Mercurial > repos > iuc > bigwig_outlier_bed

changeset 1:8377a6abb4da draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 92ffe42a6ad6e81f3f157bbc9b942c000d450416
author iuc
date Sun, 21 Jul 2024 11:03:36 +0000
parents ebcd48f183b3
children 61946b8bd43b
files bigwig_outlier_bed.py bigwig_outlier_bed.xml test-data/bedouthi2_sample test-data/bedouthi_qlo_notset_sample test-data/bedouthi_sample test-data/bedouthilo2_sample test-data/bedouthilo_qlo_notset_sample test-data/bedouthilo_sample test-data/bedoutlo2_sample test-data/bedoutlo_sample test-data/table2_sample test-data/table3_sample test-data/table_qlo_notset_sample test-data/table_sample
diffstat 14 files changed, 4754 insertions(+), 630 deletions(-) [+]
line wrap: on
line diff
--- a/bigwig_outlier_bed.py	Fri Jul 05 06:00:15 2024 +0000
+++ b/bigwig_outlier_bed.py	Sun Jul 21 11:03:36 2024 +0000
@@ -28,8 +28,6 @@
         self.bwnames = args.bigwig
         self.bwlabels = args.bigwiglabels
         self.bedwin = args.minwin
-        self.qlo = args.qlo
-        self.qhi = args.qhi
         self.outbeds = args.outbeds
         self.bedouthi = args.bedouthi
         self.bedoutlo = args.bedoutlo
@@ -37,7 +35,13 @@
         self.tableoutfile = args.tableoutfile
         self.bedwin = args.minwin
         self.qhi = args.qhi
-        self.qlo = args.qlo
+        self.qlo = None
+        try:
+            f = float(args.qlo)
+            self.qlo = f
+        except Exception as e:
+            s = str(e)
+            print(s, ' qlo=', args.qlo)
         nbw = len(args.bigwig)
         nlab = len(args.bigwiglabels)
         if nlab < nbw:
@@ -90,13 +94,13 @@
             bwmax,
         )
         if self.qhi is not None:
-            row += "\t%f" % self.bwtop
+            row += "\t%.2f" % self.bwtop
         else:
-            row += "\t"
+            row += "\tnoqhi"
         if self.qlo is not None:
-            row += "\t%f" % self.bwbot
+            row += "\t%.2f" % self.bwbot
         else:
-            row += "\t"
+            row += "\tnoqlo"
         return row
 
     def makeBed(self):
@@ -125,13 +129,31 @@
                     bwhi = self.processVals(bw, isTop=True)
                     for j, seg in enumerate(bwhi):
                         if seg[1] - seg[0] >= self.bedwin:
-                            bedhi.append((chr, seg[0], seg[1], "%s_hi" % (bwlabel), 1))
+                            score = np.sum(bw[seg[0]:seg[1]])
+                            bedhi.append(
+                                (
+                                    chr,
+                                    seg[0],
+                                    seg[1],
+                                    "%s_%d" % (bwlabel, score),
+                                    score,
+                                )
+                            )
                 if self.qlo is not None:
                     self.bwbot = np.quantile(bw, self.qlo)
                     bwlo = self.processVals(bw, isTop=False)
                     for j, seg in enumerate(bwlo):
                         if seg[1] - seg[0] >= self.bedwin:
-                            bedlo.append((chr, seg[0], seg[1], "%s_lo" % (bwlabel), -1))
+                            score = -1 * np.sum(bw[seg[0]:seg[1]])
+                            bedlo.append(
+                                (
+                                    chr,
+                                    seg[0],
+                                    seg[1],
+                                    "%s_%d" % (bwlabel, score),
+                                    score,
+                                )
+                            )
                 if self.tableoutfile:
                     row = self.makeTableRow(bw, bwlabel, chr)
                     restab.append(copy.copy(row))
@@ -164,7 +186,7 @@
     parser = argparse.ArgumentParser()
     a = parser.add_argument
     a("-m", "--minwin", default=10, type=int)
-    a("-l", "--qlo", default=None, type=float)
+    a("-l", "--qlo", default=None)
     a("-i", "--qhi", default=None, type=float)
     a("--bedouthi", default=None)
     a("--bedoutlo", default=None)
--- a/bigwig_outlier_bed.xml	Fri Jul 05 06:00:15 2024 +0000
+++ b/bigwig_outlier_bed.xml	Sun Jul 21 11:03:36 2024 +0000
@@ -1,5 +1,10 @@
-<tool name="Bigwig extremes to bed features" id="bigwig_outlier_bed" version="0.1.4" profile="22.05">
+<tool name="Bigwig extremes to bed features" id="bigwig_outlier_bed" version="@TOOL_VERSION@" profile="22.05">
   <description>Writes high and low bigwig runs as features in a bed file</description>
+  <macros>
+  <token name="@TOOL_VERSION@">0.2.0</token>
+  <token name="@NUMPY_VERSION@">2.0.0</token>
+  <token name="@PYTHON_VERSION@">3.12.3</token>
+  </macros>
   <edam_topics>
       <edam_topic>topic_0157</edam_topic>
       <edam_topic>topic_0092</edam_topic>
@@ -11,9 +16,9 @@
     <xref type="bio.tools">bigtools</xref>
   </xrefs>
   <requirements>
-    <requirement type="package" version="3.12.3">python</requirement>
-    <requirement type="package" version="2.0.0">numpy</requirement>
-    <requirement type="package" version="0.1.4">pybigtools</requirement>
+    <requirement type="package" version="@PYTHON_VERSION@">python</requirement>
+    <requirement type="package" version="@NUMPY_VERSION@">numpy</requirement>
+    <requirement type="package" version="@TOOL_VERSION@">pybigtools</requirement>
   </requirements>
   <required_files>
       <include path="bigwig_outlier_bed.py"/>
@@ -102,15 +107,25 @@
       <param name="qlo" value="0.01"/>
       <param name="tableout" value="create"/>
     </test>
+    <test expect_num_outputs="2">
+      <output name="bedouthi" value="bedouthi_qlo_notset_sample" compare="diff" lines_diff="0"/>
+      <output name="tableoutfile" value="table_qlo_notset_sample" compare="diff" lines_diff="0"/>
+      <param name="outbeds" value="outhi"/>
+      <param name="bigwig" value="bigwig_sample"/>
+      <param name="minwin" value="10"/>
+      <param name="qhi" value="0.99"/>
+      <param name="qlo" value=""/>
+      <param name="tableout" value="create"/>
+    </test>
     <test expect_num_outputs="3">
       <output name="bedouthi" value="bedouthi_sample" compare="diff" lines_diff="0"/>
       <output name="bedoutlo" value="bedoutlo_sample" compare="diff" lines_diff="0"/>
-      <output name="tableoutfile" value="table_sample" compare="diff" lines_diff="0"/>
+      <output name="tableoutfile" value="table3_sample" compare="diff" lines_diff="0"/>
       <param name="outbeds" value="outlohi"/>
       <param name="bigwig" value="bigwig_sample"/>
-      <param name="minwin" value="10"/>
-      <param name="qhi" value="0.99"/>
-      <param name="qlo" value="0.01"/>
+      <param name="minwin" value="1"/>
+      <param name="qhi" value="0.9"/>
+      <param name="qlo" value="0.1"/>
       <param name="tableout" value="create"/>
     </test>
     <test expect_num_outputs="4">
@@ -120,9 +135,9 @@
       <output name="tableoutfile" value="table2_sample" compare="diff" lines_diff="0"/>
       <param name="outbeds" value="outall"/>
       <param name="bigwig" value="bigwig_sample,1.bigwig"/>
-      <param name="minwin" value="10"/>
-      <param name="qhi" value="0.99"/>
-      <param name="qlo" value="0.01"/>
+      <param name="minwin" value="1"/>
+      <param name="qhi" value="0.9"/>
+      <param name="qlo" value="0.1"/>
       <param name="tableout" value="create"/>
     </test>
   </tests>
--- a/test-data/bedouthi2_sample	Fri Jul 05 06:00:15 2024 +0000
+++ b/test-data/bedouthi2_sample	Sun Jul 21 11:03:36 2024 +0000
@@ -1,73 +1,1347 @@
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+Merlin	62759	62769	bigwig_sample_318380	318380
+Merlin	62789	62799	bigwig_sample_316090	316090
+Merlin	62819	62829	bigwig_sample_245080	245080
+Merlin	62859	62869	bigwig_sample_293490	293490
+Merlin	62969	62979	bigwig_sample_284130	284130
+Merlin	63009	63019	bigwig_sample_251470	251470
+Merlin	63039	63049	bigwig_sample_320480	320480
+Merlin	63069	63089	bigwig_sample_585530	585530
+Merlin	63099	63129	bigwig_sample_871360	871360
+Merlin	63139	63159	bigwig_sample_640730	640730
+Merlin	63169	63179	bigwig_sample_283990	283990
+Merlin	63189	63199	bigwig_sample_287750	287750
+Merlin	63259	63269	bigwig_sample_260300	260300
+Merlin	63339	63349	bigwig_sample_327450	327450
+Merlin	63359	63369	bigwig_sample_326830	326830
+Merlin	63389	63399	bigwig_sample_273500	273500
+Merlin	63419	63479	bigwig_sample_1692710	1692710
+Merlin	63499	63509	bigwig_sample_279330	279330
+Merlin	63519	63529	bigwig_sample_319530	319530
+Merlin	63539	63549	bigwig_sample_255950	255950
+Merlin	63579	63589	bigwig_sample_253750	253750
+Merlin	63609	63619	bigwig_sample_253980	253980
+Merlin	63699	63749	bigwig_sample_1332790	1332790
+Merlin	63799	63809	bigwig_sample_316710	316710
+Merlin	63829	63839	bigwig_sample_308560	308560
+Merlin	63899	63909	bigwig_sample_284670	284670
+Merlin	63919	63929	bigwig_sample_278630	278630
+Merlin	63949	63959	bigwig_sample_323380	323380
+Merlin	63969	63979	bigwig_sample_321670	321670
+Merlin	63989	63999	bigwig_sample_279080	279080
+Merlin	64039	64049	bigwig_sample_273860	273860
+Merlin	64119	64129	bigwig_sample_314550	314550
+Merlin	64179	64199	bigwig_sample_560810	560810
+Merlin	64209	64229	bigwig_sample_564200	564200
+Merlin	64239	64249	bigwig_sample_282750	282750
+Merlin	64299	64309	bigwig_sample_306220	306220
+Merlin	64359	64369	bigwig_sample_321860	321860
+Merlin	64459	64479	bigwig_sample_551980	551980
+Merlin	64509	64519	bigwig_sample_291350	291350
+Merlin	64559	64569	bigwig_sample_298470	298470
+Merlin	64649	64659	bigwig_sample_258490	258490
+Merlin	64789	64799	bigwig_sample_305600	305600
+Merlin	64809	64829	bigwig_sample_545840	545840
+Merlin	64849	64859	bigwig_sample_312360	312360
+Merlin	64929	64939	bigwig_sample_271280	271280
+Merlin	64989	64999	bigwig_sample_319060	319060
+Merlin	65069	65079	bigwig_sample_283550	283550
+Merlin	65099	65109	bigwig_sample_261470	261470
+Merlin	65179	65199	bigwig_sample_538420	538420
+Merlin	65219	65229	bigwig_sample_298760	298760
+Merlin	65269	65279	bigwig_sample_248740	248740
+Merlin	65349	65359	bigwig_sample_297330	297330
+Merlin	65379	65399	bigwig_sample_509610	509610
+Merlin	65469	65479	bigwig_sample_250110	250110
+Merlin	65519	65529	bigwig_sample_257160	257160
+Merlin	65549	65559	bigwig_sample_303810	303810
+Merlin	65599	65609	bigwig_sample_300010	300010
+Merlin	65669	65679	bigwig_sample_303010	303010
+Merlin	65709	65719	bigwig_sample_314860	314860
+Merlin	65749	65779	bigwig_sample_863280	863280
+Merlin	65839	65849	bigwig_sample_265310	265310
+Merlin	65889	65909	bigwig_sample_527880	527880
+Merlin	65949	65959	bigwig_sample_282930	282930
+Merlin	65969	66009	bigwig_sample_1162560	1162560
+Merlin	66019	66029	bigwig_sample_272140	272140
+Merlin	66129	66139	bigwig_sample_260910	260910
+Merlin	66169	66179	bigwig_sample_248770	248770
+Merlin	66189	66199	bigwig_sample_256250	256250
+Merlin	66219	66249	bigwig_sample_860960	860960
+Merlin	66269	66279	bigwig_sample_315640	315640
+Merlin	66299	66309	bigwig_sample_272920	272920
+Merlin	66319	66329	bigwig_sample_313380	313380
+Merlin	66429	66439	bigwig_sample_308770	308770
+Merlin	66449	66459	bigwig_sample_260470	260470
+Merlin	66469	66479	bigwig_sample_267460	267460
+Merlin	66519	66529	bigwig_sample_327310	327310
+Merlin	66539	66559	bigwig_sample_576210	576210
+Merlin	66579	66589	bigwig_sample_256720	256720
+Merlin	66679	66689	bigwig_sample_297390	297390
+Merlin	66699	66709	bigwig_sample_243750	243750
+Merlin	66729	66739	bigwig_sample_297820	297820
+Merlin	66809	66819	bigwig_sample_300330	300330
+Merlin	66859	66869	bigwig_sample_325520	325520
+Merlin	66879	66899	bigwig_sample_561300	561300
+Merlin	66959	66969	bigwig_sample_314100	314100
+Merlin	66989	66999	bigwig_sample_283810	283810
+Merlin	67049	67069	bigwig_sample_601150	601150
+Merlin	67139	67149	bigwig_sample_258810	258810
+Merlin	67169	67179	bigwig_sample_256650	256650
+Merlin	67189	67199	bigwig_sample_308580	308580
+Merlin	67209	67239	bigwig_sample_891580	891580
+Merlin	67249	67259	bigwig_sample_323350	323350
+Merlin	67309	67319	bigwig_sample_290480	290480
+Merlin	67489	67499	bigwig_sample_249030	249030
+Merlin	67509	67519	bigwig_sample_253760	253760
+Merlin	67529	67539	bigwig_sample_317750	317750
+Merlin	67559	67569	bigwig_sample_313420	313420
+Merlin	67649	67659	bigwig_sample_257120	257120
+Merlin	67669	67679	bigwig_sample_318900	318900
+Merlin	67699	67709	bigwig_sample_326970	326970
+Merlin	67719	67729	bigwig_sample_308250	308250
+Merlin	67829	67839	bigwig_sample_308360	308360
+Merlin	67849	67869	bigwig_sample_574680	574680
+Merlin	67909	67919	bigwig_sample_262360	262360
+Merlin	67959	67969	bigwig_sample_282720	282720
+Merlin	67989	67999	bigwig_sample_296470	296470
+Merlin	68199	68209	bigwig_sample_318490	318490
+Merlin	68299	68309	bigwig_sample_302570	302570
+Merlin	68379	68389	bigwig_sample_263330	263330
+Merlin	68399	68409	bigwig_sample_255710	255710
+Merlin	68439	68449	bigwig_sample_258110	258110
+Merlin	68529	68539	bigwig_sample_260100	260100
+Merlin	68569	68579	bigwig_sample_276830	276830
+Merlin	68599	68609	bigwig_sample_292640	292640
+Merlin	68649	68659	bigwig_sample_323020	323020
+Merlin	68689	68699	bigwig_sample_275040	275040
+Merlin	68749	68759	bigwig_sample_292720	292720
+Merlin	68769	68799	bigwig_sample_954320	954320
+Merlin	68899	68909	bigwig_sample_286420	286420
+Merlin	68919	68929	bigwig_sample_264980	264980
+Merlin	68989	68999	bigwig_sample_319610	319610
+Merlin	69069	69079	bigwig_sample_278970	278970
+Merlin	69099	69109	bigwig_sample_257030	257030
+Merlin	69119	69149	bigwig_sample_872070	872070
+Merlin	69179	69189	bigwig_sample_269340	269340
+Merlin	69199	69209	bigwig_sample_258020	258020
+Merlin	69259	69269	bigwig_sample_320570	320570
+Merlin	69279	69289	bigwig_sample_251800	251800
+Merlin	69329	69339	bigwig_sample_282140	282140
+Merlin	69409	69419	bigwig_sample_277610	277610
+Merlin	69439	69459	bigwig_sample_522930	522930
+Merlin	69509	69519	bigwig_sample_262190	262190
+Merlin	69579	69589	bigwig_sample_320980	320980
+Merlin	69769	69779	bigwig_sample_281620	281620
+Merlin	69809	69829	bigwig_sample_636960	636960
+Merlin	69859	69869	bigwig_sample_326630	326630
+Merlin	69879	69909	bigwig_sample_838070	838070
+Merlin	69949	69959	bigwig_sample_309600	309600
+Merlin	69979	69989	bigwig_sample_309730	309730
+chr21	0	48129895	1.bigwig_165850	165850
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bedouthi_qlo_notset_sample	Sun Jul 21 11:03:36 2024 +0000
@@ -0,0 +1,178 @@
+Merlin	29	39	bigwig_sample_324550	324550
+Merlin	199	209	bigwig_sample_325430	325430
+Merlin	299	309	bigwig_sample_322440	322440
+Merlin	1579	1589	bigwig_sample_326050	326050
+Merlin	1729	1749	bigwig_sample_645520	645520
+Merlin	1859	1869	bigwig_sample_325690	325690
+Merlin	1889	1899	bigwig_sample_324060	324060
+Merlin	2589	2599	bigwig_sample_319990	319990
+Merlin	3409	3419	bigwig_sample_327310	327310
+Merlin	3659	3669	bigwig_sample_320520	320520
+Merlin	4039	4049	bigwig_sample_326360	326360
+Merlin	4409	4419	bigwig_sample_319410	319410
+Merlin	7129	7139	bigwig_sample_324490	324490
+Merlin	7269	7279	bigwig_sample_322880	322880
+Merlin	7869	7879	bigwig_sample_327240	327240
+Merlin	8079	8089	bigwig_sample_320310	320310
+Merlin	8289	8299	bigwig_sample_325450	325450
+Merlin	8739	8749	bigwig_sample_320050	320050
+Merlin	9039	9049	bigwig_sample_322170	322170
+Merlin	9259	9269	bigwig_sample_321140	321140
+Merlin	9459	9469	bigwig_sample_322600	322600
+Merlin	9549	9559	bigwig_sample_321080	321080
+Merlin	10209	10219	bigwig_sample_321070	321070
+Merlin	10829	10839	bigwig_sample_327660	327660
+Merlin	11219	11229	bigwig_sample_320890	320890
+Merlin	12049	12059	bigwig_sample_323710	323710
+Merlin	12169	12179	bigwig_sample_321700	321700
+Merlin	12509	12519	bigwig_sample_322540	322540
+Merlin	12969	12979	bigwig_sample_319320	319320
+Merlin	13319	13329	bigwig_sample_326950	326950
+Merlin	13749	13759	bigwig_sample_323640	323640
+Merlin	14419	14429	bigwig_sample_320290	320290
+Merlin	14469	14479	bigwig_sample_322500	322500
+Merlin	14749	14759	bigwig_sample_322480	322480
+Merlin	15499	15509	bigwig_sample_321250	321250
+Merlin	15979	15989	bigwig_sample_320790	320790
+Merlin	16559	16569	bigwig_sample_323020	323020
+Merlin	16589	16599	bigwig_sample_323850	323850
+Merlin	17579	17589	bigwig_sample_324630	324630
+Merlin	17949	17959	bigwig_sample_325800	325800
+Merlin	17989	17999	bigwig_sample_322480	322480
+Merlin	18349	18359	bigwig_sample_327370	327370
+Merlin	18819	18829	bigwig_sample_325440	325440
+Merlin	19159	19169	bigwig_sample_320050	320050
+Merlin	19999	20009	bigwig_sample_321990	321990
+Merlin	20509	20519	bigwig_sample_321290	321290
+Merlin	20799	20809	bigwig_sample_323260	323260
+Merlin	21149	21159	bigwig_sample_323350	323350
+Merlin	21169	21179	bigwig_sample_321840	321840
+Merlin	21309	21319	bigwig_sample_323520	323520
+Merlin	21329	21339	bigwig_sample_323370	323370
+Merlin	21569	21579	bigwig_sample_322070	322070
+Merlin	22319	22329	bigwig_sample_326130	326130
+Merlin	22369	22379	bigwig_sample_323350	323350
+Merlin	22729	22739	bigwig_sample_319650	319650
+Merlin	22799	22809	bigwig_sample_322710	322710
+Merlin	22879	22889	bigwig_sample_319180	319180
+Merlin	23289	23299	bigwig_sample_320030	320030
+Merlin	23769	23779	bigwig_sample_324230	324230
+Merlin	23939	23949	bigwig_sample_322460	322460
+Merlin	24449	24459	bigwig_sample_319810	319810
+Merlin	24589	24599	bigwig_sample_327010	327010
+Merlin	24869	24879	bigwig_sample_324030	324030
+Merlin	24899	24919	bigwig_sample_644190	644190
+Merlin	25709	25719	bigwig_sample_324990	324990
+Merlin	25769	25779	bigwig_sample_323240	323240
+Merlin	26459	26469	bigwig_sample_324360	324360
+Merlin	26559	26569	bigwig_sample_322030	322030
+Merlin	27229	27239	bigwig_sample_325090	325090
+Merlin	27289	27299	bigwig_sample_327670	327670
+Merlin	27529	27539	bigwig_sample_322100	322100
+Merlin	27919	27929	bigwig_sample_319260	319260
+Merlin	28509	28519	bigwig_sample_326280	326280
+Merlin	28589	28599	bigwig_sample_321920	321920
+Merlin	29069	29079	bigwig_sample_319210	319210
+Merlin	29189	29199	bigwig_sample_319390	319390
+Merlin	29749	29759	bigwig_sample_327090	327090
+Merlin	29849	29859	bigwig_sample_323760	323760
+Merlin	29889	29899	bigwig_sample_321420	321420
+Merlin	30299	30309	bigwig_sample_323820	323820
+Merlin	31549	31559	bigwig_sample_323870	323870
+Merlin	31899	31909	bigwig_sample_325720	325720
+Merlin	32049	32059	bigwig_sample_320970	320970
+Merlin	32949	32959	bigwig_sample_320190	320190
+Merlin	32979	32989	bigwig_sample_325360	325360
+Merlin	33729	33739	bigwig_sample_320630	320630
+Merlin	33989	33999	bigwig_sample_325710	325710
+Merlin	35449	35459	bigwig_sample_324510	324510
+Merlin	36159	36169	bigwig_sample_321880	321880
+Merlin	36399	36409	bigwig_sample_319330	319330
+Merlin	36519	36529	bigwig_sample_326860	326860
+Merlin	36589	36599	bigwig_sample_323540	323540
+Merlin	37939	37949	bigwig_sample_321110	321110
+Merlin	38549	38559	bigwig_sample_319180	319180
+Merlin	39529	39539	bigwig_sample_321650	321650
+Merlin	39699	39709	bigwig_sample_326150	326150
+Merlin	40149	40159	bigwig_sample_322240	322240
+Merlin	40359	40369	bigwig_sample_327280	327280
+Merlin	40559	40569	bigwig_sample_325970	325970
+Merlin	40699	40709	bigwig_sample_322980	322980
+Merlin	40789	40799	bigwig_sample_326120	326120
+Merlin	41399	41409	bigwig_sample_327300	327300
+Merlin	41949	41959	bigwig_sample_323970	323970
+Merlin	42479	42489	bigwig_sample_323900	323900
+Merlin	42569	42579	bigwig_sample_323990	323990
+Merlin	42739	42749	bigwig_sample_325060	325060
+Merlin	42759	42769	bigwig_sample_322590	322590
+Merlin	43019	43029	bigwig_sample_324260	324260
+Merlin	43049	43059	bigwig_sample_321650	321650
+Merlin	43919	43929	bigwig_sample_327210	327210
+Merlin	44029	44039	bigwig_sample_321790	321790
+Merlin	44189	44199	bigwig_sample_319430	319430
+Merlin	44679	44689	bigwig_sample_325010	325010
+Merlin	45249	45259	bigwig_sample_321770	321770
+Merlin	45649	45659	bigwig_sample_321720	321720
+Merlin	46019	46029	bigwig_sample_324410	324410
+Merlin	46479	46489	bigwig_sample_326850	326850
+Merlin	46889	46899	bigwig_sample_321120	321120
+Merlin	47439	47449	bigwig_sample_320620	320620
+Merlin	49379	49389	bigwig_sample_325310	325310
+Merlin	50069	50079	bigwig_sample_320990	320990
+Merlin	50319	50329	bigwig_sample_326410	326410
+Merlin	50939	50949	bigwig_sample_321760	321760
+Merlin	51109	51119	bigwig_sample_321510	321510
+Merlin	51549	51559	bigwig_sample_323060	323060
+Merlin	52449	52459	bigwig_sample_319440	319440
+Merlin	52589	52599	bigwig_sample_319130	319130
+Merlin	52989	52999	bigwig_sample_326030	326030
+Merlin	53149	53159	bigwig_sample_320540	320540
+Merlin	53649	53659	bigwig_sample_322240	322240
+Merlin	54459	54469	bigwig_sample_323000	323000
+Merlin	54509	54519	bigwig_sample_321550	321550
+Merlin	54639	54649	bigwig_sample_325760	325760
+Merlin	54759	54769	bigwig_sample_323340	323340
+Merlin	54969	54979	bigwig_sample_319230	319230
+Merlin	55439	55449	bigwig_sample_325210	325210
+Merlin	56209	56219	bigwig_sample_319070	319070
+Merlin	56459	56469	bigwig_sample_325990	325990
+Merlin	56639	56649	bigwig_sample_325740	325740
+Merlin	56719	56729	bigwig_sample_320050	320050
+Merlin	57139	57149	bigwig_sample_323350	323350
+Merlin	57619	57629	bigwig_sample_324660	324660
+Merlin	57799	57809	bigwig_sample_324110	324110
+Merlin	57909	57919	bigwig_sample_322520	322520
+Merlin	58049	58059	bigwig_sample_320380	320380
+Merlin	58739	58749	bigwig_sample_327260	327260
+Merlin	59249	59259	bigwig_sample_321560	321560
+Merlin	59369	59379	bigwig_sample_325920	325920
+Merlin	59459	59469	bigwig_sample_326500	326500
+Merlin	60219	60229	bigwig_sample_326590	326590
+Merlin	60309	60319	bigwig_sample_323670	323670
+Merlin	61119	61129	bigwig_sample_325180	325180
+Merlin	61679	61689	bigwig_sample_323700	323700
+Merlin	62179	62189	bigwig_sample_320550	320550
+Merlin	62479	62489	bigwig_sample_325380	325380
+Merlin	63039	63049	bigwig_sample_320480	320480
+Merlin	63149	63159	bigwig_sample_322560	322560
+Merlin	63339	63349	bigwig_sample_327450	327450
+Merlin	63359	63369	bigwig_sample_326830	326830
+Merlin	63469	63479	bigwig_sample_319260	319260
+Merlin	63519	63529	bigwig_sample_319530	319530
+Merlin	63949	63959	bigwig_sample_323380	323380
+Merlin	63969	63979	bigwig_sample_321670	321670
+Merlin	64359	64369	bigwig_sample_321860	321860
+Merlin	65999	66009	bigwig_sample_321670	321670
+Merlin	66219	66229	bigwig_sample_326610	326610
+Merlin	66519	66529	bigwig_sample_327310	327310
+Merlin	66859	66869	bigwig_sample_325520	325520
+Merlin	67249	67259	bigwig_sample_323350	323350
+Merlin	67699	67709	bigwig_sample_326970	326970
+Merlin	68649	68659	bigwig_sample_323020	323020
+Merlin	68769	68789	bigwig_sample_648580	648580
+Merlin	68989	68999	bigwig_sample_319610	319610
+Merlin	69259	69269	bigwig_sample_320570	320570
+Merlin	69579	69589	bigwig_sample_320980	320980
+Merlin	69819	69829	bigwig_sample_320470	320470
+Merlin	69859	69869	bigwig_sample_326630	326630
+Merlin	69889	69899	bigwig_sample_319940	319940
--- a/test-data/bedouthi_sample	Fri Jul 05 06:00:15 2024 +0000
+++ b/test-data/bedouthi_sample	Sun Jul 21 11:03:36 2024 +0000
@@ -1,70 +1,1346 @@
-Merlin	20	30	bigwig_sample_hi	1
-Merlin	190	200	bigwig_sample_hi	1
-Merlin	1570	1580	bigwig_sample_hi	1
-Merlin	1730	1740	bigwig_sample_hi	1
-Merlin	1850	1860	bigwig_sample_hi	1
-Merlin	1880	1890	bigwig_sample_hi	1
-Merlin	3400	3410	bigwig_sample_hi	1
-Merlin	4030	4040	bigwig_sample_hi	1
-Merlin	7120	7130	bigwig_sample_hi	1
-Merlin	7860	7870	bigwig_sample_hi	1
-Merlin	8280	8290	bigwig_sample_hi	1
-Merlin	10820	10830	bigwig_sample_hi	1
-Merlin	13310	13320	bigwig_sample_hi	1
-Merlin	17570	17580	bigwig_sample_hi	1
-Merlin	17940	17950	bigwig_sample_hi	1
-Merlin	18340	18350	bigwig_sample_hi	1
-Merlin	18810	18820	bigwig_sample_hi	1
-Merlin	22310	22320	bigwig_sample_hi	1
-Merlin	23760	23770	bigwig_sample_hi	1
-Merlin	24580	24590	bigwig_sample_hi	1
-Merlin	24860	24870	bigwig_sample_hi	1
-Merlin	25700	25710	bigwig_sample_hi	1
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--- a/test-data/bedouthilo2_sample	Fri Jul 05 06:00:15 2024 +0000
+++ b/test-data/bedouthilo2_sample	Sun Jul 21 11:03:36 2024 +0000
@@ -1,164 +1,1457 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bedouthilo_qlo_notset_sample	Sun Jul 21 11:03:36 2024 +0000
@@ -0,0 +1,70 @@
+Merlin	20	30	bigwig_sample_hi	1
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--- a/test-data/bedouthilo_sample	Fri Jul 05 06:00:15 2024 +0000
+++ b/test-data/bedouthilo_sample	Sun Jul 21 11:03:36 2024 +0000
@@ -1,139 +1,179 @@
-Merlin	20	30	bigwig_sample_hi	1
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+Merlin	63039	63049	bigwig_sample_320480	320480
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+Merlin	63469	63479	bigwig_sample_319260	319260
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+Merlin	65999	66009	bigwig_sample_321670	321670
+Merlin	66219	66229	bigwig_sample_326610	326610
+Merlin	66519	66529	bigwig_sample_327310	327310
+Merlin	66859	66869	bigwig_sample_325520	325520
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+Merlin	69889	69899	bigwig_sample_319940	319940
+Merlin	70049	180929	bigwig_sample_0	0
--- a/test-data/bedoutlo2_sample	Fri Jul 05 06:00:15 2024 +0000
+++ b/test-data/bedoutlo2_sample	Sun Jul 21 11:03:36 2024 +0000
@@ -1,91 +1,110 @@
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+chr21	9412565	9412570	1.bigwig_0	0
+chr21	9412590	9412595	1.bigwig_0	0
+chr21	9412640	9412650	1.bigwig_0	0
+chr21	9412670	9412675	1.bigwig_0	0
+chr21	9412690	9412700	1.bigwig_0	0
+chr21	9412770	9412775	1.bigwig_0	0
+chr21	9412815	9412820	1.bigwig_0	0
+chr21	9412835	9412840	1.bigwig_0	0
+chr21	9412845	9412850	1.bigwig_0	0
+chr21	9412900	9412905	1.bigwig_0	0
+chr21	9412970	9412975	1.bigwig_0	0
+chr21	9412990	9412995	1.bigwig_0	0
+chr21	9413040	9413045	1.bigwig_0	0
+chr21	9413055	9413065	1.bigwig_0	0
+chr21	9413095	9413100	1.bigwig_0	0
+chr21	9413130	9413135	1.bigwig_0	0
+chr21	9413155	9413160	1.bigwig_0	0
+chr21	9413170	9413180	1.bigwig_0	0
+chr21	9413205	9413210	1.bigwig_0	0
+chr21	9413250	9413255	1.bigwig_0	0
+chr21	9413280	9413285	1.bigwig_0	0
+chr21	9413310	9413315	1.bigwig_0	0
+chr21	9413345	9413350	1.bigwig_0	0
+chr21	9413400	9413405	1.bigwig_0	0
+chr21	9413510	9413515	1.bigwig_0	0
+chr21	9413665	9413670	1.bigwig_0	0
+chr21	9414040	9414045	1.bigwig_0	0
+chr21	9414055	9414060	1.bigwig_0	0
+chr21	9414100	9414105	1.bigwig_0	0
+chr21	9414150	9414160	1.bigwig_0	0
+chr21	9414175	9414180	1.bigwig_0	0
+chr21	9414215	9414225	1.bigwig_0	0
+chr21	9414255	9414260	1.bigwig_0	0
+chr21	9414265	9414270	1.bigwig_0	0
+chr21	9414280	9414285	1.bigwig_0	0
+chr21	9414305	9414310	1.bigwig_0	0
+chr21	9414435	9414440	1.bigwig_0	0
+chr21	9414525	9414530	1.bigwig_0	0
+chr21	9414585	9414590	1.bigwig_0	0
+chr21	9414595	9414600	1.bigwig_0	0
+chr21	9414655	9414665	1.bigwig_0	0
+chr21	9414680	9414690	1.bigwig_0	0
+chr21	9414695	9414700	1.bigwig_0	0
+chr21	9414705	9414710	1.bigwig_0	0
+chr21	9414720	9414725	1.bigwig_0	0
+chr21	9414755	9414760	1.bigwig_0	0
+chr21	9414775	9414780	1.bigwig_0	0
+chr21	9414785	9414790	1.bigwig_0	0
+chr21	9414820	9414825	1.bigwig_0	0
+chr21	9414835	9414840	1.bigwig_0	0
+chr21	9414850	9414855	1.bigwig_0	0
+chr21	9414860	9414870	1.bigwig_0	0
+chr21	9414905	9414910	1.bigwig_0	0
+chr21	9414925	9414930	1.bigwig_0	0
+chr21	9414955	9414960	1.bigwig_0	0
+chr21	9414975	9414980	1.bigwig_0	0
+chr21	9414995	9415000	1.bigwig_0	0
+chr21	9415040	9415055	1.bigwig_0	0
+chr21	9415065	9415075	1.bigwig_0	0
+chr21	9415095	9415100	1.bigwig_0	0
+chr21	9415105	9415115	1.bigwig_0	0
+chr21	9415135	9415140	1.bigwig_0	0
+chr21	9415150	9415155	1.bigwig_0	0
+chr21	9415170	9415175	1.bigwig_0	0
+chr21	9415270	9415275	1.bigwig_0	0
+chr21	9415320	9415325	1.bigwig_0	0
+chr21	9415385	9415390	1.bigwig_0	0
+chr21	9415470	9415475	1.bigwig_0	0
+chr21	9415535	9415540	1.bigwig_0	0
+chr21	9415595	9415600	1.bigwig_0	0
+chr21	9415665	9415670	1.bigwig_0	0
+chr21	9415685	9415700	1.bigwig_0	0
+chr21	9415710	9415715	1.bigwig_0	0
+chr21	9415820	9415830	1.bigwig_0	0
+chr21	9415880	9415885	1.bigwig_0	0
+chr21	9416020	9416025	1.bigwig_0	0
+chr21	9416080	9416085	1.bigwig_0	0
+chr21	9416095	9416100	1.bigwig_0	0
+chr21	9416130	9416135	1.bigwig_0	0
+chr21	9416150	9416155	1.bigwig_0	0
+chr21	9416165	9416175	1.bigwig_0	0
+chr21	9416185	48129895	1.bigwig_0	0
--- a/test-data/bedoutlo_sample	Fri Jul 05 06:00:15 2024 +0000
+++ b/test-data/bedoutlo_sample	Sun Jul 21 11:03:36 2024 +0000
@@ -1,69 +1,2 @@
-Merlin	80	90	bigwig_sample_lo	-1
-Merlin	430	440	bigwig_sample_lo	-1
-Merlin	1230	1240	bigwig_sample_lo	-1
-Merlin	2670	2680	bigwig_sample_lo	-1
-Merlin	3740	3750	bigwig_sample_lo	-1
-Merlin	4700	4710	bigwig_sample_lo	-1
-Merlin	5870	5890	bigwig_sample_lo	-1
-Merlin	6290	6300	bigwig_sample_lo	-1
-Merlin	8860	8870	bigwig_sample_lo	-1
-Merlin	10520	10530	bigwig_sample_lo	-1
-Merlin	11190	11200	bigwig_sample_lo	-1
-Merlin	11380	11390	bigwig_sample_lo	-1
-Merlin	11810	11820	bigwig_sample_lo	-1
-Merlin	12660	12670	bigwig_sample_lo	-1
-Merlin	14160	14170	bigwig_sample_lo	-1
-Merlin	14750	14760	bigwig_sample_lo	-1
-Merlin	16270	16280	bigwig_sample_lo	-1
-Merlin	17240	17250	bigwig_sample_lo	-1
-Merlin	18290	18300	bigwig_sample_lo	-1
-Merlin	19080	19090	bigwig_sample_lo	-1
-Merlin	19220	19230	bigwig_sample_lo	-1
-Merlin	20240	20250	bigwig_sample_lo	-1
-Merlin	21650	21660	bigwig_sample_lo	-1
-Merlin	21810	21820	bigwig_sample_lo	-1
-Merlin	23630	23640	bigwig_sample_lo	-1
-Merlin	25030	25040	bigwig_sample_lo	-1
-Merlin	26260	26270	bigwig_sample_lo	-1
-Merlin	26560	26570	bigwig_sample_lo	-1
-Merlin	26610	26620	bigwig_sample_lo	-1
-Merlin	27670	27680	bigwig_sample_lo	-1
-Merlin	27970	27980	bigwig_sample_lo	-1
-Merlin	29400	29410	bigwig_sample_lo	-1
-Merlin	29910	29920	bigwig_sample_lo	-1
-Merlin	33460	33470	bigwig_sample_lo	-1
-Merlin	33910	33920	bigwig_sample_lo	-1
-Merlin	34470	34490	bigwig_sample_lo	-1
-Merlin	35320	35330	bigwig_sample_lo	-1
-Merlin	35620	35630	bigwig_sample_lo	-1
-Merlin	35880	35890	bigwig_sample_lo	-1
-Merlin	36810	36820	bigwig_sample_lo	-1
-Merlin	37230	37240	bigwig_sample_lo	-1
-Merlin	37560	37570	bigwig_sample_lo	-1
-Merlin	37750	37760	bigwig_sample_lo	-1
-Merlin	38330	38340	bigwig_sample_lo	-1
-Merlin	39600	39610	bigwig_sample_lo	-1
-Merlin	41900	41910	bigwig_sample_lo	-1
-Merlin	42050	42060	bigwig_sample_lo	-1
-Merlin	44440	44450	bigwig_sample_lo	-1
-Merlin	46610	46620	bigwig_sample_lo	-1
-Merlin	49290	49300	bigwig_sample_lo	-1
-Merlin	50880	50890	bigwig_sample_lo	-1
-Merlin	52230	52240	bigwig_sample_lo	-1
-Merlin	52460	52470	bigwig_sample_lo	-1
-Merlin	52740	52750	bigwig_sample_lo	-1
-Merlin	52770	52780	bigwig_sample_lo	-1
-Merlin	53150	53160	bigwig_sample_lo	-1
-Merlin	54830	54840	bigwig_sample_lo	-1
-Merlin	56020	56030	bigwig_sample_lo	-1
-Merlin	57220	57230	bigwig_sample_lo	-1
-Merlin	61250	61260	bigwig_sample_lo	-1
-Merlin	63190	63200	bigwig_sample_lo	-1
-Merlin	63290	63300	bigwig_sample_lo	-1
-Merlin	64660	64670	bigwig_sample_lo	-1
-Merlin	65050	65060	bigwig_sample_lo	-1
-Merlin	66660	66670	bigwig_sample_lo	-1
-Merlin	66900	66910	bigwig_sample_lo	-1
-Merlin	67150	67160	bigwig_sample_lo	-1
-Merlin	68790	68800	bigwig_sample_lo	-1
-Merlin	69660	69670	bigwig_sample_lo	-1
+Merlin	0	9	bigwig_sample_0	0
+Merlin	70049	180929	bigwig_sample_0	0
--- a/test-data/table2_sample	Fri Jul 05 06:00:15 2024 +0000
+++ b/test-data/table2_sample	Sun Jul 21 11:03:36 2024 +0000
@@ -1,3 +1,3 @@
 bigwig	contig	n	mean	std	min	max	qtop	qbot
-bigwig_sample	Merlin	70040	16414.614934	9523.634628	13.000000	32767.000000	32387.000000	323.000000
-1.bigwig	chr21	4995	33.203203	21.071159	0.000000	100.000000	80.000000	0.000000
+bigwig_sample	Merlin	180929	6354.313736	9951.749936	0.000000	32767.000000	24359.00	0.00
+1.bigwig	chr21	48129895	0.003446	0.400601	0.000000	100.000000	0.00	0.00
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/table3_sample	Sun Jul 21 11:03:36 2024 +0000
@@ -0,0 +1,2 @@
+bigwig	contig	n	mean	std	min	max	qtop	qbot
+bigwig_sample	Merlin	180929	6354.313736	9951.749936	0.000000	32767.000000	24359.00	0.00
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/table_qlo_notset_sample	Sun Jul 21 11:03:36 2024 +0000
@@ -0,0 +1,2 @@
+bigwig	contig	n	mean	std	min	max	qtop	qbot
+bigwig_sample	Merlin	180929	6354.313736	9951.749936	0.000000	32767.000000	31906.72	noqlo
--- a/test-data/table_sample	Fri Jul 05 06:00:15 2024 +0000
+++ b/test-data/table_sample	Sun Jul 21 11:03:36 2024 +0000
@@ -1,2 +1,2 @@
 bigwig	contig	n	mean	std	min	max	qtop	qbot
-bigwig_sample	Merlin	70040	16414.614934	9523.634628	13.000000	32767.000000	32387.000000	323.000000
+bigwig_sample	Merlin	180929	6354.313736	9951.749936	0.000000	32767.000000	31906.72	0.00