBtr0080660	72	23	F	6
-input1.bam	FBtr0080660	72	24	F	6
-input1.bam	FBtr0080660	72	25	F	6
-input1.bam	FBtr0080660	72	26	F	6
-input1.bam	FBtr0080660	72	27	F	6
-input1.bam	FBtr0080660	72	72	F	0
-input1.bam	FBtr0080663	71	1	F	22
-input1.bam	FBtr0080663	71	2	F	22
-input1.bam	FBtr0080663	71	3	F	78
-input1.bam	FBtr0080663	71	4	F	82
-input1.bam	FBtr0080663	71	5	F	82
-input1.bam	FBtr0080663	71	6	F	82
-input1.bam	FBtr0080663	71	7	F	83
-input1.bam	FBtr0080663	71	8	F	87
-input1.bam	FBtr0080663	71	9	F	87
-input1.bam	FBtr0080663	71	10	F	87
-input1.bam	FBtr0080663	71	11	F	87
-input1.bam	FBtr0080663	71	12	F	89
-input1.bam	FBtr0080663	71	13	F	89
-input1.bam	FBtr0080663	71	14	F	91
-input1.bam	FBtr0080663	71	15	F	92
-input1.bam	FBtr0080663	71	16	F	93
-input1.bam	FBtr0080663	71	17	F	89
-input1.bam	FBtr0080663	71	18	F	86
-input1.bam	FBtr0080663	71	19	F	86
-input1.bam	FBtr0080663	71	20	F	86
-input1.bam	FBtr0080663	71	21	F	86
-input1.bam	FBtr0080663	71	22	F	86
-input1.bam	FBtr0080663	71	23	F	78
-input1.bam	FBtr0080663	71	24	F	77
-input1.bam	FBtr0080663	71	25	F	77
-input1.bam	FBtr0080663	71	26	F	70
-input1.bam	FBtr0080663	71	27	F	34
-input1.bam	FBtr0080663	71	28	F	21
-input1.bam	FBtr0080663	71	29	F	14
-input1.bam	FBtr0080663	71	30	F	14
-input1.bam	FBtr0080663	71	31	F	13
-input1.bam	FBtr0080663	71	32	F	7
-input1.bam	FBtr0080663	71	33	F	4
-input1.bam	FBtr0080663	71	34	F	4
-input1.bam	FBtr0080663	71	35	F	3
-input1.bam	FBtr0080663	71	36	F	3
-input1.bam	FBtr0080663	71	37	F	3
-input1.bam	FBtr0080663	71	38	F	3
-input1.bam	FBtr0080663	71	39	F	3
-input1.bam	FBtr0080663	71	40	F	3
-input1.bam	FBtr0080663	71	41	F	3
-input1.bam	FBtr0080663	71	42	F	3
-input1.bam	FBtr0080663	71	43	F	3
-input1.bam	FBtr0080663	71	44	F	2
-input1.bam	FBtr0080663	71	45	F	2
-input1.bam	FBtr0080663	71	46	F	2
-input1.bam	FBtr0080663	71	47	F	1
-input1.bam	FBtr0080663	71	50	F	1
-input1.bam	FBtr0080663	71	51	F	10
-input1.bam	FBtr0080663	71	52	F	10
-input1.bam	FBtr0080663	71	53	F	10
-input1.bam	FBtr0080663	71	54	F	10
-input1.bam	FBtr0080663	71	55	F	10
-input1.bam	FBtr0080663	71	56	F	10
-input1.bam	FBtr0080663	71	57	F	10
-input1.bam	FBtr0080663	71	58	F	10
-input1.bam	FBtr0080663	71	59	F	10
-input1.bam	FBtr0080663	71	60	F	10
-input1.bam	FBtr0080663	71	61	F	10
-input1.bam	FBtr0080663	71	62	F	10
-input1.bam	FBtr0080663	71	63	F	10
-input1.bam	FBtr0080663	71	64	F	10
-input1.bam	FBtr0080663	71	65	F	10
-input1.bam	FBtr0080663	71	66	F	2
-input1.bam	FBtr0080663	71	67	F	1
-input1.bam	FBtr0080663	71	68	F	1
-input1.bam	FBtr0080663	71	69	F	1
-input1.bam	FBtr0080663	71	70	F	1
-input1.bam	FBtr0080663	71	71	F	0
-input1.bam	FBtr0080664	71	1	F	16
-input1.bam	FBtr0080664	71	2	F	16
-input1.bam	FBtr0080664	71	3	F	72
-input1.bam	FBtr0080664	71	4	F	76
-input1.bam	FBtr0080664	71	5	F	76
-input1.bam	FBtr0080664	71	6	F	77
-input1.bam	FBtr0080664	71	7	F	78
-input1.bam	FBtr0080664	71	8	F	82
-input1.bam	FBtr0080664	71	9	F	83
-input1.bam	FBtr0080664	71	10	F	83
-input1.bam	FBtr0080664	71	11	F	86
-input1.bam	FBtr0080664	71	12	F	89
-input1.bam	FBtr0080664	71	13	F	91
-input1.bam	FBtr0080664	71	14	F	94
-input1.bam	FBtr0080664	71	15	F	94
-input1.bam	FBtr0080664	71	16	F	95
-input1.bam	FBtr0080664	71	17	F	100
-input1.bam	FBtr0080664	71	18	F	98
-input1.bam	FBtr0080664	71	19	F	97
-input1.bam	FBtr0080664	71	20	F	97
-input1.bam	FBtr0080664	71	21	F	97
-input1.bam	FBtr0080664	71	22	F	97
-input1.bam	FBtr0080664	71	23	F	93
-input1.bam	FBtr0080664	71	24	F	88
-input1.bam	FBtr0080664	71	25	F	88
-input1.bam	FBtr0080664	71	26	F	82
-input1.bam	FBtr0080664	71	27	F	47
-input1.bam	FBtr0080664	71	28	F	33
-input1.bam	FBtr0080664	71	29	F	23
-input1.bam	FBtr0080664	71	30	F	23
-input1.bam	FBtr0080664	71	31	F	20
-input1.bam	FBtr0080664	71	32	F	13
-input1.bam	FBtr0080664	71	33	F	6
-input1.bam	FBtr0080664	71	34	F	7
-input1.bam	FBtr0080664	71	35	F	8
-input1.bam	FBtr0080664	71	36	F	7
-input1.bam	FBtr0080664	71	37	F	8
-input1.bam	FBtr0080664	71	38	F	9
-input1.bam	FBtr0080664	71	39	F	9
-input1.bam	FBtr0080664	71	40	F	9
-input1.bam	FBtr0080664	71	41	F	9
-input1.bam	FBtr0080664	71	42	F	9
-input1.bam	FBtr0080664	71	43	F	9
-input1.bam	FBtr0080664	71	44	F	7
-input1.bam	FBtr0080664	71	45	F	7
-input1.bam	FBtr0080664	71	46	F	7
-input1.bam	FBtr0080664	71	47	F	6
-input1.bam	FBtr0080664	71	48	F	6
-input1.bam	FBtr0080664	71	49	F	6
-input1.bam	FBtr0080664	71	50	F	6
-input1.bam	FBtr0080664	71	51	F	13
-input1.bam	FBtr0080664	71	52	F	14
-input1.bam	FBtr0080664	71	53	F	12
-input1.bam	FBtr0080664	71	54	F	12
-input1.bam	FBtr0080664	71	55	F	11
-input1.bam	FBtr0080664	71	56	F	12
-input1.bam	FBtr0080664	71	57	F	11
-input1.bam	FBtr0080664	71	58	F	11
-input1.bam	FBtr0080664	71	59	F	11
-input1.bam	FBtr0080664	71	60	F	11
-input1.bam	FBtr0080664	71	61	F	11
-input1.bam	FBtr0080664	71	62	F	11
-input1.bam	FBtr0080664	71	63	F	11
-input1.bam	FBtr0080664	71	64	F	11
-input1.bam	FBtr0080664	71	65	F	11
-input1.bam	FBtr0080664	71	66	F	2
-input1.bam	FBtr0080664	71	67	F	1
-input1.bam	FBtr0080664	71	68	F	1
-input1.bam	FBtr0080664	71	69	F	1
-input1.bam	FBtr0080664	71	70	F	1
-input1.bam	FBtr0080664	71	71	F	1
diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/input1_input2_counts.tab
--- a/test-data/input1_input2_counts.tab	Wed Apr 10 06:38:33 2019 -0400
+++ b/test-data/input1_input2_counts.tab	Sun Apr 14 14:43:44 2019 -0400
@@ -1,617 +1,392 @@
 Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts
-input1.bam	FBtr0070001	72	1	F	1
-input1.bam	FBtr0070001	72	7	F	6
+input1.bam	FBtr0070001	72	1	F	0
+input1.bam	FBtr0070001	72	7	F	5
 input1.bam	FBtr0070001	72	8	F	3
 input1.bam	FBtr0070001	72	11	F	2
 input1.bam	FBtr0070001	72	16	F	1
 input1.bam	FBtr0070001	72	17	F	1
-input1.bam	FBtr0070001	72	18	F	1
 input1.bam	FBtr0070001	72	27	F	2
 input1.bam	FBtr0070001	72	30	F	1
 input1.bam	FBtr0070001	72	31	F	11
 input1.bam	FBtr0070001	72	32	F	27
 input1.bam	FBtr0070001	72	34	F	1
 input1.bam	FBtr0070001	72	72	F	0
-input1.bam	FBtr0070533	72	1	F	1
-input1.bam	FBtr0070533	72	12	F	2
-input1.bam	FBtr0070533	72	15	F	1
+input1.bam	FBtr0070533	72	1	F	0
 input1.bam	FBtr0070533	72	19	F	5
 input1.bam	FBtr0070533	72	20	F	1
-input1.bam	FBtr0070533	72	21	F	1
 input1.bam	FBtr0070533	72	22	F	1
-input1.bam	FBtr0070533	72	25	F	1
-input1.bam	FBtr0070533	72	26	F	1
 input1.bam	FBtr0070533	72	28	F	1
-input1.bam	FBtr0070533	72	32	F	4
+input1.bam	FBtr0070533	72	32	F	3
 input1.bam	FBtr0070533	72	35	F	1
 input1.bam	FBtr0070533	72	37	F	2
-input1.bam	FBtr0070533	72	38	F	2
 input1.bam	FBtr0070533	72	72	F	0
-input1.bam	FBtr0070603	72	1	F	2
+input1.bam	FBtr0070603	72	1	F	0
 input1.bam	FBtr0070603	72	3	F	1
 input1.bam	FBtr0070603	72	4	F	1
-input1.bam	FBtr0070603	72	6	F	1
-input1.bam	FBtr0070603	72	7	F	7
-input1.bam	FBtr0070603	72	8	F	4
-input1.bam	FBtr0070603	72	9	F	7
-input1.bam	FBtr0070603	72	12	F	2
+input1.bam	FBtr0070603	72	12	F	1
 input1.bam	FBtr0070603	72	13	F	1
-input1.bam	FBtr0070603	72	15	F	2
-input1.bam	FBtr0070603	72	16	F	2
+input1.bam	FBtr0070603	72	15	F	1
+input1.bam	FBtr0070603	72	16	F	1
 input1.bam	FBtr0070603	72	17	F	3
-input1.bam	FBtr0070603	72	18	F	1
-input1.bam	FBtr0070603	72	19	F	9
-input1.bam	FBtr0070603	72	20	F	3
+input1.bam	FBtr0070603	72	19	F	8
+input1.bam	FBtr0070603	72	20	F	2
 input1.bam	FBtr0070603	72	21	F	1
 input1.bam	FBtr0070603	72	22	F	3
-input1.bam	FBtr0070603	72	24	F	2
+input1.bam	FBtr0070603	72	24	F	1
 input1.bam	FBtr0070603	72	25	F	1
 input1.bam	FBtr0070603	72	26	F	6
 input1.bam	FBtr0070603	72	27	F	3
 input1.bam	FBtr0070603	72	32	F	1
-input1.bam	FBtr0070603	72	34	F	3
-input1.bam	FBtr0070603	72	38	F	1
+input1.bam	FBtr0070603	72	34	F	2
 input1.bam	FBtr0070603	72	42	F	1
-input1.bam	FBtr0070603	72	51	F	1
-input1.bam	FBtr0070603	72	56	F	1
 input1.bam	FBtr0070603	72	72	F	0
-input1.bam	FBtr0070604	72	1	F	1
+input1.bam	FBtr0070604	72	1	F	0
 input1.bam	FBtr0070604	72	18	F	1
 input1.bam	FBtr0070604	72	22	F	1
-input1.bam	FBtr0070604	72	30	F	2
 input1.bam	FBtr0070604	72	31	F	10
 input1.bam	FBtr0070604	72	32	F	24
-input1.bam	FBtr0070604	72	57	F	1
 input1.bam	FBtr0070604	72	72	F	0
 input1.bam	FBtr0070911	73	1	F	0
 input1.bam	FBtr0070911	73	15	F	1
-input1.bam	FBtr0070911	73	38	F	1
 input1.bam	FBtr0070911	73	73	F	0
 input1.bam	FBtr0078490	72	1	F	0
-input1.bam	FBtr0078490	72	13	F	2
-input1.bam	FBtr0078490	72	17	F	1
-input1.bam	FBtr0078490	72	18	F	1
-input1.bam	FBtr0078490	72	25	F	1
-input1.bam	FBtr0078490	72	28	F	2
-input1.bam	FBtr0078490	72	38	F	1
+input1.bam	FBtr0078490	72	28	F	1
 input1.bam	FBtr0078490	72	72	F	0
-input1.bam	FBtr0078580	72	1	F	1041
+input1.bam	FBtr0078580	72	1	F	420
 input1.bam	FBtr0078580	72	3	F	3
 input1.bam	FBtr0078580	72	4	F	4
 input1.bam	FBtr0078580	72	5	F	5
-input1.bam	FBtr0078580	72	6	F	4
+input1.bam	FBtr0078580	72	6	F	2
 input1.bam	FBtr0078580	72	7	F	1
-input1.bam	FBtr0078580	72	8	F	2
+input1.bam	FBtr0078580	72	8	F	1
 input1.bam	FBtr0078580	72	11	F	1
-input1.bam	FBtr0078580	72	12	F	13
-input1.bam	FBtr0078580	72	14	F	7
-input1.bam	FBtr0078580	72	15	F	1
-input1.bam	FBtr0078580	72	16	F	4
-input1.bam	FBtr0078580	72	17	F	1
+input1.bam	FBtr0078580	72	12	F	3
+input1.bam	FBtr0078580	72	16	F	3
 input1.bam	FBtr0078580	72	19	F	1
 input1.bam	FBtr0078580	72	20	F	2
-input1.bam	FBtr0078580	72	21	F	5
-input1.bam	FBtr0078580	72	24	F	3
+input1.bam	FBtr0078580	72	21	F	4
 input1.bam	FBtr0078580	72	25	F	2
-input1.bam	FBtr0078580	72	29	F	1
-input1.bam	FBtr0078580	72	31	F	1
-input1.bam	FBtr0078580	72	52	F	2
 input1.bam	FBtr0078580	72	72	F	0
 input1.bam	FBtr0078790	73	1	F	1
-input1.bam	FBtr0078790	73	17	F	2
 input1.bam	FBtr0078790	73	33	F	1
-input1.bam	FBtr0078790	73	42	F	4
+input1.bam	FBtr0078790	73	42	F	2
 input1.bam	FBtr0078790	73	44	F	2
-input1.bam	FBtr0078790	73	46	F	1
-input1.bam	FBtr0078790	73	47	F	1
 input1.bam	FBtr0078790	73	52	F	1
-input1.bam	FBtr0078790	73	69	R	1
 input1.bam	FBtr0078790	73	73	F	0
-input1.bam	FBtr0079064	72	1	F	1
+input1.bam	FBtr0079064	72	1	F	0
 input1.bam	FBtr0079064	72	3	F	1
-input1.bam	FBtr0079064	72	33	F	1
-input1.bam	FBtr0079064	72	52	F	1
 input1.bam	FBtr0079064	72	72	F	0
-input1.bam	FBtr0079090	72	1	F	2
+input1.bam	FBtr0079090	72	1	F	1
 input1.bam	FBtr0079090	72	26	F	1
-input1.bam	FBtr0079090	72	33	F	1
-input1.bam	FBtr0079090	72	53	F	1
 input1.bam	FBtr0079090	72	56	R	1
 input1.bam	FBtr0079090	72	72	F	0
 input1.bam	FBtr0079338	73	1	F	0
-input1.bam	FBtr0079338	73	12	F	1
-input1.bam	FBtr0079338	73	13	F	2
-input1.bam	FBtr0079338	73	14	F	1
-input1.bam	FBtr0079338	73	17	F	1
-input1.bam	FBtr0079338	73	25	F	1
+input1.bam	FBtr0079338	73	13	F	1
 input1.bam	FBtr0079338	73	42	F	8
 input1.bam	FBtr0079338	73	43	F	1
-input1.bam	FBtr0079338	73	46	F	1
 input1.bam	FBtr0079338	73	73	F	0
-input1.bam	FBtr0079528	71	1	F	19
+input1.bam	FBtr0079528	71	1	F	10
 input1.bam	FBtr0079528	71	3	F	55
 input1.bam	FBtr0079528	71	4	F	2
-input1.bam	FBtr0079528	71	8	F	4
+input1.bam	FBtr0079528	71	8	F	3
 input1.bam	FBtr0079528	71	10	F	1
-input1.bam	FBtr0079528	71	11	F	2
-input1.bam	FBtr0079528	71	13	F	1
-input1.bam	FBtr0079528	71	14	F	4
-input1.bam	FBtr0079528	71	16	F	1
-input1.bam	FBtr0079528	71	17	F	4
-input1.bam	FBtr0079528	71	18	F	4
-input1.bam	FBtr0079528	71	28	F	1
-input1.bam	FBtr0079528	71	35	F	1
+input1.bam	FBtr0079528	71	11	F	1
+input1.bam	FBtr0079528	71	14	F	2
+input1.bam	FBtr0079528	71	18	F	3
 input1.bam	FBtr0079528	71	36	F	1
-input1.bam	FBtr0079528	71	37	F	1
-input1.bam	FBtr0079528	71	51	F	5
 input1.bam	FBtr0079528	71	71	F	0
-input1.bam	FBtr0079596	73	1	F	13
-input1.bam	FBtr0079596	73	3	F	13
+input1.bam	FBtr0079596	73	1	F	3
+input1.bam	FBtr0079596	73	3	F	11
 input1.bam	FBtr0079596	73	4	F	31
-input1.bam	FBtr0079596	73	5	F	2
-input1.bam	FBtr0079596	73	6	F	11
-input1.bam	FBtr0079596	73	8	F	9
-input1.bam	FBtr0079596	73	9	F	12
-input1.bam	FBtr0079596	73	10	F	3
-input1.bam	FBtr0079596	73	11	F	19
-input1.bam	FBtr0079596	73	12	F	1
-input1.bam	FBtr0079596	73	13	F	20
-input1.bam	FBtr0079596	73	14	F	6
-input1.bam	FBtr0079596	73	15	F	1
-input1.bam	FBtr0079596	73	16	F	3
-input1.bam	FBtr0079596	73	17	F	2
-input1.bam	FBtr0079596	73	18	F	1
-input1.bam	FBtr0079596	73	19	F	1
-input1.bam	FBtr0079596	73	53	F	2
+input1.bam	FBtr0079596	73	5	F	1
+input1.bam	FBtr0079596	73	6	F	4
+input1.bam	FBtr0079596	73	13	F	1
+input1.bam	FBtr0079596	73	53	F	1
 input1.bam	FBtr0079596	73	54	F	2
 input1.bam	FBtr0079596	73	73	F	0
 input1.bam	FBtr0079677	72	1	F	1
 input1.bam	FBtr0079677	72	5	F	1
 input1.bam	FBtr0079677	72	52	F	1
-input1.bam	FBtr0079677	72	53	F	1
 input1.bam	FBtr0079677	72	72	F	0
-input1.bam	FBtr0079690	72	1	F	1
-input1.bam	FBtr0079690	72	22	F	1
+input1.bam	FBtr0079690	72	1	F	0
 input1.bam	FBtr0079690	72	27	F	1
-input1.bam	FBtr0079690	72	33	F	2
 input1.bam	FBtr0079690	72	72	F	0
-input1.bam	FBtr0079692	73	1	F	3
-input1.bam	FBtr0079692	73	18	F	1
-input1.bam	FBtr0079692	73	25	F	1
+input1.bam	FBtr0079692	73	1	F	2
 input1.bam	FBtr0079692	73	32	F	1
 input1.bam	FBtr0079692	73	73	F	0
-input1.bam	FBtr0079693	72	1	F	5
+input1.bam	FBtr0079693	72	1	F	1
 input1.bam	FBtr0079693	72	25	F	1
 input1.bam	FBtr0079693	72	72	F	0
-input1.bam	FBtr0079694	72	1	F	5
+input1.bam	FBtr0079694	72	1	F	3
 input1.bam	FBtr0079694	72	18	F	1
-input1.bam	FBtr0079694	72	52	F	1
 input1.bam	FBtr0079694	72	72	F	0
-input1.bam	FBtr0079702	72	1	F	1
-input1.bam	FBtr0079702	72	19	F	2
-input1.bam	FBtr0079702	72	56	F	1
+input1.bam	FBtr0079702	72	1	F	0
 input1.bam	FBtr0079702	72	72	F	0
-input1.bam	FBtr0079728	72	1	F	2
+input1.bam	FBtr0079728	72	1	F	0
 input1.bam	FBtr0079728	72	8	F	1
 input1.bam	FBtr0079728	72	19	F	1
-input1.bam	FBtr0079728	72	33	F	3
-input1.bam	FBtr0079728	72	56	F	1
 input1.bam	FBtr0079728	72	72	F	0
-input1.bam	FBtr0079729	72	1	F	1
+input1.bam	FBtr0079729	72	1	F	0
 input1.bam	FBtr0079729	72	13	F	1
-input1.bam	FBtr0079729	72	52	F	1
-input1.bam	FBtr0079729	72	57	F	1
 input1.bam	FBtr0079729	72	72	F	0
-input1.bam	FBtr0079752	72	1	F	2
+input1.bam	FBtr0079752	72	1	F	1
 input1.bam	FBtr0079752	72	7	F	1
-input1.bam	FBtr0079752	72	12	F	1
-input1.bam	FBtr0079752	72	33	F	2
 input1.bam	FBtr0079752	72	52	F	2
 input1.bam	FBtr0079752	72	72	F	0
 input1.bam	FBtr0079820	74	1	F	0
 input1.bam	FBtr0079820	74	45	F	1
-input1.bam	FBtr0079820	74	46	F	2
-input1.bam	FBtr0079820	74	48	F	1
 input1.bam	FBtr0079820	74	49	F	1
 input1.bam	FBtr0079820	74	51	F	1
-input1.bam	FBtr0079820	74	54	F	4
-input1.bam	FBtr0079820	74	55	F	1
-input1.bam	FBtr0079820	74	56	F	2
+input1.bam	FBtr0079820	74	54	F	2
+input1.bam	FBtr0079820	74	56	F	1
 input1.bam	FBtr0079820	74	74	F	0
-input1.bam	FBtr0080609	72	1	F	13
+input1.bam	FBtr0080609	72	1	F	3
 input1.bam	FBtr0080609	72	3	F	2
 input1.bam	FBtr0080609	72	4	F	10
 input1.bam	FBtr0080609	72	5	F	2
-input1.bam	FBtr0080609	72	7	F	19
-input1.bam	FBtr0080609	72	8	F	4
-input1.bam	FBtr0080609	72	9	F	3
 input1.bam	FBtr0080609	72	12	F	1
 input1.bam	FBtr0080609	72	15	F	1
 input1.bam	FBtr0080609	72	16	F	1
-input1.bam	FBtr0080609	72	17	F	2
+input1.bam	FBtr0080609	72	17	F	1
 input1.bam	FBtr0080609	72	19	F	1
 input1.bam	FBtr0080609	72	20	F	1
 input1.bam	FBtr0080609	72	42	F	1
-input1.bam	FBtr0080609	72	51	F	1
-input1.bam	FBtr0080609	72	52	F	1
 input1.bam	FBtr0080609	72	72	F	0
 input1.bam	FBtr0080644	72	1	F	1
-input1.bam	FBtr0080644	72	4	F	2
-input1.bam	FBtr0080644	72	7	F	1
-input1.bam	FBtr0080644	72	12	F	2
+input1.bam	FBtr0080644	72	4	F	1
 input1.bam	FBtr0080644	72	72	F	0
-input1.bam	FBtr0080646	72	1	F	1
+input1.bam	FBtr0080646	72	1	F	0
 input1.bam	FBtr0080646	72	6	F	1
 input1.bam	FBtr0080646	72	7	F	1
 input1.bam	FBtr0080646	72	72	F	0
-input1.bam	FBtr0080647	72	1	F	3
-input1.bam	FBtr0080647	72	3	F	1
-input1.bam	FBtr0080647	72	6	F	2
+input1.bam	FBtr0080647	72	1	F	0
+input1.bam	FBtr0080647	72	6	F	1
 input1.bam	FBtr0080647	72	8	F	1
-input1.bam	FBtr0080647	72	11	F	2
-input1.bam	FBtr0080647	72	12	F	1
 input1.bam	FBtr0080647	72	72	F	0
 input1.bam	FBtr0080660	72	1	F	0
 input1.bam	FBtr0080660	72	4	F	4
-input1.bam	FBtr0080660	72	7	F	3
+input1.bam	FBtr0080660	72	7	F	2
 input1.bam	FBtr0080660	72	72	F	0
-input1.bam	FBtr0080663	71	1	F	22
+input1.bam	FBtr0080663	71	1	F	6
 input1.bam	FBtr0080663	71	3	F	56
 input1.bam	FBtr0080663	71	4	F	4
-input1.bam	FBtr0080663	71	7	F	1
-input1.bam	FBtr0080663	71	8	F	4
-input1.bam	FBtr0080663	71	12	F	2
+input1.bam	FBtr0080663	71	8	F	3
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-input1.bam	FBtr0080663	71	15	F	1
-input1.bam	FBtr0080663	71	16	F	3
-input1.bam	FBtr0080663	71	17	F	7
-input1.bam	FBtr0080663	71	26	F	1
-input1.bam	FBtr0080663	71	32	F	2
-input1.bam	FBtr0080663	71	50	F	1
-input1.bam	FBtr0080663	71	51	F	9
+input1.bam	FBtr0080663	71	51	F	1
 input1.bam	FBtr0080663	71	71	F	0
-input1.bam	FBtr0080664	71	1	F	16
+input1.bam	FBtr0080664	71	1	F	6
 input1.bam	FBtr0080664	71	3	F	56
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-input1.bam	FBtr0080664	71	11	F	3
-input1.bam	FBtr0080664	71	12	F	3
+input1.bam	FBtr0080664	71	12	F	1
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-input1.bam	FBtr0080664	71	17	F	10
-input1.bam	FBtr0080664	71	18	F	1
-input1.bam	FBtr0080664	71	21	F	1
-input1.bam	FBtr0080664	71	28	F	2
-input1.bam	FBtr0080664	71	32	F	1
+input1.bam	FBtr0080664	71	14	F	1
+input1.bam	FBtr0080664	71	17	F	1
 input1.bam	FBtr0080664	71	33	F	1
-input1.bam	FBtr0080664	71	34	F	1
-input1.bam	FBtr0080664	71	35	F	1
 input1.bam	FBtr0080664	71	36	F	1
-input1.bam	FBtr0080664	71	37	F	1
-input1.bam	FBtr0080664	71	38	F	1
-input1.bam	FBtr0080664	71	50	F	2
-input1.bam	FBtr0080664	71	51	F	7
-input1.bam	FBtr0080664	71	52	F	1
-input1.bam	FBtr0080664	71	56	F	1
 input1.bam	FBtr0080664	71	71	F	0
-input2.bam	FBtr0070001	72	1	F	1
-input2.bam	FBtr0070001	72	12	F	1
+input2.bam	FBtr0070001	72	1	F	0
 input2.bam	FBtr0070001	72	13	F	1
-input2.bam	FBtr0070001	72	18	F	1
 input2.bam	FBtr0070001	72	19	F	1
 input2.bam	FBtr0070001	72	28	F	1
 input2.bam	FBtr0070001	72	32	F	3
-input2.bam	FBtr0070001	72	53	F	2
-input2.bam	FBtr0070001	72	56	F	2
-input2.bam	FBtr0070001	72	57	F	1
-input2.bam	FBtr0070001	72	58	F	10
+input2.bam	FBtr0070001	72	53	F	1
 input2.bam	FBtr0070001	72	72	F	0
 input2.bam	FBtr0070533	72	1	F	0
-input2.bam	FBtr0070533	72	15	F	1
-input2.bam	FBtr0070533	72	16	F	2
-input2.bam	FBtr0070533	72	17	F	2
+input2.bam	FBtr0070533	72	16	F	1
 input2.bam	FBtr0070533	72	19	F	1
 input2.bam	FBtr0070533	72	20	F	1
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diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/input1_input2_coverage.tab
--- a/test-data/input1_input2_coverage.tab	Wed Apr 10 06:38:33 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3109 +0,0 @@
-Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Coverage
-input1.bam	FBtr0070001	72	1	F	1
-input1.bam	FBtr0070001	72	2	F	1
-input1.bam	FBtr0070001	72	3	F	1
-input1.bam	FBtr0070001	72	4	F	1
-input1.bam	FBtr0070001	72	5	F	1
-input1.bam	FBtr0070001	72	6	F	1
-input1.bam	FBtr0070001	72	7	F	7
-input1.bam	FBtr0070001	72	8	F	10
-input1.bam	FBtr0070001	72	9	F	10
-input1.bam	FBtr0070001	72	10	F	10
-input1.bam	FBtr0070001	72	11	F	12
-input1.bam	FBtr0070001	72	12	F	12
-input1.bam	FBtr0070001	72	13	F	12
-input1.bam	FBtr0070001	72	14	F	12
-input1.bam	FBtr0070001	72	15	F	12
-input1.bam	FBtr0070001	72	16	F	13
-input1.bam	FBtr0070001	72	17	F	14
-input1.bam	FBtr0070001	72	18	F	14
-input1.bam	FBtr0070001	72	19	F	14
-input1.bam	FBtr0070001	72	20	F	14
-input1.bam	FBtr0070001	72	21	F	14
-input1.bam	FBtr0070001	72	22	F	14
-input1.bam	FBtr0070001	72	23	F	13
-input1.bam	FBtr0070001	72	24	F	13
-input1.bam	FBtr0070001	72	25	F	13
-input1.bam	FBtr0070001	72	26	F	13
-input1.bam	FBtr0070001	72	27	F	14
-input1.bam	FBtr0070001	72	28	F	11
-input1.bam	FBtr0070001	72	29	F	8
-input1.bam	FBtr0070001	72	30	F	9
-input1.bam	FBtr0070001	72	31	F	18
-input1.bam	FBtr0070001	72	32	F	44
-input1.bam	FBtr0070001	72	33	F	44
-input1.bam	FBtr0070001	72	34	F	44
-input1.bam	FBtr0070001	72	35	F	43
-input1.bam	FBtr0070001	72	36	F	43
-input1.bam	FBtr0070001	72	37	F	43
-input1.bam	FBtr0070001	72	38	F	43
-input1.bam	FBtr0070001	72	39	F	43
-input1.bam	FBtr0070001	72	40	F	42
-input1.bam	FBtr0070001	72	41	F	42
-input1.bam	FBtr0070001	72	42	F	42
-input1.bam	FBtr0070001	72	43	F	42
-input1.bam	FBtr0070001	72	44	F	42
-input1.bam	FBtr0070001	72	45	F	42
-input1.bam	FBtr0070001	72	46	F	42
-input1.bam	FBtr0070001	72	47	F	42
-input1.bam	FBtr0070001	72	48	F	42
-input1.bam	FBtr0070001	72	49	F	42
-input1.bam	FBtr0070001	72	50	F	41
-input1.bam	FBtr0070001	72	51	F	40
-input1.bam	FBtr0070001	72	52	F	40
-input1.bam	FBtr0070001	72	53	F	39
-input1.bam	FBtr0070001	72	72	F	0
-input1.bam	FBtr0070533	72	1	F	1
-input1.bam	FBtr0070533	72	2	F	1
-input1.bam	FBtr0070533	72	3	F	1
-input1.bam	FBtr0070533	72	4	F	1
-input1.bam	FBtr0070533	72	5	F	1
-input1.bam	FBtr0070533	72	6	F	1
-input1.bam	FBtr0070533	72	7	F	1
-input1.bam	FBtr0070533	72	8	F	1
-input1.bam	FBtr0070533	72	9	F	1
-input1.bam	FBtr0070533	72	10	F	1
-input1.bam	FBtr0070533	72	11	F	1
-input1.bam	FBtr0070533	72	12	F	3
-input1.bam	FBtr0070533	72	13	F	3
-input1.bam	FBtr0070533	72	14	F	3
-input1.bam	FBtr0070533	72	15	F	4
-input1.bam	FBtr0070533	72	16	F	3
-input1.bam	FBtr0070533	72	17	F	3
-input1.bam	FBtr0070533	72	18	F	3
-input1.bam	FBtr0070533	72	19	F	8
-input1.bam	FBtr0070533	72	20	F	9
-input1.bam	FBtr0070533	72	21	F	10
-input1.bam	FBtr0070533	72	22	F	11
-input1.bam	FBtr0070533	72	23	F	11
-input1.bam	FBtr0070533	72	24	F	11
-input1.bam	FBtr0070533	72	25	F	12
-input1.bam	FBtr0070533	72	26	F	13
-input1.bam	FBtr0070533	72	27	F	13
-input1.bam	FBtr0070533	72	28	F	14
-input1.bam	FBtr0070533	72	29	F	14
-input1.bam	FBtr0070533	72	30	F	11
-input1.bam	FBtr0070533	72	31	F	11
-input1.bam	FBtr0070533	72	32	F	15
-input1.bam	FBtr0070533	72	33	F	15
-input1.bam	FBtr0070533	72	34	F	15
-input1.bam	FBtr0070533	72	35	F	16
-input1.bam	FBtr0070533	72	36	F	16
-input1.bam	FBtr0070533	72	37	F	18
-input1.bam	FBtr0070533	72	38	F	20
-input1.bam	FBtr0070533	72	39	F	19
-input1.bam	FBtr0070533	72	40	F	17
-input1.bam	FBtr0070533	72	41	F	15
-input1.bam	FBtr0070533	72	42	F	11
-input1.bam	FBtr0070533	72	43	F	10
-input1.bam	FBtr0070533	72	44	F	10
-input1.bam	FBtr0070533	72	45	F	10
-input1.bam	FBtr0070533	72	46	F	10
-input1.bam	FBtr0070533	72	47	F	10
-input1.bam	FBtr0070533	72	48	F	10
-input1.bam	FBtr0070533	72	49	F	10
-input1.bam	FBtr0070533	72	50	F	9
-input1.bam	FBtr0070533	72	51	F	9
-input1.bam	FBtr0070533	72	52	F	8
-input1.bam	FBtr0070533	72	53	F	7
-input1.bam	FBtr0070533	72	54	F	4
-input1.bam	FBtr0070533	72	55	F	4
-input1.bam	FBtr0070533	72	72	F	0
-input1.bam	FBtr0070603	72	1	F	2
-input1.bam	FBtr0070603	72	2	F	2
-input1.bam	FBtr0070603	72	3	F	3
-input1.bam	FBtr0070603	72	4	F	4
-input1.bam	FBtr0070603	72	5	F	4
-input1.bam	FBtr0070603	72	6	F	5
-input1.bam	FBtr0070603	72	7	F	12
-input1.bam	FBtr0070603	72	8	F	16
-input1.bam	FBtr0070603	72	9	F	23
-input1.bam	FBtr0070603	72	10	F	23
-input1.bam	FBtr0070603	72	11	F	23
-input1.bam	FBtr0070603	72	12	F	25
-input1.bam	FBtr0070603	72	13	F	26
-input1.bam	FBtr0070603	72	14	F	26
-input1.bam	FBtr0070603	72	15	F	28
-input1.bam	FBtr0070603	72	16	F	29
-input1.bam	FBtr0070603	72	17	F	32
-input1.bam	FBtr0070603	72	18	F	33
-input1.bam	FBtr0070603	72	19	F	41
-input1.bam	FBtr0070603	72	20	F	44
-input1.bam	FBtr0070603	72	21	F	45
-input1.bam	FBtr0070603	72	22	F	48
-input1.bam	FBtr0070603	72	23	F	48
-input1.bam	FBtr0070603	72	24	F	30
-input1.bam	FBtr0070603	72	25	F	30
-input1.bam	FBtr0070603	72	26	F	36
-input1.bam	FBtr0070603	72	27	F	39
-input1.bam	FBtr0070603	72	28	F	39
-input1.bam	FBtr0070603	72	29	F	38
-input1.bam	FBtr0070603	72	30	F	38
-input1.bam	FBtr0070603	72	31	F	38
-input1.bam	FBtr0070603	72	32	F	38
-input1.bam	FBtr0070603	72	33	F	37
-input1.bam	FBtr0070603	72	34	F	39
-input1.bam	FBtr0070603	72	35	F	35
-input1.bam	FBtr0070603	72	36	F	34
-input1.bam	FBtr0070603	72	37	F	34
-input1.bam	FBtr0070603	72	38	F	35
-input1.bam	FBtr0070603	72	39	F	34
-input1.bam	FBtr0070603	72	40	F	33
-input1.bam	FBtr0070603	72	41	F	32
-input1.bam	FBtr0070603	72	42	F	21
-input1.bam	FBtr0070603	72	43	F	21
-input1.bam	FBtr0070603	72	44	F	20
-input1.bam	FBtr0070603	72	45	F	18
-input1.bam	FBtr0070603	72	46	F	16
-input1.bam	FBtr0070603	72	47	F	16
-input1.bam	FBtr0070603	72	48	F	15
-input1.bam	FBtr0070603	72	49	F	15
-input1.bam	FBtr0070603	72	50	F	14
-input1.bam	FBtr0070603	72	51	F	14
-input1.bam	FBtr0070603	72	52	F	10
-input1.bam	FBtr0070603	72	53	F	6
-input1.bam	FBtr0070603	72	54	F	3
-input1.bam	FBtr0070603	72	55	F	3
-input1.bam	FBtr0070603	72	56	F	3
-input1.bam	FBtr0070603	72	57	F	3
-input1.bam	FBtr0070603	72	58	F	3
-input1.bam	FBtr0070603	72	59	F	3
-input1.bam	FBtr0070603	72	60	F	3
-input1.bam	FBtr0070603	72	61	F	3
-input1.bam	FBtr0070603	72	62	F	3
-input1.bam	FBtr0070603	72	63	F	2
-input1.bam	FBtr0070603	72	64	F	2
-input1.bam	FBtr0070603	72	65	F	2
-input1.bam	FBtr0070603	72	66	F	2
-input1.bam	FBtr0070603	72	67	F	2
-input1.bam	FBtr0070603	72	68	F	2
-input1.bam	FBtr0070603	72	69	F	1
-input1.bam	FBtr0070603	72	70	F	1
-input1.bam	FBtr0070603	72	71	F	1
-input1.bam	FBtr0070603	72	72	F	0
-input1.bam	FBtr0070604	72	1	F	1
-input1.bam	FBtr0070604	72	2	F	1
-input1.bam	FBtr0070604	72	3	F	1
-input1.bam	FBtr0070604	72	4	F	1
-input1.bam	FBtr0070604	72	5	F	1
-input1.bam	FBtr0070604	72	6	F	1
-input1.bam	FBtr0070604	72	7	F	1
-input1.bam	FBtr0070604	72	8	F	1
-input1.bam	FBtr0070604	72	9	F	1
-input1.bam	FBtr0070604	72	10	F	1
-input1.bam	FBtr0070604	72	11	F	1
-input1.bam	FBtr0070604	72	12	F	1
-input1.bam	FBtr0070604	72	13	F	1
-input1.bam	FBtr0070604	72	14	F	1
-input1.bam	FBtr0070604	72	15	F	1
-input1.bam	FBtr0070604	72	18	F	1
-input1.bam	FBtr0070604	72	19	F	1
-input1.bam	FBtr0070604	72	20	F	1
-input1.bam	FBtr0070604	72	21	F	1
-input1.bam	FBtr0070604	72	22	F	2
-input1.bam	FBtr0070604	72	23	F	2
-input1.bam	FBtr0070604	72	24	F	2
-input1.bam	FBtr0070604	72	25	F	2
-input1.bam	FBtr0070604	72	26	F	2
-input1.bam	FBtr0070604	72	27	F	2
-input1.bam	FBtr0070604	72	28	F	2
-input1.bam	FBtr0070604	72	29	F	2
-input1.bam	FBtr0070604	72	30	F	4
-input1.bam	FBtr0070604	72	31	F	14
-input1.bam	FBtr0070604	72	32	F	38
-input1.bam	FBtr0070604	72	33	F	38
-input1.bam	FBtr0070604	72	34	F	38
-input1.bam	FBtr0070604	72	35	F	38
-input1.bam	FBtr0070604	72	36	F	38
-input1.bam	FBtr0070604	72	37	F	38
-input1.bam	FBtr0070604	72	38	F	38
-input1.bam	FBtr0070604	72	39	F	38
-input1.bam	FBtr0070604	72	40	F	38
-input1.bam	FBtr0070604	72	41	F	36
-input1.bam	FBtr0070604	72	42	F	36
-input1.bam	FBtr0070604	72	43	F	36
-input1.bam	FBtr0070604	72	44	F	36
-input1.bam	FBtr0070604	72	45	F	36
-input1.bam	FBtr0070604	72	46	F	35
-input1.bam	FBtr0070604	72	47	F	36
-input1.bam	FBtr0070604	72	48	F	34
-input1.bam	FBtr0070604	72	49	F	34
-input1.bam	FBtr0070604	72	50	F	33
-input1.bam	FBtr0070604	72	51	F	33
-input1.bam	FBtr0070604	72	52	F	33
-input1.bam	FBtr0070604	72	53	F	31
-input1.bam	FBtr0070604	72	57	F	1
-input1.bam	FBtr0070604	72	58	F	1
-input1.bam	FBtr0070604	72	59	F	1
-input1.bam	FBtr0070604	72	60	F	1
-input1.bam	FBtr0070604	72	61	F	1
-input1.bam	FBtr0070604	72	62	F	1
-input1.bam	FBtr0070604	72	63	F	1
-input1.bam	FBtr0070604	72	64	F	1
-input1.bam	FBtr0070604	72	65	F	1
-input1.bam	FBtr0070604	72	66	F	1
-input1.bam	FBtr0070604	72	67	F	1
-input1.bam	FBtr0070604	72	68	F	1
-input1.bam	FBtr0070604	72	69	F	1
-input1.bam	FBtr0070604	72	70	F	1
-input1.bam	FBtr0070604	72	71	F	1
-input1.bam	FBtr0070604	72	72	F	0
-input1.bam	FBtr0070911	73	1	F	0
-input1.bam	FBtr0070911	73	15	F	1
-input1.bam	FBtr0070911	73	16	F	1
-input1.bam	FBtr0070911	73	17	F	1
-input1.bam	FBtr0070911	73	18	F	1
-input1.bam	FBtr0070911	73	19	F	1
-input1.bam	FBtr0070911	73	20	F	1
-input1.bam	FBtr0070911	73	21	F	1
-input1.bam	FBtr0070911	73	22	F	1
-input1.bam	FBtr0070911	73	23	F	1
-input1.bam	FBtr0070911	73	24	F	1
-input1.bam	FBtr0070911	73	25	F	1
-input1.bam	FBtr0070911	73	26	F	1
-input1.bam	FBtr0070911	73	27	F	1
-input1.bam	FBtr0070911	73	28	F	1
-input1.bam	FBtr0070911	73	29	F	1
-input1.bam	FBtr0070911	73	30	F	1
-input1.bam	FBtr0070911	73	31	F	1
-input1.bam	FBtr0070911	73	32	F	1
-input1.bam	FBtr0070911	73	33	F	1
-input1.bam	FBtr0070911	73	34	F	1
-input1.bam	FBtr0070911	73	35	F	1
-input1.bam	FBtr0070911	73	38	F	1
-input1.bam	FBtr0070911	73	39	F	1
-input1.bam	FBtr0070911	73	40	F	1
-input1.bam	FBtr0070911	73	41	F	1
-input1.bam	FBtr0070911	73	42	F	1
-input1.bam	FBtr0070911	73	43	F	1
-input1.bam	FBtr0070911	73	44	F	1
-input1.bam	FBtr0070911	73	45	F	1
-input1.bam	FBtr0070911	73	46	F	1
-input1.bam	FBtr0070911	73	47	F	1
-input1.bam	FBtr0070911	73	48	F	1
-input1.bam	FBtr0070911	73	49	F	1
-input1.bam	FBtr0070911	73	50	F	1
-input1.bam	FBtr0070911	73	51	F	1
-input1.bam	FBtr0070911	73	52	F	1
-input1.bam	FBtr0070911	73	73	F	0
-input1.bam	FBtr0078490	72	1	F	0
-input1.bam	FBtr0078490	72	13	F	2
-input1.bam	FBtr0078490	72	14	F	2
-input1.bam	FBtr0078490	72	15	F	2
-input1.bam	FBtr0078490	72	16	F	2
-input1.bam	FBtr0078490	72	17	F	3
-input1.bam	FBtr0078490	72	18	F	4
-input1.bam	FBtr0078490	72	19	F	4
-input1.bam	FBtr0078490	72	20	F	4
-input1.bam	FBtr0078490	72	21	F	4
-input1.bam	FBtr0078490	72	22	F	4
-input1.bam	FBtr0078490	72	23	F	4
-input1.bam	FBtr0078490	72	24	F	4
-input1.bam	FBtr0078490	72	25	F	5
-input1.bam	FBtr0078490	72	26	F	5
-input1.bam	FBtr0078490	72	27	F	5
-input1.bam	FBtr0078490	72	28	F	7
-input1.bam	FBtr0078490	72	29	F	5
-input1.bam	FBtr0078490	72	30	F	5
-input1.bam	FBtr0078490	72	31	F	5
-input1.bam	FBtr0078490	72	32	F	5
-input1.bam	FBtr0078490	72	33	F	3
-input1.bam	FBtr0078490	72	34	F	3
-input1.bam	FBtr0078490	72	35	F	3
-input1.bam	FBtr0078490	72	36	F	3
-input1.bam	FBtr0078490	72	37	F	3
-input1.bam	FBtr0078490	72	38	F	4
-input1.bam	FBtr0078490	72	39	F	4
-input1.bam	FBtr0078490	72	40	F	3
-input1.bam	FBtr0078490	72	41	F	3
-input1.bam	FBtr0078490	72	42	F	3
-input1.bam	FBtr0078490	72	43	F	2
-input1.bam	FBtr0078490	72	44	F	2
-input1.bam	FBtr0078490	72	45	F	2
-input1.bam	FBtr0078490	72	46	F	2
-input1.bam	FBtr0078490	72	47	F	2
-input1.bam	FBtr0078490	72	48	F	2
-input1.bam	FBtr0078490	72	49	F	2
-input1.bam	FBtr0078490	72	50	F	2
-input1.bam	FBtr0078490	72	51	F	1
-input1.bam	FBtr0078490	72	52	F	1
-input1.bam	FBtr0078490	72	53	F	1
-input1.bam	FBtr0078490	72	54	F	1
-input1.bam	FBtr0078490	72	55	F	1
-input1.bam	FBtr0078490	72	72	F	0
-input1.bam	FBtr0078580	72	1	F	1041
-input1.bam	FBtr0078580	72	2	F	1041
-input1.bam	FBtr0078580	72	3	F	1044
-input1.bam	FBtr0078580	72	4	F	1048
-input1.bam	FBtr0078580	72	5	F	1053
-input1.bam	FBtr0078580	72	6	F	1057
-input1.bam	FBtr0078580	72	7	F	1058
-input1.bam	FBtr0078580	72	8	F	1060
-input1.bam	FBtr0078580	72	9	F	1060
-input1.bam	FBtr0078580	72	10	F	1060
-input1.bam	FBtr0078580	72	11	F	1061
-input1.bam	FBtr0078580	72	12	F	1074
-input1.bam	FBtr0078580	72	13	F	1074
-input1.bam	FBtr0078580	72	14	F	1081
-input1.bam	FBtr0078580	72	15	F	1082
-input1.bam	FBtr0078580	72	16	F	502
-input1.bam	FBtr0078580	72	17	F	487
-input1.bam	FBtr0078580	72	18	F	473
-input1.bam	FBtr0078580	72	19	F	467
-input1.bam	FBtr0078580	72	20	F	466
-input1.bam	FBtr0078580	72	21	F	468
-input1.bam	FBtr0078580	72	22	F	468
-input1.bam	FBtr0078580	72	23	F	457
-input1.bam	FBtr0078580	72	24	F	457
-input1.bam	FBtr0078580	72	25	F	276
-input1.bam	FBtr0078580	72	26	F	66
-input1.bam	FBtr0078580	72	27	F	62
-input1.bam	FBtr0078580	72	28	F	61
-input1.bam	FBtr0078580	72	29	F	30
-input1.bam	FBtr0078580	72	30	F	24
-input1.bam	FBtr0078580	72	31	F	22
-input1.bam	FBtr0078580	72	32	F	22
-input1.bam	FBtr0078580	72	33	F	22
-input1.bam	FBtr0078580	72	34	F	19
-input1.bam	FBtr0078580	72	35	F	16
-input1.bam	FBtr0078580	72	36	F	16
-input1.bam	FBtr0078580	72	37	F	15
-input1.bam	FBtr0078580	72	38	F	15
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-input2.bam	FBtr0080663	71	22	F	97
-input2.bam	FBtr0080663	71	23	F	95
-input2.bam	FBtr0080663	71	24	F	95
-input2.bam	FBtr0080663	71	25	F	95
-input2.bam	FBtr0080663	71	26	F	95
-input2.bam	FBtr0080663	71	27	F	95
-input2.bam	FBtr0080663	71	28	F	95
-input2.bam	FBtr0080663	71	29	F	95
-input2.bam	FBtr0080663	71	30	F	95
-input2.bam	FBtr0080663	71	31	F	96
-input2.bam	FBtr0080663	71	32	F	62
-input2.bam	FBtr0080663	71	33	F	41
-input2.bam	FBtr0080663	71	34	F	40
-input2.bam	FBtr0080663	71	35	F	34
-input2.bam	FBtr0080663	71	36	F	12
-input2.bam	FBtr0080663	71	37	F	6
-input2.bam	FBtr0080663	71	38	F	5
-input2.bam	FBtr0080663	71	39	F	4
-input2.bam	FBtr0080663	71	40	F	3
-input2.bam	FBtr0080663	71	41	F	2
-input2.bam	FBtr0080663	71	42	F	1
-input2.bam	FBtr0080663	71	43	F	1
-input2.bam	FBtr0080663	71	44	F	1
-input2.bam	FBtr0080663	71	45	F	1
-input2.bam	FBtr0080663	71	46	F	1
-input2.bam	FBtr0080663	71	47	F	1
-input2.bam	FBtr0080663	71	50	F	2
-input2.bam	FBtr0080663	71	51	F	3
-input2.bam	FBtr0080663	71	52	F	5
-input2.bam	FBtr0080663	71	53	F	5
-input2.bam	FBtr0080663	71	54	F	5
-input2.bam	FBtr0080663	71	55	F	5
-input2.bam	FBtr0080663	71	56	F	5
-input2.bam	FBtr0080663	71	57	F	8
-input2.bam	FBtr0080663	71	58	F	8
-input2.bam	FBtr0080663	71	59	F	8
-input2.bam	FBtr0080663	71	60	F	8
-input2.bam	FBtr0080663	71	61	F	8
-input2.bam	FBtr0080663	71	62	F	8
-input2.bam	FBtr0080663	71	63	F	8
-input2.bam	FBtr0080663	71	64	F	8
-input2.bam	FBtr0080663	71	65	F	7
-input2.bam	FBtr0080663	71	66	F	6
-input2.bam	FBtr0080663	71	67	F	4
-input2.bam	FBtr0080663	71	68	F	4
-input2.bam	FBtr0080663	71	69	F	4
-input2.bam	FBtr0080663	71	70	F	3
-input2.bam	FBtr0080663	71	71	F	3
-input2.bam	FBtr0080664	71	1	F	1
-input2.bam	FBtr0080664	71	2	F	1
-input2.bam	FBtr0080664	71	3	F	3
-input2.bam	FBtr0080664	71	4	F	3
-input2.bam	FBtr0080664	71	5	F	3
-input2.bam	FBtr0080664	71	6	F	3
-input2.bam	FBtr0080664	71	7	F	3
-input2.bam	FBtr0080664	71	8	F	3
-input2.bam	FBtr0080664	71	9	F	3
-input2.bam	FBtr0080664	71	10	F	4
-input2.bam	FBtr0080664	71	11	F	6
-input2.bam	FBtr0080664	71	12	F	9
-input2.bam	FBtr0080664	71	13	F	20
-input2.bam	FBtr0080664	71	14	F	31
-input2.bam	FBtr0080664	71	15	F	48
-input2.bam	FBtr0080664	71	16	F	63
-input2.bam	FBtr0080664	71	17	F	76
-input2.bam	FBtr0080664	71	18	F	86
-input2.bam	FBtr0080664	71	19	F	94
-input2.bam	FBtr0080664	71	20	F	95
-input2.bam	FBtr0080664	71	21	F	110
-input2.bam	FBtr0080664	71	22	F	116
-input2.bam	FBtr0080664	71	23	F	114
-input2.bam	FBtr0080664	71	24	F	115
-input2.bam	FBtr0080664	71	25	F	115
-input2.bam	FBtr0080664	71	26	F	115
-input2.bam	FBtr0080664	71	27	F	115
-input2.bam	FBtr0080664	71	28	F	115
-input2.bam	FBtr0080664	71	29	F	113
-input2.bam	FBtr0080664	71	30	F	113
-input2.bam	FBtr0080664	71	31	F	117
-input2.bam	FBtr0080664	71	32	F	127
-input2.bam	FBtr0080664	71	33	F	97
-input2.bam	FBtr0080664	71	34	F	134
-input2.bam	FBtr0080664	71	35	F	265
-input2.bam	FBtr0080664	71	36	F	249
-input2.bam	FBtr0080664	71	37	F	266
-input2.bam	FBtr0080664	71	38	F	268
-input2.bam	FBtr0080664	71	39	F	263
-input2.bam	FBtr0080664	71	40	F	263
-input2.bam	FBtr0080664	71	41	F	262
-input2.bam	FBtr0080664	71	42	F	262
-input2.bam	FBtr0080664	71	43	F	260
-input2.bam	FBtr0080664	71	44	F	263
-input2.bam	FBtr0080664	71	45	F	263
-input2.bam	FBtr0080664	71	46	F	263
-input2.bam	FBtr0080664	71	47	F	264
-input2.bam	FBtr0080664	71	48	F	264
-input2.bam	FBtr0080664	71	49	F	254
-input2.bam	FBtr0080664	71	50	F	72
-input2.bam	FBtr0080664	71	51	F	63
-input2.bam	FBtr0080664	71	52	F	61
-input2.bam	FBtr0080664	71	53	F	31
-input2.bam	FBtr0080664	71	54	F	30
-input2.bam	FBtr0080664	71	55	F	21
-input2.bam	FBtr0080664	71	56	F	16
-input2.bam	FBtr0080664	71	57	F	18
-input2.bam	FBtr0080664	71	58	F	18
-input2.bam	FBtr0080664	71	59	F	18
-input2.bam	FBtr0080664	71	60	F	17
-input2.bam	FBtr0080664	71	61	F	16
-input2.bam	FBtr0080664	71	62	F	12
-input2.bam	FBtr0080664	71	62	R	12
-input2.bam	FBtr0080664	71	63	F	8
-input2.bam	FBtr0080664	71	64	F	8
-input2.bam	FBtr0080664	71	65	F	7
-input2.bam	FBtr0080664	71	66	F	6
-input2.bam	FBtr0080664	71	67	F	6
-input2.bam	FBtr0080664	71	68	F	5
-input2.bam	FBtr0080664	71	69	F	5
-input2.bam	FBtr0080664	71	70	F	5
-input2.bam	FBtr0080664	71	71	F	5
-input2.bam	FBtr0080664	71	71	R	5
diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/input1_input2_double_plot_counts_size_ylimneg5_5.pdf
Binary file test-data/input1_input2_double_plot_counts_size_ylimneg5_5.pdf has changed
diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/input1_input2_double_plot_coverage_mean_ylim20_25.pdf
Binary file test-data/input1_input2_double_plot_coverage_mean_ylim20_25.pdf has changed
diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/input1_input2_mean.tab
--- a/test-data/input1_input2_mean.tab	Wed Apr 10 06:38:33 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,617 +0,0 @@
-Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Mean
-input1.bam	FBtr0070001	72	1	F	17.0
-input1.bam	FBtr0070001	72	7	F	20.3
-input1.bam	FBtr0070001	72	8	F	21.3
-input1.bam	FBtr0070001	72	11	F	20.5
-input1.bam	FBtr0070001	72	16	F	19.0
-input1.bam	FBtr0070001	72	17	F	23.0
-input1.bam	FBtr0070001	72	18	F	16.0
-input1.bam	FBtr0070001	72	27	F	23.5
-input1.bam	FBtr0070001	72	30	F	23.0
-input1.bam	FBtr0070001	72	31	F	23.0
-input1.bam	FBtr0070001	72	32	F	22.0
-input1.bam	FBtr0070001	72	34	F	20.0
-input1.bam	FBtr0070001	72	72	F	0
-input1.bam	FBtr0070533	72	1	F	15.0
-input1.bam	FBtr0070533	72	12	F	18.0
-input1.bam	FBtr0070533	72	15	F	15.0
-input1.bam	FBtr0070533	72	19	F	21.8
-input1.bam	FBtr0070533	72	20	F	23.0
-input1.bam	FBtr0070533	72	21	F	18.0
-input1.bam	FBtr0070533	72	22	F	20.0
-input1.bam	FBtr0070533	72	25	F	17.0
-input1.bam	FBtr0070533	72	26	F	16.0
-input1.bam	FBtr0070533	72	28	F	25.0
-input1.bam	FBtr0070533	72	32	F	20.5
-input1.bam	FBtr0070533	72	35	F	19.0
-input1.bam	FBtr0070533	72	37	F	19.0
-input1.bam	FBtr0070533	72	38	F	18.0
-input1.bam	FBtr0070533	72	72	F	0
-input1.bam	FBtr0070603	72	1	F	16.5
-input1.bam	FBtr0070603	72	3	F	21.0
-input1.bam	FBtr0070603	72	4	F	20.0
-input1.bam	FBtr0070603	72	6	F	18.0
-input1.bam	FBtr0070603	72	7	F	17.1
-input1.bam	FBtr0070603	72	8	F	16.0
-input1.bam	FBtr0070603	72	9	F	15.0
-input1.bam	FBtr0070603	72	12	F	20.0
-input1.bam	FBtr0070603	72	13	F	22.0
-input1.bam	FBtr0070603	72	15	F	18.5
-input1.bam	FBtr0070603	72	16	F	20.5
-input1.bam	FBtr0070603	72	17	F	24.0
-input1.bam	FBtr0070603	72	18	F	16.0
-input1.bam	FBtr0070603	72	19	F	22.6
-input1.bam	FBtr0070603	72	20	F	21.0
-input1.bam	FBtr0070603	72	21	F	25.0
-input1.bam	FBtr0070603	72	22	F	20.7
-input1.bam	FBtr0070603	72	24	F	19.5
-input1.bam	FBtr0070603	72	25	F	23.0
-input1.bam	FBtr0070603	72	26	F	25.8
-input1.bam	FBtr0070603	72	27	F	26.3
-input1.bam	FBtr0070603	72	32	F	20.0
-input1.bam	FBtr0070603	72	34	F	19.3
-input1.bam	FBtr0070603	72	38	F	18.0
-input1.bam	FBtr0070603	72	42	F	21.0
-input1.bam	FBtr0070603	72	51	F	18.0
-input1.bam	FBtr0070603	72	56	F	16.0
-input1.bam	FBtr0070603	72	72	F	0
-input1.bam	FBtr0070604	72	1	F	15.0
-input1.bam	FBtr0070604	72	18	F	23.0
-input1.bam	FBtr0070604	72	22	F	19.0
-input1.bam	FBtr0070604	72	30	F	18.0
-input1.bam	FBtr0070604	72	31	F	22.6
-input1.bam	FBtr0070604	72	32	F	22.0
-input1.bam	FBtr0070604	72	57	F	15.0
-input1.bam	FBtr0070604	72	72	F	0
-input1.bam	FBtr0070911	73	1	F	0
-input1.bam	FBtr0070911	73	15	F	21.0
-input1.bam	FBtr0070911	73	38	F	15.0
-input1.bam	FBtr0070911	73	73	F	0
-input1.bam	FBtr0078490	72	1	F	0
-input1.bam	FBtr0078490	72	13	F	16.0
-input1.bam	FBtr0078490	72	17	F	16.0
-input1.bam	FBtr0078490	72	18	F	15.0
-input1.bam	FBtr0078490	72	25	F	15.0
-input1.bam	FBtr0078490	72	28	F	19.0
-input1.bam	FBtr0078490	72	38	F	18.0
-input1.bam	FBtr0078490	72	72	F	0
-input1.bam	FBtr0078580	72	1	F	18.9
-input1.bam	FBtr0078580	72	3	F	22.0
-input1.bam	FBtr0078580	72	4	F	25.3
-input1.bam	FBtr0078580	72	5	F	21.0
-input1.bam	FBtr0078580	72	6	F	19.0
-input1.bam	FBtr0078580	72	7	F	22.0
-input1.bam	FBtr0078580	72	8	F	18.0
-input1.bam	FBtr0078580	72	11	F	23.0
-input1.bam	FBtr0078580	72	12	F	18.0
-input1.bam	FBtr0078580	72	14	F	15.3
-input1.bam	FBtr0078580	72	15	F	16.0
-input1.bam	FBtr0078580	72	16	F	19.0
-input1.bam	FBtr0078580	72	17	F	17.0
-input1.bam	FBtr0078580	72	19	F	24.0
-input1.bam	FBtr0078580	72	20	F	21.0
-input1.bam	FBtr0078580	72	21	F	19.4
-input1.bam	FBtr0078580	72	24	F	17.0
-input1.bam	FBtr0078580	72	25	F	27.5
-input1.bam	FBtr0078580	72	29	F	17.0
-input1.bam	FBtr0078580	72	31	F	17.0
-input1.bam	FBtr0078580	72	52	F	16.0
-input1.bam	FBtr0078580	72	72	F	0
-input1.bam	FBtr0078790	73	1	F	19.0
-input1.bam	FBtr0078790	73	17	F	16.0
-input1.bam	FBtr0078790	73	33	F	23.0
-input1.bam	FBtr0078790	73	42	F	18.5
-input1.bam	FBtr0078790	73	44	F	19.5
-input1.bam	FBtr0078790	73	46	F	17.0
-input1.bam	FBtr0078790	73	47	F	18.0
-input1.bam	FBtr0078790	73	52	F	20.0
-input1.bam	FBtr0078790	73	69	R	15.0
-input1.bam	FBtr0078790	73	73	F	0
-input1.bam	FBtr0079064	72	1	F	15.0
-input1.bam	FBtr0079064	72	3	F	21.0
-input1.bam	FBtr0079064	72	33	F	15.0
-input1.bam	FBtr0079064	72	52	F	17.0
-input1.bam	FBtr0079064	72	72	F	0
-input1.bam	FBtr0079090	72	1	F	21.5
-input1.bam	FBtr0079090	72	26	F	24.0
-input1.bam	FBtr0079090	72	33	F	16.0
-input1.bam	FBtr0079090	72	53	F	18.0
-input1.bam	FBtr0079090	72	56	R	21.0
-input1.bam	FBtr0079090	72	72	F	0
-input1.bam	FBtr0079338	73	1	F	0
-input1.bam	FBtr0079338	73	12	F	17.0
-input1.bam	FBtr0079338	73	13	F	17.5
-input1.bam	FBtr0079338	73	14	F	15.0
-input1.bam	FBtr0079338	73	17	F	15.0
-input1.bam	FBtr0079338	73	25	F	16.0
-input1.bam	FBtr0079338	73	42	F	21.8
-input1.bam	FBtr0079338	73	43	F	21.0
-input1.bam	FBtr0079338	73	46	F	18.0
-input1.bam	FBtr0079338	73	73	F	0
-input1.bam	FBtr0079528	71	1	F	20.8
-input1.bam	FBtr0079528	71	3	F	23.6
-input1.bam	FBtr0079528	71	4	F	24.0
-input1.bam	FBtr0079528	71	8	F	20.3
-input1.bam	FBtr0079528	71	10	F	21.0
-input1.bam	FBtr0079528	71	11	F	19.0
-input1.bam	FBtr0079528	71	13	F	16.0
-input1.bam	FBtr0079528	71	14	F	18.5
-input1.bam	FBtr0079528	71	16	F	15.0
-input1.bam	FBtr0079528	71	17	F	15.3
-input1.bam	FBtr0079528	71	18	F	19.8
-input1.bam	FBtr0079528	71	28	F	16.0
-input1.bam	FBtr0079528	71	35	F	15.0
-input1.bam	FBtr0079528	71	36	F	20.0
-input1.bam	FBtr0079528	71	37	F	18.0
-input1.bam	FBtr0079528	71	51	F	15.0
-input1.bam	FBtr0079528	71	71	F	0
-input1.bam	FBtr0079596	73	1	F	16.2
-input1.bam	FBtr0079596	73	3	F	21.8
-input1.bam	FBtr0079596	73	4	F	21.5
-input1.bam	FBtr0079596	73	5	F	18.5
-input1.bam	FBtr0079596	73	6	F	17.5
-input1.bam	FBtr0079596	73	8	F	16.6
-input1.bam	FBtr0079596	73	9	F	16.1
-input1.bam	FBtr0079596	73	10	F	15.3
-input1.bam	FBtr0079596	73	11	F	15.2
-input1.bam	FBtr0079596	73	12	F	17.0
-input1.bam	FBtr0079596	73	13	F	16.1
-input1.bam	FBtr0079596	73	14	F	15.0
-input1.bam	FBtr0079596	73	15	F	18.0
-input1.bam	FBtr0079596	73	16	F	16.7
-input1.bam	FBtr0079596	73	17	F	16.0
-input1.bam	FBtr0079596	73	18	F	15.0
-input1.bam	FBtr0079596	73	19	F	15.0
-input1.bam	FBtr0079596	73	53	F	18.5
-input1.bam	FBtr0079596	73	54	F	19.5
-input1.bam	FBtr0079596	73	73	F	0
-input1.bam	FBtr0079677	72	1	F	23.0
-input1.bam	FBtr0079677	72	5	F	19.0
-input1.bam	FBtr0079677	72	52	F	19.0
-input1.bam	FBtr0079677	72	53	F	18.0
-input1.bam	FBtr0079677	72	72	F	0
-input1.bam	FBtr0079690	72	1	F	15.0
-input1.bam	FBtr0079690	72	22	F	15.0
-input1.bam	FBtr0079690	72	27	F	25.0
-input1.bam	FBtr0079690	72	33	F	16.0
-input1.bam	FBtr0079690	72	72	F	0
-input1.bam	FBtr0079692	73	1	F	19.3
-input1.bam	FBtr0079692	73	18	F	18.0
-input1.bam	FBtr0079692	73	25	F	17.0
-input1.bam	FBtr0079692	73	32	F	20.0
-input1.bam	FBtr0079692	73	73	F	0
-input1.bam	FBtr0079693	72	1	F	17.2
-input1.bam	FBtr0079693	72	25	F	23.0
-input1.bam	FBtr0079693	72	72	F	0
-input1.bam	FBtr0079694	72	1	F	20.4
-input1.bam	FBtr0079694	72	18	F	19.0
-input1.bam	FBtr0079694	72	52	F	17.0
-input1.bam	FBtr0079694	72	72	F	0
-input1.bam	FBtr0079702	72	1	F	15.0
-input1.bam	FBtr0079702	72	19	F	18.0
-input1.bam	FBtr0079702	72	56	F	15.0
-input1.bam	FBtr0079702	72	72	F	0
-input1.bam	FBtr0079728	72	1	F	16.0
-input1.bam	FBtr0079728	72	8	F	20.0
-input1.bam	FBtr0079728	72	19	F	24.0
-input1.bam	FBtr0079728	72	33	F	15.7
-input1.bam	FBtr0079728	72	56	F	15.0
-input1.bam	FBtr0079728	72	72	F	0
-input1.bam	FBtr0079729	72	1	F	15.0
-input1.bam	FBtr0079729	72	13	F	22.0
-input1.bam	FBtr0079729	72	52	F	18.0
-input1.bam	FBtr0079729	72	57	F	16.0
-input1.bam	FBtr0079729	72	72	F	0
-input1.bam	FBtr0079752	72	1	F	19.5
-input1.bam	FBtr0079752	72	7	F	20.0
-input1.bam	FBtr0079752	72	12	F	16.0
-input1.bam	FBtr0079752	72	33	F	16.0
-input1.bam	FBtr0079752	72	52	F	19.5
-input1.bam	FBtr0079752	72	72	F	0
-input1.bam	FBtr0079820	74	1	F	0
-input1.bam	FBtr0079820	74	45	F	20.0
-input1.bam	FBtr0079820	74	46	F	17.0
-input1.bam	FBtr0079820	74	48	F	18.0
-input1.bam	FBtr0079820	74	49	F	24.0
-input1.bam	FBtr0079820	74	51	F	20.0
-input1.bam	FBtr0079820	74	54	F	17.0
-input1.bam	FBtr0079820	74	55	F	18.0
-input1.bam	FBtr0079820	74	56	F	18.5
-input1.bam	FBtr0079820	74	74	F	0
-input1.bam	FBtr0080609	72	1	F	18.8
-input1.bam	FBtr0080609	72	3	F	21.0
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-input2.bam	FBtr0080663	71	20	F	16.7
-input2.bam	FBtr0080663	71	21	F	15.5
-input2.bam	FBtr0080663	71	22	F	15.3
-input2.bam	FBtr0080663	71	31	F	17.0
-input2.bam	FBtr0080663	71	50	F	15.5
-input2.bam	FBtr0080663	71	51	F	19.0
-input2.bam	FBtr0080663	71	52	F	15.0
-input2.bam	FBtr0080663	71	57	F	15.0
-input2.bam	FBtr0080663	71	71	F	0
-input2.bam	FBtr0080664	71	1	F	22.0
-input2.bam	FBtr0080664	71	3	F	23.0
-input2.bam	FBtr0080664	71	10	F	23.0
-input2.bam	FBtr0080664	71	11	F	22.0
-input2.bam	FBtr0080664	71	12	F	21.0
-input2.bam	FBtr0080664	71	13	F	19.7
-input2.bam	FBtr0080664	71	14	F	18.3
-input2.bam	FBtr0080664	71	15	F	18.1
-input2.bam	FBtr0080664	71	16	F	17.3
-input2.bam	FBtr0080664	71	17	F	15.8
-input2.bam	FBtr0080664	71	18	F	18.9
-input2.bam	FBtr0080664	71	19	F	19.0
-input2.bam	FBtr0080664	71	20	F	16.0
-input2.bam	FBtr0080664	71	21	F	15.3
-input2.bam	FBtr0080664	71	22	F	16.2
-input2.bam	FBtr0080664	71	24	F	15.0
-input2.bam	FBtr0080664	71	30	F	21.0
-input2.bam	FBtr0080664	71	31	F	18.7
-input2.bam	FBtr0080664	71	32	F	18.3
-input2.bam	FBtr0080664	71	33	F	17.5
-input2.bam	FBtr0080664	71	34	F	16.1
-input2.bam	FBtr0080664	71	35	F	15.2
-input2.bam	FBtr0080664	71	36	F	19.9
-input2.bam	FBtr0080664	71	37	F	17.7
-input2.bam	FBtr0080664	71	38	F	18.1
-input2.bam	FBtr0080664	71	39	F	17.0
-input2.bam	FBtr0080664	71	42	F	20.0
-input2.bam	FBtr0080664	71	47	F	15.0
-input2.bam	FBtr0080664	71	50	F	15.5
-input2.bam	FBtr0080664	71	52	F	16.0
-input2.bam	FBtr0080664	71	53	F	19.0
-input2.bam	FBtr0080664	71	56	F	16.0
-input2.bam	FBtr0080664	71	57	F	15.0
-input2.bam	FBtr0080664	71	62	R	23.0
-input2.bam	FBtr0080664	71	71	F	0
-input2.bam	FBtr0080664	71	71	R	22.0
diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/input1_input2_norm_1_2_counts.tab
--- a/test-data/input1_input2_norm_1_2_counts.tab	Wed Apr 10 06:38:33 2019 -0400
+++ b/test-data/input1_input2_norm_1_2_counts.tab	Sun Apr 14 14:43:44 2019 -0400
@@ -1,617 +1,392 @@
 Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts
-input1.bam	FBtr0070001	72	1	F	1
-input1.bam	FBtr0070001	72	7	F	6
+input1.bam	FBtr0070001	72	1	F	0
+input1.bam	FBtr0070001	72	7	F	5
 input1.bam	FBtr0070001	72	8	F	3
 input1.bam	FBtr0070001	72	11	F	2
 input1.bam	FBtr0070001	72	16	F	1
 input1.bam	FBtr0070001	72	17	F	1
-input1.bam	FBtr0070001	72	18	F	1
 input1.bam	FBtr0070001	72	27	F	2
 input1.bam	FBtr0070001	72	30	F	1
 input1.bam	FBtr0070001	72	31	F	11
 input1.bam	FBtr0070001	72	32	F	27
 input1.bam	FBtr0070001	72	34	F	1
 input1.bam	FBtr0070001	72	72	F	0
-input1.bam	FBtr0070533	72	1	F	1
-input1.bam	FBtr0070533	72	12	F	2
-input1.bam	FBtr0070533	72	15	F	1
+input1.bam	FBtr0070533	72	1	F	0
 input1.bam	FBtr0070533	72	19	F	5
 input1.bam	FBtr0070533	72	20	F	1
-input1.bam	FBtr0070533	72	21	F	1
 input1.bam	FBtr0070533	72	22	F	1
-input1.bam	FBtr0070533	72	25	F	1
-input1.bam	FBtr0070533	72	26	F	1
 input1.bam	FBtr0070533	72	28	F	1
-input1.bam	FBtr0070533	72	32	F	4
+input1.bam	FBtr0070533	72	32	F	3
 input1.bam	FBtr0070533	72	35	F	1
 input1.bam	FBtr0070533	72	37	F	2
-input1.bam	FBtr0070533	72	38	F	2
 input1.bam	FBtr0070533	72	72	F	0
-input1.bam	FBtr0070603	72	1	F	2
+input1.bam	FBtr0070603	72	1	F	0
 input1.bam	FBtr0070603	72	3	F	1
 input1.bam	FBtr0070603	72	4	F	1
-input1.bam	FBtr0070603	72	6	F	1
-input1.bam	FBtr0070603	72	7	F	7
-input1.bam	FBtr0070603	72	8	F	4
-input1.bam	FBtr0070603	72	9	F	7
-input1.bam	FBtr0070603	72	12	F	2
+input1.bam	FBtr0070603	72	12	F	1
 input1.bam	FBtr0070603	72	13	F	1
-input1.bam	FBtr0070603	72	15	F	2
-input1.bam	FBtr0070603	72	16	F	2
+input1.bam	FBtr0070603	72	15	F	1
+input1.bam	FBtr0070603	72	16	F	1
 input1.bam	FBtr0070603	72	17	F	3
-input1.bam	FBtr0070603	72	18	F	1
-input1.bam	FBtr0070603	72	19	F	9
-input1.bam	FBtr0070603	72	20	F	3
+input1.bam	FBtr0070603	72	19	F	8
+input1.bam	FBtr0070603	72	20	F	2
 input1.bam	FBtr0070603	72	21	F	1
 input1.bam	FBtr0070603	72	22	F	3
-input1.bam	FBtr0070603	72	24	F	2
+input1.bam	FBtr0070603	72	24	F	1
 input1.bam	FBtr0070603	72	25	F	1
 input1.bam	FBtr0070603	72	26	F	6
 input1.bam	FBtr0070603	72	27	F	3
 input1.bam	FBtr0070603	72	32	F	1
-input1.bam	FBtr0070603	72	34	F	3
-input1.bam	FBtr0070603	72	38	F	1
+input1.bam	FBtr0070603	72	34	F	2
 input1.bam	FBtr0070603	72	42	F	1
-input1.bam	FBtr0070603	72	51	F	1
-input1.bam	FBtr0070603	72	56	F	1
 input1.bam	FBtr0070603	72	72	F	0
-input1.bam	FBtr0070604	72	1	F	1
+input1.bam	FBtr0070604	72	1	F	0
 input1.bam	FBtr0070604	72	18	F	1
 input1.bam	FBtr0070604	72	22	F	1
-input1.bam	FBtr0070604	72	30	F	2
 input1.bam	FBtr0070604	72	31	F	10
 input1.bam	FBtr0070604	72	32	F	24
-input1.bam	FBtr0070604	72	57	F	1
 input1.bam	FBtr0070604	72	72	F	0
 input1.bam	FBtr0070911	73	1	F	0
 input1.bam	FBtr0070911	73	15	F	1
-input1.bam	FBtr0070911	73	38	F	1
 input1.bam	FBtr0070911	73	73	F	0
 input1.bam	FBtr0078490	72	1	F	0
-input1.bam	FBtr0078490	72	13	F	2
-input1.bam	FBtr0078490	72	17	F	1
-input1.bam	FBtr0078490	72	18	F	1
-input1.bam	FBtr0078490	72	25	F	1
-input1.bam	FBtr0078490	72	28	F	2
-input1.bam	FBtr0078490	72	38	F	1
+input1.bam	FBtr0078490	72	28	F	1
 input1.bam	FBtr0078490	72	72	F	0
-input1.bam	FBtr0078580	72	1	F	1041
+input1.bam	FBtr0078580	72	1	F	420
 input1.bam	FBtr0078580	72	3	F	3
 input1.bam	FBtr0078580	72	4	F	4
 input1.bam	FBtr0078580	72	5	F	5
-input1.bam	FBtr0078580	72	6	F	4
+input1.bam	FBtr0078580	72	6	F	2
 input1.bam	FBtr0078580	72	7	F	1
-input1.bam	FBtr0078580	72	8	F	2
+input1.bam	FBtr0078580	72	8	F	1
 input1.bam	FBtr0078580	72	11	F	1
-input1.bam	FBtr0078580	72	12	F	13
-input1.bam	FBtr0078580	72	14	F	7
-input1.bam	FBtr0078580	72	15	F	1
-input1.bam	FBtr0078580	72	16	F	4
-input1.bam	FBtr0078580	72	17	F	1
+input1.bam	FBtr0078580	72	12	F	3
+input1.bam	FBtr0078580	72	16	F	3
 input1.bam	FBtr0078580	72	19	F	1
 input1.bam	FBtr0078580	72	20	F	2
-input1.bam	FBtr0078580	72	21	F	5
-input1.bam	FBtr0078580	72	24	F	3
+input1.bam	FBtr0078580	72	21	F	4
 input1.bam	FBtr0078580	72	25	F	2
-input1.bam	FBtr0078580	72	29	F	1
-input1.bam	FBtr0078580	72	31	F	1
-input1.bam	FBtr0078580	72	52	F	2
 input1.bam	FBtr0078580	72	72	F	0
 input1.bam	FBtr0078790	73	1	F	1
-input1.bam	FBtr0078790	73	17	F	2
 input1.bam	FBtr0078790	73	33	F	1
-input1.bam	FBtr0078790	73	42	F	4
+input1.bam	FBtr0078790	73	42	F	2
 input1.bam	FBtr0078790	73	44	F	2
-input1.bam	FBtr0078790	73	46	F	1
-input1.bam	FBtr0078790	73	47	F	1
 input1.bam	FBtr0078790	73	52	F	1
-input1.bam	FBtr0078790	73	69	R	1
 input1.bam	FBtr0078790	73	73	F	0
-input1.bam	FBtr0079064	72	1	F	1
+input1.bam	FBtr0079064	72	1	F	0
 input1.bam	FBtr0079064	72	3	F	1
-input1.bam	FBtr0079064	72	33	F	1
-input1.bam	FBtr0079064	72	52	F	1
 input1.bam	FBtr0079064	72	72	F	0
-input1.bam	FBtr0079090	72	1	F	2
+input1.bam	FBtr0079090	72	1	F	1
 input1.bam	FBtr0079090	72	26	F	1
-input1.bam	FBtr0079090	72	33	F	1
-input1.bam	FBtr0079090	72	53	F	1
 input1.bam	FBtr0079090	72	56	R	1
 input1.bam	FBtr0079090	72	72	F	0
 input1.bam	FBtr0079338	73	1	F	0
-input1.bam	FBtr0079338	73	12	F	1
-input1.bam	FBtr0079338	73	13	F	2
-input1.bam	FBtr0079338	73	14	F	1
-input1.bam	FBtr0079338	73	17	F	1
-input1.bam	FBtr0079338	73	25	F	1
+input1.bam	FBtr0079338	73	13	F	1
 input1.bam	FBtr0079338	73	42	F	8
 input1.bam	FBtr0079338	73	43	F	1
-input1.bam	FBtr0079338	73	46	F	1
 input1.bam	FBtr0079338	73	73	F	0
-input1.bam	FBtr0079528	71	1	F	19
+input1.bam	FBtr0079528	71	1	F	10
 input1.bam	FBtr0079528	71	3	F	55
 input1.bam	FBtr0079528	71	4	F	2
-input1.bam	FBtr0079528	71	8	F	4
+input1.bam	FBtr0079528	71	8	F	3
 input1.bam	FBtr0079528	71	10	F	1
-input1.bam	FBtr0079528	71	11	F	2
-input1.bam	FBtr0079528	71	13	F	1
-input1.bam	FBtr0079528	71	14	F	4
-input1.bam	FBtr0079528	71	16	F	1
-input1.bam	FBtr0079528	71	17	F	4
-input1.bam	FBtr0079528	71	18	F	4
-input1.bam	FBtr0079528	71	28	F	1
-input1.bam	FBtr0079528	71	35	F	1
+input1.bam	FBtr0079528	71	11	F	1
+input1.bam	FBtr0079528	71	14	F	2
+input1.bam	FBtr0079528	71	18	F	3
 input1.bam	FBtr0079528	71	36	F	1
-input1.bam	FBtr0079528	71	37	F	1
-input1.bam	FBtr0079528	71	51	F	5
 input1.bam	FBtr0079528	71	71	F	0
-input1.bam	FBtr0079596	73	1	F	13
-input1.bam	FBtr0079596	73	3	F	13
+input1.bam	FBtr0079596	73	1	F	3
+input1.bam	FBtr0079596	73	3	F	11
 input1.bam	FBtr0079596	73	4	F	31
-input1.bam	FBtr0079596	73	5	F	2
-input1.bam	FBtr0079596	73	6	F	11
-input1.bam	FBtr0079596	73	8	F	9
-input1.bam	FBtr0079596	73	9	F	12
-input1.bam	FBtr0079596	73	10	F	3
-input1.bam	FBtr0079596	73	11	F	19
-input1.bam	FBtr0079596	73	12	F	1
-input1.bam	FBtr0079596	73	13	F	20
-input1.bam	FBtr0079596	73	14	F	6
-input1.bam	FBtr0079596	73	15	F	1
-input1.bam	FBtr0079596	73	16	F	3
-input1.bam	FBtr0079596	73	17	F	2
-input1.bam	FBtr0079596	73	18	F	1
-input1.bam	FBtr0079596	73	19	F	1
-input1.bam	FBtr0079596	73	53	F	2
+input1.bam	FBtr0079596	73	5	F	1
+input1.bam	FBtr0079596	73	6	F	4
+input1.bam	FBtr0079596	73	13	F	1
+input1.bam	FBtr0079596	73	53	F	1
 input1.bam	FBtr0079596	73	54	F	2
 input1.bam	FBtr0079596	73	73	F	0
 input1.bam	FBtr0079677	72	1	F	1
 input1.bam	FBtr0079677	72	5	F	1
 input1.bam	FBtr0079677	72	52	F	1
-input1.bam	FBtr0079677	72	53	F	1
 input1.bam	FBtr0079677	72	72	F	0
-input1.bam	FBtr0079690	72	1	F	1
-input1.bam	FBtr0079690	72	22	F	1
+input1.bam	FBtr0079690	72	1	F	0
 input1.bam	FBtr0079690	72	27	F	1
-input1.bam	FBtr0079690	72	33	F	2
 input1.bam	FBtr0079690	72	72	F	0
-input1.bam	FBtr0079692	73	1	F	3
-input1.bam	FBtr0079692	73	18	F	1
-input1.bam	FBtr0079692	73	25	F	1
+input1.bam	FBtr0079692	73	1	F	2
 input1.bam	FBtr0079692	73	32	F	1
 input1.bam	FBtr0079692	73	73	F	0
-input1.bam	FBtr0079693	72	1	F	5
+input1.bam	FBtr0079693	72	1	F	1
 input1.bam	FBtr0079693	72	25	F	1
 input1.bam	FBtr0079693	72	72	F	0
-input1.bam	FBtr0079694	72	1	F	5
+input1.bam	FBtr0079694	72	1	F	3
 input1.bam	FBtr0079694	72	18	F	1
-input1.bam	FBtr0079694	72	52	F	1
 input1.bam	FBtr0079694	72	72	F	0
-input1.bam	FBtr0079702	72	1	F	1
-input1.bam	FBtr0079702	72	19	F	2
-input1.bam	FBtr0079702	72	56	F	1
+input1.bam	FBtr0079702	72	1	F	0
 input1.bam	FBtr0079702	72	72	F	0
-input1.bam	FBtr0079728	72	1	F	2
+input1.bam	FBtr0079728	72	1	F	0
 input1.bam	FBtr0079728	72	8	F	1
 input1.bam	FBtr0079728	72	19	F	1
-input1.bam	FBtr0079728	72	33	F	3
-input1.bam	FBtr0079728	72	56	F	1
 input1.bam	FBtr0079728	72	72	F	0
-input1.bam	FBtr0079729	72	1	F	1
+input1.bam	FBtr0079729	72	1	F	0
 input1.bam	FBtr0079729	72	13	F	1
-input1.bam	FBtr0079729	72	52	F	1
-input1.bam	FBtr0079729	72	57	F	1
 input1.bam	FBtr0079729	72	72	F	0
-input1.bam	FBtr0079752	72	1	F	2
+input1.bam	FBtr0079752	72	1	F	1
 input1.bam	FBtr0079752	72	7	F	1
-input1.bam	FBtr0079752	72	12	F	1
-input1.bam	FBtr0079752	72	33	F	2
 input1.bam	FBtr0079752	72	52	F	2
 input1.bam	FBtr0079752	72	72	F	0
 input1.bam	FBtr0079820	74	1	F	0
 input1.bam	FBtr0079820	74	45	F	1
-input1.bam	FBtr0079820	74	46	F	2
-input1.bam	FBtr0079820	74	48	F	1
 input1.bam	FBtr0079820	74	49	F	1
 input1.bam	FBtr0079820	74	51	F	1
-input1.bam	FBtr0079820	74	54	F	4
-input1.bam	FBtr0079820	74	55	F	1
-input1.bam	FBtr0079820	74	56	F	2
+input1.bam	FBtr0079820	74	54	F	2
+input1.bam	FBtr0079820	74	56	F	1
 input1.bam	FBtr0079820	74	74	F	0
-input1.bam	FBtr0080609	72	1	F	13
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 input1.bam	FBtr0080609	72	3	F	2
 input1.bam	FBtr0080609	72	4	F	10
 input1.bam	FBtr0080609	72	5	F	2
-input1.bam	FBtr0080609	72	7	F	19
-input1.bam	FBtr0080609	72	8	F	4
-input1.bam	FBtr0080609	72	9	F	3
 input1.bam	FBtr0080609	72	12	F	1
 input1.bam	FBtr0080609	72	15	F	1
 input1.bam	FBtr0080609	72	16	F	1
-input1.bam	FBtr0080609	72	17	F	2
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 input1.bam	FBtr0080609	72	19	F	1
 input1.bam	FBtr0080609	72	20	F	1
 input1.bam	FBtr0080609	72	42	F	1
-input1.bam	FBtr0080609	72	51	F	1
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 input1.bam	FBtr0080609	72	72	F	0
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-input1.bam	FBtr0080644	72	4	F	2
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-input1.bam	FBtr0080644	72	12	F	2
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 input1.bam	FBtr0080644	72	72	F	0
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 input1.bam	FBtr0080646	72	6	F	1
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-input1.bam	FBtr0080647	72	1	F	3
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-input1.bam	FBtr0080647	72	6	F	2
+input1.bam	FBtr0080647	72	1	F	0
+input1.bam	FBtr0080647	72	6	F	1
 input1.bam	FBtr0080647	72	8	F	1
-input1.bam	FBtr0080647	72	11	F	2
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-input1.bam	FBtr0080660	72	7	F	3
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 input1.bam	FBtr0080660	72	72	F	0
-input1.bam	FBtr0080663	71	1	F	22
+input1.bam	FBtr0080663	71	1	F	6
 input1.bam	FBtr0080663	71	3	F	56
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-input1.bam	FBtr0080663	71	7	F	1
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-input1.bam	FBtr0080663	71	15	F	1
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-input1.bam	FBtr0080663	71	17	F	7
-input1.bam	FBtr0080663	71	26	F	1
-input1.bam	FBtr0080663	71	32	F	2
-input1.bam	FBtr0080663	71	50	F	1
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 input2.bam	FBtr0080663	71	51	F	1
-input2.bam	FBtr0080663	71	52	F	2
-input2.bam	FBtr0080663	71	57	F	3
 input2.bam	FBtr0080663	71	71	F	0
 input2.bam	FBtr0080664	71	1	F	1
 input2.bam	FBtr0080664	71	3	F	2
 input2.bam	FBtr0080664	71	10	F	1
 input2.bam	FBtr0080664	71	11	F	2
 input2.bam	FBtr0080664	71	12	F	3
-input2.bam	FBtr0080664	71	13	F	11
-input2.bam	FBtr0080664	71	14	F	11
-input2.bam	FBtr0080664	71	15	F	17
-input2.bam	FBtr0080664	71	16	F	15
-input2.bam	FBtr0080664	71	17	F	13
-input2.bam	FBtr0080664	71	18	F	10
-input2.bam	FBtr0080664	71	19	F	8
-input2.bam	FBtr0080664	71	20	F	1
-input2.bam	FBtr0080664	71	21	F	15
-input2.bam	FBtr0080664	71	22	F	6
-input2.bam	FBtr0080664	71	24	F	1
+input2.bam	FBtr0080664	71	13	F	10
+input2.bam	FBtr0080664	71	14	F	3
+input2.bam	FBtr0080664	71	15	F	2
+input2.bam	FBtr0080664	71	16	F	4
+input2.bam	FBtr0080664	71	18	F	5
+input2.bam	FBtr0080664	71	19	F	5
+input2.bam	FBtr0080664	71	22	F	1
 input2.bam	FBtr0080664	71	30	F	1
-input2.bam	FBtr0080664	71	31	F	3
-input2.bam	FBtr0080664	71	32	F	39
-input2.bam	FBtr0080664	71	33	F	4
-input2.bam	FBtr0080664	71	34	F	37
-input2.bam	FBtr0080664	71	35	F	135
-input2.bam	FBtr0080664	71	36	F	8
-input2.bam	FBtr0080664	71	37	F	25
-input2.bam	FBtr0080664	71	38	F	8
-input2.bam	FBtr0080664	71	39	F	1
+input2.bam	FBtr0080664	71	31	F	2
+input2.bam	FBtr0080664	71	32	F	8
+input2.bam	FBtr0080664	71	33	F	1
+input2.bam	FBtr0080664	71	34	F	4
+input2.bam	FBtr0080664	71	36	F	4
+input2.bam	FBtr0080664	71	37	F	5
+input2.bam	FBtr0080664	71	38	F	2
 input2.bam	FBtr0080664	71	42	F	1
-input2.bam	FBtr0080664	71	47	F	1
-input2.bam	FBtr0080664	71	50	F	2
-input2.bam	FBtr0080664	71	52	F	1
 input2.bam	FBtr0080664	71	53	F	1
-input2.bam	FBtr0080664	71	56	F	1
-input2.bam	FBtr0080664	71	57	F	2
 input2.bam	FBtr0080664	71	62	R	1
 input2.bam	FBtr0080664	71	71	F	0
 input2.bam	FBtr0080664	71	71	R	1
diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/input1_input2_norm_1_2_coverage.tab
--- a/test-data/input1_input2_norm_1_2_coverage.tab	Wed Apr 10 06:38:33 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3109 +0,0 @@
-Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Coverage
-input1.bam	FBtr0070001	72	1	F	1
-input1.bam	FBtr0070001	72	2	F	1
-input1.bam	FBtr0070001	72	3	F	1
-input1.bam	FBtr0070001	72	4	F	1
-input1.bam	FBtr0070001	72	5	F	1
-input1.bam	FBtr0070001	72	6	F	1
-input1.bam	FBtr0070001	72	7	F	7
-input1.bam	FBtr0070001	72	8	F	10
-input1.bam	FBtr0070001	72	9	F	10
-input1.bam	FBtr0070001	72	10	F	10
-input1.bam	FBtr0070001	72	11	F	12
-input1.bam	FBtr0070001	72	12	F	12
-input1.bam	FBtr0070001	72	13	F	12
-input1.bam	FBtr0070001	72	14	F	12
-input1.bam	FBtr0070001	72	15	F	12
-input1.bam	FBtr0070001	72	16	F	13
-input1.bam	FBtr0070001	72	17	F	14
-input1.bam	FBtr0070001	72	18	F	14
-input1.bam	FBtr0070001	72	19	F	14
-input1.bam	FBtr0070001	72	20	F	14
-input1.bam	FBtr0070001	72	21	F	14
-input1.bam	FBtr0070001	72	22	F	14
-input1.bam	FBtr0070001	72	23	F	13
-input1.bam	FBtr0070001	72	24	F	13
-input1.bam	FBtr0070001	72	25	F	13
-input1.bam	FBtr0070001	72	26	F	13
-input1.bam	FBtr0070001	72	27	F	14
-input1.bam	FBtr0070001	72	28	F	11
-input1.bam	FBtr0070001	72	29	F	8
-input1.bam	FBtr0070001	72	30	F	9
-input1.bam	FBtr0070001	72	31	F	18
-input1.bam	FBtr0070001	72	32	F	44
-input1.bam	FBtr0070001	72	33	F	44
-input1.bam	FBtr0070001	72	34	F	44
-input1.bam	FBtr0070001	72	35	F	43
-input1.bam	FBtr0070001	72	36	F	43
-input1.bam	FBtr0070001	72	37	F	43
-input1.bam	FBtr0070001	72	38	F	43
-input1.bam	FBtr0070001	72	39	F	43
-input1.bam	FBtr0070001	72	40	F	42
-input1.bam	FBtr0070001	72	41	F	42
-input1.bam	FBtr0070001	72	42	F	42
-input1.bam	FBtr0070001	72	43	F	42
-input1.bam	FBtr0070001	72	44	F	42
-input1.bam	FBtr0070001	72	45	F	42
-input1.bam	FBtr0070001	72	46	F	42
-input1.bam	FBtr0070001	72	47	F	42
-input1.bam	FBtr0070001	72	48	F	42
-input1.bam	FBtr0070001	72	49	F	42
-input1.bam	FBtr0070001	72	50	F	41
-input1.bam	FBtr0070001	72	51	F	40
-input1.bam	FBtr0070001	72	52	F	40
-input1.bam	FBtr0070001	72	53	F	39
-input1.bam	FBtr0070001	72	72	F	0
-input1.bam	FBtr0070533	72	1	F	1
-input1.bam	FBtr0070533	72	2	F	1
-input1.bam	FBtr0070533	72	3	F	1
-input1.bam	FBtr0070533	72	4	F	1
-input1.bam	FBtr0070533	72	5	F	1
-input1.bam	FBtr0070533	72	6	F	1
-input1.bam	FBtr0070533	72	7	F	1
-input1.bam	FBtr0070533	72	8	F	1
-input1.bam	FBtr0070533	72	9	F	1
-input1.bam	FBtr0070533	72	10	F	1
-input1.bam	FBtr0070533	72	11	F	1
-input1.bam	FBtr0070533	72	12	F	3
-input1.bam	FBtr0070533	72	13	F	3
-input1.bam	FBtr0070533	72	14	F	3
-input1.bam	FBtr0070533	72	15	F	4
-input1.bam	FBtr0070533	72	16	F	3
-input1.bam	FBtr0070533	72	17	F	3
-input1.bam	FBtr0070533	72	18	F	3
-input1.bam	FBtr0070533	72	19	F	8
-input1.bam	FBtr0070533	72	20	F	9
-input1.bam	FBtr0070533	72	21	F	10
-input1.bam	FBtr0070533	72	22	F	11
-input1.bam	FBtr0070533	72	23	F	11
-input1.bam	FBtr0070533	72	24	F	11
-input1.bam	FBtr0070533	72	25	F	12
-input1.bam	FBtr0070533	72	26	F	13
-input1.bam	FBtr0070533	72	27	F	13
-input1.bam	FBtr0070533	72	28	F	14
-input1.bam	FBtr0070533	72	29	F	14
-input1.bam	FBtr0070533	72	30	F	11
-input1.bam	FBtr0070533	72	31	F	11
-input1.bam	FBtr0070533	72	32	F	15
-input1.bam	FBtr0070533	72	33	F	15
-input1.bam	FBtr0070533	72	34	F	15
-input1.bam	FBtr0070533	72	35	F	16
-input1.bam	FBtr0070533	72	36	F	16
-input1.bam	FBtr0070533	72	37	F	18
-input1.bam	FBtr0070533	72	38	F	20
-input1.bam	FBtr0070533	72	39	F	19
-input1.bam	FBtr0070533	72	40	F	17
-input1.bam	FBtr0070533	72	41	F	15
-input1.bam	FBtr0070533	72	42	F	11
-input1.bam	FBtr0070533	72	43	F	10
-input1.bam	FBtr0070533	72	44	F	10
-input1.bam	FBtr0070533	72	45	F	10
-input1.bam	FBtr0070533	72	46	F	10
-input1.bam	FBtr0070533	72	47	F	10
-input1.bam	FBtr0070533	72	48	F	10
-input1.bam	FBtr0070533	72	49	F	10
-input1.bam	FBtr0070533	72	50	F	9
-input1.bam	FBtr0070533	72	51	F	9
-input1.bam	FBtr0070533	72	52	F	8
-input1.bam	FBtr0070533	72	53	F	7
-input1.bam	FBtr0070533	72	54	F	4
-input1.bam	FBtr0070533	72	55	F	4
-input1.bam	FBtr0070533	72	72	F	0
-input1.bam	FBtr0070603	72	1	F	2
-input1.bam	FBtr0070603	72	2	F	2
-input1.bam	FBtr0070603	72	3	F	3
-input1.bam	FBtr0070603	72	4	F	4
-input1.bam	FBtr0070603	72	5	F	4
-input1.bam	FBtr0070603	72	6	F	5
-input1.bam	FBtr0070603	72	7	F	12
-input1.bam	FBtr0070603	72	8	F	16
-input1.bam	FBtr0070603	72	9	F	23
-input1.bam	FBtr0070603	72	10	F	23
-input1.bam	FBtr0070603	72	11	F	23
-input1.bam	FBtr0070603	72	12	F	25
-input1.bam	FBtr0070603	72	13	F	26
-input1.bam	FBtr0070603	72	14	F	26
-input1.bam	FBtr0070603	72	15	F	28
-input1.bam	FBtr0070603	72	16	F	29
-input1.bam	FBtr0070603	72	17	F	32
-input1.bam	FBtr0070603	72	18	F	33
-input1.bam	FBtr0070603	72	19	F	41
-input1.bam	FBtr0070603	72	20	F	44
-input1.bam	FBtr0070603	72	21	F	45
-input1.bam	FBtr0070603	72	22	F	48
-input1.bam	FBtr0070603	72	23	F	48
-input1.bam	FBtr0070603	72	24	F	30
-input1.bam	FBtr0070603	72	25	F	30
-input1.bam	FBtr0070603	72	26	F	36
-input1.bam	FBtr0070603	72	27	F	39
-input1.bam	FBtr0070603	72	28	F	39
-input1.bam	FBtr0070603	72	29	F	38
-input1.bam	FBtr0070603	72	30	F	38
-input1.bam	FBtr0070603	72	31	F	38
-input1.bam	FBtr0070603	72	32	F	38
-input1.bam	FBtr0070603	72	33	F	37
-input1.bam	FBtr0070603	72	34	F	39
-input1.bam	FBtr0070603	72	35	F	35
-input1.bam	FBtr0070603	72	36	F	34
-input1.bam	FBtr0070603	72	37	F	34
-input1.bam	FBtr0070603	72	38	F	35
-input1.bam	FBtr0070603	72	39	F	34
-input1.bam	FBtr0070603	72	40	F	33
-input1.bam	FBtr0070603	72	41	F	32
-input1.bam	FBtr0070603	72	42	F	21
-input1.bam	FBtr0070603	72	43	F	21
-input1.bam	FBtr0070603	72	44	F	20
-input1.bam	FBtr0070603	72	45	F	18
-input1.bam	FBtr0070603	72	46	F	16
-input1.bam	FBtr0070603	72	47	F	16
-input1.bam	FBtr0070603	72	48	F	15
-input1.bam	FBtr0070603	72	49	F	15
-input1.bam	FBtr0070603	72	50	F	14
-input1.bam	FBtr0070603	72	51	F	14
-input1.bam	FBtr0070603	72	52	F	10
-input1.bam	FBtr0070603	72	53	F	6
-input1.bam	FBtr0070603	72	54	F	3
-input1.bam	FBtr0070603	72	55	F	3
-input1.bam	FBtr0070603	72	56	F	3
-input1.bam	FBtr0070603	72	57	F	3
-input1.bam	FBtr0070603	72	58	F	3
-input1.bam	FBtr0070603	72	59	F	3
-input1.bam	FBtr0070603	72	60	F	3
-input1.bam	FBtr0070603	72	61	F	3
-input1.bam	FBtr0070603	72	62	F	3
-input1.bam	FBtr0070603	72	63	F	2
-input1.bam	FBtr0070603	72	64	F	2
-input1.bam	FBtr0070603	72	65	F	2
-input1.bam	FBtr0070603	72	66	F	2
-input1.bam	FBtr0070603	72	67	F	2
-input1.bam	FBtr0070603	72	68	F	2
-input1.bam	FBtr0070603	72	69	F	1
-input1.bam	FBtr0070603	72	70	F	1
-input1.bam	FBtr0070603	72	71	F	1
-input1.bam	FBtr0070603	72	72	F	0
-input1.bam	FBtr0070604	72	1	F	1
-input1.bam	FBtr0070604	72	2	F	1
-input1.bam	FBtr0070604	72	3	F	1
-input1.bam	FBtr0070604	72	4	F	1
-input1.bam	FBtr0070604	72	5	F	1
-input1.bam	FBtr0070604	72	6	F	1
-input1.bam	FBtr0070604	72	7	F	1
-input1.bam	FBtr0070604	72	8	F	1
-input1.bam	FBtr0070604	72	9	F	1
-input1.bam	FBtr0070604	72	10	F	1
-input1.bam	FBtr0070604	72	11	F	1
-input1.bam	FBtr0070604	72	12	F	1
-input1.bam	FBtr0070604	72	13	F	1
-input1.bam	FBtr0070604	72	14	F	1
-input1.bam	FBtr0070604	72	15	F	1
-input1.bam	FBtr0070604	72	18	F	1
-input1.bam	FBtr0070604	72	19	F	1
-input1.bam	FBtr0070604	72	20	F	1
-input1.bam	FBtr0070604	72	21	F	1
-input1.bam	FBtr0070604	72	22	F	2
-input1.bam	FBtr0070604	72	23	F	2
-input1.bam	FBtr0070604	72	24	F	2
-input1.bam	FBtr0070604	72	25	F	2
-input1.bam	FBtr0070604	72	26	F	2
-input1.bam	FBtr0070604	72	27	F	2
-input1.bam	FBtr0070604	72	28	F	2
-input1.bam	FBtr0070604	72	29	F	2
-input1.bam	FBtr0070604	72	30	F	4
-input1.bam	FBtr0070604	72	31	F	14
-input1.bam	FBtr0070604	72	32	F	38
-input1.bam	FBtr0070604	72	33	F	38
-input1.bam	FBtr0070604	72	34	F	38
-input1.bam	FBtr0070604	72	35	F	38
-input1.bam	FBtr0070604	72	36	F	38
-input1.bam	FBtr0070604	72	37	F	38
-input1.bam	FBtr0070604	72	38	F	38
-input1.bam	FBtr0070604	72	39	F	38
-input1.bam	FBtr0070604	72	40	F	38
-input1.bam	FBtr0070604	72	41	F	36
-input1.bam	FBtr0070604	72	42	F	36
-input1.bam	FBtr0070604	72	43	F	36
-input1.bam	FBtr0070604	72	44	F	36
-input1.bam	FBtr0070604	72	45	F	36
-input1.bam	FBtr0070604	72	46	F	35
-input1.bam	FBtr0070604	72	47	F	36
-input1.bam	FBtr0070604	72	48	F	34
-input1.bam	FBtr0070604	72	49	F	34
-input1.bam	FBtr0070604	72	50	F	33
-input1.bam	FBtr0070604	72	51	F	33
-input1.bam	FBtr0070604	72	52	F	33
-input1.bam	FBtr0070604	72	53	F	31
-input1.bam	FBtr0070604	72	57	F	1
-input1.bam	FBtr0070604	72	58	F	1
-input1.bam	FBtr0070604	72	59	F	1
-input1.bam	FBtr0070604	72	60	F	1
-input1.bam	FBtr0070604	72	61	F	1
-input1.bam	FBtr0070604	72	62	F	1
-input1.bam	FBtr0070604	72	63	F	1
-input1.bam	FBtr0070604	72	64	F	1
-input1.bam	FBtr0070604	72	65	F	1
-input1.bam	FBtr0070604	72	66	F	1
-input1.bam	FBtr0070604	72	67	F	1
-input1.bam	FBtr0070604	72	68	F	1
-input1.bam	FBtr0070604	72	69	F	1
-input1.bam	FBtr0070604	72	70	F	1
-input1.bam	FBtr0070604	72	71	F	1
-input1.bam	FBtr0070604	72	72	F	0
-input1.bam	FBtr0070911	73	1	F	0
-input1.bam	FBtr0070911	73	15	F	1
-input1.bam	FBtr0070911	73	16	F	1
-input1.bam	FBtr0070911	73	17	F	1
-input1.bam	FBtr0070911	73	18	F	1
-input1.bam	FBtr0070911	73	19	F	1
-input1.bam	FBtr0070911	73	20	F	1
-input1.bam	FBtr0070911	73	21	F	1
-input1.bam	FBtr0070911	73	22	F	1
-input1.bam	FBtr0070911	73	23	F	1
-input1.bam	FBtr0070911	73	24	F	1
-input1.bam	FBtr0070911	73	25	F	1
-input1.bam	FBtr0070911	73	26	F	1
-input1.bam	FBtr0070911	73	27	F	1
-input1.bam	FBtr0070911	73	28	F	1
-input1.bam	FBtr0070911	73	29	F	1
-input1.bam	FBtr0070911	73	30	F	1
-input1.bam	FBtr0070911	73	31	F	1
-input1.bam	FBtr0070911	73	32	F	1
-input1.bam	FBtr0070911	73	33	F	1
-input1.bam	FBtr0070911	73	34	F	1
-input1.bam	FBtr0070911	73	35	F	1
-input1.bam	FBtr0070911	73	38	F	1
-input1.bam	FBtr0070911	73	39	F	1
-input1.bam	FBtr0070911	73	40	F	1
-input1.bam	FBtr0070911	73	41	F	1
-input1.bam	FBtr0070911	73	42	F	1
-input1.bam	FBtr0070911	73	43	F	1
-input1.bam	FBtr0070911	73	44	F	1
-input1.bam	FBtr0070911	73	45	F	1
-input1.bam	FBtr0070911	73	46	F	1
-input1.bam	FBtr0070911	73	47	F	1
-input1.bam	FBtr0070911	73	48	F	1
-input1.bam	FBtr0070911	73	49	F	1
-input1.bam	FBtr0070911	73	50	F	1
-input1.bam	FBtr0070911	73	51	F	1
-input1.bam	FBtr0070911	73	52	F	1
-input1.bam	FBtr0070911	73	73	F	0
-input1.bam	FBtr0078490	72	1	F	0
-input1.bam	FBtr0078490	72	13	F	2
-input1.bam	FBtr0078490	72	14	F	2
-input1.bam	FBtr0078490	72	15	F	2
-input1.bam	FBtr0078490	72	16	F	2
-input1.bam	FBtr0078490	72	17	F	3
-input1.bam	FBtr0078490	72	18	F	4
-input1.bam	FBtr0078490	72	19	F	4
-input1.bam	FBtr0078490	72	20	F	4
-input1.bam	FBtr0078490	72	21	F	4
-input1.bam	FBtr0078490	72	22	F	4
-input1.bam	FBtr0078490	72	23	F	4
-input1.bam	FBtr0078490	72	24	F	4
-input1.bam	FBtr0078490	72	25	F	5
-input1.bam	FBtr0078490	72	26	F	5
-input1.bam	FBtr0078490	72	27	F	5
-input1.bam	FBtr0078490	72	28	F	7
-input1.bam	FBtr0078490	72	29	F	5
-input1.bam	FBtr0078490	72	30	F	5
-input1.bam	FBtr0078490	72	31	F	5
-input1.bam	FBtr0078490	72	32	F	5
-input1.bam	FBtr0078490	72	33	F	3
-input1.bam	FBtr0078490	72	34	F	3
-input1.bam	FBtr0078490	72	35	F	3
-input1.bam	FBtr0078490	72	36	F	3
-input1.bam	FBtr0078490	72	37	F	3
-input1.bam	FBtr0078490	72	38	F	4
-input1.bam	FBtr0078490	72	39	F	4
-input1.bam	FBtr0078490	72	40	F	3
-input1.bam	FBtr0078490	72	41	F	3
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-input2.bam	FBtr0080647	72	17	F	1
-input2.bam	FBtr0080647	72	18	F	1
-input2.bam	FBtr0080647	72	57	F	4
-input2.bam	FBtr0080647	72	58	F	11
-input2.bam	FBtr0080647	72	59	F	11
-input2.bam	FBtr0080647	72	60	F	11
-input2.bam	FBtr0080647	72	61	F	11
-input2.bam	FBtr0080647	72	62	F	11
-input2.bam	FBtr0080647	72	63	F	11
-input2.bam	FBtr0080647	72	64	F	11
-input2.bam	FBtr0080647	72	65	F	11
-input2.bam	FBtr0080647	72	66	F	11
-input2.bam	FBtr0080647	72	67	F	11
-input2.bam	FBtr0080647	72	68	F	11
-input2.bam	FBtr0080647	72	69	F	11
-input2.bam	FBtr0080647	72	70	F	11
-input2.bam	FBtr0080647	72	71	F	11
-input2.bam	FBtr0080647	72	72	F	9
-input2.bam	FBtr0080660	72	1	F	0
-input2.bam	FBtr0080660	72	58	F	11
-input2.bam	FBtr0080660	72	59	F	11
-input2.bam	FBtr0080660	72	60	F	11
-input2.bam	FBtr0080660	72	61	F	11
-input2.bam	FBtr0080660	72	62	F	11
-input2.bam	FBtr0080660	72	63	F	11
-input2.bam	FBtr0080660	72	64	F	11
-input2.bam	FBtr0080660	72	65	F	11
-input2.bam	FBtr0080660	72	66	F	11
-input2.bam	FBtr0080660	72	67	F	11
-input2.bam	FBtr0080660	72	68	F	11
-input2.bam	FBtr0080660	72	69	F	11
-input2.bam	FBtr0080660	72	70	F	11
-input2.bam	FBtr0080660	72	71	F	11
-input2.bam	FBtr0080660	72	72	F	11
-input2.bam	FBtr0080663	71	1	F	2
-input2.bam	FBtr0080663	71	2	F	2
-input2.bam	FBtr0080663	71	3	F	2
-input2.bam	FBtr0080663	71	4	F	2
-input2.bam	FBtr0080663	71	5	F	2
-input2.bam	FBtr0080663	71	6	F	2
-input2.bam	FBtr0080663	71	7	F	2
-input2.bam	FBtr0080663	71	8	F	2
-input2.bam	FBtr0080663	71	9	F	2
-input2.bam	FBtr0080663	71	10	F	2
-input2.bam	FBtr0080663	71	11	F	3
-input2.bam	FBtr0080663	71	12	F	7
-input2.bam	FBtr0080663	71	13	F	11
-input2.bam	FBtr0080663	71	14	F	33
-input2.bam	FBtr0080663	71	15	F	47
-input2.bam	FBtr0080663	71	16	F	52
-input2.bam	FBtr0080663	71	17	F	64
-input2.bam	FBtr0080663	71	18	F	69
-input2.bam	FBtr0080663	71	19	F	75
-input2.bam	FBtr0080663	71	20	F	81
-input2.bam	FBtr0080663	71	21	F	94
-input2.bam	FBtr0080663	71	22	F	97
-input2.bam	FBtr0080663	71	23	F	95
-input2.bam	FBtr0080663	71	24	F	95
-input2.bam	FBtr0080663	71	25	F	95
-input2.bam	FBtr0080663	71	26	F	95
-input2.bam	FBtr0080663	71	27	F	95
-input2.bam	FBtr0080663	71	28	F	95
-input2.bam	FBtr0080663	71	29	F	95
-input2.bam	FBtr0080663	71	30	F	95
-input2.bam	FBtr0080663	71	31	F	96
-input2.bam	FBtr0080663	71	32	F	62
-input2.bam	FBtr0080663	71	33	F	41
-input2.bam	FBtr0080663	71	34	F	40
-input2.bam	FBtr0080663	71	35	F	34
-input2.bam	FBtr0080663	71	36	F	12
-input2.bam	FBtr0080663	71	37	F	6
-input2.bam	FBtr0080663	71	38	F	5
-input2.bam	FBtr0080663	71	39	F	4
-input2.bam	FBtr0080663	71	40	F	3
-input2.bam	FBtr0080663	71	41	F	2
-input2.bam	FBtr0080663	71	42	F	1
-input2.bam	FBtr0080663	71	43	F	1
-input2.bam	FBtr0080663	71	44	F	1
-input2.bam	FBtr0080663	71	45	F	1
-input2.bam	FBtr0080663	71	46	F	1
-input2.bam	FBtr0080663	71	47	F	1
-input2.bam	FBtr0080663	71	50	F	2
-input2.bam	FBtr0080663	71	51	F	3
-input2.bam	FBtr0080663	71	52	F	5
-input2.bam	FBtr0080663	71	53	F	5
-input2.bam	FBtr0080663	71	54	F	5
-input2.bam	FBtr0080663	71	55	F	5
-input2.bam	FBtr0080663	71	56	F	5
-input2.bam	FBtr0080663	71	57	F	8
-input2.bam	FBtr0080663	71	58	F	8
-input2.bam	FBtr0080663	71	59	F	8
-input2.bam	FBtr0080663	71	60	F	8
-input2.bam	FBtr0080663	71	61	F	8
-input2.bam	FBtr0080663	71	62	F	8
-input2.bam	FBtr0080663	71	63	F	8
-input2.bam	FBtr0080663	71	64	F	8
-input2.bam	FBtr0080663	71	65	F	7
-input2.bam	FBtr0080663	71	66	F	6
-input2.bam	FBtr0080663	71	67	F	4
-input2.bam	FBtr0080663	71	68	F	4
-input2.bam	FBtr0080663	71	69	F	4
-input2.bam	FBtr0080663	71	70	F	3
-input2.bam	FBtr0080663	71	71	F	3
-input2.bam	FBtr0080664	71	1	F	1
-input2.bam	FBtr0080664	71	2	F	1
-input2.bam	FBtr0080664	71	3	F	3
-input2.bam	FBtr0080664	71	4	F	3
-input2.bam	FBtr0080664	71	5	F	3
-input2.bam	FBtr0080664	71	6	F	3
-input2.bam	FBtr0080664	71	7	F	3
-input2.bam	FBtr0080664	71	8	F	3
-input2.bam	FBtr0080664	71	9	F	3
-input2.bam	FBtr0080664	71	10	F	4
-input2.bam	FBtr0080664	71	11	F	6
-input2.bam	FBtr0080664	71	12	F	9
-input2.bam	FBtr0080664	71	13	F	20
-input2.bam	FBtr0080664	71	14	F	31
-input2.bam	FBtr0080664	71	15	F	48
-input2.bam	FBtr0080664	71	16	F	63
-input2.bam	FBtr0080664	71	17	F	76
-input2.bam	FBtr0080664	71	18	F	86
-input2.bam	FBtr0080664	71	19	F	94
-input2.bam	FBtr0080664	71	20	F	95
-input2.bam	FBtr0080664	71	21	F	110
-input2.bam	FBtr0080664	71	22	F	116
-input2.bam	FBtr0080664	71	23	F	114
-input2.bam	FBtr0080664	71	24	F	115
-input2.bam	FBtr0080664	71	25	F	115
-input2.bam	FBtr0080664	71	26	F	115
-input2.bam	FBtr0080664	71	27	F	115
-input2.bam	FBtr0080664	71	28	F	115
-input2.bam	FBtr0080664	71	29	F	113
-input2.bam	FBtr0080664	71	30	F	113
-input2.bam	FBtr0080664	71	31	F	117
-input2.bam	FBtr0080664	71	32	F	127
-input2.bam	FBtr0080664	71	33	F	97
-input2.bam	FBtr0080664	71	34	F	134
-input2.bam	FBtr0080664	71	35	F	265
-input2.bam	FBtr0080664	71	36	F	249
-input2.bam	FBtr0080664	71	37	F	266
-input2.bam	FBtr0080664	71	38	F	268
-input2.bam	FBtr0080664	71	39	F	263
-input2.bam	FBtr0080664	71	40	F	263
-input2.bam	FBtr0080664	71	41	F	262
-input2.bam	FBtr0080664	71	42	F	262
-input2.bam	FBtr0080664	71	43	F	260
-input2.bam	FBtr0080664	71	44	F	263
-input2.bam	FBtr0080664	71	45	F	263
-input2.bam	FBtr0080664	71	46	F	263
-input2.bam	FBtr0080664	71	47	F	264
-input2.bam	FBtr0080664	71	48	F	264
-input2.bam	FBtr0080664	71	49	F	254
-input2.bam	FBtr0080664	71	50	F	72
-input2.bam	FBtr0080664	71	51	F	63
-input2.bam	FBtr0080664	71	52	F	61
-input2.bam	FBtr0080664	71	53	F	31
-input2.bam	FBtr0080664	71	54	F	30
-input2.bam	FBtr0080664	71	55	F	21
-input2.bam	FBtr0080664	71	56	F	16
-input2.bam	FBtr0080664	71	57	F	18
-input2.bam	FBtr0080664	71	58	F	18
-input2.bam	FBtr0080664	71	59	F	18
-input2.bam	FBtr0080664	71	60	F	17
-input2.bam	FBtr0080664	71	61	F	16
-input2.bam	FBtr0080664	71	62	F	12
-input2.bam	FBtr0080664	71	62	R	12
-input2.bam	FBtr0080664	71	63	F	8
-input2.bam	FBtr0080664	71	64	F	8
-input2.bam	FBtr0080664	71	65	F	7
-input2.bam	FBtr0080664	71	66	F	6
-input2.bam	FBtr0080664	71	67	F	6
-input2.bam	FBtr0080664	71	68	F	5
-input2.bam	FBtr0080664	71	69	F	5
-input2.bam	FBtr0080664	71	70	F	5
-input2.bam	FBtr0080664	71	71	F	5
-input2.bam	FBtr0080664	71	71	R	5
diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/input1_input2_norm_1_2_single_plot_counts.pdf
Binary file test-data/input1_input2_norm_1_2_single_plot_counts.pdf has changed
diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/input1_input2_norm_1_2_single_plot_coverage.pdf
Binary file test-data/input1_input2_norm_1_2_single_plot_coverage.pdf has changed
diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/input1_input2_size.tab
--- a/test-data/input1_input2_size.tab	Wed Apr 10 06:38:33 2019 -0400
+++ b/test-data/input1_input2_size.tab	Sun Apr 14 14:43:44 2019 -0400
@@ -1,1045 +1,694 @@
 Dataset	Chromosome	Polarity	Size	Counts	Strandness	z-score
-input1.bam	FBtr0070001	F	16	2	1.0	-0.476603123819
-input1.bam	FBtr0070001	F	17	1	1.0	-0.586588460085
-input1.bam	FBtr0070001	F	18	0	1.0	-0.696573796351
-input1.bam	FBtr0070001	F	19	1	1.0	-0.586588460085
-input1.bam	FBtr0070001	F	20	4	1.0	-0.256632451287
-input1.bam	FBtr0070001	F	21	4	1.0	-0.256632451287
-input1.bam	FBtr0070001	F	22	29	1.0	2.49300095536
-input1.bam	FBtr0070001	F	23	15	1.0	0.953206247639
-input1.bam	FBtr0070001	F	24	1	1.0	-0.586588460085
-input1.bam	FBtr0070001	R	16	0	1.0	-0.476603123819
-input1.bam	FBtr0070001	R	17	0	1.0	-0.586588460085
-input1.bam	FBtr0070001	R	18	0	1.0	-0.696573796351
-input1.bam	FBtr0070001	R	19	0	1.0	-0.586588460085
-input1.bam	FBtr0070001	R	20	0	1.0	-0.256632451287
-input1.bam	FBtr0070001	R	21	0	1.0	-0.256632451287
-input1.bam	FBtr0070001	R	22	0	1.0	2.49300095536
-input1.bam	FBtr0070001	R	23	0	1.0	0.953206247639
-input1.bam	FBtr0070001	R	24	0	1.0	-0.586588460085
-input1.bam	FBtr0070533	F	15	2	1.0	-0.114707866935
-input1.bam	FBtr0070533	F	16	1	1.0	-0.745601135079
-input1.bam	FBtr0070533	F	17	1	1.0	-0.745601135079
-input1.bam	FBtr0070533	F	18	6	1.0	2.40886520564
-input1.bam	FBtr0070533	F	19	3	1.0	0.516185401209
-input1.bam	FBtr0070533	F	20	2	1.0	-0.114707866935
-input1.bam	FBtr0070533	F	21	2	1.0	-0.114707866935
-input1.bam	FBtr0070533	F	22	4	1.0	1.14707866935
-input1.bam	FBtr0070533	F	23	2	1.0	-0.114707866935
-input1.bam	FBtr0070533	F	24	0	1.0	-1.37649440322
-input1.bam	FBtr0070533	F	25	1	1.0	-0.745601135079
-input1.bam	FBtr0070533	R	15	0	1.0	-0.114707866935
-input1.bam	FBtr0070533	R	16	0	1.0	-0.745601135079
-input1.bam	FBtr0070533	R	17	0	1.0	-0.745601135079
-input1.bam	FBtr0070533	R	18	0	1.0	2.40886520564
-input1.bam	FBtr0070533	R	19	0	1.0	0.516185401209
-input1.bam	FBtr0070533	R	20	0	1.0	-0.114707866935
-input1.bam	FBtr0070533	R	21	0	1.0	-0.114707866935
-input1.bam	FBtr0070533	R	22	0	1.0	1.14707866935
-input1.bam	FBtr0070533	R	23	0	1.0	-0.114707866935
-input1.bam	FBtr0070533	R	24	0	1.0	-1.37649440322
-input1.bam	FBtr0070533	R	25	0	1.0	-0.745601135079
-input1.bam	FBtr0070603	F	15	9	1.0	1.25973222843
-input1.bam	FBtr0070603	F	16	6	1.0	0.214422506968
-input1.bam	FBtr0070603	F	17	10	1.0	1.60816880226
-input1.bam	FBtr0070603	F	18	7	1.0	0.56285908079
-input1.bam	FBtr0070603	F	19	1	1.0	-1.52776036214
-input1.bam	FBtr0070603	F	20	6	1.0	0.214422506968
-input1.bam	FBtr0070603	F	21	3	1.0	-0.830887214499
-input1.bam	FBtr0070603	F	22	3	1.0	-0.830887214499
-input1.bam	FBtr0070603	F	23	10	1.0	1.60816880226
-input1.bam	FBtr0070603	F	24	2	1.0	-1.17932378832
-input1.bam	FBtr0070603	F	25	5	1.0	-0.134014066855
-input1.bam	FBtr0070603	F	26	5	1.0	-0.134014066855
-input1.bam	FBtr0070603	F	27	3	1.0	-0.830887214499
-input1.bam	FBtr0070603	R	15	0	1.0	1.25973222843
-input1.bam	FBtr0070603	R	16	0	1.0	0.214422506968
-input1.bam	FBtr0070603	R	17	0	1.0	1.60816880226
-input1.bam	FBtr0070603	R	18	0	1.0	0.56285908079
-input1.bam	FBtr0070603	R	19	0	1.0	-1.52776036214
-input1.bam	FBtr0070603	R	20	0	1.0	0.214422506968
-input1.bam	FBtr0070603	R	21	0	1.0	-0.830887214499
-input1.bam	FBtr0070603	R	22	0	1.0	-0.830887214499
-input1.bam	FBtr0070603	R	23	0	1.0	1.60816880226
-input1.bam	FBtr0070603	R	24	0	1.0	-1.17932378832
-input1.bam	FBtr0070603	R	25	0	1.0	-0.134014066855
-input1.bam	FBtr0070603	R	26	0	1.0	-0.134014066855
-input1.bam	FBtr0070603	R	27	0	1.0	-0.830887214499
-input1.bam	FBtr0070604	F	15	2	1.0	-0.340359959259
-input1.bam	FBtr0070604	F	16	0	1.0	-0.618836289562
-input1.bam	FBtr0070604	F	17	0	1.0	-0.618836289562
-input1.bam	FBtr0070604	F	18	2	1.0	-0.340359959259
-input1.bam	FBtr0070604	F	19	2	1.0	-0.340359959259
-input1.bam	FBtr0070604	F	20	0	1.0	-0.618836289562
-input1.bam	FBtr0070604	F	21	1	1.0	-0.479598124411
-input1.bam	FBtr0070604	F	22	23	1.0	2.58364150892
-input1.bam	FBtr0070604	F	23	10	1.0	0.773545361953
-input1.bam	FBtr0070604	R	15	0	1.0	-0.340359959259
-input1.bam	FBtr0070604	R	16	0	1.0	-0.618836289562
-input1.bam	FBtr0070604	R	17	0	1.0	-0.618836289562
-input1.bam	FBtr0070604	R	18	0	1.0	-0.340359959259
-input1.bam	FBtr0070604	R	19	0	1.0	-0.340359959259
-input1.bam	FBtr0070604	R	20	0	1.0	-0.618836289562
-input1.bam	FBtr0070604	R	21	0	1.0	-0.479598124411
-input1.bam	FBtr0070604	R	22	0	1.0	2.58364150892
-input1.bam	FBtr0070604	R	23	0	1.0	0.773545361953
-input1.bam	FBtr0070911	F	15	1	1.0	1.58113883008
-input1.bam	FBtr0070911	F	16	0	1.0	-0.632455532034
-input1.bam	FBtr0070911	F	17	0	1.0	-0.632455532034
-input1.bam	FBtr0070911	F	18	0	1.0	-0.632455532034
-input1.bam	FBtr0070911	F	19	0	1.0	-0.632455532034
-input1.bam	FBtr0070911	F	20	0	1.0	-0.632455532034
-input1.bam	FBtr0070911	F	21	1	1.0	1.58113883008
-input1.bam	FBtr0070911	R	15	0	1.0	1.58113883008
-input1.bam	FBtr0070911	R	16	0	1.0	-0.632455532034
-input1.bam	FBtr0070911	R	17	0	1.0	-0.632455532034
-input1.bam	FBtr0070911	R	18	0	1.0	-0.632455532034
-input1.bam	FBtr0070911	R	19	0	1.0	-0.632455532034
-input1.bam	FBtr0070911	R	20	0	1.0	-0.632455532034
-input1.bam	FBtr0070911	R	21	0	1.0	1.58113883008
-input1.bam	FBtr0078490	F	15	3	1.0	1.76410571268
-input1.bam	FBtr0078490	F	16	3	1.0	1.76410571268
-input1.bam	FBtr0078490	F	17	0	1.0	-0.742781352708
-input1.bam	FBtr0078490	F	18	1	1.0	0.0928476690885
-input1.bam	FBtr0078490	F	19	0	1.0	-0.742781352708
-input1.bam	FBtr0078490	F	20	0	1.0	-0.742781352708
-input1.bam	FBtr0078490	F	21	0	1.0	-0.742781352708
-input1.bam	FBtr0078490	F	22	0	1.0	-0.742781352708
-input1.bam	FBtr0078490	F	23	1	1.0	0.0928476690885
-input1.bam	FBtr0078490	R	15	0	1.0	1.76410571268
-input1.bam	FBtr0078490	R	16	0	1.0	1.76410571268
-input1.bam	FBtr0078490	R	17	0	1.0	-0.742781352708
-input1.bam	FBtr0078490	R	18	0	1.0	0.0928476690885
-input1.bam	FBtr0078490	R	19	0	1.0	-0.742781352708
-input1.bam	FBtr0078490	R	20	0	1.0	-0.742781352708
-input1.bam	FBtr0078490	R	21	0	1.0	-0.742781352708
-input1.bam	FBtr0078490	R	22	0	1.0	-0.742781352708
-input1.bam	FBtr0078490	R	23	0	1.0	0.0928476690885
-input1.bam	FBtr0078580	F	15	592	1.0	3.27906790103
-input1.bam	FBtr0078580	F	16	20	1.0	-0.376106897334
-input1.bam	FBtr0078580	F	17	31	1.0	-0.305815074288
-input1.bam	FBtr0078580	F	18	9	1.0	-0.446398720379
-input1.bam	FBtr0078580	F	19	8	1.0	-0.45278888611
-input1.bam	FBtr0078580	F	20	9	1.0	-0.446398720379
-input1.bam	FBtr0078580	F	21	5	1.0	-0.471959383305
-input1.bam	FBtr0078580	F	22	13	1.0	-0.420838057453
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+input2.bam	FBtr0079752	F	24	1	1.0	3.16227766017
+input2.bam	FBtr0079752	F	25	0	1.0	-0.316227766017
+input2.bam	FBtr0079752	F	26	0	1.0	-0.316227766017
+input2.bam	FBtr0079752	F	27	0	1.0	-0.316227766017
+input2.bam	FBtr0079752	F	28	0	1.0	-0.316227766017
+input2.bam	FBtr0079752	F	29	0	1.0	-0.316227766017
+input2.bam	FBtr0079820	F	19	25	1.0	2.1262475074
+input2.bam	FBtr0079820	F	20	24	1.0	2.01895978913
+input2.bam	FBtr0079820	F	21	7	1.0	0.19506857866
+input2.bam	FBtr0079820	F	22	1	1.0	-0.448657730919
+input2.bam	FBtr0079820	F	23	0	1.0	-0.555945449182
+input2.bam	FBtr0079820	F	24	0	1.0	-0.555945449182
+input2.bam	FBtr0079820	F	25	0	1.0	-0.555945449182
+input2.bam	FBtr0079820	F	26	0	1.0	-0.555945449182
+input2.bam	FBtr0079820	F	27	0	1.0	-0.555945449182
+input2.bam	FBtr0079820	F	28	0	1.0	-0.555945449182
+input2.bam	FBtr0079820	F	29	0	1.0	-0.555945449182
+input2.bam	FBtr0080609	F	19	2	1.0	2.35747583396
+input2.bam	FBtr0080609	F	20	0	1.0	-0.693375245282
+input2.bam	FBtr0080609	F	21	0	1.0	-0.693375245282
+input2.bam	FBtr0080609	F	22	1	1.0	0.832050294338
+input2.bam	FBtr0080609	F	23	1	1.0	0.832050294338
+input2.bam	FBtr0080609	F	24	0	1.0	-0.693375245282
+input2.bam	FBtr0080609	F	25	1	1.0	0.832050294338
+input2.bam	FBtr0080609	F	26	0	1.0	-0.693375245282
+input2.bam	FBtr0080609	F	27	0	1.0	-0.693375245282
+input2.bam	FBtr0080609	F	28	0	1.0	-0.693375245282
+input2.bam	FBtr0080609	F	29	0	1.0	-0.693375245282
+input2.bam	FBtr0080644	F	19	0	2	0
+input2.bam	FBtr0080644	F	20	0	2	0
+input2.bam	FBtr0080644	F	21	0	2	0
+input2.bam	FBtr0080644	F	22	0	2	0
+input2.bam	FBtr0080644	F	23	0	2	0
+input2.bam	FBtr0080644	F	24	0	2	0
+input2.bam	FBtr0080644	F	25	0	2	0
+input2.bam	FBtr0080644	F	26	0	2	0
+input2.bam	FBtr0080644	F	27	0	2	0
+input2.bam	FBtr0080644	F	28	0	2	0
+input2.bam	FBtr0080644	F	29	0	2	0
+input2.bam	FBtr0080646	F	19	0	1.0	-0.316227766017
+input2.bam	FBtr0080646	F	20	0	1.0	-0.316227766017
+input2.bam	FBtr0080646	F	21	1	1.0	3.16227766017
+input2.bam	FBtr0080646	F	22	0	1.0	-0.316227766017
+input2.bam	FBtr0080646	F	23	0	1.0	-0.316227766017
+input2.bam	FBtr0080646	F	24	0	1.0	-0.316227766017
+input2.bam	FBtr0080646	F	25	0	1.0	-0.316227766017
+input2.bam	FBtr0080646	F	26	0	1.0	-0.316227766017
+input2.bam	FBtr0080646	F	27	0	1.0	-0.316227766017
+input2.bam	FBtr0080646	F	28	0	1.0	-0.316227766017
+input2.bam	FBtr0080646	F	29	0	1.0	-0.316227766017
+input2.bam	FBtr0080647	F	19	0	2	0
+input2.bam	FBtr0080647	F	20	0	2	0
+input2.bam	FBtr0080647	F	21	0	2	0
+input2.bam	FBtr0080647	F	22	0	2	0
+input2.bam	FBtr0080647	F	23	0	2	0
+input2.bam	FBtr0080647	F	24	0	2	0
+input2.bam	FBtr0080647	F	25	0	2	0
+input2.bam	FBtr0080647	F	26	0	2	0
+input2.bam	FBtr0080647	F	27	0	2	0
+input2.bam	FBtr0080647	F	28	0	2	0
+input2.bam	FBtr0080647	F	29	0	2	0
+input2.bam	FBtr0080660	F	19	0	2	0
+input2.bam	FBtr0080660	F	20	0	2	0
+input2.bam	FBtr0080660	F	21	0	2	0
+input2.bam	FBtr0080660	F	22	0	2	0
+input2.bam	FBtr0080660	F	23	0	2	0
+input2.bam	FBtr0080660	F	24	0	2	0
+input2.bam	FBtr0080660	F	25	0	2	0
+input2.bam	FBtr0080660	F	26	0	2	0
+input2.bam	FBtr0080660	F	27	0	2	0
+input2.bam	FBtr0080660	F	28	0	2	0
+input2.bam	FBtr0080660	F	29	0	2	0
+input2.bam	FBtr0080663	F	19	9	1.0	2.09341857157
+input2.bam	FBtr0080663	F	20	7	1.0	1.46252530342
+input2.bam	FBtr0080663	F	21	4	1.0	0.516185401209
+input2.bam	FBtr0080663	F	22	5	1.0	0.831632035281
+input2.bam	FBtr0080663	F	23	0	1.0	-0.745601135079
+input2.bam	FBtr0080663	F	24	1	1.0	-0.430154501007
+input2.bam	FBtr0080663	F	25	0	1.0	-0.745601135079
+input2.bam	FBtr0080663	F	26	0	1.0	-0.745601135079
+input2.bam	FBtr0080663	F	27	0	1.0	-0.745601135079
+input2.bam	FBtr0080663	F	28	0	1.0	-0.745601135079
+input2.bam	FBtr0080663	F	29	0	1.0	-0.745601135079
+input2.bam	FBtr0080664	F	19	24	0.971428571429	2.19436796542
+input2.bam	FBtr0080664	F	20	21	0.971428571429	1.8210991878
+input2.bam	FBtr0080664	F	21	8	0.971428571429	0.203601151431
+input2.bam	FBtr0080664	F	22	4	0.971428571429	-0.169667626192
+input2.bam	FBtr0080664	F	23	4	0.971428571429	-0.169667626192
+input2.bam	FBtr0080664	F	24	0	0.971428571429	-0.791782255563
+input2.bam	FBtr0080664	F	25	3	0.971428571429	-0.418513477941
+input2.bam	FBtr0080664	F	26	4	0.971428571429	-0.294090552066
+input2.bam	FBtr0080664	F	27	0	0.971428571429	-0.791782255563
+input2.bam	FBtr0080664	F	28	0	0.971428571429	-0.791782255563
+input2.bam	FBtr0080664	F	29	0	0.971428571429	-0.791782255563
+input2.bam	FBtr0080664	R	19	0	0.971428571429	2.19436796542
+input2.bam	FBtr0080664	R	20	0	0.971428571429	1.8210991878
+input2.bam	FBtr0080664	R	21	0	0.971428571429	0.203601151431
+input2.bam	FBtr0080664	R	22	1	0.971428571429	-0.169667626192
+input2.bam	FBtr0080664	R	23	1	0.971428571429	-0.169667626192
+input2.bam	FBtr0080664	R	24	0	0.971428571429	-0.791782255563
+input2.bam	FBtr0080664	R	25	0	0.971428571429	-0.418513477941
+input2.bam	FBtr0080664	R	26	0	0.971428571429	-0.294090552066
+input2.bam	FBtr0080664	R	27	0	0.971428571429	-0.791782255563
+input2.bam	FBtr0080664	R	28	0	0.971428571429	-0.791782255563
+input2.bam	FBtr0080664	R	29	0	0.971428571429	-0.791782255563
diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/input1_input2new_norm_1_2_counts.tab
--- a/test-data/input1_input2new_norm_1_2_counts.tab	Wed Apr 10 06:38:33 2019 -0400
+++ b/test-data/input1_input2new_norm_1_2_counts.tab	Sun Apr 14 14:43:44 2019 -0400
@@ -1,616 +1,392 @@
 Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts
-input1.bam	FBtr0070001	72	1	F	1
-input1.bam	FBtr0070001	72	7	F	6
+input1.bam	FBtr0070001	72	1	F	0
+input1.bam	FBtr0070001	72	7	F	5
 input1.bam	FBtr0070001	72	8	F	3
 input1.bam	FBtr0070001	72	11	F	2
 input1.bam	FBtr0070001	72	16	F	1
 input1.bam	FBtr0070001	72	17	F	1
-input1.bam	FBtr0070001	72	18	F	1
 input1.bam	FBtr0070001	72	27	F	2
 input1.bam	FBtr0070001	72	30	F	1
 input1.bam	FBtr0070001	72	31	F	11
 input1.bam	FBtr0070001	72	32	F	27
 input1.bam	FBtr0070001	72	34	F	1
 input1.bam	FBtr0070001	72	72	F	0
-input1.bam	FBtr0070533	72	1	F	1
-input1.bam	FBtr0070533	72	12	F	2
-input1.bam	FBtr0070533	72	15	F	1
+input1.bam	FBtr0070533	72	1	F	0
 input1.bam	FBtr0070533	72	19	F	5
 input1.bam	FBtr0070533	72	20	F	1
-input1.bam	FBtr0070533	72	21	F	1
 input1.bam	FBtr0070533	72	22	F	1
-input1.bam	FBtr0070533	72	25	F	1
-input1.bam	FBtr0070533	72	26	F	1
 input1.bam	FBtr0070533	72	28	F	1
-input1.bam	FBtr0070533	72	32	F	4
+input1.bam	FBtr0070533	72	32	F	3
 input1.bam	FBtr0070533	72	35	F	1
 input1.bam	FBtr0070533	72	37	F	2
-input1.bam	FBtr0070533	72	38	F	2
 input1.bam	FBtr0070533	72	72	F	0
-input1.bam	FBtr0070603	72	1	F	2
+input1.bam	FBtr0070603	72	1	F	0
 input1.bam	FBtr0070603	72	3	F	1
 input1.bam	FBtr0070603	72	4	F	1
-input1.bam	FBtr0070603	72	6	F	1
-input1.bam	FBtr0070603	72	7	F	7
-input1.bam	FBtr0070603	72	8	F	4
-input1.bam	FBtr0070603	72	9	F	7
-input1.bam	FBtr0070603	72	12	F	2
+input1.bam	FBtr0070603	72	12	F	1
 input1.bam	FBtr0070603	72	13	F	1
-input1.bam	FBtr0070603	72	15	F	2
-input1.bam	FBtr0070603	72	16	F	2
+input1.bam	FBtr0070603	72	15	F	1
+input1.bam	FBtr0070603	72	16	F	1
 input1.bam	FBtr0070603	72	17	F	3
-input1.bam	FBtr0070603	72	18	F	1
-input1.bam	FBtr0070603	72	19	F	9
-input1.bam	FBtr0070603	72	20	F	3
+input1.bam	FBtr0070603	72	19	F	8
+input1.bam	FBtr0070603	72	20	F	2
 input1.bam	FBtr0070603	72	21	F	1
 input1.bam	FBtr0070603	72	22	F	3
-input1.bam	FBtr0070603	72	24	F	2
+input1.bam	FBtr0070603	72	24	F	1
 input1.bam	FBtr0070603	72	25	F	1
 input1.bam	FBtr0070603	72	26	F	6
 input1.bam	FBtr0070603	72	27	F	3
 input1.bam	FBtr0070603	72	32	F	1
-input1.bam	FBtr0070603	72	34	F	3
-input1.bam	FBtr0070603	72	38	F	1
+input1.bam	FBtr0070603	72	34	F	2
 input1.bam	FBtr0070603	72	42	F	1
-input1.bam	FBtr0070603	72	51	F	1
-input1.bam	FBtr0070603	72	56	F	1
 input1.bam	FBtr0070603	72	72	F	0
-input1.bam	FBtr0070604	72	1	F	1
+input1.bam	FBtr0070604	72	1	F	0
 input1.bam	FBtr0070604	72	18	F	1
 input1.bam	FBtr0070604	72	22	F	1
-input1.bam	FBtr0070604	72	30	F	2
 input1.bam	FBtr0070604	72	31	F	10
 input1.bam	FBtr0070604	72	32	F	24
-input1.bam	FBtr0070604	72	57	F	1
 input1.bam	FBtr0070604	72	72	F	0
 input1.bam	FBtr0070911	73	1	F	0
 input1.bam	FBtr0070911	73	15	F	1
-input1.bam	FBtr0070911	73	38	F	1
 input1.bam	FBtr0070911	73	73	F	0
 input1.bam	FBtr0078490	72	1	F	0
-input1.bam	FBtr0078490	72	13	F	2
-input1.bam	FBtr0078490	72	17	F	1
-input1.bam	FBtr0078490	72	18	F	1
-input1.bam	FBtr0078490	72	25	F	1
-input1.bam	FBtr0078490	72	28	F	2
-input1.bam	FBtr0078490	72	38	F	1
+input1.bam	FBtr0078490	72	28	F	1
 input1.bam	FBtr0078490	72	72	F	0
-input1.bam	FBtr0078580	72	1	F	1041
+input1.bam	FBtr0078580	72	1	F	420
 input1.bam	FBtr0078580	72	3	F	3
 input1.bam	FBtr0078580	72	4	F	4
 input1.bam	FBtr0078580	72	5	F	5
-input1.bam	FBtr0078580	72	6	F	4
+input1.bam	FBtr0078580	72	6	F	2
 input1.bam	FBtr0078580	72	7	F	1
-input1.bam	FBtr0078580	72	8	F	2
+input1.bam	FBtr0078580	72	8	F	1
 input1.bam	FBtr0078580	72	11	F	1
-input1.bam	FBtr0078580	72	12	F	13
-input1.bam	FBtr0078580	72	14	F	7
-input1.bam	FBtr0078580	72	15	F	1
-input1.bam	FBtr0078580	72	16	F	4
-input1.bam	FBtr0078580	72	17	F	1
+input1.bam	FBtr0078580	72	12	F	3
+input1.bam	FBtr0078580	72	16	F	3
 input1.bam	FBtr0078580	72	19	F	1
 input1.bam	FBtr0078580	72	20	F	2
-input1.bam	FBtr0078580	72	21	F	5
-input1.bam	FBtr0078580	72	24	F	3
+input1.bam	FBtr0078580	72	21	F	4
 input1.bam	FBtr0078580	72	25	F	2
-input1.bam	FBtr0078580	72	29	F	1
-input1.bam	FBtr0078580	72	31	F	1
-input1.bam	FBtr0078580	72	52	F	2
 input1.bam	FBtr0078580	72	72	F	0
 input1.bam	FBtr0078790	73	1	F	1
-input1.bam	FBtr0078790	73	17	F	2
 input1.bam	FBtr0078790	73	33	F	1
-input1.bam	FBtr0078790	73	42	F	4
+input1.bam	FBtr0078790	73	42	F	2
 input1.bam	FBtr0078790	73	44	F	2
-input1.bam	FBtr0078790	73	46	F	1
-input1.bam	FBtr0078790	73	47	F	1
 input1.bam	FBtr0078790	73	52	F	1
-input1.bam	FBtr0078790	73	69	R	1
 input1.bam	FBtr0078790	73	73	F	0
-input1.bam	FBtr0079064	72	1	F	1
+input1.bam	FBtr0079064	72	1	F	0
 input1.bam	FBtr0079064	72	3	F	1
-input1.bam	FBtr0079064	72	33	F	1
-input1.bam	FBtr0079064	72	52	F	1
 input1.bam	FBtr0079064	72	72	F	0
-input1.bam	FBtr0079090	72	1	F	2
+input1.bam	FBtr0079090	72	1	F	1
 input1.bam	FBtr0079090	72	26	F	1
-input1.bam	FBtr0079090	72	33	F	1
-input1.bam	FBtr0079090	72	53	F	1
 input1.bam	FBtr0079090	72	56	R	1
 input1.bam	FBtr0079090	72	72	F	0
 input1.bam	FBtr0079338	73	1	F	0
-input1.bam	FBtr0079338	73	12	F	1
-input1.bam	FBtr0079338	73	13	F	2
-input1.bam	FBtr0079338	73	14	F	1
-input1.bam	FBtr0079338	73	17	F	1
-input1.bam	FBtr0079338	73	25	F	1
+input1.bam	FBtr0079338	73	13	F	1
 input1.bam	FBtr0079338	73	42	F	8
 input1.bam	FBtr0079338	73	43	F	1
-input1.bam	FBtr0079338	73	46	F	1
 input1.bam	FBtr0079338	73	73	F	0
-input1.bam	FBtr0079528	71	1	F	19
+input1.bam	FBtr0079528	71	1	F	10
 input1.bam	FBtr0079528	71	3	F	55
 input1.bam	FBtr0079528	71	4	F	2
-input1.bam	FBtr0079528	71	8	F	4
+input1.bam	FBtr0079528	71	8	F	3
 input1.bam	FBtr0079528	71	10	F	1
-input1.bam	FBtr0079528	71	11	F	2
-input1.bam	FBtr0079528	71	13	F	1
-input1.bam	FBtr0079528	71	14	F	4
-input1.bam	FBtr0079528	71	16	F	1
-input1.bam	FBtr0079528	71	17	F	4
-input1.bam	FBtr0079528	71	18	F	4
-input1.bam	FBtr0079528	71	28	F	1
-input1.bam	FBtr0079528	71	35	F	1
+input1.bam	FBtr0079528	71	11	F	1
+input1.bam	FBtr0079528	71	14	F	2
+input1.bam	FBtr0079528	71	18	F	3
 input1.bam	FBtr0079528	71	36	F	1
-input1.bam	FBtr0079528	71	37	F	1
-input1.bam	FBtr0079528	71	51	F	5
 input1.bam	FBtr0079528	71	71	F	0
-input1.bam	FBtr0079596	73	1	F	13
-input1.bam	FBtr0079596	73	3	F	13
+input1.bam	FBtr0079596	73	1	F	3
+input1.bam	FBtr0079596	73	3	F	11
 input1.bam	FBtr0079596	73	4	F	31
-input1.bam	FBtr0079596	73	5	F	2
-input1.bam	FBtr0079596	73	6	F	11
-input1.bam	FBtr0079596	73	8	F	9
-input1.bam	FBtr0079596	73	9	F	12
-input1.bam	FBtr0079596	73	10	F	3
-input1.bam	FBtr0079596	73	11	F	19
-input1.bam	FBtr0079596	73	12	F	1
-input1.bam	FBtr0079596	73	13	F	20
-input1.bam	FBtr0079596	73	14	F	6
-input1.bam	FBtr0079596	73	15	F	1
-input1.bam	FBtr0079596	73	16	F	3
-input1.bam	FBtr0079596	73	17	F	2
-input1.bam	FBtr0079596	73	18	F	1
-input1.bam	FBtr0079596	73	19	F	1
-input1.bam	FBtr0079596	73	53	F	2
+input1.bam	FBtr0079596	73	5	F	1
+input1.bam	FBtr0079596	73	6	F	4
+input1.bam	FBtr0079596	73	13	F	1
+input1.bam	FBtr0079596	73	53	F	1
 input1.bam	FBtr0079596	73	54	F	2
 input1.bam	FBtr0079596	73	73	F	0
 input1.bam	FBtr0079677	72	1	F	1
 input1.bam	FBtr0079677	72	5	F	1
 input1.bam	FBtr0079677	72	52	F	1
-input1.bam	FBtr0079677	72	53	F	1
 input1.bam	FBtr0079677	72	72	F	0
-input1.bam	FBtr0079690	72	1	F	1
-input1.bam	FBtr0079690	72	22	F	1
+input1.bam	FBtr0079690	72	1	F	0
 input1.bam	FBtr0079690	72	27	F	1
-input1.bam	FBtr0079690	72	33	F	2
 input1.bam	FBtr0079690	72	72	F	0
-input1.bam	FBtr0079692	73	1	F	3
-input1.bam	FBtr0079692	73	18	F	1
-input1.bam	FBtr0079692	73	25	F	1
+input1.bam	FBtr0079692	73	1	F	2
 input1.bam	FBtr0079692	73	32	F	1
 input1.bam	FBtr0079692	73	73	F	0
-input1.bam	FBtr0079693	72	1	F	5
+input1.bam	FBtr0079693	72	1	F	1
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 input_new2.bam	FBtr0079596	73	59	R	1
 input_new2.bam	FBtr0079596	73	73	F	0
-input_new2.bam	FBtr0079677	72	1	F	2
+input_new2.bam	FBtr0079677	72	1	F	0
 input_new2.bam	FBtr0079677	72	15	F	1
-input_new2.bam	FBtr0079677	72	24	F	1
 input_new2.bam	FBtr0079677	72	43	F	1
-input_new2.bam	FBtr0079677	72	52	F	1
-input_new2.bam	FBtr0079677	72	54	F	1
 input_new2.bam	FBtr0079677	72	72	F	0
-input_new2.bam	FBtr0079690	72	1	F	1
+input_new2.bam	FBtr0079690	72	1	F	0
 input_new2.bam	FBtr0079690	72	15	F	1
 input_new2.bam	FBtr0079690	72	17	F	1
 input_new2.bam	FBtr0079690	72	19	F	1
-input_new2.bam	FBtr0079690	72	21	F	1
 input_new2.bam	FBtr0079690	72	72	F	0
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-input_new2.bam	FBtr0079692	73	4	F	1
-input_new2.bam	FBtr0079692	73	7	F	1
 input_new2.bam	FBtr0079692	73	12	F	1
 input_new2.bam	FBtr0079692	73	15	F	1
 input_new2.bam	FBtr0079692	73	73	F	0
-input_new2.bam	FBtr0079693	72	1	F	3
-input_new2.bam	FBtr0079693	72	17	F	2
-input_new2.bam	FBtr0079693	72	20	F	1
-input_new2.bam	FBtr0079693	72	45	F	1
+input_new2.bam	FBtr0079693	72	1	F	0
+input_new2.bam	FBtr0079693	72	17	F	1
 input_new2.bam	FBtr0079693	72	52	F	1
-input_new2.bam	FBtr0079693	72	54	F	1
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-input_new2.bam	FBtr0079694	72	1	F	2
+input_new2.bam	FBtr0079694	72	1	F	0
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-input_new2.bam	FBtr0079694	72	52	F	1
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-input_new2.bam	FBtr0079702	72	1	F	2
-input_new2.bam	FBtr0079702	72	52	F	2
+input_new2.bam	FBtr0079702	72	1	F	0
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-input_new2.bam	FBtr0079728	72	1	F	3
-input_new2.bam	FBtr0079728	72	20	F	1
-input_new2.bam	FBtr0079728	72	52	F	2
+input_new2.bam	FBtr0079728	72	1	F	0
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-input_new2.bam	FBtr0079729	72	1	F	1
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-input_new2.bam	FBtr0079729	72	33	F	1
-input_new2.bam	FBtr0079729	72	53	F	1
+input_new2.bam	FBtr0079729	72	1	F	0
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 input_new2.bam	FBtr0079752	72	1	F	0
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-input_new2.bam	FBtr0079752	72	52	F	1
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-input_new2.bam	FBtr0079820	74	39	F	1
 input_new2.bam	FBtr0079820	74	52	F	1
-input_new2.bam	FBtr0079820	74	53	F	28
+input_new2.bam	FBtr0079820	74	53	F	25
 input_new2.bam	FBtr0079820	74	54	F	26
-input_new2.bam	FBtr0079820	74	55	F	10
-input_new2.bam	FBtr0079820	74	56	F	2
-input_new2.bam	FBtr0079820	74	57	F	6
-input_new2.bam	FBtr0079820	74	58	F	5
-input_new2.bam	FBtr0079820	74	59	F	11
-input_new2.bam	FBtr0079820	74	60	F	19
+input_new2.bam	FBtr0079820	74	55	F	5
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-input_new2.bam	FBtr0080609	72	21	F	2
+input_new2.bam	FBtr0080609	72	21	F	1
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-input_new2.bam	FBtr0080609	72	39	F	1
-input_new2.bam	FBtr0080609	72	52	F	1
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-input_new2.bam	FBtr0080644	72	57	F	1
-input_new2.bam	FBtr0080644	72	58	F	7
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-input_new2.bam	FBtr0080646	72	57	F	2
-input_new2.bam	FBtr0080646	72	58	F	9
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-input_new2.bam	FBtr0080647	72	1	F	1
-input_new2.bam	FBtr0080647	72	57	F	4
-input_new2.bam	FBtr0080647	72	58	F	7
+input_new2.bam	FBtr0080647	72	1	F	0
 input_new2.bam	FBtr0080647	72	72	F	0
 input_new2.bam	FBtr0080660	72	1	F	0
-input_new2.bam	FBtr0080660	72	58	F	11
 input_new2.bam	FBtr0080660	72	72	F	0
 input_new2.bam	FBtr0080663	71	1	F	2
 input_new2.bam	FBtr0080663	71	11	F	1
 input_new2.bam	FBtr0080663	71	12	F	4
 input_new2.bam	FBtr0080663	71	13	F	4
-input_new2.bam	FBtr0080663	71	14	F	22
-input_new2.bam	FBtr0080663	71	15	F	14
-input_new2.bam	FBtr0080663	71	16	F	5
-input_new2.bam	FBtr0080663	71	17	F	12
-input_new2.bam	FBtr0080663	71	18	F	5
-input_new2.bam	FBtr0080663	71	19	F	6
-input_new2.bam	FBtr0080663	71	20	F	6
-input_new2.bam	FBtr0080663	71	21	F	13
-input_new2.bam	FBtr0080663	71	22	F	3
-input_new2.bam	FBtr0080663	71	31	F	1
-input_new2.bam	FBtr0080663	71	50	F	2
+input_new2.bam	FBtr0080663	71	14	F	7
+input_new2.bam	FBtr0080663	71	15	F	2
+input_new2.bam	FBtr0080663	71	16	F	1
+input_new2.bam	FBtr0080663	71	18	F	1
+input_new2.bam	FBtr0080663	71	19	F	1
+input_new2.bam	FBtr0080663	71	20	F	1
+input_new2.bam	FBtr0080663	71	21	F	1
 input_new2.bam	FBtr0080663	71	51	F	1
-input_new2.bam	FBtr0080663	71	52	F	2
-input_new2.bam	FBtr0080663	71	57	F	3
 input_new2.bam	FBtr0080663	71	71	F	0
 input_new2.bam	FBtr0080664	71	1	F	1
 input_new2.bam	FBtr0080664	71	3	F	2
 input_new2.bam	FBtr0080664	71	10	F	1
 input_new2.bam	FBtr0080664	71	11	F	2
 input_new2.bam	FBtr0080664	71	12	F	3
-input_new2.bam	FBtr0080664	71	13	F	11
-input_new2.bam	FBtr0080664	71	14	F	11
-input_new2.bam	FBtr0080664	71	15	F	17
-input_new2.bam	FBtr0080664	71	16	F	15
-input_new2.bam	FBtr0080664	71	17	F	13
-input_new2.bam	FBtr0080664	71	18	F	10
-input_new2.bam	FBtr0080664	71	19	F	8
-input_new2.bam	FBtr0080664	71	20	F	1
-input_new2.bam	FBtr0080664	71	21	F	15
-input_new2.bam	FBtr0080664	71	22	F	6
-input_new2.bam	FBtr0080664	71	24	F	1
+input_new2.bam	FBtr0080664	71	13	F	10
+input_new2.bam	FBtr0080664	71	14	F	3
+input_new2.bam	FBtr0080664	71	15	F	2
+input_new2.bam	FBtr0080664	71	16	F	4
+input_new2.bam	FBtr0080664	71	18	F	5
+input_new2.bam	FBtr0080664	71	19	F	5
+input_new2.bam	FBtr0080664	71	22	F	1
 input_new2.bam	FBtr0080664	71	30	F	1
-input_new2.bam	FBtr0080664	71	31	F	3
-input_new2.bam	FBtr0080664	71	32	F	39
-input_new2.bam	FBtr0080664	71	33	F	4
-input_new2.bam	FBtr0080664	71	34	F	37
-input_new2.bam	FBtr0080664	71	35	F	135
-input_new2.bam	FBtr0080664	71	36	F	8
-input_new2.bam	FBtr0080664	71	37	F	25
-input_new2.bam	FBtr0080664	71	38	F	8
-input_new2.bam	FBtr0080664	71	39	F	1
+input_new2.bam	FBtr0080664	71	31	F	2
+input_new2.bam	FBtr0080664	71	32	F	8
+input_new2.bam	FBtr0080664	71	33	F	1
+input_new2.bam	FBtr0080664	71	34	F	4
+input_new2.bam	FBtr0080664	71	36	F	4
+input_new2.bam	FBtr0080664	71	37	F	5
+input_new2.bam	FBtr0080664	71	38	F	2
 input_new2.bam	FBtr0080664	71	42	F	1
-input_new2.bam	FBtr0080664	71	47	F	1
-input_new2.bam	FBtr0080664	71	50	F	2
-input_new2.bam	FBtr0080664	71	52	F	1
 input_new2.bam	FBtr0080664	71	53	F	1
-input_new2.bam	FBtr0080664	71	56	F	1
-input_new2.bam	FBtr0080664	71	57	F	2
 input_new2.bam	FBtr0080664	71	62	R	1
 input_new2.bam	FBtr0080664	71	71	F	0
 input_new2.bam	FBtr0080664	71	71	R	1
diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/input1_input2new_norm_1_2_single_plot_counts.pdf
Binary file test-data/input1_input2new_norm_1_2_single_plot_counts.pdf has changed
diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/input1_mean.tab
--- a/test-data/input1_mean.tab	Wed Apr 10 06:38:33 2019 -0400
+++ b/test-data/input1_mean.tab	Sun Apr 14 14:43:44 2019 -0400
@@ -1,300 +1,190 @@
 Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Mean
-input1.bam	FBtr0070001	72	1	F	17.0
-input1.bam	FBtr0070001	72	7	F	20.3
+input1.bam	FBtr0070001	72	1	F	0
+input1.bam	FBtr0070001	72	7	F	21.2
 input1.bam	FBtr0070001	72	8	F	21.3
 input1.bam	FBtr0070001	72	11	F	20.5
 input1.bam	FBtr0070001	72	16	F	19.0
 input1.bam	FBtr0070001	72	17	F	23.0
-input1.bam	FBtr0070001	72	18	F	16.0
 input1.bam	FBtr0070001	72	27	F	23.5
 input1.bam	FBtr0070001	72	30	F	23.0
 input1.bam	FBtr0070001	72	31	F	23.0
 input1.bam	FBtr0070001	72	32	F	22.0
 input1.bam	FBtr0070001	72	34	F	20.0
 input1.bam	FBtr0070001	72	72	F	0
-input1.bam	FBtr0070533	72	1	F	15.0
-input1.bam	FBtr0070533	72	12	F	18.0
-input1.bam	FBtr0070533	72	15	F	15.0
+input1.bam	FBtr0070533	72	1	F	0
 input1.bam	FBtr0070533	72	19	F	21.8
 input1.bam	FBtr0070533	72	20	F	23.0
-input1.bam	FBtr0070533	72	21	F	18.0
 input1.bam	FBtr0070533	72	22	F	20.0
-input1.bam	FBtr0070533	72	25	F	17.0
-input1.bam	FBtr0070533	72	26	F	16.0
 input1.bam	FBtr0070533	72	28	F	25.0
-input1.bam	FBtr0070533	72	32	F	20.5
+input1.bam	FBtr0070533	72	32	F	21.3
 input1.bam	FBtr0070533	72	35	F	19.0
 input1.bam	FBtr0070533	72	37	F	19.0
-input1.bam	FBtr0070533	72	38	F	18.0
 input1.bam	FBtr0070533	72	72	F	0
-input1.bam	FBtr0070603	72	1	F	16.5
+input1.bam	FBtr0070603	72	1	F	0
 input1.bam	FBtr0070603	72	3	F	21.0
 input1.bam	FBtr0070603	72	4	F	20.0
-input1.bam	FBtr0070603	72	6	F	18.0
-input1.bam	FBtr0070603	72	7	F	17.1
-input1.bam	FBtr0070603	72	8	F	16.0
-input1.bam	FBtr0070603	72	9	F	15.0
-input1.bam	FBtr0070603	72	12	F	20.0
+input1.bam	FBtr0070603	72	12	F	23.0
 input1.bam	FBtr0070603	72	13	F	22.0
-input1.bam	FBtr0070603	72	15	F	18.5
-input1.bam	FBtr0070603	72	16	F	20.5
+input1.bam	FBtr0070603	72	15	F	20.0
+input1.bam	FBtr0070603	72	16	F	24.0
 input1.bam	FBtr0070603	72	17	F	24.0
-input1.bam	FBtr0070603	72	18	F	16.0
-input1.bam	FBtr0070603	72	19	F	22.6
-input1.bam	FBtr0070603	72	20	F	21.0
+input1.bam	FBtr0070603	72	19	F	23.3
+input1.bam	FBtr0070603	72	20	F	24.0
 input1.bam	FBtr0070603	72	21	F	25.0
 input1.bam	FBtr0070603	72	22	F	20.7
-input1.bam	FBtr0070603	72	24	F	19.5
+input1.bam	FBtr0070603	72	24	F	21.0
 input1.bam	FBtr0070603	72	25	F	23.0
 input1.bam	FBtr0070603	72	26	F	25.8
 input1.bam	FBtr0070603	72	27	F	26.3
 input1.bam	FBtr0070603	72	32	F	20.0
-input1.bam	FBtr0070603	72	34	F	19.3
-input1.bam	FBtr0070603	72	38	F	18.0
+input1.bam	FBtr0070603	72	34	F	20.0
 input1.bam	FBtr0070603	72	42	F	21.0
-input1.bam	FBtr0070603	72	51	F	18.0
-input1.bam	FBtr0070603	72	56	F	16.0
 input1.bam	FBtr0070603	72	72	F	0
-input1.bam	FBtr0070604	72	1	F	15.0
+input1.bam	FBtr0070604	72	1	F	0
 input1.bam	FBtr0070604	72	18	F	23.0
 input1.bam	FBtr0070604	72	22	F	19.0
-input1.bam	FBtr0070604	72	30	F	18.0
 input1.bam	FBtr0070604	72	31	F	22.6
 input1.bam	FBtr0070604	72	32	F	22.0
-input1.bam	FBtr0070604	72	57	F	15.0
 input1.bam	FBtr0070604	72	72	F	0
 input1.bam	FBtr0070911	73	1	F	0
 input1.bam	FBtr0070911	73	15	F	21.0
-input1.bam	FBtr0070911	73	38	F	15.0
 input1.bam	FBtr0070911	73	73	F	0
 input1.bam	FBtr0078490	72	1	F	0
-input1.bam	FBtr0078490	72	13	F	16.0
-input1.bam	FBtr0078490	72	17	F	16.0
-input1.bam	FBtr0078490	72	18	F	15.0
-input1.bam	FBtr0078490	72	25	F	15.0
-input1.bam	FBtr0078490	72	28	F	19.0
-input1.bam	FBtr0078490	72	38	F	18.0
+input1.bam	FBtr0078490	72	28	F	23.0
 input1.bam	FBtr0078490	72	72	F	0
-input1.bam	FBtr0078580	72	1	F	18.9
+input1.bam	FBtr0078580	72	1	F	24.5
 input1.bam	FBtr0078580	72	3	F	22.0
 input1.bam	FBtr0078580	72	4	F	25.3
 input1.bam	FBtr0078580	72	5	F	21.0
-input1.bam	FBtr0078580	72	6	F	19.0
+input1.bam	FBtr0078580	72	6	F	21.0
 input1.bam	FBtr0078580	72	7	F	22.0
-input1.bam	FBtr0078580	72	8	F	18.0
+input1.bam	FBtr0078580	72	8	F	19.0
 input1.bam	FBtr0078580	72	11	F	23.0
-input1.bam	FBtr0078580	72	12	F	18.0
-input1.bam	FBtr0078580	72	14	F	15.3
-input1.bam	FBtr0078580	72	15	F	16.0
-input1.bam	FBtr0078580	72	16	F	19.0
-input1.bam	FBtr0078580	72	17	F	17.0
+input1.bam	FBtr0078580	72	12	F	21.3
+input1.bam	FBtr0078580	72	16	F	20.3
 input1.bam	FBtr0078580	72	19	F	24.0
 input1.bam	FBtr0078580	72	20	F	21.0
-input1.bam	FBtr0078580	72	21	F	19.4
-input1.bam	FBtr0078580	72	24	F	17.0
+input1.bam	FBtr0078580	72	21	F	20.3
 input1.bam	FBtr0078580	72	25	F	27.5
-input1.bam	FBtr0078580	72	29	F	17.0
-input1.bam	FBtr0078580	72	31	F	17.0
-input1.bam	FBtr0078580	72	52	F	16.0
 input1.bam	FBtr0078580	72	72	F	0
 input1.bam	FBtr0078790	73	1	F	19.0
-input1.bam	FBtr0078790	73	17	F	16.0
 input1.bam	FBtr0078790	73	33	F	23.0
-input1.bam	FBtr0078790	73	42	F	18.5
+input1.bam	FBtr0078790	73	42	F	22.0
 input1.bam	FBtr0078790	73	44	F	19.5
-input1.bam	FBtr0078790	73	46	F	17.0
-input1.bam	FBtr0078790	73	47	F	18.0
 input1.bam	FBtr0078790	73	52	F	20.0
-input1.bam	FBtr0078790	73	69	R	15.0
 input1.bam	FBtr0078790	73	73	F	0
-input1.bam	FBtr0079064	72	1	F	15.0
+input1.bam	FBtr0079064	72	1	F	0
 input1.bam	FBtr0079064	72	3	F	21.0
-input1.bam	FBtr0079064	72	33	F	15.0
-input1.bam	FBtr0079064	72	52	F	17.0
 input1.bam	FBtr0079064	72	72	F	0
-input1.bam	FBtr0079090	72	1	F	21.5
+input1.bam	FBtr0079090	72	1	F	28.0
 input1.bam	FBtr0079090	72	26	F	24.0
-input1.bam	FBtr0079090	72	33	F	16.0
-input1.bam	FBtr0079090	72	53	F	18.0
 input1.bam	FBtr0079090	72	56	R	21.0
 input1.bam	FBtr0079090	72	72	F	0
 input1.bam	FBtr0079338	73	1	F	0
-input1.bam	FBtr0079338	73	12	F	17.0
-input1.bam	FBtr0079338	73	13	F	17.5
-input1.bam	FBtr0079338	73	14	F	15.0
-input1.bam	FBtr0079338	73	17	F	15.0
-input1.bam	FBtr0079338	73	25	F	16.0
+input1.bam	FBtr0079338	73	13	F	19.0
 input1.bam	FBtr0079338	73	42	F	21.8
 input1.bam	FBtr0079338	73	43	F	21.0
-input1.bam	FBtr0079338	73	46	F	18.0
 input1.bam	FBtr0079338	73	73	F	0
-input1.bam	FBtr0079528	71	1	F	20.8
+input1.bam	FBtr0079528	71	1	F	25.3
 input1.bam	FBtr0079528	71	3	F	23.6
 input1.bam	FBtr0079528	71	4	F	24.0
-input1.bam	FBtr0079528	71	8	F	20.3
+input1.bam	FBtr0079528	71	8	F	21.0
 input1.bam	FBtr0079528	71	10	F	21.0
-input1.bam	FBtr0079528	71	11	F	19.0
-input1.bam	FBtr0079528	71	13	F	16.0
-input1.bam	FBtr0079528	71	14	F	18.5
-input1.bam	FBtr0079528	71	16	F	15.0
-input1.bam	FBtr0079528	71	17	F	15.3
-input1.bam	FBtr0079528	71	18	F	19.8
-input1.bam	FBtr0079528	71	28	F	16.0
-input1.bam	FBtr0079528	71	35	F	15.0
+input1.bam	FBtr0079528	71	11	F	22.0
+input1.bam	FBtr0079528	71	14	F	19.0
+input1.bam	FBtr0079528	71	18	F	20.3
 input1.bam	FBtr0079528	71	36	F	20.0
-input1.bam	FBtr0079528	71	37	F	18.0
-input1.bam	FBtr0079528	71	51	F	15.0
 input1.bam	FBtr0079528	71	71	F	0
-input1.bam	FBtr0079596	73	1	F	16.2
-input1.bam	FBtr0079596	73	3	F	21.8
+input1.bam	FBtr0079596	73	1	F	19.0
+input1.bam	FBtr0079596	73	3	F	23.1
 input1.bam	FBtr0079596	73	4	F	21.5
-input1.bam	FBtr0079596	73	5	F	18.5
-input1.bam	FBtr0079596	73	6	F	17.5
-input1.bam	FBtr0079596	73	8	F	16.6
-input1.bam	FBtr0079596	73	9	F	16.1
-input1.bam	FBtr0079596	73	10	F	15.3
-input1.bam	FBtr0079596	73	11	F	15.2
-input1.bam	FBtr0079596	73	12	F	17.0
-input1.bam	FBtr0079596	73	13	F	16.1
-input1.bam	FBtr0079596	73	14	F	15.0
-input1.bam	FBtr0079596	73	15	F	18.0
-input1.bam	FBtr0079596	73	16	F	16.7
-input1.bam	FBtr0079596	73	17	F	16.0
-input1.bam	FBtr0079596	73	18	F	15.0
-input1.bam	FBtr0079596	73	19	F	15.0
-input1.bam	FBtr0079596	73	53	F	18.5
+input1.bam	FBtr0079596	73	5	F	19.0
+input1.bam	FBtr0079596	73	6	F	19.0
+input1.bam	FBtr0079596	73	13	F	21.0
+input1.bam	FBtr0079596	73	53	F	20.0
 input1.bam	FBtr0079596	73	54	F	19.5
 input1.bam	FBtr0079596	73	73	F	0
 input1.bam	FBtr0079677	72	1	F	23.0
 input1.bam	FBtr0079677	72	5	F	19.0
 input1.bam	FBtr0079677	72	52	F	19.0
-input1.bam	FBtr0079677	72	53	F	18.0
 input1.bam	FBtr0079677	72	72	F	0
-input1.bam	FBtr0079690	72	1	F	15.0
-input1.bam	FBtr0079690	72	22	F	15.0
+input1.bam	FBtr0079690	72	1	F	0
 input1.bam	FBtr0079690	72	27	F	25.0
-input1.bam	FBtr0079690	72	33	F	16.0
 input1.bam	FBtr0079690	72	72	F	0
-input1.bam	FBtr0079692	73	1	F	19.3
-input1.bam	FBtr0079692	73	18	F	18.0
-input1.bam	FBtr0079692	73	25	F	17.0
+input1.bam	FBtr0079692	73	1	F	21.0
 input1.bam	FBtr0079692	73	32	F	20.0
 input1.bam	FBtr0079692	73	73	F	0
-input1.bam	FBtr0079693	72	1	F	17.2
+input1.bam	FBtr0079693	72	1	F	24.0
 input1.bam	FBtr0079693	72	25	F	23.0
 input1.bam	FBtr0079693	72	72	F	0
-input1.bam	FBtr0079694	72	1	F	20.4
+input1.bam	FBtr0079694	72	1	F	24.0
 input1.bam	FBtr0079694	72	18	F	19.0
-input1.bam	FBtr0079694	72	52	F	17.0
 input1.bam	FBtr0079694	72	72	F	0
-input1.bam	FBtr0079702	72	1	F	15.0
-input1.bam	FBtr0079702	72	19	F	18.0
-input1.bam	FBtr0079702	72	56	F	15.0
+input1.bam	FBtr0079702	72	1	F	0
 input1.bam	FBtr0079702	72	72	F	0
-input1.bam	FBtr0079728	72	1	F	16.0
+input1.bam	FBtr0079728	72	1	F	0
 input1.bam	FBtr0079728	72	8	F	20.0
 input1.bam	FBtr0079728	72	19	F	24.0
-input1.bam	FBtr0079728	72	33	F	15.7
-input1.bam	FBtr0079728	72	56	F	15.0
 input1.bam	FBtr0079728	72	72	F	0
-input1.bam	FBtr0079729	72	1	F	15.0
+input1.bam	FBtr0079729	72	1	F	0
 input1.bam	FBtr0079729	72	13	F	22.0
-input1.bam	FBtr0079729	72	52	F	18.0
-input1.bam	FBtr0079729	72	57	F	16.0
 input1.bam	FBtr0079729	72	72	F	0
-input1.bam	FBtr0079752	72	1	F	19.5
+input1.bam	FBtr0079752	72	1	F	24.0
 input1.bam	FBtr0079752	72	7	F	20.0
-input1.bam	FBtr0079752	72	12	F	16.0
-input1.bam	FBtr0079752	72	33	F	16.0
 input1.bam	FBtr0079752	72	52	F	19.5
 input1.bam	FBtr0079752	72	72	F	0
 input1.bam	FBtr0079820	74	1	F	0
 input1.bam	FBtr0079820	74	45	F	20.0
-input1.bam	FBtr0079820	74	46	F	17.0
-input1.bam	FBtr0079820	74	48	F	18.0
 input1.bam	FBtr0079820	74	49	F	24.0
 input1.bam	FBtr0079820	74	51	F	20.0
-input1.bam	FBtr0079820	74	54	F	17.0
-input1.bam	FBtr0079820	74	55	F	18.0
-input1.bam	FBtr0079820	74	56	F	18.5
+input1.bam	FBtr0079820	74	54	F	19.0
+input1.bam	FBtr0079820	74	56	F	19.0
 input1.bam	FBtr0079820	74	74	F	0
-input1.bam	FBtr0080609	72	1	F	18.8
+input1.bam	FBtr0080609	72	1	F	22.3
 input1.bam	FBtr0080609	72	3	F	21.0
 input1.bam	FBtr0080609	72	4	F	20.0
 input1.bam	FBtr0080609	72	5	F	19.0
-input1.bam	FBtr0080609	72	7	F	17.1
-input1.bam	FBtr0080609	72	8	F	16.0
-input1.bam	FBtr0080609	72	9	F	15.0
 input1.bam	FBtr0080609	72	12	F	23.0
 input1.bam	FBtr0080609	72	15	F	19.0
 input1.bam	FBtr0080609	72	16	F	23.0
-input1.bam	FBtr0080609	72	17	F	20.5
+input1.bam	FBtr0080609	72	17	F	24.0
 input1.bam	FBtr0080609	72	19	F	26.0
 input1.bam	FBtr0080609	72	20	F	25.0
 input1.bam	FBtr0080609	72	42	F	21.0
-input1.bam	FBtr0080609	72	51	F	18.0
-input1.bam	FBtr0080609	72	52	F	15.0
 input1.bam	FBtr0080609	72	72	F	0
 input1.bam	FBtr0080644	72	1	F	27.0
-input1.bam	FBtr0080644	72	4	F	20.5
-input1.bam	FBtr0080644	72	7	F	16.0
-input1.bam	FBtr0080644	72	12	F	16.0
+input1.bam	FBtr0080644	72	4	F	24.0
 input1.bam	FBtr0080644	72	72	F	0
-input1.bam	FBtr0080646	72	1	F	16.0
+input1.bam	FBtr0080646	72	1	F	0
 input1.bam	FBtr0080646	72	6	F	22.0
 input1.bam	FBtr0080646	72	7	F	21.0
 input1.bam	FBtr0080646	72	72	F	0
-input1.bam	FBtr0080647	72	1	F	16.3
-input1.bam	FBtr0080647	72	3	F	16.0
-input1.bam	FBtr0080647	72	6	F	19.0
+input1.bam	FBtr0080647	72	1	F	0
+input1.bam	FBtr0080647	72	6	F	22.0
 input1.bam	FBtr0080647	72	8	F	20.0
-input1.bam	FBtr0080647	72	11	F	17.0
-input1.bam	FBtr0080647	72	12	F	16.0
 input1.bam	FBtr0080647	72	72	F	0
 input1.bam	FBtr0080660	72	1	F	0
 input1.bam	FBtr0080660	72	4	F	24.0
-input1.bam	FBtr0080660	72	7	F	19.3
+input1.bam	FBtr0080660	72	7	F	21.0
 input1.bam	FBtr0080660	72	72	F	0
-input1.bam	FBtr0080663	71	1	F	18.8
+input1.bam	FBtr0080663	71	1	F	26.0
 input1.bam	FBtr0080663	71	3	F	23.7
 input1.bam	FBtr0080663	71	4	F	23.3
-input1.bam	FBtr0080663	71	7	F	16.0
-input1.bam	FBtr0080663	71	8	F	19.3
-input1.bam	FBtr0080663	71	12	F	16.0
+input1.bam	FBtr0080663	71	8	F	19.7
 input1.bam	FBtr0080663	71	14	F	19.0
-input1.bam	FBtr0080663	71	15	F	17.0
-input1.bam	FBtr0080663	71	16	F	15.7
-input1.bam	FBtr0080663	71	17	F	15.6
-input1.bam	FBtr0080663	71	26	F	18.0
-input1.bam	FBtr0080663	71	32	F	15.5
-input1.bam	FBtr0080663	71	50	F	17.0
-input1.bam	FBtr0080663	71	51	F	15.6
+input1.bam	FBtr0080663	71	51	F	20.0
 input1.bam	FBtr0080663	71	71	F	0
-input1.bam	FBtr0080664	71	1	F	19.5
+input1.bam	FBtr0080664	71	1	F	24.7
 input1.bam	FBtr0080664	71	3	F	23.8
 input1.bam	FBtr0080664	71	4	F	23.5
 input1.bam	FBtr0080664	71	6	F	23.0
 input1.bam	FBtr0080664	71	7	F	21.0
 input1.bam	FBtr0080664	71	8	F	20.5
 input1.bam	FBtr0080664	71	9	F	20.0
-input1.bam	FBtr0080664	71	11	F	16.7
-input1.bam	FBtr0080664	71	12	F	18.0
+input1.bam	FBtr0080664	71	12	F	20.0
 input1.bam	FBtr0080664	71	13	F	20.0
-input1.bam	FBtr0080664	71	14	F	18.3
-input1.bam	FBtr0080664	71	16	F	15.0
-input1.bam	FBtr0080664	71	17	F	15.8
-input1.bam	FBtr0080664	71	18	F	15.0
-input1.bam	FBtr0080664	71	21	F	15.0
-input1.bam	FBtr0080664	71	28	F	16.0
-input1.bam	FBtr0080664	71	32	F	15.0
+input1.bam	FBtr0080664	71	14	F	19.0
+input1.bam	FBtr0080664	71	17	F	19.0
 input1.bam	FBtr0080664	71	33	F	20.0
-input1.bam	FBtr0080664	71	34	F	16.0
-input1.bam	FBtr0080664	71	35	F	15.0
 input1.bam	FBtr0080664	71	36	F	21.0
-input1.bam	FBtr0080664	71	37	F	18.0
-input1.bam	FBtr0080664	71	38	F	15.0
-input1.bam	FBtr0080664	71	50	F	16.0
-input1.bam	FBtr0080664	71	51	F	15.0
-input1.bam	FBtr0080664	71	52	F	15.0
-input1.bam	FBtr0080664	71	56	F	16.0
 input1.bam	FBtr0080664	71	71	F	0
diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/input1_median.tab
--- a/test-data/input1_median.tab	Wed Apr 10 06:38:33 2019 -0400
+++ b/test-data/input1_median.tab	Sun Apr 14 14:43:44 2019 -0400
@@ -1,300 +1,190 @@
 Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Median
-input1.bam	FBtr0070001	72	1	F	17.0
+input1.bam	FBtr0070001	72	1	F	0
 input1.bam	FBtr0070001	72	7	F	21.0
 input1.bam	FBtr0070001	72	8	F	21.0
 input1.bam	FBtr0070001	72	11	F	20.5
 input1.bam	FBtr0070001	72	16	F	19.0
 input1.bam	FBtr0070001	72	17	F	23.0
-input1.bam	FBtr0070001	72	18	F	16.0
 input1.bam	FBtr0070001	72	27	F	23.5
 input1.bam	FBtr0070001	72	30	F	23.0
 input1.bam	FBtr0070001	72	31	F	23.0
 input1.bam	FBtr0070001	72	32	F	22.0
 input1.bam	FBtr0070001	72	34	F	20.0
 input1.bam	FBtr0070001	72	72	F	0
-input1.bam	FBtr0070533	72	1	F	15.0
-input1.bam	FBtr0070533	72	12	F	18.0
-input1.bam	FBtr0070533	72	15	F	15.0
+input1.bam	FBtr0070533	72	1	F	0
 input1.bam	FBtr0070533	72	19	F	22.0
 input1.bam	FBtr0070533	72	20	F	23.0
-input1.bam	FBtr0070533	72	21	F	18.0
 input1.bam	FBtr0070533	72	22	F	20.0
-input1.bam	FBtr0070533	72	25	F	17.0
-input1.bam	FBtr0070533	72	26	F	16.0
 input1.bam	FBtr0070533	72	28	F	25.0
-input1.bam	FBtr0070533	72	32	F	21.0
+input1.bam	FBtr0070533	72	32	F	22.0
 input1.bam	FBtr0070533	72	35	F	19.0
 input1.bam	FBtr0070533	72	37	F	19.0
-input1.bam	FBtr0070533	72	38	F	18.0
 input1.bam	FBtr0070533	72	72	F	0
-input1.bam	FBtr0070603	72	1	F	16.5
+input1.bam	FBtr0070603	72	1	F	0
 input1.bam	FBtr0070603	72	3	F	21.0
 input1.bam	FBtr0070603	72	4	F	20.0
-input1.bam	FBtr0070603	72	6	F	18.0
-input1.bam	FBtr0070603	72	7	F	17.0
-input1.bam	FBtr0070603	72	8	F	16.0
-input1.bam	FBtr0070603	72	9	F	15.0
-input1.bam	FBtr0070603	72	12	F	20.0
+input1.bam	FBtr0070603	72	12	F	23.0
 input1.bam	FBtr0070603	72	13	F	22.0
-input1.bam	FBtr0070603	72	15	F	18.5
-input1.bam	FBtr0070603	72	16	F	20.5
+input1.bam	FBtr0070603	72	15	F	20.0
+input1.bam	FBtr0070603	72	16	F	24.0
 input1.bam	FBtr0070603	72	17	F	25.0
-input1.bam	FBtr0070603	72	18	F	16.0
 input1.bam	FBtr0070603	72	19	F	23.0
-input1.bam	FBtr0070603	72	20	F	22.0
+input1.bam	FBtr0070603	72	20	F	24.0
 input1.bam	FBtr0070603	72	21	F	25.0
 input1.bam	FBtr0070603	72	22	F	20.0
-input1.bam	FBtr0070603	72	24	F	19.5
+input1.bam	FBtr0070603	72	24	F	21.0
 input1.bam	FBtr0070603	72	25	F	23.0
 input1.bam	FBtr0070603	72	26	F	26.0
 input1.bam	FBtr0070603	72	27	F	26.0
 input1.bam	FBtr0070603	72	32	F	20.0
 input1.bam	FBtr0070603	72	34	F	20.0
-input1.bam	FBtr0070603	72	38	F	18.0
 input1.bam	FBtr0070603	72	42	F	21.0
-input1.bam	FBtr0070603	72	51	F	18.0
-input1.bam	FBtr0070603	72	56	F	16.0
 input1.bam	FBtr0070603	72	72	F	0
-input1.bam	FBtr0070604	72	1	F	15.0
+input1.bam	FBtr0070604	72	1	F	0
 input1.bam	FBtr0070604	72	18	F	23.0
 input1.bam	FBtr0070604	72	22	F	19.0
-input1.bam	FBtr0070604	72	30	F	18.0
 input1.bam	FBtr0070604	72	31	F	23.0
 input1.bam	FBtr0070604	72	32	F	22.0
-input1.bam	FBtr0070604	72	57	F	15.0
 input1.bam	FBtr0070604	72	72	F	0
 input1.bam	FBtr0070911	73	1	F	0
 input1.bam	FBtr0070911	73	15	F	21.0
-input1.bam	FBtr0070911	73	38	F	15.0
 input1.bam	FBtr0070911	73	73	F	0
 input1.bam	FBtr0078490	72	1	F	0
-input1.bam	FBtr0078490	72	13	F	16.0
-input1.bam	FBtr0078490	72	17	F	16.0
-input1.bam	FBtr0078490	72	18	F	15.0
-input1.bam	FBtr0078490	72	25	F	15.0
-input1.bam	FBtr0078490	72	28	F	19.0
-input1.bam	FBtr0078490	72	38	F	18.0
+input1.bam	FBtr0078490	72	28	F	23.0
 input1.bam	FBtr0078490	72	72	F	0
-input1.bam	FBtr0078580	72	1	F	15.0
+input1.bam	FBtr0078580	72	1	F	25.0
 input1.bam	FBtr0078580	72	3	F	22.0
 input1.bam	FBtr0078580	72	4	F	25.0
 input1.bam	FBtr0078580	72	5	F	20.0
-input1.bam	FBtr0078580	72	6	F	19.0
+input1.bam	FBtr0078580	72	6	F	21.0
 input1.bam	FBtr0078580	72	7	F	22.0
-input1.bam	FBtr0078580	72	8	F	18.0
+input1.bam	FBtr0078580	72	8	F	19.0
 input1.bam	FBtr0078580	72	11	F	23.0
-input1.bam	FBtr0078580	72	12	F	17.0
-input1.bam	FBtr0078580	72	14	F	15.0
-input1.bam	FBtr0078580	72	15	F	16.0
+input1.bam	FBtr0078580	72	12	F	22.0
 input1.bam	FBtr0078580	72	16	F	19.0
-input1.bam	FBtr0078580	72	17	F	17.0
 input1.bam	FBtr0078580	72	19	F	24.0
 input1.bam	FBtr0078580	72	20	F	21.0
 input1.bam	FBtr0078580	72	21	F	20.0
-input1.bam	FBtr0078580	72	24	F	17.0
 input1.bam	FBtr0078580	72	25	F	27.5
-input1.bam	FBtr0078580	72	29	F	17.0
-input1.bam	FBtr0078580	72	31	F	17.0
-input1.bam	FBtr0078580	72	52	F	16.0
 input1.bam	FBtr0078580	72	72	F	0
 input1.bam	FBtr0078790	73	1	F	19.0
-input1.bam	FBtr0078790	73	17	F	16.0
 input1.bam	FBtr0078790	73	33	F	23.0
-input1.bam	FBtr0078790	73	42	F	18.5
+input1.bam	FBtr0078790	73	42	F	22.0
 input1.bam	FBtr0078790	73	44	F	19.5
-input1.bam	FBtr0078790	73	46	F	17.0
-input1.bam	FBtr0078790	73	47	F	18.0
 input1.bam	FBtr0078790	73	52	F	20.0
-input1.bam	FBtr0078790	73	69	R	15.0
 input1.bam	FBtr0078790	73	73	F	0
-input1.bam	FBtr0079064	72	1	F	15.0
+input1.bam	FBtr0079064	72	1	F	0
 input1.bam	FBtr0079064	72	3	F	21.0
-input1.bam	FBtr0079064	72	33	F	15.0
-input1.bam	FBtr0079064	72	52	F	17.0
 input1.bam	FBtr0079064	72	72	F	0
-input1.bam	FBtr0079090	72	1	F	21.5
+input1.bam	FBtr0079090	72	1	F	28.0
 input1.bam	FBtr0079090	72	26	F	24.0
-input1.bam	FBtr0079090	72	33	F	16.0
-input1.bam	FBtr0079090	72	53	F	18.0
 input1.bam	FBtr0079090	72	56	R	21.0
 input1.bam	FBtr0079090	72	72	F	0
 input1.bam	FBtr0079338	73	1	F	0
-input1.bam	FBtr0079338	73	12	F	17.0
-input1.bam	FBtr0079338	73	13	F	17.5
-input1.bam	FBtr0079338	73	14	F	15.0
-input1.bam	FBtr0079338	73	17	F	15.0
-input1.bam	FBtr0079338	73	25	F	16.0
+input1.bam	FBtr0079338	73	13	F	19.0
 input1.bam	FBtr0079338	73	42	F	22.0
 input1.bam	FBtr0079338	73	43	F	21.0
-input1.bam	FBtr0079338	73	46	F	18.0
 input1.bam	FBtr0079338	73	73	F	0
-input1.bam	FBtr0079528	71	1	F	20.0
+input1.bam	FBtr0079528	71	1	F	26.0
 input1.bam	FBtr0079528	71	3	F	24.0
 input1.bam	FBtr0079528	71	4	F	24.0
-input1.bam	FBtr0079528	71	8	F	19.5
+input1.bam	FBtr0079528	71	8	F	20.0
 input1.bam	FBtr0079528	71	10	F	21.0
-input1.bam	FBtr0079528	71	11	F	19.0
-input1.bam	FBtr0079528	71	13	F	16.0
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diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/input1_min0_max10000_cluster0_single_plot_counts.pdf
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diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/input1_min0_max10000_cluster0_ylimneg5_pos5_single_plot_counts.pdf
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diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/input1_min0_max10000_cluster5_single_plot_counts.pdf
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diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/input1_min20_max30_cluster0_single_plot_counts.pdf
Binary file test-data/input1_min20_max30_cluster0_single_plot_counts.pdf has changed
diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/input1_min20_max30_counts.tab
--- a/test-data/input1_min20_max30_counts.tab	Wed Apr 10 06:38:33 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,171 +0,0 @@
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-input1.bam	FBtr0080609	72	17	F	1
-input1.bam	FBtr0080609	72	19	F	1
-input1.bam	FBtr0080609	72	20	F	1
-input1.bam	FBtr0080609	72	42	F	1
-input1.bam	FBtr0080609	72	72	F	0
-input1.bam	FBtr0080644	72	1	F	1
-input1.bam	FBtr0080644	72	4	F	1
-input1.bam	FBtr0080644	72	72	F	0
-input1.bam	FBtr0080646	72	1	F	0
-input1.bam	FBtr0080646	72	6	F	1
-input1.bam	FBtr0080646	72	7	F	1
-input1.bam	FBtr0080646	72	72	F	0
-input1.bam	FBtr0080647	72	1	F	0
-input1.bam	FBtr0080647	72	6	F	1
-input1.bam	FBtr0080647	72	8	F	1
-input1.bam	FBtr0080647	72	72	F	0
-input1.bam	FBtr0080660	72	1	F	0
-input1.bam	FBtr0080660	72	4	F	4
-input1.bam	FBtr0080660	72	7	F	2
-input1.bam	FBtr0080660	72	72	F	0
-input1.bam	FBtr0080663	71	1	F	6
-input1.bam	FBtr0080663	71	3	F	56
-input1.bam	FBtr0080663	71	4	F	4
-input1.bam	FBtr0080663	71	8	F	2
-input1.bam	FBtr0080663	71	51	F	1
-input1.bam	FBtr0080663	71	71	F	0
-input1.bam	FBtr0080664	71	1	F	6
-input1.bam	FBtr0080664	71	3	F	56
-input1.bam	FBtr0080664	71	4	F	4
-input1.bam	FBtr0080664	71	6	F	1
-input1.bam	FBtr0080664	71	7	F	1
-input1.bam	FBtr0080664	71	8	F	3
-input1.bam	FBtr0080664	71	9	F	1
-input1.bam	FBtr0080664	71	12	F	1
-input1.bam	FBtr0080664	71	13	F	2
-input1.bam	FBtr0080664	71	33	F	1
-input1.bam	FBtr0080664	71	36	F	1
-input1.bam	FBtr0080664	71	71	F	0
diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/input1_min20_max30_single_plot_size.pdf
Binary file test-data/input1_min20_max30_single_plot_size.pdf has changed
diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/input1_min20_max30_size.tab
--- a/test-data/input1_min20_max30_size.tab	Wed Apr 10 06:38:33 2019 -0400
+++ b/test-data/input1_min20_max30_size.tab	Sun Apr 14 14:43:44 2019 -0400
@@ -1,265 +1,342 @@
 Dataset	Chromosome	Polarity	Size	Counts	Strandness	z-score
-input1.bam	FBtr0070001	F	20	4	1.0	-0.63673824446
-input1.bam	FBtr0070001	F	21	4	1.0	-0.63673824446
-input1.bam	FBtr0070001	F	22	29	1.0	1.77514904516
-input1.bam	FBtr0070001	F	23	15	1.0	0.424492162973
-input1.bam	FBtr0070001	F	24	1	1.0	-0.926164719215
-input1.bam	FBtr0070001	R	20	0	1.0	-0.63673824446
-input1.bam	FBtr0070001	R	21	0	1.0	-0.63673824446
-input1.bam	FBtr0070001	R	22	0	1.0	1.77514904516
-input1.bam	FBtr0070001	R	23	0	1.0	0.424492162973
-input1.bam	FBtr0070001	R	24	0	1.0	-0.926164719215
-input1.bam	FBtr0070533	F	20	2	1.0	0.137360563949
-input1.bam	FBtr0070533	F	21	2	1.0	0.137360563949
-input1.bam	FBtr0070533	F	22	4	1.0	1.78568733133
-input1.bam	FBtr0070533	F	23	2	1.0	0.137360563949
-input1.bam	FBtr0070533	F	24	0	1.0	-1.51096620344
-input1.bam	FBtr0070533	F	25	1	1.0	-0.686802819743
-input1.bam	FBtr0070533	R	20	0	1.0	0.137360563949
-input1.bam	FBtr0070533	R	21	0	1.0	0.137360563949
-input1.bam	FBtr0070533	R	22	0	1.0	1.78568733133
-input1.bam	FBtr0070533	R	23	0	1.0	0.137360563949
-input1.bam	FBtr0070533	R	24	0	1.0	-1.51096620344
-input1.bam	FBtr0070533	R	25	0	1.0	-0.686802819743
-input1.bam	FBtr0070603	F	20	6	1.0	0.574195326069
-input1.bam	FBtr0070603	F	21	3	1.0	-0.678594476263
-input1.bam	FBtr0070603	F	22	3	1.0	-0.678594476263
-input1.bam	FBtr0070603	F	23	10	1.0	2.24458172918
-input1.bam	FBtr0070603	F	24	2	1.0	-1.09619107704
-input1.bam	FBtr0070603	F	25	5	1.0	0.156598725292
-input1.bam	FBtr0070603	F	26	5	1.0	0.156598725292
-input1.bam	FBtr0070603	F	27	3	1.0	-0.678594476263
-input1.bam	FBtr0070603	R	20	0	1.0	0.574195326069
-input1.bam	FBtr0070603	R	21	0	1.0	-0.678594476263
-input1.bam	FBtr0070603	R	22	0	1.0	-0.678594476263
-input1.bam	FBtr0070603	R	23	0	1.0	2.24458172918
-input1.bam	FBtr0070603	R	24	0	1.0	-1.09619107704
-input1.bam	FBtr0070603	R	25	0	1.0	0.156598725292
-input1.bam	FBtr0070603	R	26	0	1.0	0.156598725292
-input1.bam	FBtr0070603	R	27	0	1.0	-0.678594476263
-input1.bam	FBtr0070604	F	21	1	1.0	-1.14423087931
-input1.bam	FBtr0070604	F	22	23	1.0	1.29187357342
-input1.bam	FBtr0070604	F	23	10	1.0	-0.147642694105
-input1.bam	FBtr0070604	R	21	0	1.0	-1.14423087931
-input1.bam	FBtr0070604	R	22	0	1.0	1.29187357342
-input1.bam	FBtr0070604	R	23	0	1.0	-0.147642694105
-input1.bam	FBtr0070911	F	21	1	1.0	0
-input1.bam	FBtr0070911	R	21	0	1.0	0
-input1.bam	FBtr0078490	F	23	1	1.0	0
-input1.bam	FBtr0078490	R	23	0	1.0	0
-input1.bam	FBtr0078580	F	20	9	1.0	-0.511163173122
-input1.bam	FBtr0078580	F	21	5	1.0	-0.561857041531
-input1.bam	FBtr0078580	F	22	13	1.0	-0.460469304713
-input1.bam	FBtr0078580	F	23	5	1.0	-0.561857041531
-input1.bam	FBtr0078580	F	24	180	1.0	1.65599970135
-input1.bam	FBtr0078580	F	25	212	1.0	2.06155064863
-input1.bam	FBtr0078580	F	26	1	1.0	-0.61255090994
-input1.bam	FBtr0078580	F	27	2	1.0	-0.599877442838
-input1.bam	FBtr0078580	F	28	17	1.0	-0.409775436305
-input1.bam	FBtr0078580	R	20	0	1.0	-0.511163173122
-input1.bam	FBtr0078580	R	21	0	1.0	-0.561857041531
-input1.bam	FBtr0078580	R	22	0	1.0	-0.460469304713
-input1.bam	FBtr0078580	R	23	0	1.0	-0.561857041531
-input1.bam	FBtr0078580	R	24	0	1.0	1.65599970135
-input1.bam	FBtr0078580	R	25	0	1.0	2.06155064863
-input1.bam	FBtr0078580	R	26	0	1.0	-0.61255090994
-input1.bam	FBtr0078580	R	27	0	1.0	-0.599877442838
-input1.bam	FBtr0078580	R	28	0	1.0	-0.409775436305
-input1.bam	FBtr0078790	F	20	2	1.0	0.904534033733
-input1.bam	FBtr0078790	F	21	0	1.0	-1.50755672289
-input1.bam	FBtr0078790	F	22	2	1.0	0.904534033733
-input1.bam	FBtr0078790	F	23	1	1.0	-0.301511344578
-input1.bam	FBtr0078790	R	20	0	1.0	0.904534033733
-input1.bam	FBtr0078790	R	21	0	1.0	-1.50755672289
-input1.bam	FBtr0078790	R	22	0	1.0	0.904534033733
-input1.bam	FBtr0078790	R	23	0	1.0	-0.301511344578
-input1.bam	FBtr0079064	F	21	1	1.0	0
-input1.bam	FBtr0079064	R	21	0	1.0	0
-input1.bam	FBtr0079090	F	21	0	0.666666666667	1.29099444874
-input1.bam	FBtr0079090	F	22	0	0.666666666667	-0.774596669241
-input1.bam	FBtr0079090	F	23	0	0.666666666667	-0.774596669241
-input1.bam	FBtr0079090	F	24	1	0.666666666667	1.29099444874
-input1.bam	FBtr0079090	F	25	0	0.666666666667	-0.774596669241
-input1.bam	FBtr0079090	F	26	0	0.666666666667	-0.774596669241
-input1.bam	FBtr0079090	F	27	0	0.666666666667	-0.774596669241
-input1.bam	FBtr0079090	F	28	1	0.666666666667	1.29099444874
-input1.bam	FBtr0079090	R	21	1	0.666666666667	1.29099444874
-input1.bam	FBtr0079090	R	22	0	0.666666666667	-0.774596669241
-input1.bam	FBtr0079090	R	23	0	0.666666666667	-0.774596669241
-input1.bam	FBtr0079090	R	24	0	0.666666666667	1.29099444874
-input1.bam	FBtr0079090	R	25	0	0.666666666667	-0.774596669241
-input1.bam	FBtr0079090	R	26	0	0.666666666667	-0.774596669241
-input1.bam	FBtr0079090	R	27	0	0.666666666667	-0.774596669241
-input1.bam	FBtr0079090	R	28	0	0.666666666667	1.29099444874
-input1.bam	FBtr0079338	F	21	3	1.0	-1.0
-input1.bam	FBtr0079338	F	22	6	1.0	1.0
-input1.bam	FBtr0079338	R	21	0	1.0	-1.0
-input1.bam	FBtr0079338	R	22	0	1.0	1.0
-input1.bam	FBtr0079528	F	20	12	1.0	0.457174252464
-input1.bam	FBtr0079528	F	21	3	1.0	-0.437297111052
-input1.bam	FBtr0079528	F	22	2	1.0	-0.53668281811
-input1.bam	FBtr0079528	F	23	3	1.0	-0.437297111052
-input1.bam	FBtr0079528	F	24	36	1.0	2.84243122184
-input1.bam	FBtr0079528	F	25	8	1.0	0.0596314242344
-input1.bam	FBtr0079528	F	26	5	1.0	-0.238525696938
-input1.bam	FBtr0079528	F	27	2	1.0	-0.53668281811
-input1.bam	FBtr0079528	F	28	2	1.0	-0.53668281811
-input1.bam	FBtr0079528	F	29	1	1.0	-0.636068525167
-input1.bam	FBtr0079528	R	20	0	1.0	0.457174252464
-input1.bam	FBtr0079528	R	21	0	1.0	-0.437297111052
-input1.bam	FBtr0079528	R	22	0	1.0	-0.53668281811
-input1.bam	FBtr0079528	R	23	0	1.0	-0.437297111052
-input1.bam	FBtr0079528	R	24	0	1.0	2.84243122184
-input1.bam	FBtr0079528	R	25	0	1.0	0.0596314242344
-input1.bam	FBtr0079528	R	26	0	1.0	-0.238525696938
-input1.bam	FBtr0079528	R	27	0	1.0	-0.53668281811
-input1.bam	FBtr0079528	R	28	0	1.0	-0.53668281811
-input1.bam	FBtr0079528	R	29	0	1.0	-0.636068525167
-input1.bam	FBtr0079596	F	20	13	1.0	1.30066495429
-input1.bam	FBtr0079596	F	21	3	1.0	-0.433554984762
-input1.bam	FBtr0079596	F	22	16	1.0	1.820930936
-input1.bam	FBtr0079596	F	23	8	1.0	0.433554984762
-input1.bam	FBtr0079596	F	24	0	1.0	-0.953820966477
-input1.bam	FBtr0079596	F	25	0	1.0	-0.953820966477
-input1.bam	FBtr0079596	F	26	3	1.0	-0.433554984762
-input1.bam	FBtr0079596	F	27	1	1.0	-0.780398972572
-input1.bam	FBtr0079596	R	20	0	1.0	1.30066495429
-input1.bam	FBtr0079596	R	21	0	1.0	-0.433554984762
-input1.bam	FBtr0079596	R	22	0	1.0	1.820930936
-input1.bam	FBtr0079596	R	23	0	1.0	0.433554984762
-input1.bam	FBtr0079596	R	24	0	1.0	-0.953820966477
-input1.bam	FBtr0079596	R	25	0	1.0	-0.953820966477
-input1.bam	FBtr0079596	R	26	0	1.0	-0.433554984762
-input1.bam	FBtr0079596	R	27	0	1.0	-0.780398972572
-input1.bam	FBtr0079677	F	23	1	1.0	0
-input1.bam	FBtr0079677	R	23	0	1.0	0
-input1.bam	FBtr0079690	F	25	1	1.0	0
-input1.bam	FBtr0079690	R	25	0	1.0	0
-input1.bam	FBtr0079692	F	20	1	1.0	1.0
-input1.bam	FBtr0079692	F	21	0	1.0	-1.0
-input1.bam	FBtr0079692	F	22	0	1.0	-1.0
-input1.bam	FBtr0079692	F	23	1	1.0	1.0
-input1.bam	FBtr0079692	R	20	0	1.0	1.0
-input1.bam	FBtr0079692	R	21	0	1.0	-1.0
-input1.bam	FBtr0079692	R	22	0	1.0	-1.0
-input1.bam	FBtr0079692	R	23	0	1.0	1.0
-input1.bam	FBtr0079693	F	23	1	1.0	0
-input1.bam	FBtr0079693	F	24	1	1.0	0
-input1.bam	FBtr0079693	R	23	0	1.0	0
-input1.bam	FBtr0079693	R	24	0	1.0	0
-input1.bam	FBtr0079694	F	23	1	1.0	0
-input1.bam	FBtr0079694	F	24	1	1.0	0
-input1.bam	FBtr0079694	F	25	1	1.0	0
-input1.bam	FBtr0079694	R	23	0	1.0	0
-input1.bam	FBtr0079694	R	24	0	1.0	0
-input1.bam	FBtr0079694	R	25	0	1.0	0
-input1.bam	FBtr0079702	F	10	0	2	0
-input1.bam	FBtr0079702	R	10	0	2	0
-input1.bam	FBtr0079728	F	20	1	1.0	1.22474487139
-input1.bam	FBtr0079728	F	21	0	1.0	-0.816496580928
-input1.bam	FBtr0079728	F	22	0	1.0	-0.816496580928
-input1.bam	FBtr0079728	F	23	0	1.0	-0.816496580928
-input1.bam	FBtr0079728	F	24	1	1.0	1.22474487139
-input1.bam	FBtr0079728	R	20	0	1.0	1.22474487139
-input1.bam	FBtr0079728	R	21	0	1.0	-0.816496580928
-input1.bam	FBtr0079728	R	22	0	1.0	-0.816496580928
-input1.bam	FBtr0079728	R	23	0	1.0	-0.816496580928
-input1.bam	FBtr0079728	R	24	0	1.0	1.22474487139
-input1.bam	FBtr0079729	F	22	1	1.0	0
-input1.bam	FBtr0079729	R	22	0	1.0	0
-input1.bam	FBtr0079752	F	20	2	1.0	1.75
-input1.bam	FBtr0079752	F	21	0	1.0	-0.75
-input1.bam	FBtr0079752	F	22	0	1.0	-0.75
-input1.bam	FBtr0079752	F	23	0	1.0	-0.75
-input1.bam	FBtr0079752	F	24	1	1.0	0.5
-input1.bam	FBtr0079752	R	20	0	1.0	1.75
-input1.bam	FBtr0079752	R	21	0	1.0	-0.75
-input1.bam	FBtr0079752	R	22	0	1.0	-0.75
-input1.bam	FBtr0079752	R	23	0	1.0	-0.75
-input1.bam	FBtr0079752	R	24	0	1.0	0.5
-input1.bam	FBtr0079820	F	20	2	1.0	1.75
-input1.bam	FBtr0079820	F	21	0	1.0	-0.75
-input1.bam	FBtr0079820	F	22	0	1.0	-0.75
-input1.bam	FBtr0079820	F	23	0	1.0	-0.75
-input1.bam	FBtr0079820	F	24	1	1.0	0.5
-input1.bam	FBtr0079820	R	20	0	1.0	1.75
-input1.bam	FBtr0079820	R	21	0	1.0	-0.75
-input1.bam	FBtr0079820	R	22	0	1.0	-0.75
-input1.bam	FBtr0079820	R	23	0	1.0	-0.75
-input1.bam	FBtr0079820	R	24	0	1.0	0.5
-input1.bam	FBtr0080609	F	20	10	1.0	2.18263347562
-input1.bam	FBtr0080609	F	21	4	1.0	0.311804782231
-input1.bam	FBtr0080609	F	22	0	1.0	-0.935414346693
-input1.bam	FBtr0080609	F	23	4	1.0	0.311804782231
-input1.bam	FBtr0080609	F	24	1	1.0	-0.623609564462
-input1.bam	FBtr0080609	F	25	1	1.0	-0.623609564462
-input1.bam	FBtr0080609	F	26	1	1.0	-0.623609564462
-input1.bam	FBtr0080609	R	20	0	1.0	2.18263347562
-input1.bam	FBtr0080609	R	21	0	1.0	0.311804782231
-input1.bam	FBtr0080609	R	22	0	1.0	-0.935414346693
-input1.bam	FBtr0080609	R	23	0	1.0	0.311804782231
-input1.bam	FBtr0080609	R	24	0	1.0	-0.623609564462
-input1.bam	FBtr0080609	R	25	0	1.0	-0.623609564462
-input1.bam	FBtr0080609	R	26	0	1.0	-0.623609564462
-input1.bam	FBtr0080644	F	24	1	1.0	1.0
-input1.bam	FBtr0080644	F	25	0	1.0	-1.0
-input1.bam	FBtr0080644	F	26	0	1.0	-1.0
-input1.bam	FBtr0080644	F	27	1	1.0	1.0
-input1.bam	FBtr0080644	R	24	0	1.0	1.0
-input1.bam	FBtr0080644	R	25	0	1.0	-1.0
-input1.bam	FBtr0080644	R	26	0	1.0	-1.0
-input1.bam	FBtr0080644	R	27	0	1.0	1.0
-input1.bam	FBtr0080646	F	21	1	1.0	0
-input1.bam	FBtr0080646	F	22	1	1.0	0
-input1.bam	FBtr0080646	R	21	0	1.0	0
-input1.bam	FBtr0080646	R	22	0	1.0	0
-input1.bam	FBtr0080647	F	20	1	1.0	0.707106781187
-input1.bam	FBtr0080647	F	21	0	1.0	-1.41421356237
-input1.bam	FBtr0080647	F	22	1	1.0	0.707106781187
-input1.bam	FBtr0080647	R	20	0	1.0	0.707106781187
-input1.bam	FBtr0080647	R	21	0	1.0	-1.41421356237
-input1.bam	FBtr0080647	R	22	0	1.0	0.707106781187
-input1.bam	FBtr0080660	F	21	2	1.0	0.301511344578
-input1.bam	FBtr0080660	F	22	0	1.0	-0.904534033733
-input1.bam	FBtr0080660	F	23	0	1.0	-0.904534033733
-input1.bam	FBtr0080660	F	24	4	1.0	1.50755672289
-input1.bam	FBtr0080660	R	21	0	1.0	0.301511344578
-input1.bam	FBtr0080660	R	22	0	1.0	-0.904534033733
-input1.bam	FBtr0080660	R	23	0	1.0	-0.904534033733
-input1.bam	FBtr0080660	R	24	0	1.0	1.50755672289
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+input1.bam	FBtr0079702	F	25	0	2	0
+input1.bam	FBtr0079702	F	26	0	2	0
+input1.bam	FBtr0079702	F	27	0	2	0
+input1.bam	FBtr0079702	F	28	0	2	0
+input1.bam	FBtr0079702	F	29	0	2	0
+input1.bam	FBtr0079728	F	19	0	1.0	-0.471404520791
+input1.bam	FBtr0079728	F	20	1	1.0	2.12132034356
+input1.bam	FBtr0079728	F	21	0	1.0	-0.471404520791
+input1.bam	FBtr0079728	F	22	0	1.0	-0.471404520791
+input1.bam	FBtr0079728	F	23	0	1.0	-0.471404520791
+input1.bam	FBtr0079728	F	24	1	1.0	2.12132034356
+input1.bam	FBtr0079728	F	25	0	1.0	-0.471404520791
+input1.bam	FBtr0079728	F	26	0	1.0	-0.471404520791
+input1.bam	FBtr0079728	F	27	0	1.0	-0.471404520791
+input1.bam	FBtr0079728	F	28	0	1.0	-0.471404520791
+input1.bam	FBtr0079728	F	29	0	1.0	-0.471404520791
+input1.bam	FBtr0079729	F	19	0	1.0	-0.316227766017
+input1.bam	FBtr0079729	F	20	0	1.0	-0.316227766017
+input1.bam	FBtr0079729	F	21	0	1.0	-0.316227766017
+input1.bam	FBtr0079729	F	22	1	1.0	3.16227766017
+input1.bam	FBtr0079729	F	23	0	1.0	-0.316227766017
+input1.bam	FBtr0079729	F	24	0	1.0	-0.316227766017
+input1.bam	FBtr0079729	F	25	0	1.0	-0.316227766017
+input1.bam	FBtr0079729	F	26	0	1.0	-0.316227766017
+input1.bam	FBtr0079729	F	27	0	1.0	-0.316227766017
+input1.bam	FBtr0079729	F	28	0	1.0	-0.316227766017
+input1.bam	FBtr0079729	F	29	0	1.0	-0.316227766017
+input1.bam	FBtr0079752	F	19	1	1.0	0.989949493661
+input1.bam	FBtr0079752	F	20	2	1.0	2.54558441227
+input1.bam	FBtr0079752	F	21	0	1.0	-0.565685424949
+input1.bam	FBtr0079752	F	22	0	1.0	-0.565685424949
+input1.bam	FBtr0079752	F	23	0	1.0	-0.565685424949
+input1.bam	FBtr0079752	F	24	1	1.0	0.989949493661
+input1.bam	FBtr0079752	F	25	0	1.0	-0.565685424949
+input1.bam	FBtr0079752	F	26	0	1.0	-0.565685424949
+input1.bam	FBtr0079752	F	27	0	1.0	-0.565685424949
+input1.bam	FBtr0079752	F	28	0	1.0	-0.565685424949
+input1.bam	FBtr0079752	F	29	0	1.0	-0.565685424949
+input1.bam	FBtr0079820	F	19	3	1.0	2.48555146833
+input1.bam	FBtr0079820	F	20	2	1.0	1.47291938864
+input1.bam	FBtr0079820	F	21	0	1.0	-0.552344770739
+input1.bam	FBtr0079820	F	22	0	1.0	-0.552344770739
+input1.bam	FBtr0079820	F	23	0	1.0	-0.552344770739
+input1.bam	FBtr0079820	F	24	1	1.0	0.460287308949
+input1.bam	FBtr0079820	F	25	0	1.0	-0.552344770739
+input1.bam	FBtr0079820	F	26	0	1.0	-0.552344770739
+input1.bam	FBtr0079820	F	27	0	1.0	-0.552344770739
+input1.bam	FBtr0079820	F	28	0	1.0	-0.552344770739
+input1.bam	FBtr0079820	F	29	0	1.0	-0.552344770739
+input1.bam	FBtr0080609	F	19	3	1.0	0.283473354757
+input1.bam	FBtr0080609	F	20	10	1.0	2.7087453899
+input1.bam	FBtr0080609	F	21	4	1.0	0.629940788349
+input1.bam	FBtr0080609	F	22	0	1.0	-0.755928946018
+input1.bam	FBtr0080609	F	23	4	1.0	0.629940788349
+input1.bam	FBtr0080609	F	24	1	1.0	-0.409461512427
+input1.bam	FBtr0080609	F	25	1	1.0	-0.409461512427
+input1.bam	FBtr0080609	F	26	1	1.0	-0.409461512427
+input1.bam	FBtr0080609	F	27	0	1.0	-0.755928946018
+input1.bam	FBtr0080609	F	28	0	1.0	-0.755928946018
+input1.bam	FBtr0080609	F	29	0	1.0	-0.755928946018
+input1.bam	FBtr0080644	F	19	0	1.0	-0.471404520791
+input1.bam	FBtr0080644	F	20	0	1.0	-0.471404520791
+input1.bam	FBtr0080644	F	21	0	1.0	-0.471404520791
+input1.bam	FBtr0080644	F	22	0	1.0	-0.471404520791
+input1.bam	FBtr0080644	F	23	0	1.0	-0.471404520791
+input1.bam	FBtr0080644	F	24	1	1.0	2.12132034356
+input1.bam	FBtr0080644	F	25	0	1.0	-0.471404520791
+input1.bam	FBtr0080644	F	26	0	1.0	-0.471404520791
+input1.bam	FBtr0080644	F	27	1	1.0	2.12132034356
+input1.bam	FBtr0080644	F	28	0	1.0	-0.471404520791
+input1.bam	FBtr0080644	F	29	0	1.0	-0.471404520791
+input1.bam	FBtr0080646	F	19	0	1.0	-0.471404520791
+input1.bam	FBtr0080646	F	20	0	1.0	-0.471404520791
+input1.bam	FBtr0080646	F	21	1	1.0	2.12132034356
+input1.bam	FBtr0080646	F	22	1	1.0	2.12132034356
+input1.bam	FBtr0080646	F	23	0	1.0	-0.471404520791
+input1.bam	FBtr0080646	F	24	0	1.0	-0.471404520791
+input1.bam	FBtr0080646	F	25	0	1.0	-0.471404520791
+input1.bam	FBtr0080646	F	26	0	1.0	-0.471404520791
+input1.bam	FBtr0080646	F	27	0	1.0	-0.471404520791
+input1.bam	FBtr0080646	F	28	0	1.0	-0.471404520791
+input1.bam	FBtr0080646	F	29	0	1.0	-0.471404520791
+input1.bam	FBtr0080647	F	19	0	1.0	-0.471404520791
+input1.bam	FBtr0080647	F	20	1	1.0	2.12132034356
+input1.bam	FBtr0080647	F	21	0	1.0	-0.471404520791
+input1.bam	FBtr0080647	F	22	1	1.0	2.12132034356
+input1.bam	FBtr0080647	F	23	0	1.0	-0.471404520791
+input1.bam	FBtr0080647	F	24	0	1.0	-0.471404520791
+input1.bam	FBtr0080647	F	25	0	1.0	-0.471404520791
+input1.bam	FBtr0080647	F	26	0	1.0	-0.471404520791
+input1.bam	FBtr0080647	F	27	0	1.0	-0.471404520791
+input1.bam	FBtr0080647	F	28	0	1.0	-0.471404520791
+input1.bam	FBtr0080647	F	29	0	1.0	-0.471404520791
+input1.bam	FBtr0080660	F	19	0	1.0	-0.442325868465
+input1.bam	FBtr0080660	F	20	0	1.0	-0.442325868465
+input1.bam	FBtr0080660	F	21	2	1.0	1.17953564924
+input1.bam	FBtr0080660	F	22	0	1.0	-0.442325868465
+input1.bam	FBtr0080660	F	23	0	1.0	-0.442325868465
+input1.bam	FBtr0080660	F	24	4	1.0	2.80139716694
+input1.bam	FBtr0080660	F	25	0	1.0	-0.442325868465
+input1.bam	FBtr0080660	F	26	0	1.0	-0.442325868465
+input1.bam	FBtr0080660	F	27	0	1.0	-0.442325868465
+input1.bam	FBtr0080660	F	28	0	1.0	-0.442325868465
+input1.bam	FBtr0080660	F	29	0	1.0	-0.442325868465
+input1.bam	FBtr0080663	F	19	3	1.0	-0.388372247691
+input1.bam	FBtr0080663	F	20	10	1.0	0.37841398493
+input1.bam	FBtr0080663	F	21	0	1.0	-0.716994918814
+input1.bam	FBtr0080663	F	22	1	1.0	-0.60745402844
+input1.bam	FBtr0080663	F	23	7	1.0	0.0497913138066
+input1.bam	FBtr0080663	F	24	33	1.0	2.89785446354
+input1.bam	FBtr0080663	F	25	10	1.0	0.37841398493
+input1.bam	FBtr0080663	F	26	6	1.0	-0.0597495765679
+input1.bam	FBtr0080663	F	27	0	1.0	-0.716994918814
+input1.bam	FBtr0080663	F	28	2	1.0	-0.497913138066
+input1.bam	FBtr0080663	F	29	0	1.0	-0.716994918814
+input1.bam	FBtr0080664	F	19	3	1.0	-0.465643333651
+input1.bam	FBtr0080664	F	20	12	1.0	0.515179858507
+input1.bam	FBtr0080664	F	21	5	1.0	-0.247682624282
+input1.bam	FBtr0080664	F	22	0	1.0	-0.792584397704
+input1.bam	FBtr0080664	F	23	11	1.0	0.406199503823
+input1.bam	FBtr0080664	F	24	33	1.0	2.80376730688
+input1.bam	FBtr0080664	F	25	10	1.0	0.297219149139
+input1.bam	FBtr0080664	F	26	4	1.0	-0.356662978967
+input1.bam	FBtr0080664	F	27	0	1.0	-0.792584397704
+input1.bam	FBtr0080664	F	28	2	1.0	-0.574623688335
+input1.bam	FBtr0080664	F	29	0	1.0	-0.792584397704
diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/input1_single_plot_median.pdf
Binary file test-data/input1_single_plot_median.pdf has changed
diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/input1_size.tab
--- a/test-data/input1_size.tab	Wed Apr 10 06:38:33 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,605 +0,0 @@
-Dataset	Chromosome	Polarity	Size	Counts
-input1.bam	FBtr0070001	F	16	2
-input1.bam	FBtr0070001	F	17	1
-input1.bam	FBtr0070001	F	18	0
-input1.bam	FBtr0070001	F	19	1
-input1.bam	FBtr0070001	F	20	4
-input1.bam	FBtr0070001	F	21	4
-input1.bam	FBtr0070001	F	22	29
-input1.bam	FBtr0070001	F	23	15
-input1.bam	FBtr0070001	F	24	1
-input1.bam	FBtr0070001	R	16	0
-input1.bam	FBtr0070001	R	17	0
-input1.bam	FBtr0070001	R	18	0
-input1.bam	FBtr0070001	R	19	0
-input1.bam	FBtr0070001	R	20	0
-input1.bam	FBtr0070001	R	21	0
-input1.bam	FBtr0070001	R	22	0
-input1.bam	FBtr0070001	R	23	0
-input1.bam	FBtr0070001	R	24	0
-input1.bam	FBtr0070533	F	15	2
-input1.bam	FBtr0070533	F	16	1
-input1.bam	FBtr0070533	F	17	1
-input1.bam	FBtr0070533	F	18	6
-input1.bam	FBtr0070533	F	19	3
-input1.bam	FBtr0070533	F	20	2
-input1.bam	FBtr0070533	F	21	2
-input1.bam	FBtr0070533	F	22	4
-input1.bam	FBtr0070533	F	23	2
-input1.bam	FBtr0070533	F	24	0
-input1.bam	FBtr0070533	F	25	1
-input1.bam	FBtr0070533	R	15	0
-input1.bam	FBtr0070533	R	16	0
-input1.bam	FBtr0070533	R	17	0
-input1.bam	FBtr0070533	R	18	0
-input1.bam	FBtr0070533	R	19	0
-input1.bam	FBtr0070533	R	20	0
-input1.bam	FBtr0070533	R	21	0
-input1.bam	FBtr0070533	R	22	0
-input1.bam	FBtr0070533	R	23	0
-input1.bam	FBtr0070533	R	24	0
-input1.bam	FBtr0070533	R	25	0
-input1.bam	FBtr0070603	F	15	9
-input1.bam	FBtr0070603	F	16	6
-input1.bam	FBtr0070603	F	17	10
-input1.bam	FBtr0070603	F	18	7
-input1.bam	FBtr0070603	F	19	1
-input1.bam	FBtr0070603	F	20	6
-input1.bam	FBtr0070603	F	21	3
-input1.bam	FBtr0070603	F	22	3
-input1.bam	FBtr0070603	F	23	10
-input1.bam	FBtr0070603	F	24	2
-input1.bam	FBtr0070603	F	25	5
-input1.bam	FBtr0070603	F	26	5
-input1.bam	FBtr0070603	F	27	3
-input1.bam	FBtr0070603	R	15	0
-input1.bam	FBtr0070603	R	16	0
-input1.bam	FBtr0070603	R	17	0
-input1.bam	FBtr0070603	R	18	0
-input1.bam	FBtr0070603	R	19	0
-input1.bam	FBtr0070603	R	20	0
-input1.bam	FBtr0070603	R	21	0
-input1.bam	FBtr0070603	R	22	0
-input1.bam	FBtr0070603	R	23	0
-input1.bam	FBtr0070603	R	24	0
-input1.bam	FBtr0070603	R	25	0
-input1.bam	FBtr0070603	R	26	0
-input1.bam	FBtr0070603	R	27	0
-input1.bam	FBtr0070604	F	15	2
-input1.bam	FBtr0070604	F	16	0
-input1.bam	FBtr0070604	F	17	0
-input1.bam	FBtr0070604	F	18	2
-input1.bam	FBtr0070604	F	19	2
-input1.bam	FBtr0070604	F	20	0
-input1.bam	FBtr0070604	F	21	1
-input1.bam	FBtr0070604	F	22	23
-input1.bam	FBtr0070604	F	23	10
-input1.bam	FBtr0070604	R	15	0
-input1.bam	FBtr0070604	R	16	0
-input1.bam	FBtr0070604	R	17	0
-input1.bam	FBtr0070604	R	18	0
-input1.bam	FBtr0070604	R	19	0
-input1.bam	FBtr0070604	R	20	0
-input1.bam	FBtr0070604	R	21	0
-input1.bam	FBtr0070604	R	22	0
-input1.bam	FBtr0070604	R	23	0
-input1.bam	FBtr0070911	F	15	1
-input1.bam	FBtr0070911	F	16	0
-input1.bam	FBtr0070911	F	17	0
-input1.bam	FBtr0070911	F	18	0
-input1.bam	FBtr0070911	F	19	0
-input1.bam	FBtr0070911	F	20	0
-input1.bam	FBtr0070911	F	21	1
-input1.bam	FBtr0070911	R	15	0
-input1.bam	FBtr0070911	R	16	0
-input1.bam	FBtr0070911	R	17	0
-input1.bam	FBtr0070911	R	18	0
-input1.bam	FBtr0070911	R	19	0
-input1.bam	FBtr0070911	R	20	0
-input1.bam	FBtr0070911	R	21	0
-input1.bam	FBtr0078490	F	15	3
-input1.bam	FBtr0078490	F	16	3
-input1.bam	FBtr0078490	F	17	0
-input1.bam	FBtr0078490	F	18	1
-input1.bam	FBtr0078490	F	19	0
-input1.bam	FBtr0078490	F	20	0
-input1.bam	FBtr0078490	F	21	0
-input1.bam	FBtr0078490	F	22	0
-input1.bam	FBtr0078490	F	23	1
-input1.bam	FBtr0078490	R	15	0
-input1.bam	FBtr0078490	R	16	0
-input1.bam	FBtr0078490	R	17	0
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-input1.bam	FBtr0078490	R	23	0
-input1.bam	FBtr0078580	F	15	592
-input1.bam	FBtr0078580	F	16	20
-input1.bam	FBtr0078580	F	17	31
-input1.bam	FBtr0078580	F	18	9
-input1.bam	FBtr0078580	F	19	8
-input1.bam	FBtr0078580	F	20	9
-input1.bam	FBtr0078580	F	21	5
-input1.bam	FBtr0078580	F	22	13
-input1.bam	FBtr0078580	F	23	5
-input1.bam	FBtr0078580	F	24	180
-input1.bam	FBtr0078580	F	25	212
-input1.bam	FBtr0078580	F	26	1
-input1.bam	FBtr0078580	F	27	2
-input1.bam	FBtr0078580	F	28	17
-input1.bam	FBtr0078580	R	15	0
-input1.bam	FBtr0078580	R	16	0
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-input1.bam	FBtr0078580	R	18	0
-input1.bam	FBtr0078580	R	19	0
-input1.bam	FBtr0078580	R	20	0
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-input1.bam	FBtr0078580	R	22	0
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-input1.bam	FBtr0078580	R	26	0
-input1.bam	FBtr0078580	R	27	0
-input1.bam	FBtr0078580	R	28	0
-input1.bam	FBtr0078790	F	15	2
-input1.bam	FBtr0078790	F	16	2
-input1.bam	FBtr0078790	F	17	1
-input1.bam	FBtr0078790	F	18	1
-input1.bam	FBtr0078790	F	19	2
-input1.bam	FBtr0078790	F	20	2
-input1.bam	FBtr0078790	F	21	0
-input1.bam	FBtr0078790	F	22	2
-input1.bam	FBtr0078790	F	23	1
-input1.bam	FBtr0078790	R	15	1
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-input1.bam	FBtr0078790	R	17	0
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-input1.bam	FBtr0079064	F	15	2
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-input1.bam	FBtr0079064	F	21	1
-input1.bam	FBtr0079064	R	15	0
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-input1.bam	FBtr0079090	F	15	1
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-input1.bam	FBtr0079090	F	18	1
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-input1.bam	FBtr0079090	F	23	0
-input1.bam	FBtr0079090	F	24	1
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-input1.bam	FBtr0079090	F	26	0
-input1.bam	FBtr0079090	F	27	0
-input1.bam	FBtr0079090	F	28	1
-input1.bam	FBtr0079090	R	15	0
-input1.bam	FBtr0079090	R	16	0
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-input1.bam	FBtr0079090	R	20	0
-input1.bam	FBtr0079090	R	21	1
-input1.bam	FBtr0079090	R	22	0
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diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/input1_yminneg5_5_single_plot_counts.pdf
Binary file test-data/input1_yminneg5_5_single_plot_counts.pdf has changed
diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/input_single_chr_x_6_single_plot_coverage.pdf
Binary file test-data/input_single_chr_x_6_single_plot_coverage.pdf has changed
diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/input_single_chr_x_6_single_plot_coverage.tab
--- a/test-data/input_single_chr_x_6_single_plot_coverage.tab	Wed Apr 10 06:38:33 2019 -0400
+++ b/test-data/input_single_chr_x_6_single_plot_coverage.tab	Sun Apr 14 14:43:44 2019 -0400
@@ -1,481 +1,13 @@
 Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Coverage
-input_single_chr.bam_0	1	80	1	F	1
-input_single_chr.bam_0	1	80	2	F	1
-input_single_chr.bam_0	1	80	3	F	1
-input_single_chr.bam_0	1	80	4	F	1
-input_single_chr.bam_0	1	80	5	F	1
-input_single_chr.bam_0	1	80	6	F	1
-input_single_chr.bam_0	1	80	7	F	1
-input_single_chr.bam_0	1	80	8	F	1
-input_single_chr.bam_0	1	80	9	F	1
-input_single_chr.bam_0	1	80	10	F	1
-input_single_chr.bam_0	1	80	11	F	1
-input_single_chr.bam_0	1	80	12	F	1
-input_single_chr.bam_0	1	80	13	F	1
-input_single_chr.bam_0	1	80	14	F	1
-input_single_chr.bam_0	1	80	15	F	1
-input_single_chr.bam_0	1	80	16	F	1
-input_single_chr.bam_0	1	80	17	F	1
-input_single_chr.bam_0	1	80	18	F	1
-input_single_chr.bam_0	1	80	19	F	1
-input_single_chr.bam_0	1	80	20	F	1
-input_single_chr.bam_0	1	80	21	F	1
-input_single_chr.bam_0	1	80	22	F	1
-input_single_chr.bam_0	1	80	23	F	1
-input_single_chr.bam_0	1	80	24	F	1
-input_single_chr.bam_0	1	80	25	F	1
-input_single_chr.bam_0	1	80	26	F	1
-input_single_chr.bam_0	1	80	27	F	1
-input_single_chr.bam_0	1	80	28	F	1
-input_single_chr.bam_0	1	80	29	F	1
-input_single_chr.bam_0	1	80	30	F	1
-input_single_chr.bam_0	1	80	31	F	1
-input_single_chr.bam_0	1	80	32	F	1
-input_single_chr.bam_0	1	80	33	F	1
-input_single_chr.bam_0	1	80	34	F	1
-input_single_chr.bam_0	1	80	35	F	1
-input_single_chr.bam_0	1	80	36	F	1
-input_single_chr.bam_0	1	80	37	F	1
-input_single_chr.bam_0	1	80	38	F	1
-input_single_chr.bam_0	1	80	39	F	1
-input_single_chr.bam_0	1	80	40	F	1
-input_single_chr.bam_0	1	80	41	F	1
-input_single_chr.bam_0	1	80	42	F	1
-input_single_chr.bam_0	1	80	43	F	1
-input_single_chr.bam_0	1	80	44	F	1
-input_single_chr.bam_0	1	80	45	F	1
-input_single_chr.bam_0	1	80	46	F	1
-input_single_chr.bam_0	1	80	47	F	1
-input_single_chr.bam_0	1	80	48	F	1
-input_single_chr.bam_0	1	80	49	F	1
-input_single_chr.bam_0	1	80	50	F	1
-input_single_chr.bam_0	1	80	51	F	1
-input_single_chr.bam_0	1	80	52	F	1
-input_single_chr.bam_0	1	80	53	F	1
-input_single_chr.bam_0	1	80	54	F	1
-input_single_chr.bam_0	1	80	55	F	1
-input_single_chr.bam_0	1	80	56	F	1
-input_single_chr.bam_0	1	80	57	F	1
-input_single_chr.bam_0	1	80	58	F	1
-input_single_chr.bam_0	1	80	59	F	1
-input_single_chr.bam_0	1	80	60	F	1
-input_single_chr.bam_0	1	80	61	F	1
-input_single_chr.bam_0	1	80	62	F	1
-input_single_chr.bam_0	1	80	63	F	1
-input_single_chr.bam_0	1	80	64	F	1
-input_single_chr.bam_0	1	80	65	F	1
-input_single_chr.bam_0	1	80	66	F	1
-input_single_chr.bam_0	1	80	67	F	1
-input_single_chr.bam_0	1	80	68	F	1
-input_single_chr.bam_0	1	80	69	F	1
-input_single_chr.bam_0	1	80	70	F	1
-input_single_chr.bam_0	1	80	71	F	1
-input_single_chr.bam_0	1	80	72	F	1
-input_single_chr.bam_0	1	80	73	F	1
-input_single_chr.bam_0	1	80	74	F	1
-input_single_chr.bam_0	1	80	75	F	1
-input_single_chr.bam_0	1	80	76	F	1
-input_single_chr.bam_0	1	80	77	F	1
-input_single_chr.bam_0	1	80	78	F	1
-input_single_chr.bam_0	1	80	79	F	1
-input_single_chr.bam_0	1	80	80	F	1
-input_single_chr.bam_1	1	80	1	F	1
-input_single_chr.bam_1	1	80	2	F	1
-input_single_chr.bam_1	1	80	3	F	1
-input_single_chr.bam_1	1	80	4	F	1
-input_single_chr.bam_1	1	80	5	F	1
-input_single_chr.bam_1	1	80	6	F	1
-input_single_chr.bam_1	1	80	7	F	1
-input_single_chr.bam_1	1	80	8	F	1
-input_single_chr.bam_1	1	80	9	F	1
-input_single_chr.bam_1	1	80	10	F	1
-input_single_chr.bam_1	1	80	11	F	1
-input_single_chr.bam_1	1	80	12	F	1
-input_single_chr.bam_1	1	80	13	F	1
-input_single_chr.bam_1	1	80	14	F	1
-input_single_chr.bam_1	1	80	15	F	1
-input_single_chr.bam_1	1	80	16	F	1
-input_single_chr.bam_1	1	80	17	F	1
-input_single_chr.bam_1	1	80	18	F	1
-input_single_chr.bam_1	1	80	19	F	1
-input_single_chr.bam_1	1	80	20	F	1
-input_single_chr.bam_1	1	80	21	F	1
-input_single_chr.bam_1	1	80	22	F	1
-input_single_chr.bam_1	1	80	23	F	1
-input_single_chr.bam_1	1	80	24	F	1
-input_single_chr.bam_1	1	80	25	F	1
-input_single_chr.bam_1	1	80	26	F	1
-input_single_chr.bam_1	1	80	27	F	1
-input_single_chr.bam_1	1	80	28	F	1
-input_single_chr.bam_1	1	80	29	F	1
-input_single_chr.bam_1	1	80	30	F	1
-input_single_chr.bam_1	1	80	31	F	1
-input_single_chr.bam_1	1	80	32	F	1
-input_single_chr.bam_1	1	80	33	F	1
-input_single_chr.bam_1	1	80	34	F	1
-input_single_chr.bam_1	1	80	35	F	1
-input_single_chr.bam_1	1	80	36	F	1
-input_single_chr.bam_1	1	80	37	F	1
-input_single_chr.bam_1	1	80	38	F	1
-input_single_chr.bam_1	1	80	39	F	1
-input_single_chr.bam_1	1	80	40	F	1
-input_single_chr.bam_1	1	80	41	F	1
-input_single_chr.bam_1	1	80	42	F	1
-input_single_chr.bam_1	1	80	43	F	1
-input_single_chr.bam_1	1	80	44	F	1
-input_single_chr.bam_1	1	80	45	F	1
-input_single_chr.bam_1	1	80	46	F	1
-input_single_chr.bam_1	1	80	47	F	1
-input_single_chr.bam_1	1	80	48	F	1
-input_single_chr.bam_1	1	80	49	F	1
-input_single_chr.bam_1	1	80	50	F	1
-input_single_chr.bam_1	1	80	51	F	1
-input_single_chr.bam_1	1	80	52	F	1
-input_single_chr.bam_1	1	80	53	F	1
-input_single_chr.bam_1	1	80	54	F	1
-input_single_chr.bam_1	1	80	55	F	1
-input_single_chr.bam_1	1	80	56	F	1
-input_single_chr.bam_1	1	80	57	F	1
-input_single_chr.bam_1	1	80	58	F	1
-input_single_chr.bam_1	1	80	59	F	1
-input_single_chr.bam_1	1	80	60	F	1
-input_single_chr.bam_1	1	80	61	F	1
-input_single_chr.bam_1	1	80	62	F	1
-input_single_chr.bam_1	1	80	63	F	1
-input_single_chr.bam_1	1	80	64	F	1
-input_single_chr.bam_1	1	80	65	F	1
-input_single_chr.bam_1	1	80	66	F	1
-input_single_chr.bam_1	1	80	67	F	1
-input_single_chr.bam_1	1	80	68	F	1
-input_single_chr.bam_1	1	80	69	F	1
-input_single_chr.bam_1	1	80	70	F	1
-input_single_chr.bam_1	1	80	71	F	1
-input_single_chr.bam_1	1	80	72	F	1
-input_single_chr.bam_1	1	80	73	F	1
-input_single_chr.bam_1	1	80	74	F	1
-input_single_chr.bam_1	1	80	75	F	1
-input_single_chr.bam_1	1	80	76	F	1
-input_single_chr.bam_1	1	80	77	F	1
-input_single_chr.bam_1	1	80	78	F	1
-input_single_chr.bam_1	1	80	79	F	1
-input_single_chr.bam_1	1	80	80	F	1
-input_single_chr.bam_2	1	80	1	F	1
-input_single_chr.bam_2	1	80	2	F	1
-input_single_chr.bam_2	1	80	3	F	1
-input_single_chr.bam_2	1	80	4	F	1
-input_single_chr.bam_2	1	80	5	F	1
-input_single_chr.bam_2	1	80	6	F	1
-input_single_chr.bam_2	1	80	7	F	1
-input_single_chr.bam_2	1	80	8	F	1
-input_single_chr.bam_2	1	80	9	F	1
-input_single_chr.bam_2	1	80	10	F	1
-input_single_chr.bam_2	1	80	11	F	1
-input_single_chr.bam_2	1	80	12	F	1
-input_single_chr.bam_2	1	80	13	F	1
-input_single_chr.bam_2	1	80	14	F	1
-input_single_chr.bam_2	1	80	15	F	1
-input_single_chr.bam_2	1	80	16	F	1
-input_single_chr.bam_2	1	80	17	F	1
-input_single_chr.bam_2	1	80	18	F	1
-input_single_chr.bam_2	1	80	19	F	1
-input_single_chr.bam_2	1	80	20	F	1
-input_single_chr.bam_2	1	80	21	F	1
-input_single_chr.bam_2	1	80	22	F	1
-input_single_chr.bam_2	1	80	23	F	1
-input_single_chr.bam_2	1	80	24	F	1
-input_single_chr.bam_2	1	80	25	F	1
-input_single_chr.bam_2	1	80	26	F	1
-input_single_chr.bam_2	1	80	27	F	1
-input_single_chr.bam_2	1	80	28	F	1
-input_single_chr.bam_2	1	80	29	F	1
-input_single_chr.bam_2	1	80	30	F	1
-input_single_chr.bam_2	1	80	31	F	1
-input_single_chr.bam_2	1	80	32	F	1
-input_single_chr.bam_2	1	80	33	F	1
-input_single_chr.bam_2	1	80	34	F	1
-input_single_chr.bam_2	1	80	35	F	1
-input_single_chr.bam_2	1	80	36	F	1
-input_single_chr.bam_2	1	80	37	F	1
-input_single_chr.bam_2	1	80	38	F	1
-input_single_chr.bam_2	1	80	39	F	1
-input_single_chr.bam_2	1	80	40	F	1
-input_single_chr.bam_2	1	80	41	F	1
-input_single_chr.bam_2	1	80	42	F	1
-input_single_chr.bam_2	1	80	43	F	1
-input_single_chr.bam_2	1	80	44	F	1
-input_single_chr.bam_2	1	80	45	F	1
-input_single_chr.bam_2	1	80	46	F	1
-input_single_chr.bam_2	1	80	47	F	1
-input_single_chr.bam_2	1	80	48	F	1
-input_single_chr.bam_2	1	80	49	F	1
-input_single_chr.bam_2	1	80	50	F	1
-input_single_chr.bam_2	1	80	51	F	1
-input_single_chr.bam_2	1	80	52	F	1
-input_single_chr.bam_2	1	80	53	F	1
-input_single_chr.bam_2	1	80	54	F	1
-input_single_chr.bam_2	1	80	55	F	1
-input_single_chr.bam_2	1	80	56	F	1
-input_single_chr.bam_2	1	80	57	F	1
-input_single_chr.bam_2	1	80	58	F	1
-input_single_chr.bam_2	1	80	59	F	1
-input_single_chr.bam_2	1	80	60	F	1
-input_single_chr.bam_2	1	80	61	F	1
-input_single_chr.bam_2	1	80	62	F	1
-input_single_chr.bam_2	1	80	63	F	1
-input_single_chr.bam_2	1	80	64	F	1
-input_single_chr.bam_2	1	80	65	F	1
-input_single_chr.bam_2	1	80	66	F	1
-input_single_chr.bam_2	1	80	67	F	1
-input_single_chr.bam_2	1	80	68	F	1
-input_single_chr.bam_2	1	80	69	F	1
-input_single_chr.bam_2	1	80	70	F	1
-input_single_chr.bam_2	1	80	71	F	1
-input_single_chr.bam_2	1	80	72	F	1
-input_single_chr.bam_2	1	80	73	F	1
-input_single_chr.bam_2	1	80	74	F	1
-input_single_chr.bam_2	1	80	75	F	1
-input_single_chr.bam_2	1	80	76	F	1
-input_single_chr.bam_2	1	80	77	F	1
-input_single_chr.bam_2	1	80	78	F	1
-input_single_chr.bam_2	1	80	79	F	1
-input_single_chr.bam_2	1	80	80	F	1
-input_single_chr.bam_3	1	80	1	F	1
-input_single_chr.bam_3	1	80	2	F	1
-input_single_chr.bam_3	1	80	3	F	1
-input_single_chr.bam_3	1	80	4	F	1
-input_single_chr.bam_3	1	80	5	F	1
-input_single_chr.bam_3	1	80	6	F	1
-input_single_chr.bam_3	1	80	7	F	1
-input_single_chr.bam_3	1	80	8	F	1
-input_single_chr.bam_3	1	80	9	F	1
-input_single_chr.bam_3	1	80	10	F	1
-input_single_chr.bam_3	1	80	11	F	1
-input_single_chr.bam_3	1	80	12	F	1
-input_single_chr.bam_3	1	80	13	F	1
-input_single_chr.bam_3	1	80	14	F	1
-input_single_chr.bam_3	1	80	15	F	1
-input_single_chr.bam_3	1	80	16	F	1
-input_single_chr.bam_3	1	80	17	F	1
-input_single_chr.bam_3	1	80	18	F	1
-input_single_chr.bam_3	1	80	19	F	1
-input_single_chr.bam_3	1	80	20	F	1
-input_single_chr.bam_3	1	80	21	F	1
-input_single_chr.bam_3	1	80	22	F	1
-input_single_chr.bam_3	1	80	23	F	1
-input_single_chr.bam_3	1	80	24	F	1
-input_single_chr.bam_3	1	80	25	F	1
-input_single_chr.bam_3	1	80	26	F	1
-input_single_chr.bam_3	1	80	27	F	1
-input_single_chr.bam_3	1	80	28	F	1
-input_single_chr.bam_3	1	80	29	F	1
-input_single_chr.bam_3	1	80	30	F	1
-input_single_chr.bam_3	1	80	31	F	1
-input_single_chr.bam_3	1	80	32	F	1
-input_single_chr.bam_3	1	80	33	F	1
-input_single_chr.bam_3	1	80	34	F	1
-input_single_chr.bam_3	1	80	35	F	1
-input_single_chr.bam_3	1	80	36	F	1
-input_single_chr.bam_3	1	80	37	F	1
-input_single_chr.bam_3	1	80	38	F	1
-input_single_chr.bam_3	1	80	39	F	1
-input_single_chr.bam_3	1	80	40	F	1
-input_single_chr.bam_3	1	80	41	F	1
-input_single_chr.bam_3	1	80	42	F	1
-input_single_chr.bam_3	1	80	43	F	1
-input_single_chr.bam_3	1	80	44	F	1
-input_single_chr.bam_3	1	80	45	F	1
-input_single_chr.bam_3	1	80	46	F	1
-input_single_chr.bam_3	1	80	47	F	1
-input_single_chr.bam_3	1	80	48	F	1
-input_single_chr.bam_3	1	80	49	F	1
-input_single_chr.bam_3	1	80	50	F	1
-input_single_chr.bam_3	1	80	51	F	1
-input_single_chr.bam_3	1	80	52	F	1
-input_single_chr.bam_3	1	80	53	F	1
-input_single_chr.bam_3	1	80	54	F	1
-input_single_chr.bam_3	1	80	55	F	1
-input_single_chr.bam_3	1	80	56	F	1
-input_single_chr.bam_3	1	80	57	F	1
-input_single_chr.bam_3	1	80	58	F	1
-input_single_chr.bam_3	1	80	59	F	1
-input_single_chr.bam_3	1	80	60	F	1
-input_single_chr.bam_3	1	80	61	F	1
-input_single_chr.bam_3	1	80	62	F	1
-input_single_chr.bam_3	1	80	63	F	1
-input_single_chr.bam_3	1	80	64	F	1
-input_single_chr.bam_3	1	80	65	F	1
-input_single_chr.bam_3	1	80	66	F	1
-input_single_chr.bam_3	1	80	67	F	1
-input_single_chr.bam_3	1	80	68	F	1
-input_single_chr.bam_3	1	80	69	F	1
-input_single_chr.bam_3	1	80	70	F	1
-input_single_chr.bam_3	1	80	71	F	1
-input_single_chr.bam_3	1	80	72	F	1
-input_single_chr.bam_3	1	80	73	F	1
-input_single_chr.bam_3	1	80	74	F	1
-input_single_chr.bam_3	1	80	75	F	1
-input_single_chr.bam_3	1	80	76	F	1
-input_single_chr.bam_3	1	80	77	F	1
-input_single_chr.bam_3	1	80	78	F	1
-input_single_chr.bam_3	1	80	79	F	1
-input_single_chr.bam_3	1	80	80	F	1
-input_single_chr.bam_4	1	80	1	F	1
-input_single_chr.bam_4	1	80	2	F	1
-input_single_chr.bam_4	1	80	3	F	1
-input_single_chr.bam_4	1	80	4	F	1
-input_single_chr.bam_4	1	80	5	F	1
-input_single_chr.bam_4	1	80	6	F	1
-input_single_chr.bam_4	1	80	7	F	1
-input_single_chr.bam_4	1	80	8	F	1
-input_single_chr.bam_4	1	80	9	F	1
-input_single_chr.bam_4	1	80	10	F	1
-input_single_chr.bam_4	1	80	11	F	1
-input_single_chr.bam_4	1	80	12	F	1
-input_single_chr.bam_4	1	80	13	F	1
-input_single_chr.bam_4	1	80	14	F	1
-input_single_chr.bam_4	1	80	15	F	1
-input_single_chr.bam_4	1	80	16	F	1
-input_single_chr.bam_4	1	80	17	F	1
-input_single_chr.bam_4	1	80	18	F	1
-input_single_chr.bam_4	1	80	19	F	1
-input_single_chr.bam_4	1	80	20	F	1
-input_single_chr.bam_4	1	80	21	F	1
-input_single_chr.bam_4	1	80	22	F	1
-input_single_chr.bam_4	1	80	23	F	1
-input_single_chr.bam_4	1	80	24	F	1
-input_single_chr.bam_4	1	80	25	F	1
-input_single_chr.bam_4	1	80	26	F	1
-input_single_chr.bam_4	1	80	27	F	1
-input_single_chr.bam_4	1	80	28	F	1
-input_single_chr.bam_4	1	80	29	F	1
-input_single_chr.bam_4	1	80	30	F	1
-input_single_chr.bam_4	1	80	31	F	1
-input_single_chr.bam_4	1	80	32	F	1
-input_single_chr.bam_4	1	80	33	F	1
-input_single_chr.bam_4	1	80	34	F	1
-input_single_chr.bam_4	1	80	35	F	1
-input_single_chr.bam_4	1	80	36	F	1
-input_single_chr.bam_4	1	80	37	F	1
-input_single_chr.bam_4	1	80	38	F	1
-input_single_chr.bam_4	1	80	39	F	1
-input_single_chr.bam_4	1	80	40	F	1
-input_single_chr.bam_4	1	80	41	F	1
-input_single_chr.bam_4	1	80	42	F	1
-input_single_chr.bam_4	1	80	43	F	1
-input_single_chr.bam_4	1	80	44	F	1
-input_single_chr.bam_4	1	80	45	F	1
-input_single_chr.bam_4	1	80	46	F	1
-input_single_chr.bam_4	1	80	47	F	1
-input_single_chr.bam_4	1	80	48	F	1
-input_single_chr.bam_4	1	80	49	F	1
-input_single_chr.bam_4	1	80	50	F	1
-input_single_chr.bam_4	1	80	51	F	1
-input_single_chr.bam_4	1	80	52	F	1
-input_single_chr.bam_4	1	80	53	F	1
-input_single_chr.bam_4	1	80	54	F	1
-input_single_chr.bam_4	1	80	55	F	1
-input_single_chr.bam_4	1	80	56	F	1
-input_single_chr.bam_4	1	80	57	F	1
-input_single_chr.bam_4	1	80	58	F	1
-input_single_chr.bam_4	1	80	59	F	1
-input_single_chr.bam_4	1	80	60	F	1
-input_single_chr.bam_4	1	80	61	F	1
-input_single_chr.bam_4	1	80	62	F	1
-input_single_chr.bam_4	1	80	63	F	1
-input_single_chr.bam_4	1	80	64	F	1
-input_single_chr.bam_4	1	80	65	F	1
-input_single_chr.bam_4	1	80	66	F	1
-input_single_chr.bam_4	1	80	67	F	1
-input_single_chr.bam_4	1	80	68	F	1
-input_single_chr.bam_4	1	80	69	F	1
-input_single_chr.bam_4	1	80	70	F	1
-input_single_chr.bam_4	1	80	71	F	1
-input_single_chr.bam_4	1	80	72	F	1
-input_single_chr.bam_4	1	80	73	F	1
-input_single_chr.bam_4	1	80	74	F	1
-input_single_chr.bam_4	1	80	75	F	1
-input_single_chr.bam_4	1	80	76	F	1
-input_single_chr.bam_4	1	80	77	F	1
-input_single_chr.bam_4	1	80	78	F	1
-input_single_chr.bam_4	1	80	79	F	1
-input_single_chr.bam_4	1	80	80	F	1
-input_single_chr.bam_5	1	80	1	F	1
-input_single_chr.bam_5	1	80	2	F	1
-input_single_chr.bam_5	1	80	3	F	1
-input_single_chr.bam_5	1	80	4	F	1
-input_single_chr.bam_5	1	80	5	F	1
-input_single_chr.bam_5	1	80	6	F	1
-input_single_chr.bam_5	1	80	7	F	1
-input_single_chr.bam_5	1	80	8	F	1
-input_single_chr.bam_5	1	80	9	F	1
-input_single_chr.bam_5	1	80	10	F	1
-input_single_chr.bam_5	1	80	11	F	1
-input_single_chr.bam_5	1	80	12	F	1
-input_single_chr.bam_5	1	80	13	F	1
-input_single_chr.bam_5	1	80	14	F	1
-input_single_chr.bam_5	1	80	15	F	1
-input_single_chr.bam_5	1	80	16	F	1
-input_single_chr.bam_5	1	80	17	F	1
-input_single_chr.bam_5	1	80	18	F	1
-input_single_chr.bam_5	1	80	19	F	1
-input_single_chr.bam_5	1	80	20	F	1
-input_single_chr.bam_5	1	80	21	F	1
-input_single_chr.bam_5	1	80	22	F	1
-input_single_chr.bam_5	1	80	23	F	1
-input_single_chr.bam_5	1	80	24	F	1
-input_single_chr.bam_5	1	80	25	F	1
-input_single_chr.bam_5	1	80	26	F	1
-input_single_chr.bam_5	1	80	27	F	1
-input_single_chr.bam_5	1	80	28	F	1
-input_single_chr.bam_5	1	80	29	F	1
-input_single_chr.bam_5	1	80	30	F	1
-input_single_chr.bam_5	1	80	31	F	1
-input_single_chr.bam_5	1	80	32	F	1
-input_single_chr.bam_5	1	80	33	F	1
-input_single_chr.bam_5	1	80	34	F	1
-input_single_chr.bam_5	1	80	35	F	1
-input_single_chr.bam_5	1	80	36	F	1
-input_single_chr.bam_5	1	80	37	F	1
-input_single_chr.bam_5	1	80	38	F	1
-input_single_chr.bam_5	1	80	39	F	1
-input_single_chr.bam_5	1	80	40	F	1
-input_single_chr.bam_5	1	80	41	F	1
-input_single_chr.bam_5	1	80	42	F	1
-input_single_chr.bam_5	1	80	43	F	1
-input_single_chr.bam_5	1	80	44	F	1
-input_single_chr.bam_5	1	80	45	F	1
-input_single_chr.bam_5	1	80	46	F	1
-input_single_chr.bam_5	1	80	47	F	1
-input_single_chr.bam_5	1	80	48	F	1
-input_single_chr.bam_5	1	80	49	F	1
-input_single_chr.bam_5	1	80	50	F	1
-input_single_chr.bam_5	1	80	51	F	1
-input_single_chr.bam_5	1	80	52	F	1
-input_single_chr.bam_5	1	80	53	F	1
-input_single_chr.bam_5	1	80	54	F	1
-input_single_chr.bam_5	1	80	55	F	1
-input_single_chr.bam_5	1	80	56	F	1
-input_single_chr.bam_5	1	80	57	F	1
-input_single_chr.bam_5	1	80	58	F	1
-input_single_chr.bam_5	1	80	59	F	1
-input_single_chr.bam_5	1	80	60	F	1
-input_single_chr.bam_5	1	80	61	F	1
-input_single_chr.bam_5	1	80	62	F	1
-input_single_chr.bam_5	1	80	63	F	1
-input_single_chr.bam_5	1	80	64	F	1
-input_single_chr.bam_5	1	80	65	F	1
-input_single_chr.bam_5	1	80	66	F	1
-input_single_chr.bam_5	1	80	67	F	1
-input_single_chr.bam_5	1	80	68	F	1
-input_single_chr.bam_5	1	80	69	F	1
-input_single_chr.bam_5	1	80	70	F	1
-input_single_chr.bam_5	1	80	71	F	1
-input_single_chr.bam_5	1	80	72	F	1
-input_single_chr.bam_5	1	80	73	F	1
-input_single_chr.bam_5	1	80	74	F	1
-input_single_chr.bam_5	1	80	75	F	1
-input_single_chr.bam_5	1	80	76	F	1
-input_single_chr.bam_5	1	80	77	F	1
-input_single_chr.bam_5	1	80	78	F	1
-input_single_chr.bam_5	1	80	79	F	1
-input_single_chr.bam_5	1	80	80	F	1
+input_single_chr.bam_0	1	80	1	F	0
+input_single_chr.bam_0	1	80	80	F	0
+input_single_chr.bam_1	1	80	1	F	0
+input_single_chr.bam_1	1	80	80	F	0
+input_single_chr.bam_2	1	80	1	F	0
+input_single_chr.bam_2	1	80	80	F	0
+input_single_chr.bam_3	1	80	1	F	0
+input_single_chr.bam_3	1	80	80	F	0
+input_single_chr.bam_4	1	80	1	F	0
+input_single_chr.bam_4	1	80	80	F	0
+input_single_chr.bam_5	1	80	1	F	0
+input_single_chr.bam_5	1	80	80	F	0
diff -r 07aa8f928d4b -r 376fae7c9f32 test-data/size.tab
--- a/test-data/size.tab	Wed Apr 10 06:38:33 2019 -0400
+++ b/test-data/size.tab	Sun Apr 14 14:43:44 2019 -0400
@@ -1,1045 +1,694 @@
 Dataset	Chromosome	Polarity	Size	Counts	Strandness	z-score
-input1.bam	FBtr0070001	F	16	2	1.0	-0.476603123819
-input1.bam	FBtr0070001	F	17	1	1.0	-0.586588460085
-input1.bam	FBtr0070001	F	18	0	1.0	-0.696573796351
-input1.bam	FBtr0070001	F	19	1	1.0	-0.586588460085
-input1.bam	FBtr0070001	F	20	4	1.0	-0.256632451287
-input1.bam	FBtr0070001	F	21	4	1.0	-0.256632451287
-input1.bam	FBtr0070001	F	22	29	1.0	2.49300095536
-input1.bam	FBtr0070001	F	23	15	1.0	0.953206247639
-input1.bam	FBtr0070001	F	24	1	1.0	-0.586588460085
-input1.bam	FBtr0070001	R	16	0	1.0	-0.476603123819
-input1.bam	FBtr0070001	R	17	0	1.0	-0.586588460085
-input1.bam	FBtr0070001	R	18	0	1.0	-0.696573796351
-input1.bam	FBtr0070001	R	19	0	1.0	-0.586588460085
-input1.bam	FBtr0070001	R	20	0	1.0	-0.256632451287
-input1.bam	FBtr0070001	R	21	0	1.0	-0.256632451287
-input1.bam	FBtr0070001	R	22	0	1.0	2.49300095536
-input1.bam	FBtr0070001	R	23	0	1.0	0.953206247639
-input1.bam	FBtr0070001	R	24	0	1.0	-0.586588460085
-input1.bam	FBtr0070533	F	15	2	1.0	-0.114707866935
-input1.bam	FBtr0070533	F	16	1	1.0	-0.745601135079
-input1.bam	FBtr0070533	F	17	1	1.0	-0.745601135079
-input1.bam	FBtr0070533	F	18	6	1.0	2.40886520564
-input1.bam	FBtr0070533	F	19	3	1.0	0.516185401209
-input1.bam	FBtr0070533	F	20	2	1.0	-0.114707866935
-input1.bam	FBtr0070533	F	21	2	1.0	-0.114707866935
-input1.bam	FBtr0070533	F	22	4	1.0	1.14707866935
-input1.bam	FBtr0070533	F	23	2	1.0	-0.114707866935
-input1.bam	FBtr0070533	F	24	0	1.0	-1.37649440322
-input1.bam	FBtr0070533	F	25	1	1.0	-0.745601135079
-input1.bam	FBtr0070533	R	15	0	1.0	-0.114707866935
-input1.bam	FBtr0070533	R	16	0	1.0	-0.745601135079
-input1.bam	FBtr0070533	R	17	0	1.0	-0.745601135079
-input1.bam	FBtr0070533	R	18	0	1.0	2.40886520564
-input1.bam	FBtr0070533	R	19	0	1.0	0.516185401209
-input1.bam	FBtr0070533	R	20	0	1.0	-0.114707866935
-input1.bam	FBtr0070533	R	21	0	1.0	-0.114707866935
-input1.bam	FBtr0070533	R	22	0	1.0	1.14707866935
-input1.bam	FBtr0070533	R	23	0	1.0	-0.114707866935
-input1.bam	FBtr0070533	R	24	0	1.0	-1.37649440322
-input1.bam	FBtr0070533	R	25	0	1.0	-0.745601135079
-input1.bam	FBtr0070603	F	15	9	1.0	1.25973222843
-input1.bam	FBtr0070603	F	16	6	1.0	0.214422506968
-input1.bam	FBtr0070603	F	17	10	1.0	1.60816880226
-input1.bam	FBtr0070603	F	18	7	1.0	0.56285908079
-input1.bam	FBtr0070603	F	19	1	1.0	-1.52776036214
-input1.bam	FBtr0070603	F	20	6	1.0	0.214422506968
-input1.bam	FBtr0070603	F	21	3	1.0	-0.830887214499
-input1.bam	FBtr0070603	F	22	3	1.0	-0.830887214499
-input1.bam	FBtr0070603	F	23	10	1.0	1.60816880226
-input1.bam	FBtr0070603	F	24	2	1.0	-1.17932378832
-input1.bam	FBtr0070603	F	25	5	1.0	-0.134014066855
-input1.bam	FBtr0070603	F	26	5	1.0	-0.134014066855
-input1.bam	FBtr0070603	F	27	3	1.0	-0.830887214499
-input1.bam	FBtr0070603	R	15	0	1.0	1.25973222843
-input1.bam	FBtr0070603	R	16	0	1.0	0.214422506968
-input1.bam	FBtr0070603	R	17	0	1.0	1.60816880226
-input1.bam	FBtr0070603	R	18	0	1.0	0.56285908079
-input1.bam	FBtr0070603	R	19	0	1.0	-1.52776036214
-input1.bam	FBtr0070603	R	20	0	1.0	0.214422506968
-input1.bam	FBtr0070603	R	21	0	1.0	-0.830887214499
-input1.bam	FBtr0070603	R	22	0	1.0	-0.830887214499
-input1.bam	FBtr0070603	R	23	0	1.0	1.60816880226
-input1.bam	FBtr0070603	R	24	0	1.0	-1.17932378832
-input1.bam	FBtr0070603	R	25	0	1.0	-0.134014066855
-input1.bam	FBtr0070603	R	26	0	1.0	-0.134014066855
-input1.bam	FBtr0070603	R	27	0	1.0	-0.830887214499
-input1.bam	FBtr0070604	F	15	2	1.0	-0.340359959259
-input1.bam	FBtr0070604	F	16	0	1.0	-0.618836289562
-input1.bam	FBtr0070604	F	17	0	1.0	-0.618836289562
-input1.bam	FBtr0070604	F	18	2	1.0	-0.340359959259
-input1.bam	FBtr0070604	F	19	2	1.0	-0.340359959259
-input1.bam	FBtr0070604	F	20	0	1.0	-0.618836289562
-input1.bam	FBtr0070604	F	21	1	1.0	-0.479598124411
-input1.bam	FBtr0070604	F	22	23	1.0	2.58364150892
-input1.bam	FBtr0070604	F	23	10	1.0	0.773545361953
-input1.bam	FBtr0070604	R	15	0	1.0	-0.340359959259
-input1.bam	FBtr0070604	R	16	0	1.0	-0.618836289562
-input1.bam	FBtr0070604	R	17	0	1.0	-0.618836289562
-input1.bam	FBtr0070604	R	18	0	1.0	-0.340359959259
-input1.bam	FBtr0070604	R	19	0	1.0	-0.340359959259
-input1.bam	FBtr0070604	R	20	0	1.0	-0.618836289562
-input1.bam	FBtr0070604	R	21	0	1.0	-0.479598124411
-input1.bam	FBtr0070604	R	22	0	1.0	2.58364150892
-input1.bam	FBtr0070604	R	23	0	1.0	0.773545361953
-input1.bam	FBtr0070911	F	15	1	1.0	1.58113883008
-input1.bam	FBtr0070911	F	16	0	1.0	-0.632455532034
-input1.bam	FBtr0070911	F	17	0	1.0	-0.632455532034
-input1.bam	FBtr0070911	F	18	0	1.0	-0.632455532034
-input1.bam	FBtr0070911	F	19	0	1.0	-0.632455532034
-input1.bam	FBtr0070911	F	20	0	1.0	-0.632455532034
-input1.bam	FBtr0070911	F	21	1	1.0	1.58113883008
-input1.bam	FBtr0070911	R	15	0	1.0	1.58113883008
-input1.bam	FBtr0070911	R	16	0	1.0	-0.632455532034
-input1.bam	FBtr0070911	R	17	0	1.0	-0.632455532034
-input1.bam	FBtr0070911	R	18	0	1.0	-0.632455532034
-input1.bam	FBtr0070911	R	19	0	1.0	-0.632455532034
-input1.bam	FBtr0070911	R	20	0	1.0	-0.632455532034
-input1.bam	FBtr0070911	R	21	0	1.0	1.58113883008
-input1.bam	FBtr0078490	F	15	3	1.0	1.76410571268
-input1.bam	FBtr0078490	F	16	3	1.0	1.76410571268
-input1.bam	FBtr0078490	F	17	0	1.0	-0.742781352708
-input1.bam	FBtr0078490	F	18	1	1.0	0.0928476690885
-input1.bam	FBtr0078490	F	19	0	1.0	-0.742781352708
-input1.bam	FBtr0078490	F	20	0	1.0	-0.742781352708
-input1.bam	FBtr0078490	F	21	0	1.0	-0.742781352708
-input1.bam	FBtr0078490	F	22	0	1.0	-0.742781352708
-input1.bam	FBtr0078490	F	23	1	1.0	0.0928476690885
-input1.bam	FBtr0078490	R	15	0	1.0	1.76410571268
-input1.bam	FBtr0078490	R	16	0	1.0	1.76410571268
-input1.bam	FBtr0078490	R	17	0	1.0	-0.742781352708
-input1.bam	FBtr0078490	R	18	0	1.0	0.0928476690885
-input1.bam	FBtr0078490	R	19	0	1.0	-0.742781352708
-input1.bam	FBtr0078490	R	20	0	1.0	-0.742781352708
-input1.bam	FBtr0078490	R	21	0	1.0	-0.742781352708
-input1.bam	FBtr0078490	R	22	0	1.0	-0.742781352708
-input1.bam	FBtr0078490	R	23	0	1.0	0.0928476690885
-input1.bam	FBtr0078580	F	15	592	1.0	3.27906790103
-input1.bam	FBtr0078580	F	16	20	1.0	-0.376106897334
-input1.bam	FBtr0078580	F	17	31	1.0	-0.305815074288
-input1.bam	FBtr0078580	F	18	9	1.0	-0.446398720379
-input1.bam	FBtr0078580	F	19	8	1.0	-0.45278888611
-input1.bam	FBtr0078580	F	20	9	1.0	-0.446398720379
-input1.bam	FBtr0078580	F	21	5	1.0	-0.471959383305
-input1.bam	FBtr0078580	F	22	13	1.0	-0.420838057453
-input1.bam	FBtr0078580	F	23	5	1.0	-0.471959383305
-input1.bam	FBtr0078580	F	24	180	1.0	0.64631961969
-input1.bam	FBtr0078580	F	25	212	1.0	0.850804923095
-input1.bam	FBtr0078580	F	26	1	1.0	-0.49752004623
-input1.bam	FBtr0078580	F	27	2	1.0	-0.491129880499
-input1.bam	FBtr0078580	F	28	17	1.0	-0.395277394528
-input1.bam	FBtr0078580	R	15	0	1.0	3.27906790103
-input1.bam	FBtr0078580	R	16	0	1.0	-0.376106897334
-input1.bam	FBtr0078580	R	17	0	1.0	-0.305815074288
-input1.bam	FBtr0078580	R	18	0	1.0	-0.446398720379
-input1.bam	FBtr0078580	R	19	0	1.0	-0.45278888611
-input1.bam	FBtr0078580	R	20	0	1.0	-0.446398720379
-input1.bam	FBtr0078580	R	21	0	1.0	-0.471959383305
-input1.bam	FBtr0078580	R	22	0	1.0	-0.420838057453
-input1.bam	FBtr0078580	R	23	0	1.0	-0.471959383305
-input1.bam	FBtr0078580	R	24	0	1.0	0.64631961969
-input1.bam	FBtr0078580	R	25	0	1.0	0.850804923095
-input1.bam	FBtr0078580	R	26	0	1.0	-0.49752004623
-input1.bam	FBtr0078580	R	27	0	1.0	-0.491129880499
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