# HG changeset patch
# User iuc
# Date 1586592874 14400
# Node ID 8c8cc81b34cd0115f8af3f9fd4ab0341a12c8e7e
# Parent  26d7ec4af11952651133a80e72fe2cc9fe03d4c7
"planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit 6a45aa4c34b4f3b73ab0c6c3d9e7a315b62bf761"

diff -r 26d7ec4af119 -r 8c8cc81b34cd macros.xml
--- a/macros.xml	Fri Sep 06 09:54:27 2019 -0400
+++ b/macros.xml	Sat Apr 11 04:14:34 2020 -0400
@@ -8,16 +8,32 @@
 
     <token name="@VERSION@">1.3.4.6</token>
 
+    <token name="@DMCExample@">
+
+Example::
+
+ chr11	87	89	6	1	0.652,1	10	0.2	0,0.47	-0.8	-0.327	-0.857,-0.327	0.000318	0.00699	strongHypo
+ chr11	152	154	4	1	0.549,1	9	0.333	0.0575,0.609	-0.667	-0.113	-0.761,-0.113	0.0035	0.0699	hypo
+ chr11	258	260	3	1	0.473,1	13	0.231	0,0.466	-0.769	-0.165	-0.809,-0.165	0.00236	0.0357	hypo
+ chr11	331	333	6	0.667	0.341,0.992	22	0.227	0.0499,0.405	-0.439	-0.058	-0.66,-0.058	0.00636	0.0638	hypo
+ chr11	630	632	3	1	0.473,1	5	0	0,0.393	-1	-0.271	-1,-0.271	0.000954	0.0179	strongHypo
+ chr11	638	640	3	0.667	0.249,1	5	0.6	0.264,0.936	-0.0667	-0	-0.461,0.418	0.0286	1	hypo
+ chr11	641	643	4	1	0.549,1	5	0.4	0.064,0.736	-0.6	-0.0122	-0.748,-0.0122	0.00715	0.167	hypo
+ chr11	645	647	4	1	0.549,1	8	1	0.717,1	0	0	-0.183,0.374	0.067	1	hypo
+ chr11	666	668	4	1	0.549,1	9	0.667	0.391,0.942	-0.333	-0	-0.506,0.15	0.021	0.497	hypo
+ chr11	685	687	3	1	0.473,1	8	0	0,0.283	-1	-0.342	-1,-0.342	0.000364	0.00606	strongHypo
+
+    </token>
+
     <token name="@DMRExample@">
 
 Example::
 
- chr11	316	1705	-	35	30	5	-1
- chr11	3052	3674	-	17	16	1	-1
- chr11	18599	19013	-	9	7	3	-1
- chr11	19120	19931	-	39	39	0	-1
- chr11	22138	22618	-	14	12	3	-1
- chr11	28140	28356	-	4	4	0	-1
+ chr11	2529	2582	0.787	77	8	0.226	123	8	-0.204	3.79e-17	strongHypo
+ chr11	2976	3065	0.833	222	3	0.241	116	3	-0.339	1.69e-22	strongHypo
+ chr11	4327	5335	0.722	286	29	0.143	563	29	-0.201	2.3e-48	strongHypo
+ chr11	6544	7008	0.955	86	17	0.126	97	17	-0.223	6.5e-34	strongHypo
+
     </token>
 
     <xml name="citations">
diff -r 26d7ec4af119 -r 8c8cc81b34cd moabs.xml
--- a/moabs.xml	Fri Sep 06 09:54:27 2019 -0400
+++ b/moabs.xml	Sat Apr 11 04:14:34 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="moabs" name="MOABS" profile="16.04" version="@VERSION@">
+<tool id="moabs" name="MOABS" profile="16.04" version="@VERSION@+galaxy1">
     <description>MOdel based Analysis of Bisulfite Sequencing data</description>
     <macros>
         <import>macros.xml</import>
@@ -11,10 +11,13 @@
         #end if
         moabs -v 1 --def MMAP.p="\${GALAXY_SLOTS:-4}" --def MCALL.p="\${GALAXY_SLOTS:-4}" --def MCOMP.p="\${GALAXY_SLOTS:-4}" --cf '$cfg_file' &&
         #if "1" in $output_selector:
-            cp -f dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr '$output1' &&
+            cp -f dmc_M2_g1.G.bed_vs_g2.G.bed.txt '$output1' &&
         #end if
         #if "2" in $output_selector:
-            cp -f comp.g1.vs.g2.txt '$output2' &&
+            cp -f dmr_M2_g1.G.bed_vs_g2.G.bed.txt '$output2' &&
+        #end if
+        #if "3" in $output_selector:
+            cp -f comp.g1.vs.g2.txt '$output3' &&
         #end if
         echo Done
         ]]>
@@ -62,18 +65,54 @@
             #if str( $bsmap_advanced.bsmap_mismatch.bsmap_mismatch_selector ) != "0":
                 v=$bsmap_advanced.bsmap_mismatch.v
             #end if
+            s=$bsmap_advanced.s
+            w=$bsmap_advanced.w
+            #if $bsmap_advanced.D:
+                D=$bsmap_advanced.D
+            #end if
+            S=$bsmap_advanced.S
             n=$bsmap_advanced.n
+            q=$bsmap_advanced.q
+            z=$bsmap_advanced.z
+            f=$bsmap_advanced.f
+            #if $bsmap_advanced.A:
+                A=$bsmap_advanced.A
+            #end if
             r=$bsmap_advanced.r
-            R=''
+            #if str( $bsmap_advanced.R ) == "1":
+                R=''
+            #end if
+            #if str( $bsmap_advanced.u ) == "1":
+                u=''
+            #end if
+            m=$bsmap_advanced.m
+            x=$bsmap_advanced.x
 
             [MCALL]
             Path=mcall
             r='${reference_fasta_filename}'
+            cytosineMinScore=$mcall_advanced.cytosineMinScore
+            nextBaseMinScore=$mcall_advanced.nextBaseMinScore
+            qualityScoreBase=$mcall_advanced.qualityScoreBase
+            trimWGBSEndRepairPE2Seq=$mcall_advanced.trimWGBSEndRepairPE2Seq
+            trimWGBSEndRepairPE1Seq=$mcall_advanced.trimWGBSEndRepairPE1Seq
+            processPEOverlapSeq=$mcall_advanced.processPEOverlapSeq
+            trimRRBSEndRepairSeq=$mcall_advanced.trimRRBSEndRepairSeq
+            minFragSize=$mcall_advanced.minFragSize
+            minMMFragSize=$mcall_advanced.minMMFragSize
+            reportCpX=$mcall_advanced.reportCpX
 
             [MCOMP]
             Path=mcomp
-            reference='${reference_fasta_filename}'
             doComp=$mcomp_advanced.doComp.compare_selector
+            d=$mcomp_advanced.d
+            filterCredibleDif=$mcomp_advanced.filterCredibleDif
+            pFetDmc=$mcomp_advanced.pFetDmc
+            pFetDmr=$mcomp_advanced.pFetDmr
+            minNominalDif=$mcomp_advanced.minNominalDif
+            minCredibleDif=$mcomp_advanced.minCredibleDif
+            minDmcsInDmr=$mcomp_advanced.minDmcsInDmr
+            maxDistConsDmcs=$mcomp_advanced.maxDistConsDmcs
         </configfile>
     </configfiles>
 
@@ -134,9 +173,10 @@
             </conditional>
         </repeat>
         <section name="bsmap_advanced" title="Advanced options for BSMAP" expanded="False">
+            <param argument="-s" type="integer" value="16" min="8" max="16" label="Seed size" help="The seed size for the HASH table. BSMAP implements a seeding algorithm by indexing reference for all possible k-mers, i.e. seeds. As for the seed size, i.e. the length of k-mers, 16 is suggested for the WGBS mode, and 12 is suggested for the RRBS mode. Min=8, max=16."/>
             <conditional name="bsmap_mismatch">
-                <param name="bsmap_mismatch_selector" type="select" label="Set the mismatch rate or number?" help="">
-                    <option value="0">Do not set</option>
+                <param name="bsmap_mismatch_selector" type="select" label="Set the mismatch rate or number?" help="When `Do not set` selected, BSMAP will allow a default suggested 8% mismatch rate. Otherwise, a customized mismatch can be controlled by specifying a mismatch rate or a mismatch number.">
+                    <option value="0" selected="true">Do not set</option>
                     <option value="1">Set the mismatch rate</option>
                     <option value="2">Set the mismatch number</option>
                 </param>
@@ -147,44 +187,102 @@
                     <param argument="-v" type="integer" value="3" min="0" label="Mismatch number" help="The maximum number of mismatches allowed on a read"/>
                 </when>
             </conditional>
-            <param argument="-n" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Mapping to four strands?" help="Yes: map SE or PE reads to all 4 strands, i.e. ++, +-, -+, --; No: only map to 2 forward strands, i.e. BSW(++) and BSC(-+)"/>
-            <param argument="-r" type="select" label="How to report repeat hits" help="0=none(unique hit/pair); 1=random one; 2=all(slow)">
+            <param argument="-w" type="integer" value="1000" min="0" max="1000" label="Maximum number of equal best hits to count" help="Maximum number of equal best hits to count. When multiple mapping occurs for a read, it should control the number of records to report. Default: 1000."/>
+            <param argument="-D" type="text" label="Restriction enzyme digestion sites for RRBS mode" help="For RRBS data, this option activates RRBS mapping mode and set restriction enzyme digestion sites. Digestion position marked by '-', example: -D C-CGG for MspI digestion.  default: none (WGBS mode).">
+              <validator type="regex" message="Use A/T/C/G/- for restriction enzyme digestion sites">^[ATCG-]*$</validator>
+            </param>
+            <param argument="-S" type="integer" value="0" label="Random seed" help="Seed for random number generation used in selecting multiple hits. Other seed values generate pseudo random number based on read index number, to allow reproducible mapping results. Default=0 (get seed from system clock, mapping results not resproducible)."/>
+            <param argument="-n" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Mapping to four strands?" help="Yes: map SE or PE reads to all 4 strands, i.e. ++, +-, -+, --; No: only map to 2 forward strands, i.e. BSW(++) and BSC(-+). For example, for a traditional library construction, two forward strands, ++ and -+, are sufficient for alignments. However, a Pico library construction needs all four-strand mappings."/>
+            <param argument="-q" type="integer" value="0" min="0" max="40" label="Quality threshold in trimming" help="The quality threshold to trim read bases. To obtain an accurate mapping, low-quality bases should be skipped beforehand. Min=0, max=40. Default=0 (no trim)."/>
+            <param argument="-z" type="select" label="Base quality" help="Base quality for sequencing reads, Illumina or Sanger.">
+                <option value="33" selected="true">Sanger</option>
+                <option value="64">Illumina</option>
+            </param>
+            <param argument="-f" type="integer" value="5" min="0" label="Maximum number of Ns in a read to filter out" help="To filter out low-quality reads containing >n Ns. Default=5."/>
+            <param argument="-A" type="text" label="3' adapter sequence to trim" help="To trim 3' adapter sequence. Default: none (no trim).">
+              <validator type="regex" message="Use A/T/C/G for adapter sequences, and the length should be greater equal to 12 bases.">^[ATCG]{12,}$|^$</validator>
+            </param>
+            <param argument="-r" type="select" label="How to report repeat hits" help="0=none(unique hit/pair); 1=random one; 2=all(slow). When input reads coverage is high, it is suggested to report only unique hits (r=0). For a low-depth library, a random one from multiple mappings (r=1), or all multiple mappings (r=2) can be specified to increase read coverage, yet be cautious about bias caused by ambiguous mappings.">
                 <option value="0" selected="true">0</option>
                 <option value="1">1</option>
                 <option value="2">2</option>
             </param>
+            <param argument="-R" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Print corresponding reference sequences?" help="Yes: print corresponding reference sequences in mapping records, a `RS:` tag will be added in record attributes; No: do not print reference sequences."/>
+            <param argument="-u" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Report unmapped reads?" help="Yes: print unmapped reads; No: do not print unmapped reads."/>
+            <param argument="-m" type="integer" value="28" min="0" label="Minimal insert size allowed in paired-end mapping" help="For paired-end reads, the minimal insert size allowed in two end mapping. Default=28."/>
+            <param argument="-x" type="integer" value="1000" min="0" label="Maximal insert size allowed in paired-end mapping" help="For paired-end reads, the maximal insert size allowed in two end mapping. Default=1000."/>
+        </section>
+        <section name="mcall_advanced" title="Advanced options for MCALL" expanded="False">
+            <param argument="--cytosineMinScore" type="integer" value="20" min="0" label="Threshold for cytosine quality score" help="Threshold for cytosine quality score. Discard the base if threshold is not reached. Default=20."/>
+            <param argument="--nextBaseMinScore" type="integer" value="3" min="-1" label="Threshold for the next base quality score" help="Threshold for the next base quality score. Possible values: -1 makes the program not to check if next base matches reference; any positive integer or zero makes the program to check if next base matches reference and reaches this score threshold; default=3, i.e., better than 'B' or '#'."/>
+            <param argument="--qualityScoreBase" type="select" label="Specify the quality score system" help="Sanger, Solexa, or Illumina. See wiki FASTQ_format for details. Default: auto-detection.">
+                <option value="0" selected="true">Auto-detection</option>
+                <option value="33">Sanger</option>
+                <option value="59">Solexa</option>
+                <option value="64">Illumina</option>
+            </param>
+            <param argument="--trimWGBSEndRepairPE2Seq" type="integer" value="3" min="0" label="Bases to trim end-repair sequences from +-/--" help="To trim end-repair sequence from begin of +-/-- reads from Pair End WGBS Sequencing. 0: no trim; n (positive integer): trim n bases from begin of +-/-- reads. Default: trim 3 bases."/>
+            <param argument="--trimWGBSEndRepairPE1Seq" type="integer" value="3" min="0" label="Bases to trim end-repair sequences from ++/-+" help="To trim end-repair sequence from end of ++/-+ reads from Pair End WGBS Sequencing. 0: no trim; n (positive integer): trim n bases from end of ++/-+ reads. Default: trim 3 bases."/>
+            <param argument="--processPEOverlapSeq" type="select" label="Count once or twice the overlap sequence of two pairs" help="Two ends of paired-end reads may be overlapped in mapping. The overlap sequencce will be counted once or twice for cytosine methylation measurements. Default: once.">
+                <option value="1" selected="true">Once</option>
+                <option value="0">Twice</option>
+            </param>
+            <param argument="--trimRRBSEndRepairSeq" type="select" label="How to trim end-repair sequence for RRBS reads?" help="To trim end-repair sequence for RRBS reads. 0: no trim; 2: trim the last CG at exactly end of ++/-+ reads and trim the first CG at exactly begin of +-/-- reads like the WGBS situation. Default=2.">
+                <option value="2" selected="true">2</option>
+                <option value="0">0</option>
+            </param>
+            <param argument="--minFragSize" type="integer" value="0" min="0" label="Minimal fragment size for properly mapped reads" help="To retain properly mapped and large enough fragment sizes. The 9th field in the BAM file is the fragment size of the mapping, and non-properly-paired read has 0 at the 9th field. This option is set to require properly paired and large enough fragment size. Default=0 for all records."/>
+            <param argument="--minMMFragSize" type="integer" value="0" min="0" label="Minimal fragment size for multiply matched read" help="Same as --minFragSize but this option is only applicable to reads with flag 0x100 set as 1, i.e., reads multiply mapped. Default=0 for all records."/>
+            <param argument="--reportCpX" type="select" label="Generates CpG/A/C/T methylation?" help="To generate methylation for CpG, or CpA/CpC/CpT. Default=CpG.">
+                <option value="G" selected="true">CpG</option>
+                <option value="C">CpC</option>
+                <option value="A">CpA</option>
+                <option value="T">CpT</option>
+            </param>
         </section>
         <section name="mcomp_advanced" title="Advanced options for MCOMP" expanded="False">
             <conditional name="doComp">
                 <param name="compare_selector" type="select" label="Run the comparison or not" help="Yes: compare; No: do not compare, using the comparison result by `-c`">
-                    <option value="1">Yes</option>
+                    <option value="1" selected="true">Yes</option>
                     <option value="0">No</option>
                 </param>
                 <when value="0">
                     <param argument="-c" name="compFile" type="data" format="txt" label="Input comparison results" help="Previously generated comparison file from history"/>
                 </when>
             </conditional>
+            <param argument="-d" type="integer" value="3" min="0" label="Minimum depth for a site coverage" help="If a site has depth less than `d`, this site is ignored for statistical tests. This option affects much of nominal ratios but none of credible ratios. This option may be reset during later DMC/DMR rescan to filter sites with depth less than `d`. Default=3."/>
+            <param argument="--filterCredibleDif" type="float" value="-10" label="Minimum absolute credible methylation difference (CDIF)" help="If absolute value of CDIF for a site less than filterCredibleDif, this site is ignored for regional calculation. Use a small value, such as 0.01, to filter all sites with no difference; use 0.20 (for example) to select DMCs. Any negative number means no filter. Default=-10."/>
+            <param argument="--pFetDmc" type="float" value="0.05" min="0" max="1" label="Cutoff of Pvalue from Fisher Exact Test for DMC scan" help="Cutoff of P value from Fisher Exact Test for DMC scan. Default=`0.05`."/>
+            <param argument="--pFetDmr" type="float" value="0.05" min="0" max="1" label="Cutoff of Pvalue from Fisher Exact Test for DMR scan" help="Cutoff of P value from Fisher Exact Test for DMR scan. Default=`0.05`."/>
+            <param argument="--minNominalDif" type="float" value="0.33333" min="0" max="1" label="Minimal nominal methylation difference for DMC and DMR calling" help="Minimal nominal methylation difference for DMC and DMR. Default=`0.3333`."/>
+            <param argument="--minCredibleDif" type="float" value="0.2" min="0" max="1" label="Minimal credible methylation difference for DMC calling" help="Minimal CDIF for DMC calling. Default=`0.2`."/>
+            <param argument="--minDmcsInDmr" type="integer" value="3" min="1" label="Minimum number of DMCs in a DMR" help="Minimum number of DMCs in a DMR. Default=3."/>
+            <param argument="--maxDistConsDmcs" type="integer" value="300" min="1" label="Maximum distance between two consective DMCs for a DMR" help="Maximum distance between two consective DMCs for a DMR. Default=300."/>
         </section>
         <param name="output_selector" type="select" multiple="true" optional="true" label="Select output files" help="">
-            <option value="1"> dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr </option>
-            <option value="2"> comp.g1.vs.g2.txt </option>
-            <option value="3"> BAM files </option>
-            <option value="4"> Methylation calling BED files </option>
+            <option value="1" selected="true">dmc_M2_g1.G.bed_vs_g2.G.bed.txt</option>
+            <option value="2" selected="true">dmr_M2_g1.G.bed_vs_g2.G.bed.txt</option>
+            <option value="3" selected="true">comp.g1.vs.g2.txt</option>
+            <option value="4" selected="true">BAM files</option>
+            <option value="5" selected="true">Methylation calling BED files</option>
         </param>
     </inputs>
     <outputs>
-        <data name="output1" format="interval" label="${tool.name} on ${on_string} : dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr">
+        <data name="output1" format="interval" label="${tool.name} on ${on_string} : dmc_M2_g1.G.bed_vs_g2.G.bed.txt">
             <filter> "1" in output_selector </filter>
         </data>
-        <data name="output2" format="interval" label="${tool.name} on ${on_string} : comp.g1.vs.g2.txt">
+        <data name="output2" format="interval" label="${tool.name} on ${on_string} : dmr_M2_g1.G.bed_vs_g2.G.bed.txt">
             <filter> "2" in output_selector </filter>
         </data>
+        <data name="output3" format="interval" label="${tool.name} on ${on_string} : comp.g1.vs.g2.txt">
+            <filter> "3" in output_selector </filter>
+        </data>
         <collection name="output_collection_bam" type="list" label="BAM files">
-            <filter> "3" in output_selector </filter>
+            <filter> "4" in output_selector </filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.+\.bam$)" ext='bam'/>
         </collection>
         <collection name="output_collection_bed" type="list" label="Methylation calling BED files">
-            <filter> "4" in output_selector </filter>
+            <filter> "5" in output_selector </filter>
             <discover_datasets pattern="(?P&lt;designation&gt;g[12]\.G\.bed$)" ext='interval'/>
         </collection>
     </outputs>
@@ -226,14 +324,15 @@
                 <param name="compare_selector" value="1"/>
             </conditional>
             -->
-            <param name="output_selector" value="1,2,3,4"/>
-            <output name="output1" file="SE_dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr" ftype="interval" lines_diff="1"/>
-            <output name="output2" file="SE_comp.g1.vs.g2.txt" ftype="interval" lines_diff="1"/>
+            <param name="output_selector" value="1,2,3,4,5"/>
+            <output name="output1" file="SE_dmc_M2_g1.G.bed_vs_g2.G.bed.txt" ftype="interval" lines_diff="1"/>
+            <output name="output2" file="SE_dmr_M2_g1.G.bed_vs_g2.G.bed.txt" ftype="interval" lines_diff="1"/>
+            <output name="output3" file="SE_comp.g1.vs.g2.txt" ftype="interval" lines_diff="1"/>
             <output_collection name="output_collection_bam" count="4">
-                <element name="g1_r1.bam" file="SE_g1_r1.bam" compare="sim_size"/>
-                <element name="g1_r2.bam" file="SE_g1_r2.bam" compare="sim_size"/>
-                <element name="g2_r1.bam" file="SE_g2_r1.bam" compare="sim_size"/>
-                <element name="g2_r2.bam" file="SE_g2_r2.bam" compare="sim_size"/>
+                <element name="g1_r1.bam" file="SE_g1_r1.bam" ftype="bam" lines_diff="2"/>
+                <element name="g1_r2.bam" file="SE_g1_r2.bam" ftype="bam" lines_diff="2"/>
+                <element name="g2_r1.bam" file="SE_g2_r1.bam" ftype="bam" lines_diff="2"/>
+                <element name="g2_r2.bam" file="SE_g2_r2.bam" ftype="bam" lines_diff="2"/>
             </output_collection>
             <output_collection name="output_collection_bed" count="2">
                 <element name="g1.G.bed" file="SE_g1.G.bed" ftype="interval" lines_diff="1"/>
@@ -267,9 +366,10 @@
                 <param name="compare_selector" value="1"/>
             </conditional>
             -->
-            <param name="output_selector" value="1,2"/>
-            <output name="output1" file="PE_dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr" ftype="interval" lines_diff="1"/>
-            <output name="output2" file="PE_comp.g1.vs.g2.txt" ftype="interval" lines_diff="1"/>
+            <param name="output_selector" value="1,2,3"/>
+            <output name="output1" file="PE_dmc_M2_g1.G.bed_vs_g2.G.bed.txt" ftype="interval" lines_diff="1"/>
+            <output name="output2" file="PE_dmr_M2_g1.G.bed_vs_g2.G.bed.txt" ftype="interval" lines_diff="1"/>
+            <output name="output3" file="PE_comp.g1.vs.g2.txt" ftype="interval" lines_diff="1"/>
         </test>
         <test>
             <!-- test paired collection -->
@@ -306,9 +406,10 @@
                 <param name="compare_selector" value="1"/>
             </conditional>
             -->
-            <param name="output_selector" value="1,2"/>
-            <output name="output1" file="PE_dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr" ftype="interval" lines_diff="1"/>
-            <output name="output2" file="PE_comp.g1.vs.g2.txt" ftype="interval" lines_diff="1"/>
+            <param name="output_selector" value="1,2,3"/>
+            <output name="output1" file="PE_dmc_M2_g1.G.bed_vs_g2.G.bed.txt" ftype="interval" lines_diff="1"/>
+            <output name="output2" file="PE_dmr_M2_g1.G.bed_vs_g2.G.bed.txt" ftype="interval" lines_diff="1"/>
+            <output name="output3" file="PE_comp.g1.vs.g2.txt" ftype="interval" lines_diff="1"/>
         </test>
         <test>
             <!-- test data table reference -->
@@ -347,9 +448,10 @@
                 <param name="compare_selector" value="1"/>
             </conditional>
             -->
-            <param name="output_selector" value="1,2"/>
-            <output name="output1" file="SE_dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr" ftype="interval" lines_diff="1"/>
-            <output name="output2" file="SE_comp.g1.vs.g2.txt" ftype="interval" lines_diff="1"/>
+            <param name="output_selector" value="1,2,3"/>
+            <output name="output1" file="SE_dmc_M2_g1.G.bed_vs_g2.G.bed.txt" ftype="interval" lines_diff="1"/>
+            <output name="output2" file="SE_dmr_M2_g1.G.bed_vs_g2.G.bed.txt" ftype="interval" lines_diff="1"/>
+            <output name="output3" file="SE_comp.g1.vs.g2.txt" ftype="interval" lines_diff="1"/>
         </test>
     </tests>
     <help>
@@ -376,31 +478,63 @@
 
 **Outputs**
 
-Four output files can be selected to report, namely
+Five output files can be selected to report, namely
 
-    1. **DMR region file** - the major result file
-    2. **Comparison file between two groups** - the intermediate comparion result
-    3. **BAM files** - intermediate BAM files
-    4. **Methylation BED files** - intermediate methylation BED files
+    1. **DMC site file** - the major DMC result file
+    2. **DMR region file** - the major DMR result file
+    3. **Comparison file between two groups** - the intermediate comparion result
+    4. **BAM files** - intermediate BAM files
+    5. **Methylation BED files** - intermediate methylation BED files
 
 -----
 
-MOABS will detect differential methylated regions (DMRs) using the input BS-Seq
-reads. The output file is a tab-delimited text file (not strictly a BED
-format), representing DMRs. It has 8 columns as below.
+MOABS detects differentially methylated cytosines (DMCs) and differentially
+methylated regions (DMRs) using the input BS-Seq reads. The output DMC and DMR
+file are tab-delimited text files (not strictly a BED format), representing
+DMCs and DMRs.
+
+A DMC site file has 15 columns as below.
+
+chrom<TAB>start<TAB>end<TAB>totalC_0<TAB>nominalRatio_0<TAB>ratioCI_0<TAB>totalC_1<TAB>nominalRatio_1<TAB>ratioCI_1<TAB>nominalDif_1-0<TAB>credibleDif_1-0<TAB>difCI_1-0<TAB>p_sim_1_v_0<TAB>p_fet_1_v_0<TAB>class
 
-chrom<TAB>start<TAB>end<TAB>methylation_state<TAB>CpGsites<TAB>DMCcount<TAB>nonDMCcount<TAB>hidden_state
+    1. **chrom** - The chromosome of the CpG site.
+    2. **start** - The start genomic locus of the CpG site.
+    3. **end** - The end genomic locus of the CpG site.
+    4. **totalC_0** - The total number of CpG read coverage in group 0.
+    5. **nominalRatio_0** - The nominal methylation ratio of the CpG in group 0.
+    6. **ratioCI_0** - The confidence interval (CI) of the nominal methylation ratio at the CpG site in group 0.
+    7. **totalC_1** - The total number of CpG read coverage in group 1.
+    8. **nominalRatio_1** - The nominal methylation ratio of the CpG in group 1.
+    9. **ratioCI_1** - The confidence interval (CI) of the nominal methylation ratio at the CpG site in group 1.
+    10. **nominalDif_1-0** - The nominal methylation difference between the group 1 and the group 0.
+    11. **credibleDif_1-0** - The credible methylation difference (CDIF) between the group 1 and the group 0.
+    12. **difCI_1-0** - The difference of ratio CIs between the group 1 and the group 0.
+    13. **p_sim_1_v_0** - P-value according to the similarity probablities.
+    14. **p_fet_1_v_0** - P-value according to the Fisher exact test.
+    15. **class** - 5-state class labels by methylation differences and p-values.
+
+For example, CpGs in the DMC file are recorded in the following format.
+
+@DMCExample@
+
+A DMR result file has 12 columns as below.
+
+chrom<TAB>start<TAB>end<TAB>meanRatio_0<TAB>totalC_0<TAB>cSites_0<TAB>meanRatio_1<TAB>totalC_1<TAB>cSites_1<TAB>methDif_1-0<TAB>p_1_v_0<TAB>class_1_v_0
 
     1. **chrom** - The chromosome of the region.
     2. **start** - The start genomic locus of the region.
     3. **end** - The end genomic locus of the region.
-    4. **methylation_state** - The methylation state of the region, "+"/"-" representing hyper- or hypo-methylation regions.
-    5. **CpGsites** - Total number of CpG sites in the region.
-    6. **DMCcount** - The number of differential methylated CpG sites (DMCs) in the region.
-    7. **nonDMCcount** - The number of non-DMCs in the region.
-    8. **hidden_state** - The hidden state prediced by Hidden Markov Model (HMM), "1"/"-1" representing hyper- or hypo-methylation states.
+    4. **meanRatio_0** - Mean methylation ratio of the region in group 0.
+    5. **totalC_0** - Total cytosine coverage of the region in group 0.
+    6. **cSites_0** - The number of CpG sites of the region in group 0.
+    7. **meanRatio_1** - Mean methylation ratio of the region in group 1.
+    8. **totalC_1** - Total cytosine coverage of the region in group 1.
+    9. **cSites_1** - The number of CpG sites of the region in group 1.
+    10. **methDif_1-0** - Average methylation difference of the region between group 1 and group 0.
+    11. **p_1_v_0** - P-value from Fisher exact test of the region between group 1 and group 0.
+    12. **class_1_v_0** - 5-state class labels for the DMR.
 
-For example, six DMRs are identified in the following format.
+For example, four DMRs are identified in the following format.
 
 @DMRExample@
 
diff -r 26d7ec4af119 -r 8c8cc81b34cd test-data/PE_dmc_M2_g1.G.bed_vs_g2.G.bed.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/PE_dmc_M2_g1.G.bed_vs_g2.G.bed.txt	Sat Apr 11 04:14:34 2020 -0400
@@ -0,0 +1,122 @@
+#chrom	start	end	totalC_0	nominalRatio_0	ratioCI_0	totalC_1	nominalRatio_1	ratioCI_1	nominalDif_1-0	credibleDif_1-0	difCI_1-0	p_sim_1_v_0	p_fet_1_v_0	class
+seg	87	89	6	1	0.652,1	10	0.2	0,0.47	-0.8	-0.327	-0.857,-0.327	0.000318	0.00699	strongHypo
+seg	152	154	4	1	0.549,1	9	0.333	0.0575,0.609	-0.667	-0.113	-0.761,-0.113	0.0035	0.0699	hypo
+seg	258	260	3	1	0.473,1	13	0.231	0,0.466	-0.769	-0.165	-0.809,-0.165	0.00236	0.0357	hypo
+seg	331	333	6	0.667	0.341,0.992	22	0.227	0.0499,0.405	-0.439	-0.058	-0.66,-0.058	0.00636	0.0638	hypo
+seg	630	632	3	1	0.473,1	5	0	0,0.393	-1	-0.271	-1,-0.271	0.000954	0.0179	strongHypo
+seg	638	640	3	0.667	0.249,1	5	0.6	0.264,0.936	-0.0667	-0	-0.461,0.418	0.0286	1	hypo
+seg	641	643	4	1	0.549,1	5	0.4	0.064,0.736	-0.6	-0.0122	-0.748,-0.0122	0.00715	0.167	hypo
+seg	645	647	4	1	0.549,1	8	1	0.717,1	0	0	-0.183,0.374	0.067	1	hypo
+seg	666	668	4	1	0.549,1	9	0.667	0.391,0.942	-0.333	-0	-0.506,0.15	0.021	0.497	hypo
+seg	685	687	3	1	0.473,1	8	0	0,0.283	-1	-0.342	-1,-0.342	0.000364	0.00606	strongHypo
+seg	689	691	4	1	0.549,1	9	0.667	0.391,0.942	-0.333	-0	-0.506,0.15	0.021	0.497	hypo
+seg	697	699	3	1	0.473,1	7	0.571	0.27,0.872	-0.429	-0	-0.595,0.156	0.017	0.475	hypo
+seg	699	701	3	1	0.473,1	9	1	0.741,1	0	0	-0.149,0.454	0.0596	1	hypo
+seg	820	822	7	0.857	0.529,1	20	0.4	0.2,0.6	-0.457	-0.0729	-0.62,-0.0729	0.00528	0.0768	hypo
+seg	830	832	7	0.857	0.529,1	18	0.222	0.0252,0.419	-0.635	-0.236	-0.766,-0.236	0.000768	0.0068	strongHypo
+seg	842	844	4	0.75	0.343,1	10	0.3	0.035,0.565	-0.45	-0	-0.672,0.0536	0.0117	0.245	hypo
+seg	1172	1174	3	1	0.473,1	12	0.333	0.0889,0.578	-0.667	-0.0658	-0.738,-0.0658	0.005	0.0769	hypo
+seg	1180	1182	3	1	0.473,1	11	0.0909	0,0.339	-0.909	-0.286	-0.909,-0.286	0.000705	0.011	strongHypo
+seg	1201	1203	3	0.667	0.249,1	14	0.214	0,0.44	-0.452	-0	-0.7,0.0401	0.0118	0.191	hypo
+seg	1203	1205	3	0.667	0.249,1	13	0.308	0.0724,0.543	-0.359	-0	-0.629,0.133	0.0176	0.518	hypo
+seg	1303	1305	3	1	0.473,1	4	0	0,0.451	-1	-0.229	-1,-0.229	0.00143	0.0286	strongHypo
+seg	1333	1335	4	0.25	0,0.657	6	0.167	0,0.521	-0.0833	-0	-0.47,0.291	0.0339	1	hypo
+seg	1343	1345	3	0	0,0.527	10	0.2	0,0.47	0.2	0	-0.318,0.357	0.0363	1	hypo
+seg	2310	2312	8	1	0.717,1	11	0.455	0.198,0.711	-0.545	-0.162	-0.69,-0.162	0.00184	0.0181	hypo
+seg	2336	2338	8	1	0.717,1	5	0.6	0.264,0.936	-0.4	-0.0115	-0.656,-0.0115	0.0099	0.128	hypo
+seg	2396	2398	8	1	0.717,1	12	0.333	0.0889,0.578	-0.667	-0.273	-0.774,-0.273	0.000439	0.0047	strongHypo
+seg	2488	2490	3	0.333	0,0.751	7	0	0,0.312	-0.333	-0	-0.669,0.0603	0.0175	0.3	hypo
+seg	2516	2518	7	0.571	0.27,0.872	16	0.5	0.278,0.722	-0.0714	-0	-0.372,0.269	0.0377	1	hypo
+seg	2529	2531	7	0.571	0.27,0.872	25	0.04	0,0.17	-0.531	-0.203	-0.745,-0.203	0.000552	0.00445	strongHypo
+seg	2548	2550	10	0.7	0.435,0.965	17	0.0588	0,0.238	-0.641	-0.303	-0.787,-0.303	0.000131	0.000939	strongHypo
+seg	2550	2552	10	0.8	0.53,1	20	0.4	0.2,0.6	-0.4	-0.0665	-0.586,-0.0665	0.00582	0.0577	hypo
+seg	2556	2558	11	0.636	0.382,0.891	19	0.0526	0,0.216	-0.584	-0.271	-0.746,-0.271	0.000167	0.0011	strongHypo
+seg	2567	2569	9	0.889	0.606,1	11	0.364	0.109,0.618	-0.525	-0.135	-0.697,-0.135	0.0027	0.0281	hypo
+seg	2573	2575	10	0.9	0.636,1	12	0.167	0,0.41	-0.733	-0.352	-0.835,-0.352	0.000117	0.00191	strongHypo
+seg	2578	2580	9	0.889	0.606,1	10	0.5	0.234,0.766	-0.389	-0.0151	-0.6,-0.0151	0.0092	0.141	hypo
+seg	2580	2582	11	0.909	0.661,1	9	0.222	0,0.507	-0.687	-0.287	-0.812,-0.287	0.00036	0.00452	strongHypo
+seg	2603	2605	8	1	0.717,1	3	0.333	0,0.751	-0.667	-0.119	-0.834,-0.119	0.00328	0.0545	hypo
+seg	2625	2627	8	1	0.717,1	5	0.6	0.264,0.936	-0.4	-0.0115	-0.656,-0.0115	0.0099	0.128	hypo
+seg	2641	2643	10	0.9	0.636,1	10	0.2	0,0.47	-0.7	-0.299	-0.817,-0.299	0.00031	0.00548	strongHypo
+seg	2645	2647	9	0.667	0.391,0.942	8	0.25	0,0.55	-0.417	-0	-0.642,0.00262	0.00968	0.153	hypo
+seg	2659	2661	11	0.727	0.473,0.982	7	0.429	0.128,0.73	-0.299	-0	-0.567,0.0906	0.0183	0.332	hypo
+seg	2684	2686	9	0.778	0.493,1	10	0.5	0.234,0.766	-0.278	-0	-0.529,0.0939	0.0198	0.35	hypo
+seg	2976	2978	92	0.88	0.811,0.95	49	0.347	0.217,0.477	-0.533	-0.393	-0.639,-0.393	7.62e-11	2.14e-10	strongHypo
+seg	2986	2988	122	0.869	0.807,0.93	61	0.377	0.258,0.496	-0.492	-0.368	-0.592,-0.368	1.41e-11	1.77e-11	strongHypo
+seg	3063	3065	8	0.75	0.45,1	6	0	0,0.348	-0.75	-0.257	-0.833,-0.257	0.000785	0.00966	strongHypo
+seg	3207	3209	3	1	0.473,1	6	0.833	0.479,1	-0.167	-0	-0.397,0.333	0.0373	1	hypo
+seg	3405	3407	4	0.75	0.343,1	8	0.25	0,0.55	-0.5	-0	-0.711,0.0288	0.00979	0.222	hypo
+seg	3411	3413	4	0.75	0.343,1	9	0.111	0,0.394	-0.639	-0.112	-0.799,-0.112	0.0036	0.0517	hypo
+seg	3427	3429	4	1	0.549,1	3	0.667	0.249,1	-0.333	-0	-0.639,0.17	0.0214	0.429	hypo
+seg	3429	3431	5	0.8	0.418,1	4	0.5	0.147,0.853	-0.3	-0	-0.611,0.205	0.0214	0.524	hypo
+seg	3433	3435	5	1	0.607,1	3	0.333	0,0.751	-0.667	-0.0486	-0.815,-0.0486	0.00572	0.107	hypo
+seg	3667	3669	3	1	0.473,1	8	0.125	0,0.429	-0.875	-0.221	-0.88,-0.221	0.00146	0.0242	strongHypo
+seg	4037	4039	3	1	0.473,1	8	0.625	0.337,0.913	-0.375	-0	-0.539,0.191	0.0204	0.491	hypo
+seg	4046	4048	3	1	0.473,1	7	0.143	0,0.471	-0.857	-0.189	-0.87,-0.189	0.00194	0.0333	hypo
+seg	4057	4059	4	1	0.549,1	7	0.429	0.128,0.73	-0.571	-0.0173	-0.71,-0.0173	0.00708	0.194	hypo
+seg	4060	4062	4	1	0.549,1	6	0.333	0.0079,0.659	-0.667	-0.0776	-0.778,-0.0776	0.00455	0.0762	hypo
+seg	4277	4279	5	0.8	0.418,1	3	0	0,0.527	-0.8	-0.0985	-0.843,-0.0985	0.00381	0.143	hypo
+seg	4280	4282	5	0.6	0.264,0.936	3	0.333	0,0.751	-0.267	-0	-0.594,0.282	0.0229	1	hypo
+seg	4283	4285	5	0.6	0.264,0.936	4	0	0,0.451	-0.6	-0.0122	-0.748,-0.0122	0.00715	0.167	hypo
+seg	4320	4322	4	0.75	0.343,1	4	0	0,0.451	-0.75	-0.0938	-0.834,-0.0938	0.00397	0.143	hypo
+seg	4327	4329	4	1	0.549,1	3	0	0,0.527	-1	-0.229	-1,-0.229	0.00143	0.0286	strongHypo
+seg	4333	4335	4	1	0.549,1	3	0	0,0.527	-1	-0.229	-1,-0.229	0.00143	0.0286	strongHypo
+seg	4340	4342	3	1	0.473,1	3	0	0,0.527	-1	-0.17	-1,-0.17	0.00229	0.1	hypo
+seg	4505	4507	5	0.4	0.064,0.736	16	0	0,0.162	-0.4	-0.0844	-0.683,-0.0844	0.00444	0.0476	hypo
+seg	4511	4513	6	0.667	0.341,0.992	18	0.167	0,0.359	-0.5	-0.107	-0.709,-0.107	0.00377	0.0381	hypo
+seg	4516	4518	6	0.5	0.184,0.816	21	0.0476	0,0.198	-0.452	-0.122	-0.702,-0.122	0.00264	0.0248	hypo
+seg	4550	4552	9	0.667	0.391,0.942	23	0.13	0,0.292	-0.536	-0.205	-0.719,-0.205	0.000775	0.00564	strongHypo
+seg	4605	4607	8	0.75	0.45,1	26	0	0,0.105	-0.75	-0.408	-0.874,-0.408	2.94e-06	2.08e-05	strongHypo
+seg	4648	4650	15	0.667	0.445,0.889	39	0.179	0.0544,0.305	-0.487	-0.232	-0.653,-0.232	0.00023	0.00108	strongHypo
+seg	4738	4740	26	0.577	0.398,0.756	53	0.151	0.0496,0.252	-0.426	-0.232	-0.576,-0.232	5.23e-05	0.000172	strongHypo
+seg	4797	4799	15	0.6	0.374,0.826	45	0.0889	0,0.188	-0.511	-0.271	-0.68,-0.271	3.55e-05	0.000153	strongHypo
+seg	4829	4831	12	0.75	0.505,0.995	38	0.105	0,0.22	-0.645	-0.364	-0.782,-0.364	9.24e-06	4.74e-05	strongHypo
+seg	4846	4848	14	0.929	0.721,1	38	0.105	0,0.22	-0.823	-0.574	-0.884,-0.574	1.06e-08	4.75e-08	strongHypo
+seg	4922	4924	13	0.538	0.298,0.779	33	0.273	0.123,0.422	-0.266	-0.00424	-0.484,-0.00424	0.0135	0.167	hypo
+seg	4925	4927	13	0.615	0.377,0.854	33	0.303	0.15,0.456	-0.312	-0.0403	-0.517,-0.0403	0.00858	0.0916	hypo
+seg	4932	4934	15	0.8	0.583,1	29	0.276	0.116,0.435	-0.524	-0.251	-0.671,-0.251	0.000238	0.00138	strongHypo
+seg	4949	4951	16	0.625	0.407,0.843	23	0.13	0,0.292	-0.495	-0.224	-0.661,-0.224	0.000359	0.00203	strongHypo
+seg	4982	4984	15	0.6	0.374,0.826	11	0.455	0.198,0.711	-0.145	-0	-0.414,0.169	0.034	0.692	hypo
+seg	4984	4986	14	0.571	0.338,0.804	11	0.455	0.198,0.711	-0.117	-0	-0.393,0.198	0.0369	0.695	hypo
+seg	5011	5013	16	0.375	0.157,0.593	12	0.25	0.00535,0.495	-0.125	-0	-0.364,0.168	0.0389	0.687	hypo
+seg	5013	5015	16	0.375	0.157,0.593	11	0.455	0.198,0.711	0.0795	0	-0.215,0.359	0.0413	0.71	hypo
+seg	5049	5051	6	0.333	0.0079,0.659	8	0.125	0,0.429	-0.208	-0	-0.509,0.156	0.0277	0.538	hypo
+seg	5057	5059	4	0.75	0.343,1	7	0	0,0.312	-0.75	-0.191	-0.856,-0.191	0.00162	0.0242	hypo
+seg	5128	5130	3	1	0.473,1	9	0	0,0.259	-1	-0.356	-1,-0.356	0.00028	0.00455	strongHypo
+seg	5160	5162	4	1	0.549,1	11	0	0,0.221	-1	-0.45	-1,-0.45	5.52e-05	0.000733	strongHypo
+seg	5162	5164	4	1	0.549,1	7	0.143	0,0.471	-0.857	-0.255	-0.88,-0.255	0.00101	0.0152	strongHypo
+seg	5182	5184	3	1	0.473,1	5	0	0,0.393	-1	-0.271	-1,-0.271	0.000954	0.0179	strongHypo
+seg	5192	5194	3	1	0.473,1	6	0.167	0,0.521	-0.833	-0.149	-0.858,-0.149	0.00267	0.0476	hypo
+seg	5333	5335	14	0.857	0.637,1	21	0.143	0,0.316	-0.714	-0.42	-0.819,-0.42	6.9e-06	5.49e-05	strongHypo
+seg	5385	5387	9	0.778	0.493,1	14	0.357	0.127,0.587	-0.421	-0.0503	-0.623,-0.0503	0.00667	0.0894	hypo
+seg	5587	5589	8	1	0.717,1	18	0.778	0.581,0.975	-0.222	-0	-0.356,0.0752	0.026	0.277	hypo
+seg	5857	5859	4	0.75	0.343,1	5	0.2	0,0.582	-0.55	-0	-0.745,0.0401	0.00953	0.206	hypo
+seg	5886	5888	3	0.667	0.249,1	4	0.25	0,0.657	-0.417	-0	-0.685,0.196	0.0171	0.486	hypo
+seg	5896	5898	3	0.667	0.249,1	4	1	0.549,1	0.333	0	-0.17,0.639	0.0214	0.429	hypo
+seg	6182	6184	4	0.5	0.147,0.853	14	0.571	0.338,0.804	0.0714	0	-0.307,0.43	0.0325	1	hypo
+seg	6304	6306	6	0.5	0.184,0.816	5	0	0,0.393	-0.5	-0.00245	-0.684,-0.00245	0.00849	0.182	hypo
+seg	6332	6334	8	0.75	0.45,1	6	0.167	0,0.521	-0.583	-0.096	-0.751,-0.096	0.00412	0.103	hypo
+seg	6403	6405	7	0.857	0.529,1	3	0	0,0.527	-0.857	-0.189	-0.87,-0.189	0.00194	0.0333	hypo
+seg	6411	6413	6	1	0.652,1	4	0.75	0.343,1	-0.25	-0	-0.567,0.123	0.0255	0.4	hypo
+seg	6420	6422	4	1	0.549,1	3	0.667	0.249,1	-0.333	-0	-0.639,0.17	0.0214	0.429	hypo
+seg	6533	6535	3	0.667	0.249,1	14	0.0714	0,0.279	-0.595	-0.101	-0.805,-0.101	0.00412	0.0632	hypo
+seg	6544	6546	4	0.75	0.343,1	15	0	0,0.171	-0.75	-0.272	-0.881,-0.272	0.000332	0.00413	strongHypo
+seg	6640	6642	7	1	0.688,1	3	0.667	0.249,1	-0.333	-0	-0.669,0.0603	0.0175	0.3	hypo
+seg	6654	6656	8	0.875	0.571,1	4	0.25	0,0.657	-0.625	-0.0857	-0.789,-0.0857	0.00448	0.0667	hypo
+seg	6671	6673	9	0.778	0.493,1	9	0.222	0,0.507	-0.556	-0.135	-0.731,-0.135	0.00281	0.0567	hypo
+seg	6732	6734	3	1	0.473,1	9	0.111	0,0.394	-0.889	-0.247	-0.889,-0.247	0.00112	0.0182	strongHypo
+seg	6774	6776	6	0.833	0.479,1	7	0	0,0.312	-0.833	-0.318	-0.887,-0.318	0.000374	0.00466	strongHypo
+seg	6789	6791	6	1	0.652,1	5	0	0,0.393	-1	-0.417	-1,-0.417	0.000152	0.00216	strongHypo
+seg	6794	6796	9	1	0.741,1	7	0	0,0.312	-1	-0.549	-1,-0.549	8.26e-06	8.74e-05	strongHypo
+seg	6839	6841	3	1	0.473,1	4	0.25	0,0.657	-0.75	-0.0327	-0.822,-0.0327	0.00572	0.143	hypo
+seg	6845	6847	4	1	0.549,1	5	0.2	0,0.582	-0.8	-0.161	-0.854,-0.161	0.00238	0.0476	hypo
+seg	6855	6857	4	1	0.549,1	5	0.2	0,0.582	-0.8	-0.161	-0.854,-0.161	0.00238	0.0476	hypo
+seg	6861	6863	6	1	0.652,1	4	0.25	0,0.657	-0.75	-0.168	-0.85,-0.168	0.00212	0.0333	hypo
+seg	6940	6942	3	1	0.473,1	3	0	0,0.527	-1	-0.17	-1,-0.17	0.00229	0.1	hypo
+seg	6942	6944	4	1	0.549,1	4	0	0,0.451	-1	-0.291	-1,-0.291	0.000795	0.0286	strongHypo
+seg	6950	6952	4	1	0.549,1	4	0	0,0.451	-1	-0.291	-1,-0.291	0.000795	0.0286	strongHypo
+seg	6983	6985	3	1	0.473,1	5	0	0,0.393	-1	-0.271	-1,-0.271	0.000954	0.0179	strongHypo
+seg	7006	7008	3	1	0.473,1	4	0	0,0.451	-1	-0.229	-1,-0.229	0.00143	0.0286	strongHypo
+seg	8052	8054	4	1	0.549,1	9	0.111	0,0.394	-0.889	-0.315	-0.896,-0.315	0.0005	0.00699	strongHypo
+seg	8058	8060	4	1	0.549,1	6	0.333	0.0079,0.659	-0.667	-0.0776	-0.778,-0.0776	0.00455	0.0762	hypo
+seg	8089	8091	3	0.667	0.249,1	3	0	0,0.527	-0.667	-0	-0.791,0.054	0.00915	0.4	hypo
diff -r 26d7ec4af119 -r 8c8cc81b34cd test-data/PE_dmr_M2_g1.G.bed_vs_g2.G.bed.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/PE_dmr_M2_g1.G.bed_vs_g2.G.bed.txt	Sat Apr 11 04:14:34 2020 -0400
@@ -0,0 +1,5 @@
+#chrom	start	end	meanRatio_0	totalC_0	cSites_0	meanRatio_1	totalC_1	cSites_1	methDif_1-0	p_1_v_0	class_1_v_0
+seg	2529	2582	0.787	77	8	0.226	123	8	-0.204	3.79e-17	strongHypo
+seg	2976	3065	0.833	222	3	0.241	116	3	-0.339	1.69e-22	strongHypo
+seg	4327	5335	0.722	286	29	0.143	563	29	-0.201	2.3e-48	strongHypo
+seg	6544	7008	0.955	86	17	0.126	97	17	-0.223	6.5e-34	strongHypo
diff -r 26d7ec4af119 -r 8c8cc81b34cd test-data/PE_dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr
--- a/test-data/PE_dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr	Fri Sep 06 09:54:27 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-seg	152	1305	-	20	15	5	1
-seg	2310	7008	-	95	77	18	1
-seg	8052	8091	-	3	3	0	1
diff -r 26d7ec4af119 -r 8c8cc81b34cd test-data/SE_dmc_M2_g1.G.bed_vs_g2.G.bed.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SE_dmc_M2_g1.G.bed_vs_g2.G.bed.txt	Sat Apr 11 04:14:34 2020 -0400
@@ -0,0 +1,308 @@
+#chrom	start	end	totalC_0	nominalRatio_0	ratioCI_0	totalC_1	nominalRatio_1	ratioCI_1	nominalDif_1-0	credibleDif_1-0	difCI_1-0	p_sim_1_v_0	p_fet_1_v_0	class
+chr11	41	43	3	0	0,0.527	3	0	0,0.527	0	0	-0.391,0.391	0.0449	1	hypo
+chr11	48	50	5	0	0,0.393	3	0	0,0.527	0	0	-0.267,0.422	0.0521	1	hypo
+chr11	56	58	6	0	0,0.348	4	0	0,0.451	0	0	-0.241,0.359	0.0619	1	hypo
+chr11	59	61	8	0	0,0.283	5	0.4	0.064,0.736	0.4	0.0115	0.0115,0.656	0.0099	0.128	hyper
+chr11	101	103	13	0.0769	0,0.297	7	0.143	0,0.471	0.0659	0	-0.152,0.364	0.051	1	hypo
+chr11	140	142	16	0	0,0.162	9	0	0,0.259	0	0	-0.107,0.216	0.123	1	hypo
+chr11	144	146	14	0	0,0.181	10	0.1	0,0.364	0.1	0	-0.0722,0.317	0.0549	0.417	hypo
+chr11	210	212	15	0.133	0,0.344	12	0.417	0.169,0.664	0.283	0	-0.00696,0.507	0.0139	0.185	hypo
+chr11	215	217	19	0.263	0.0688,0.458	16	0.25	0.039,0.461	-0.0132	-0	-0.238,0.226	0.0566	1	hypo
+chr11	316	318	24	0.0833	0,0.231	26	0.846	0.692,1	0.763	0.538	0.538,0.845	9.21e-09	3.52e-08	strongHyper
+chr11	331	333	27	0.037	0,0.159	26	0.808	0.649,0.966	0.771	0.558	0.558,0.85	1.11e-09	4.05e-09	strongHyper
+chr11	400	402	34	0.0588	0,0.169	34	0.412	0.254,0.57	0.353	0.18	0.18,0.486	0.000192	0.00115	hyper
+chr11	407	409	33	0	0,0.0843	34	0.588	0.43,0.746	0.588	0.41	0.41,0.692	8.72e-09	3.39e-08	strongHyper
+chr11	445	447	25	0.08	0,0.223	33	0.606	0.447,0.766	0.526	0.316	0.316,0.648	9.32e-06	3.59e-05	strongHyper
+chr11	469	471	26	0.0385	0,0.164	34	0.588	0.43,0.746	0.55	0.352	0.352,0.661	1.43e-06	5.87e-06	strongHyper
+chr11	546	548	20	0.1	0,0.271	32	0.812	0.672,0.953	0.713	0.482	0.482,0.806	1.08e-07	4.38e-07	strongHyper
+chr11	666	668	20	0.05	0,0.207	38	0.553	0.401,0.704	0.503	0.29	0.29,0.612	2.88e-05	0.000144	strongHyper
+chr11	694	696	22	0.318	0.132,0.504	41	0.902	0.795,1	0.584	0.368	0.368,0.716	8.72e-07	2.95e-06	strongHyper
+chr11	712	714	28	0.0714	0,0.202	42	0.881	0.771,0.991	0.81	0.63	0.63,0.873	1.66e-12	4.55e-12	strongHyper
+chr11	721	723	28	0.0357	0,0.153	39	0.923	0.817,1	0.887	0.719	0.719,0.926	9.44e-15	2.57e-14	strongHyper
+chr11	737	739	27	0.037	0,0.159	37	0.622	0.471,0.772	0.585	0.393	0.393,0.687	2.21e-07	9.15e-07	strongHyper
+chr11	753	755	23	0.087	0,0.24	41	0.78	0.653,0.908	0.694	0.488	0.488,0.783	1.74e-08	5.8e-08	strongHyper
+chr11	762	764	27	0.037	0,0.159	42	0.619	0.477,0.761	0.582	0.397	0.397,0.68	1.42e-07	5.56e-07	strongHyper
+chr11	792	794	37	0.324	0.178,0.471	38	0.842	0.719,0.966	0.518	0.329	0.329,0.642	1.8e-06	6.02e-06	strongHyper
+chr11	798	800	36	0.306	0.159,0.452	40	0.875	0.761,0.989	0.569	0.384	0.384,0.685	1.25e-07	3.94e-07	strongHyper
+chr11	816	818	33	0.0303	0,0.132	34	0.912	0.793,1	0.881	0.714	0.714,0.924	5.66e-15	1.61e-14	strongHyper
+chr11	830	832	37	0.405	0.254,0.557	35	0.914	0.798,1	0.509	0.324	0.324,0.629	1.55e-06	5.05e-06	strongHyper
+chr11	954	956	47	0	0,0.0605	33	0.485	0.323,0.647	0.485	0.324	0.324,0.606	1.85e-08	4.33e-08	strongHyper
+chr11	977	979	47	0.255	0.132,0.379	37	0.703	0.559,0.847	0.447	0.264	0.264,0.579	1.7e-05	5.98e-05	strongHyper
+chr11	1006	1008	38	0	0,0.0739	38	0.526	0.374,0.678	0.526	0.364	0.364,0.633	1.27e-08	6.16e-08	strongHyper
+chr11	1066	1068	30	0.367	0.202,0.532	45	0.756	0.63,0.881	0.389	0.192	0.192,0.538	0.00027	0.00152	hyper
+chr11	1116	1118	22	0.182	0.0087,0.355	35	0.771	0.632,0.911	0.59	0.362	0.362,0.713	4.09e-06	2.32e-05	strongHyper
+chr11	1145	1147	18	0.556	0.345,0.766	26	0.538	0.358,0.719	-0.0171	-0	-0.248,0.222	0.0547	1	hypo
+chr11	1260	1262	18	0.0556	0,0.226	24	0.375	0.192,0.558	0.319	0.0943	0.0943,0.47	0.00355	0.0264	hyper
+chr11	1320	1322	17	0.118	0,0.31	25	0.64	0.461,0.819	0.522	0.26	0.26,0.661	0.000172	0.00122	strongHyper
+chr11	1559	1561	36	0.194	0.0615,0.327	27	0.852	0.702,1	0.657	0.451	0.451,0.762	5.66e-08	1.9e-07	strongHyper
+chr11	1574	1576	33	0.152	0.0184,0.285	28	0.607	0.435,0.779	0.456	0.245	0.245,0.601	7.43e-05	0.000388	strongHyper
+chr11	1592	1594	35	0.343	0.191,0.495	33	0.697	0.544,0.85	0.354	0.149	0.149,0.509	0.001	0.00421	hyper
+chr11	1609	1611	34	0.0588	0,0.169	41	0.244	0.113,0.375	0.185	0.0419	0.0419,0.305	0.0094	0.0545	hyper
+chr11	1632	1634	36	0.0556	0,0.161	45	0.2	0.0811,0.319	0.144	0.0144	0.0144,0.255	0.0193	0.1	hyper
+chr11	1642	1644	32	0.188	0.0468,0.328	41	0.268	0.134,0.402	0.0808	0	-0.0869,0.229	0.0606	0.578	hypo
+chr11	1680	1682	34	0.0882	0,0.207	54	0.611	0.485,0.738	0.523	0.354	0.354,0.626	2.25e-07	6.09e-07	strongHyper
+chr11	1689	1691	35	0.2	0.0642,0.336	51	0.471	0.338,0.603	0.271	0.095	0.095,0.408	0.00289	0.0124	hyper
+chr11	1703	1705	42	0.262	0.13,0.393	49	0.755	0.635,0.875	0.493	0.319	0.319,0.614	1.06e-06	2.93e-06	strongHyper
+chr11	1733	1735	43	0.512	0.368,0.655	51	0.745	0.626,0.864	0.233	0.0666	0.0666,0.379	0.00549	0.0305	hyper
+chr11	1766	1768	46	0.13	0.0243,0.237	48	0.312	0.184,0.441	0.182	0.0381	0.0381,0.31	0.0105	0.0473	hyper
+chr11	1869	1871	45	0.244	0.119,0.37	38	0.263	0.125,0.402	0.0187	0	-0.134,0.175	0.0834	1	hypo
+chr11	2040	2042	37	0	0,0.0758	34	0	0,0.082	0	0	-0.057,0.0639	0.31	1	hypo
+chr11	2104	2106	37	0.027	0,0.119	39	0.0513	0,0.149	0.0243	0	-0.0641,0.111	0.153	1	hypo
+chr11	2148	2150	31	0.613	0.449,0.777	34	0.588	0.43,0.746	-0.0247	-0	-0.214,0.17	0.0664	1	hypo
+chr11	2360	2362	42	0.262	0.13,0.393	26	0.538	0.358,0.719	0.277	0.0726	0.0726,0.448	0.00528	0.0373	hyper
+chr11	2384	2386	34	0.382	0.226,0.539	27	0.593	0.417,0.768	0.21	0	-0.00431,0.392	0.0176	0.126	hypo
+chr11	2454	2456	41	0.171	0.0504,0.291	28	0.107	0,0.246	-0.0636	-0	-0.189,0.0894	0.0753	0.729	hypo
+chr11	2621	2623	9	0	0,0.259	12	0	0,0.206	0	0	-0.206,0.147	0.112	1	hypo
+chr11	2648	2650	10	0	0,0.238	20	0	0,0.133	0	0	-0.202,0.0851	0.138	1	hypo
+chr11	2665	2667	13	0	0,0.193	19	0.105	0,0.283	0.105	0	-0.0832,0.237	0.0587	0.502	hypo
+chr11	2667	2669	17	0	0,0.153	20	0.1	0,0.271	0.1	0	-0.0533,0.233	0.057	0.489	hypo
+chr11	2673	2675	13	0	0,0.193	21	0.19	0.0119,0.369	0.19	0	-0.0203,0.323	0.0228	0.144	hypo
+chr11	2676	2678	17	0	0,0.153	26	0.0385	0,0.164	0.0385	0	-0.0986,0.129	0.132	1	hypo
+chr11	2685	2687	16	0.0625	0,0.25	28	0.143	0,0.288	0.0804	0	-0.113,0.211	0.0661	0.638	hypo
+chr11	2688	2690	19	0	0,0.139	28	0	0,0.0981	0	0	-0.114,0.0684	0.215	1	hypo
+chr11	2691	2693	20	0	0,0.133	29	0.276	0.116,0.435	0.276	0.0981	0.0981,0.397	0.00242	0.0148	hyper
+chr11	2713	2715	22	0	0,0.122	26	0.154	6.6e-05,0.308	0.154	0.0107	0.0107,0.277	0.0197	0.114	hyper
+chr11	2723	2725	19	0	0,0.139	25	0.12	0,0.272	0.12	0	-0.0272,0.238	0.0404	0.247	hypo
+chr11	2727	2729	20	0	0,0.133	20	0.35	0.153,0.547	0.35	0.143	0.143,0.501	0.000903	0.00832	hyper
+chr11	2731	2733	17	0.0588	0,0.238	19	0.211	0.02,0.401	0.152	0	-0.0525,0.322	0.0341	0.342	hypo
+chr11	2738	2740	18	0	0,0.146	22	0.273	0.0909,0.455	0.273	0.0783	0.0783,0.414	0.00417	0.0243	hyper
+chr11	2767	2769	15	0	0,0.171	21	0.333	0.142,0.525	0.333	0.107	0.107,0.473	0.00267	0.0273	hyper
+chr11	2778	2780	12	0.0833	0,0.316	22	0.455	0.261,0.648	0.371	0.0842	0.0842,0.526	0.00465	0.0527	hyper
+chr11	2788	2790	8	0	0,0.283	18	0.167	0,0.359	0.167	0	-0.118,0.297	0.0398	0.529	hypo
+chr11	2792	2794	7	0.143	0,0.471	22	0.318	0.132,0.504	0.175	0	-0.175,0.358	0.0341	0.635	hypo
+chr11	2810	2812	3	0	0,0.527	19	0.105	0,0.283	0.105	0	-0.4,0.187	0.0515	1	hypo
+chr11	2825	2827	4	0	0,0.451	15	0.133	0,0.344	0.133	0	-0.3,0.253	0.0491	1	hypo
+chr11	3031	3033	13	0.0769	0,0.297	15	0.4	0.174,0.626	0.323	0.038	0.038,0.511	0.00851	0.0836	hyper
+chr11	3034	3036	13	0	0,0.193	14	0.286	0.059,0.512	0.286	0.0412	0.0412,0.462	0.00859	0.0978	hyper
+chr11	3052	3054	15	0.0667	0,0.264	13	0.769	0.534,1	0.703	0.377	0.377,0.816	3.11e-05	0.000267	strongHyper
+chr11	3095	3097	11	0.273	0.0181,0.527	10	0.8	0.53,1	0.527	0.141	0.141,0.706	0.00253	0.03	hyper
+chr11	3117	3119	12	0.0833	0,0.316	14	0.571	0.338,0.804	0.488	0.161	0.161,0.655	0.00167	0.0145	hyper
+chr11	3273	3275	38	0.105	0,0.22	25	0.48	0.296,0.664	0.375	0.178	0.178,0.532	0.000337	0.00124	hyper
+chr11	3283	3285	37	0.027	0,0.119	23	0.478	0.288,0.669	0.451	0.257	0.257,0.6	1.1e-05	3.67e-05	strongHyper
+chr11	3323	3325	35	0.0571	0,0.165	24	0.625	0.442,0.808	0.568	0.358	0.358,0.698	8.63e-07	2.9e-06	strongHyper
+chr11	3424	3426	30	0.0667	0,0.189	21	0.0952	0,0.259	0.0286	0	-0.0969,0.184	0.0956	1	hypo
+chr11	3452	3454	27	0	0,0.101	17	0.588	0.374,0.803	0.588	0.349	0.349,0.729	1.79e-06	7.84e-06	strongHyper
+chr11	3484	3486	25	0.04	0,0.17	18	0.556	0.345,0.766	0.516	0.275	0.275,0.667	4.33e-05	0.000196	strongHyper
+chr11	3578	3580	19	0.263	0.0688,0.458	19	0.737	0.542,0.931	0.474	0.194	0.194,0.641	0.000789	0.00856	hyper
+chr11	3595	3597	20	0	0,0.133	21	0.238	0.0554,0.421	0.238	0.0598	0.0598,0.385	0.00603	0.0478	hyper
+chr11	3611	3613	19	0.0526	0,0.216	23	0.826	0.658,0.994	0.773	0.525	0.525,0.852	7.44e-08	3.4e-07	strongHyper
+chr11	3617	3619	19	0	0,0.139	21	0.762	0.579,0.945	0.762	0.514	0.514,0.842	7.07e-08	3.39e-07	strongHyper
+chr11	3639	3641	16	0.125	0,0.326	20	0.6	0.4,0.8	0.475	0.194	0.194,0.633	0.000772	0.00572	hyper
+chr11	3646	3648	17	0.0588	0,0.238	23	0.391	0.204,0.579	0.332	0.0973	0.0973,0.485	0.00347	0.0257	hyper
+chr11	3665	3667	13	0.0769	0,0.297	21	0.571	0.375,0.768	0.495	0.203	0.203,0.637	0.000728	0.00476	strongHyper
+chr11	3672	3674	13	0	0,0.193	23	0.348	0.163,0.532	0.348	0.106	0.106,0.476	0.00296	0.0319	hyper
+chr11	3677	3679	14	0	0,0.181	23	0.261	0.0841,0.438	0.261	0.0448	0.0448,0.391	0.00827	0.0645	hyper
+chr11	3693	3695	17	0	0,0.153	26	0.231	0.0678,0.394	0.231	0.0451	0.0451,0.355	0.0084	0.0662	hyper
+chr11	3704	3706	20	0	0,0.133	25	0.2	0.0371,0.363	0.2	0.0359	0.0359,0.329	0.0104	0.0562	hyper
+chr11	3707	3709	21	0	0,0.127	25	0.16	0.00176,0.318	0.16	0.0108	0.0108,0.286	0.019	0.114	hyper
+chr11	3717	3719	22	0.0455	0,0.19	21	0.286	0.0986,0.473	0.24	0.0455	0.0455,0.403	0.00857	0.0459	hyper
+chr11	3960	3962	21	0	0,0.127	18	0.167	0,0.359	0.167	0.011	0.011,0.326	0.0188	0.0893	hyper
+chr11	3991	3993	20	0	0,0.133	24	0.167	0.00373,0.33	0.167	0.0109	0.0109,0.296	0.0184	0.114	hyper
+chr11	4056	4058	22	0	0,0.122	24	0.292	0.115,0.468	0.292	0.111	0.111,0.431	0.0016	0.00965	hyper
+chr11	4163	4165	26	0.0769	0,0.215	30	0.0333	0,0.144	-0.0436	-0	-0.167,0.067	0.103	0.592	hypo
+chr11	4195	4197	23	0.0435	0,0.183	26	0.231	0.0678,0.394	0.187	0.0142	0.0142,0.331	0.0161	0.103	hyper
+chr11	4202	4204	21	0	0,0.127	30	0.0667	0,0.189	0.0667	0	-0.056,0.159	0.09	0.506	hypo
+chr11	4207	4209	18	0.0556	0,0.226	31	0.194	0.0495,0.338	0.138	0	-0.0495,0.266	0.0376	0.238	hypo
+chr11	4243	4245	30	0.133	0,0.271	27	0.111	0,0.254	-0.0222	-0	-0.164,0.129	0.0905	1	hypo
+chr11	4248	4250	32	0.0312	0,0.136	31	0.0323	0,0.14	0.00101	0	-0.0916,0.0963	0.165	1	hypo
+chr11	4284	4286	34	0.0882	0,0.207	31	0.226	0.0775,0.374	0.138	0	-0.014,0.281	0.0299	0.174	hypo
+chr11	4289	4291	33	0	0,0.0843	27	0.0741	0,0.208	0.0741	0	-0.0153,0.186	0.0629	0.198	hypo
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+chr11	4307	4309	31	0	0,0.0894	34	0.0294	0,0.129	0.0294	0	-0.0497,0.107	0.175	1	hypo
+chr11	4314	4316	27	0	0,0.101	33	0.0606	0,0.174	0.0606	0	-0.0384,0.149	0.094	0.497	hypo
+chr11	4320	4322	25	0.04	0,0.17	34	0.0882	0,0.207	0.0482	0	-0.082,0.153	0.0995	0.63	hypo
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+chr11	4340	4342	22	0.0455	0,0.19	31	0.0323	0,0.14	-0.0132	-0	-0.143,0.0832	0.134	1	hypo
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+chr11	4458	4460	14	0	0,0.181	16	0.0625	0,0.25	0.0625	0	-0.101,0.206	0.0874	1	hypo
+chr11	4469	4471	14	0.0714	0,0.279	13	0.154	0,0.385	0.0824	0	-0.132,0.291	0.0559	0.596	hypo
+chr11	4482	4484	15	0.0667	0,0.264	19	0	0,0.139	-0.0667	-0	-0.228,0.0612	0.0804	0.441	hypo
+chr11	4499	4501	16	0.0625	0,0.25	24	0.0417	0,0.176	-0.0208	-0	-0.189,0.102	0.101	1	hypo
+chr11	4519	4521	19	0.105	0,0.283	23	0.304	0.123,0.485	0.199	0	-0.019,0.37	0.021	0.149	hypo
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+chr11	4532	4534	20	0	0,0.133	23	0.174	0.00602,0.342	0.174	0.0155	0.0155,0.308	0.0166	0.111	hyper
+chr11	4549	4551	21	0.0476	0,0.198	26	0.231	0.0678,0.394	0.183	0.00182	0.00182,0.327	0.0191	0.112	hyper
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+chr11	4692	4694	15	0.0667	0,0.264	16	0.188	0,0.396	0.121	0	-0.0941,0.308	0.0454	0.6	hypo
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+chr11	4756	4758	19	0	0,0.139	24	0.208	0.0409,0.376	0.208	0.0368	0.0368,0.34	0.0101	0.0562	hyper
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+chr11	4799	4801	24	0.0833	0,0.231	25	0	0,0.109	-0.0833	-0	-0.203,0.0283	0.0616	0.235	hypo
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+chr11	4872	4874	26	0	0,0.105	20	0.1	0,0.271	0.1	0	-0.0148,0.243	0.0448	0.184	hypo
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+chr11	5551	5553	29	0.138	0,0.28	23	0.348	0.163,0.532	0.21	0.0113	0.0113,0.388	0.0154	0.102	hyper
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+chr11	5828	5830	12	0	0,0.206	21	0.238	0.0554,0.421	0.238	0.00538	0.00538,0.371	0.0145	0.133	hyper
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+chr11	5843	5845	11	0.0909	0,0.339	18	0.0556	0,0.226	-0.0354	-0	-0.259,0.125	0.0739	1	hypo
+chr11	5969	5971	10	0.3	0.035,0.565	15	0.267	0.0481,0.485	-0.0333	-0	-0.322,0.235	0.0461	1	hypo
+chr11	5972	5974	11	0.0909	0,0.339	15	0	0,0.171	-0.0909	-0	-0.294,0.0699	0.0601	0.423	hypo
+chr11	6023	6025	11	0.0909	0,0.339	18	0.333	0.128,0.538	0.242	0	-0.0451,0.422	0.0199	0.202	hypo
+chr11	6044	6046	10	0	0,0.238	12	0	0,0.206	0	0	-0.187,0.15	0.117	1	hypo
+chr11	6049	6051	10	0	0,0.238	12	0.0833	0,0.316	0.0833	0	-0.134,0.259	0.0677	1	hypo
+chr11	6076	6078	11	0.0909	0,0.339	7	0	0,0.312	-0.0909	-0	-0.266,0.195	0.0616	1	hypo
+chr11	6089	6091	9	0	0,0.259	10	0	0,0.238	0	0	-0.2,0.177	0.105	1	hypo
+chr11	6099	6101	6	0	0,0.348	9	0.111	0,0.394	0.111	0	-0.21,0.312	0.0524	1	hypo
+chr11	6148	6150	9	0	0,0.259	13	0	0,0.193	0	0	-0.209,0.135	0.115	1	hypo
+chr11	6156	6158	8	0	0,0.283	14	0	0,0.181	0	0	-0.235,0.121	0.111	1	hypo
+chr11	6164	6166	8	0	0,0.283	12	0	0,0.206	0	0	-0.23,0.143	0.106	1	hypo
+chr11	6168	6170	8	0.125	0,0.429	14	0	0,0.181	-0.125	-0	-0.38,0.0569	0.0427	0.364	hypo
+chr11	6208	6210	10	0.1	0,0.364	10	0.2	0,0.47	0.1	0	-0.177,0.347	0.0455	1	hypo
+chr11	6226	6228	10	0	0,0.238	10	0	0,0.238	0	0	-0.181,0.181	0.109	1	hypo
+chr11	6239	6241	5	0	0,0.393	12	0	0,0.206	0	0	-0.336,0.126	0.0829	1	hypo
+chr11	6247	6249	11	0.0909	0,0.339	11	0.0909	0,0.339	0	0	-0.226,0.226	0.0655	1	hypo
+chr11	6251	6253	13	0.0769	0,0.297	9	0.222	0,0.507	0.145	0	-0.105,0.403	0.037	0.544	hypo
+chr11	6253	6255	13	0.0769	0,0.297	9	0.111	0,0.394	0.0342	0	-0.172,0.291	0.0615	1	hypo
+chr11	6258	6260	12	0	0,0.206	11	0.0909	0,0.339	0.0909	0	-0.0993,0.287	0.0621	0.478	hypo
+chr11	6269	6271	15	0	0,0.171	12	0.0833	0,0.316	0.0833	0	-0.0753,0.272	0.0659	0.444	hypo
+chr11	6272	6274	15	0.2	0,0.417	11	0.0909	0,0.339	-0.109	-0	-0.307,0.152	0.0476	0.614	hypo
+chr11	6282	6284	15	0.0667	0,0.264	10	0.1	0,0.364	0.0333	0	-0.151,0.272	0.0675	1	hypo
+chr11	6293	6295	16	0	0,0.162	14	0.143	0,0.363	0.143	0	-0.0318,0.322	0.0346	0.209	hypo
+chr11	6297	6299	18	0	0,0.146	13	0	0,0.193	0	0	-0.103,0.155	0.154	1	hypo
+chr11	6300	6302	15	0.133	0,0.344	13	0.154	0,0.385	0.0205	0	-0.195,0.249	0.0617	1	hypo
+chr11	6304	6306	17	0.118	0,0.31	12	0.0833	0,0.316	-0.0343	-0	-0.21,0.192	0.0696	1	hypo
+chr11	6312	6314	20	0.05	0,0.207	12	0	0,0.206	-0.05	-0	-0.161,0.135	0.103	1	hypo
+chr11	6314	6316	20	0.05	0,0.207	12	0.167	0,0.41	0.117	0	-0.0623,0.337	0.044	0.54	hypo
+chr11	6318	6320	20	0.05	0,0.207	12	0	0,0.206	-0.05	-0	-0.161,0.135	0.103	1	hypo
+chr11	6321	6323	19	0	0,0.139	13	0	0,0.193	0	0	-0.0972,0.157	0.156	1	hypo
+chr11	6323	6325	20	0	0,0.133	12	0	0,0.206	0	0	-0.0897,0.171	0.153	1	hypo
+chr11	6350	6352	18	0.0556	0,0.226	12	0	0,0.206	-0.0556	-0	-0.179,0.13	0.0952	1	hypo
+chr11	6356	6358	19	0.0526	0,0.216	10	0.1	0,0.364	0.0474	0	-0.11,0.287	0.0684	1	hypo
+chr11	6358	6360	20	0.05	0,0.207	11	0	0,0.221	-0.05	-0	-0.158,0.149	0.101	1	hypo
+chr11	6365	6367	19	0	0,0.139	11	0	0,0.221	0	0	-0.0929,0.184	0.143	1	hypo
+chr11	6371	6373	18	0.0556	0,0.226	13	0.0769	0,0.297	0.0214	0	-0.135,0.219	0.0833	1	hypo
+chr11	6430	6432	14	0	0,0.181	19	0.105	0,0.283	0.105	0	-0.0731,0.239	0.0573	0.496	hypo
+chr11	6432	6434	16	0.0625	0,0.25	19	0.105	0,0.283	0.0428	0	-0.141,0.202	0.0788	1	hypo
+chr11	6442	6444	20	0.1	0,0.271	22	0.0909	0,0.249	-0.00909	-0	-0.174,0.147	0.0879	1	hypo
+chr11	6449	6451	19	0	0,0.139	24	0.0417	0,0.176	0.0417	0	-0.0824,0.143	0.126	1	hypo
+chr11	6491	6493	25	0.04	0,0.17	18	0.278	0.0771,0.478	0.238	0.0497	0.0497,0.416	0.00794	0.0672	hyper
+chr11	6526	6528	35	0.0286	0,0.125	26	0.115	0,0.263	0.0868	0	-0.0247,0.219	0.0549	0.303	hypo
+chr11	6560	6562	25	0.24	0.0727,0.407	30	0.233	0.0816,0.385	-0.00667	-0	-0.195,0.173	0.0714	1	hypo
+chr11	6596	6598	38	0.421	0.27,0.572	30	0.6	0.433,0.767	0.179	0	-0.0236,0.356	0.0237	0.222	hypo
+chr11	6730	6732	41	0.366	0.223,0.509	31	0.516	0.349,0.683	0.15	0	-0.0438,0.327	0.0316	0.236	hypo
+chr11	6857	6859	33	0.212	0.0704,0.354	46	0.239	0.116,0.362	0.027	0	-0.135,0.173	0.0826	1	hypo
+chr11	6900	6902	29	0.862	0.72,1	46	0.804	0.687,0.921	-0.0577	-0	-0.187,0.0999	0.0766	0.755	hypo
+chr11	6902	6904	29	0.483	0.311,0.655	46	0.804	0.687,0.921	0.322	0.132	0.132,0.479	0.00124	0.00524	hyper
+chr11	6979	6981	25	0.28	0.108,0.452	39	0.487	0.337,0.638	0.207	0	-0.00347,0.377	0.0177	0.123	hypo
+chr11	7085	7087	26	0.346	0.172,0.521	27	0.704	0.537,0.871	0.358	0.124	0.124,0.528	0.00216	0.0135	hyper
+chr11	7166	7168	19	0.263	0.0688,0.458	27	0.259	0.0961,0.422	-0.0039	-0	-0.221,0.195	0.0632	1	hypo
+chr11	7336	7338	17	0.294	0.0867,0.502	13	0.769	0.534,1	0.475	0.154	0.154,0.653	0.00186	0.0253	hyper
+chr11	7583	7585	26	0.154	6.6e-05,0.308	34	0.176	0.0419,0.311	0.0226	0	-0.145,0.172	0.0825	1	hypo
+chr11	7633	7635	21	0.0952	0,0.259	26	0.154	6.6e-05,0.308	0.0586	0	-0.116,0.209	0.0723	0.678	hypo
+chr11	7655	7657	15	0	0,0.171	21	0.143	0,0.316	0.143	0	-0.0375,0.275	0.0356	0.25	hypo
+chr11	7673	7675	16	0	0,0.162	17	0	0,0.153	0	0	-0.125,0.115	0.165	1	hypo
+chr11	7679	7681	17	0	0,0.153	21	0.0476	0,0.198	0.0476	0	-0.0895,0.162	0.111	1	hypo
+chr11	7688	7690	15	0	0,0.171	18	0.167	0,0.359	0.167	0	-0.0215,0.317	0.0269	0.233	hypo
+chr11	7695	7697	15	0.0667	0,0.264	21	0	0,0.127	-0.0667	-0	-0.23,0.0515	0.079	0.417	hypo
+chr11	7729	7731	14	0	0,0.181	21	0.19	0.0119,0.369	0.19	0	-0.0108,0.326	0.021	0.133	hypo
+chr11	7748	7750	15	0	0,0.171	23	0.0435	0,0.183	0.0435	0	-0.11,0.144	0.118	1	hypo
+chr11	7825	7827	18	0	0,0.146	20	0.05	0,0.207	0.05	0	-0.0806,0.171	0.107	1	hypo
+chr11	7866	7868	17	0	0,0.153	22	0.0455	0,0.19	0.0455	0	-0.0916,0.154	0.116	1	hypo
+chr11	7878	7880	15	0.0667	0,0.264	21	0.0952	0,0.259	0.0286	0	-0.161,0.177	0.0837	1	hypo
+chr11	7882	7884	13	0.0769	0,0.297	20	0.3	0.107,0.493	0.223	0	-0.0326,0.392	0.0204	0.202	hypo
+chr11	8027	8029	26	0.0385	0,0.164	18	0.167	0,0.359	0.128	0	-0.0241,0.302	0.0357	0.289	hypo
+chr11	8033	8035	27	0.037	0,0.159	16	0.0625	0,0.25	0.0255	0	-0.0862,0.195	0.103	1	hypo
+chr11	8303	8305	36	0.0556	0,0.161	23	0.0435	0,0.183	-0.0121	-0	-0.106,0.119	0.131	1	hypo
+chr11	8414	8416	16	0.0625	0,0.25	27	0.444	0.268,0.621	0.382	0.14	0.14,0.521	0.00165	0.0143	hyper
+chr11	8583	8585	24	0.0833	0,0.231	27	0.148	0,0.298	0.0648	0	-0.0948,0.209	0.0723	0.671	hypo
+chr11	8678	8680	19	0	0,0.139	17	0	0,0.153	0	0	-0.104,0.119	0.178	1	hypo
+chr11	8692	8694	23	0.0435	0,0.183	19	0.0526	0,0.216	0.00915	0	-0.116,0.155	0.113	1	hypo
+chr11	8755	8757	26	0	0,0.105	24	0.0417	0,0.176	0.0417	0	-0.0523,0.15	0.126	0.48	hypo
+chr11	8786	8788	25	0	0,0.109	19	0	0,0.139	0	0	-0.0781,0.112	0.207	1	hypo
+chr11	8812	8814	22	0.0909	0,0.249	21	0	0,0.127	-0.0909	-0	-0.217,0.038	0.0592	0.488	hypo
+chr11	8829	8831	20	0	0,0.133	22	0.136	0,0.304	0.136	0	-0.0114,0.27	0.0304	0.233	hypo
+chr11	8836	8838	21	0	0,0.127	21	0.0476	0,0.198	0.0476	0	-0.0664,0.167	0.112	1	hypo
+chr11	8855	8857	17	0.0588	0,0.238	22	0.0909	0,0.249	0.0321	0	-0.14,0.174	0.0887	1	hypo
+chr11	8902	8904	17	0	0,0.153	15	0.333	0.111,0.555	0.333	0.104	0.104,0.508	0.00262	0.0149	hyper
+chr11	8914	8916	20	0.35	0.153,0.547	13	0.308	0.0724,0.543	-0.0423	-0	-0.281,0.229	0.0495	1	hypo
+chr11	8920	8922	22	0	0,0.122	12	0	0,0.206	0	0	-0.0801,0.173	0.157	1	hypo
+chr11	8948	8950	33	0	0,0.0843	17	0.0588	0,0.238	0.0588	0	-0.0234,0.214	0.0814	0.34	hypo
+chr11	8975	8977	42	0.0476	0,0.139	19	0	0,0.139	-0.0476	-0	-0.11,0.0832	0.131	1	hypo
+chr11	9127	9129	41	0.0244	0,0.108	31	0.0968	0,0.225	0.0724	0	-0.0228,0.187	0.0662	0.308	hypo
+chr11	9136	9138	42	0.0476	0,0.139	33	0.0606	0,0.174	0.013	0	-0.0771,0.12	0.143	1	hypo
+chr11	9227	9229	45	0.0444	0,0.131	38	0.0526	0,0.153	0.00819	0	-0.0754,0.103	0.16	1	hypo
+chr11	9270	9272	40	0.025	0,0.111	33	0.0909	0,0.213	0.0659	0	-0.0287,0.175	0.0758	0.322	hypo
+chr11	9301	9303	40	0.175	0.0523,0.298	33	0.0303	0,0.132	-0.145	-0.0191	-0.253,-0.0191	0.0174	0.0652	hypo
+chr11	9371	9373	25	0	0,0.109	32	0	0,0.0868	0	0	-0.0872,0.0628	0.257	1	hypo
+chr11	9380	9382	25	0.04	0,0.17	31	0	0,0.0894	-0.04	-0	-0.147,0.0405	0.129	0.446	hypo
+chr11	9447	9449	17	0	0,0.153	30	0	0,0.0921	0	0	-0.129,0.0611	0.207	1	hypo
+chr11	9478	9480	16	0	0,0.162	21	0.0476	0,0.198	0.0476	0	-0.097,0.16	0.111	1	hypo
+chr11	9510	9512	14	0	0,0.181	23	0.0435	0,0.183	0.0435	0	-0.119,0.143	0.117	1	hypo
+chr11	9588	9590	20	0	0,0.133	18	0.111	0,0.296	0.111	0	-0.0292,0.261	0.0448	0.218	hypo
+chr11	9677	9679	11	0.0909	0,0.339	13	0.231	0,0.466	0.14	0	-0.131,0.354	0.0398	0.596	hypo
+chr11	9697	9699	14	0	0,0.181	15	0.2	0,0.417	0.2	0	-0.00842,0.371	0.02	0.224	hypo
+chr11	9709	9711	11	0	0,0.221	18	0.111	0,0.296	0.111	0	-0.104,0.245	0.0574	0.512	hypo
+chr11	9729	9731	6	0.167	0,0.521	16	0	0,0.162	-0.167	-0	-0.475,0.0224	0.0282	0.273	hypo
diff -r 26d7ec4af119 -r 8c8cc81b34cd test-data/SE_dmr_M2_g1.G.bed_vs_g2.G.bed.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SE_dmr_M2_g1.G.bed_vs_g2.G.bed.txt	Sat Apr 11 04:14:34 2020 -0400
@@ -0,0 +1,2 @@
+#chrom	start	end	meanRatio_0	totalC_0	cSites_0	meanRatio_1	totalC_1	cSites_1	methDif_1-0	p_1_v_0	class_1_v_0
+chr11	316	1705	0.148	1061	35	0.657	1278	35	0.326	3.11e-141	strongHyper
diff -r 26d7ec4af119 -r 8c8cc81b34cd test-data/SE_dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr
--- a/test-data/SE_dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr	Fri Sep 06 09:54:27 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-chr11	316	1705	-	35	30	5	-1
-chr11	3052	3674	-	17	16	1	-1