changeset 2:35d2db3753d9 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 301fc26e062ac02a28676a05aa9c82e4407e3d29
author artbio
date Sun, 24 Sep 2017 13:34:16 -0400 (2017-09-24)
parents ebe5ec2e244d
children 4f744d3aaf0b
files multicov.py probecoverage.xml test-data/coverage_pysam.tab test-data/graph.pdf test-data/graph_pysam.pdf
diffstat 5 files changed, 874 insertions(+), 12 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/multicov.py	Sun Sep 24 13:34:16 2017 -0400
@@ -0,0 +1,60 @@
+import argparse
+
+import numpy
+
+import pysam
+
+
+def Parser():
+    the_parser = argparse.ArgumentParser()
+    the_parser.add_argument('-bams', '--bams', dest='bams', required=True,
+                            nargs='+', help='list of input BAM files')
+    the_parser.add_argument('-bed', '--bed', dest='bed', required=True,
+                            help='Coordinates of probes in a bed file')
+    args = the_parser.parse_args()
+    return args
+
+
+def compute_coverage(bam, bed, quality=10):
+    bam_object = pysam.AlignmentFile(bam, 'rb')
+    bed_object = open(bed, 'r')
+    coverage_column = []
+    for line in bed_object:
+        if line[0] == '#':
+            continue
+        fields = line[:-1].split('\t')
+        chr = fields[0]
+        start = fields[1]
+        end = fields[2]
+        coverage = bam_object.count_coverage(reference=chr,
+                                             start=int(start)-1,
+                                             end=int(end),
+                                             quality_threshold=quality)
+        """ Add the 4 coverage values """
+        coverage = [sum(x) for x in zip(*coverage)]
+        coverage_column.append(numpy.mean(coverage))
+    bed_object.close()
+    return coverage_column
+
+
+def main(bams, bed):
+    column_dict = {}
+    for i, bam in enumerate(bams):
+        column_dict[i] = compute_coverage(bam, bed)
+    F = open(bed, 'r')
+    line_counter = 0
+    for line in F:
+        if line[0] == '#':
+            continue
+        prefix = line[:-1]
+        crossline = []
+        for col in sorted(column_dict):
+            crossline.append(str(column_dict[col][line_counter]))
+        line_counter += 1
+        suffix = '\t'.join(crossline)
+        print('%s\t%s' % (prefix, suffix))
+
+
+if __name__ == "__main__":
+    args = Parser()
+    main(args.bams, args.bed)
--- a/probecoverage.xml	Sat Sep 23 12:56:17 2017 -0400
+++ b/probecoverage.xml	Sun Sep 24 13:34:16 2017 -0400
@@ -1,11 +1,12 @@
-<tool id="probecoverage" name="Probe Coverage" version="0.2.0">
+<tool id="probecoverage" name="Probe Coverage" version="0.3.0">
   <description></description>
   <requirements>
         <requirement type="package" version="1.4.1">samtools</requirement>
         <requirement type="package" version="2.26.0">bedtools</requirement>
         <requirement type="package" version="1.3.2=r3.3.1_0">r-optparse</requirement>
         <requirement type="package" version="2.2.1=r3.3.1_0">r-ggplot2</requirement>
-        <requirement type="package" version="1.4.2=r3.3.1_0">r-reshape2</requirement>
+        <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
+        <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement>
   </requirements>
   <stdio>
       <exit_code range="1:" level="fatal" description="Tool exception" />
@@ -14,16 +15,25 @@
       #for $file in $inputs
           samtools index '$file' &&
       #end for
-      bedtools multicov
+      #if $method == 'pysam':
+          python $__tool_directory__/multicov.py
+      #else:
+          bedtools multicov
+      #end if
           -bams
               #for $file in $inputs
                   '$file'
               #end for
-          -bed '$bed' > $bedtools_table &&
+          -bed '$bed' > $coverage_dataframe &&
       Rscript '$__tool_directory__'/probecoverage.r
-          --input '$bedtools_table' 
+          --input '$coverage_dataframe' 
           --title 'Probe coverage depth (cumulative distribution)'
-          --xlab 'Depth'
+          --xlab
+          #if $method == 'pysam':
+              'Depth (pysam method)'
+          #else:
+              'Depth (bedtools muticov method)'
+          #end if
           --ylab 'Fraction of covered regions with coverage >= Depth'
           --output '$distribution'
           --sample "
@@ -33,13 +43,16 @@
               "
               
   ]]></command>
- <inputs>
-   <param name="inputs" type="data" format="bam" label="Select multiple Bam alignments to parse" multiple="True"/>
-   <param name="bed" type="data" format="bed" label="Select a bed file describing the genomic regions to analyze" />
- </inputs>
+<inputs>
+    <param name="inputs" type="data" format="bam" label="Select multiple Bam alignments to parse" multiple="True"/>
+    <param name="bed" type="data" format="bed" label="Select a bed file describing the genomic regions to analyze" />
+    <param name="method" type="boolean" falsevalue="bedtools" checked="false" truevalue="pysam"
+           help="coverage is computed using bedtools multicov (default) or pysam module"
+           label="Compute coverage with pysam (bedtools by default)" />
+</inputs>
 
  <outputs>
-   <data format="tabular" name="bedtools_table" label="bedtools multicov output" />
+   <data format="tabular" name="coverage_dataframe" label="coverage table" />
    <data format="pdf" name="distribution" label="Cumulative distribution of region coverages" />
 </outputs>
 
@@ -47,9 +60,17 @@
         <test>
             <param name="inputs" value="sample1,sample2,sample3" ftype="bam"/>
             <param name="bed" value="probes.bed" ftype="bed"/>
-            <output file="coverage.tab" name="bedtools_table" />
+            <param name="method" value="bedtools" />
+            <output file="coverage.tab" name="coverage_dataframe" />
             <output file="graph.pdf" name="distribution" />
         </test>
+        <test>
+            <param name="inputs" value="sample1,sample2,sample3" ftype="bam"/>
+            <param name="bed" value="probes.bed" ftype="bed"/>
+            <param name="method" value="pysam" />
+            <output file="coverage_pysam.tab" name="coverage_dataframe" />
+            <output file="graph_pysam.pdf" name="distribution" />
+        </test>
     </tests>
 
 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/coverage_pysam.tab	Sun Sep 24 13:34:16 2017 -0400
@@ -0,0 +1,781 @@
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+chr5	176820654	176820803	uc003mgk.4_exon_8_0_chr5_176820695_f	0.0	0.0	0.0
+chr5	176820994	176821219	uc003mgk.4_exon_9_0_chr5_176821029_f	0.0	0.0	0.0
+chr5	176823709	176823878	uc003mgk.4_exon_10_0_chr5_176823734_f	0.0	0.0	0.0
+chr5	176823929	176824102	uc003mgk.4_exon_11_0_chr5_176823951_f	0.0	0.0	0.0
+chr5	176824759	176825439	uc003mgk.4_exon_12_0_chr5_176824784_f	0.0	0.0	0.0
+chr5	176825449	176825857	uc003mgk.4_exon_12_0_chr5_176824784_f	0.0	0.0	0.0
+chr6	33161331	33161866	uc003odb.4_exon_0_0_chr6_33161362_r;uc003odc.4_exon_0_0_chr6_33161362_r;uc011dqr.3_exon_0_0_chr6_33161362_r	0.0	0.0	0.0
+chr6	33161886	33162617	uc003odb.4_exon_0_0_chr6_33161362_r;uc003odc.4_exon_0_0_chr6_33161362_r;uc011dqr.3_exon_0_0_chr6_33161362_r	0.0	0.0	0.0
+chr6	33162696	33162866	uc003odb.4_exon_1_0_chr6_33162722_r;uc003odc.4_exon_1_0_chr6_33162722_r;uc011dqr.3_exon_1_0_chr6_33162722_r	0.0	0.0	0.0
+chr6	33163111	33163264	uc003odb.4_exon_2_0_chr6_33163140_r;uc003odc.4_exon_2_0_chr6_33163140_r;uc011dqr.3_exon_2_0_chr6_33163140_r	0.0	0.0	0.0
+chr6	33163311	33163475	uc003odb.4_exon_3_0_chr6_33163347_r;uc003odb.4_exon_4_0_chr6_33163684_r;uc003odb.4_exon_5_0_chr6_33164211_r;uc003odc.4_exon_3_0_chr6_33163347_r;uc003odc.4_exon_4_0_chr6_33163684_r;uc003odc.4_exon_5_0_chr6_33164211_r;uc003ode.1_exon_0_0_chr6_33163562_r;uc011dqr.3_exon_3_0_chr6_33163347_r;uc011dqr.3_exon_4_0_chr6_33163684_r;uc011dqr.3_exon_5_0_chr6_33164211_r;uc011dqs.2_exon_0_0_chr6_33163388_r;uc011dqs.2_exon_1_0_chr6_33164211_r;uc011dqt.2_exon_0_0_chr6_33163562_r;uc011dqu.2_exon_0_0_chr6_33163562_r	0.0	0.0	0.0
+chr6	33163486	33164285	uc003odb.4_exon_3_0_chr6_33163347_r;uc003odb.4_exon_4_0_chr6_33163684_r;uc003odb.4_exon_5_0_chr6_33164211_r;uc003odc.4_exon_3_0_chr6_33163347_r;uc003odc.4_exon_4_0_chr6_33163684_r;uc003odc.4_exon_5_0_chr6_33164211_r;uc003ode.1_exon_0_0_chr6_33163562_r;uc011dqr.3_exon_3_0_chr6_33163347_r;uc011dqr.3_exon_4_0_chr6_33163684_r;uc011dqr.3_exon_5_0_chr6_33164211_r;uc011dqs.2_exon_0_0_chr6_33163388_r;uc011dqs.2_exon_1_0_chr6_33164211_r;uc011dqt.2_exon_0_0_chr6_33163562_r;uc011dqu.2_exon_0_0_chr6_33163562_r	0.0	0.0	0.0
+chr6	33164286	33164415	uc003odb.4_exon_3_0_chr6_33163347_r;uc003odb.4_exon_4_0_chr6_33163684_r;uc003odb.4_exon_5_0_chr6_33164211_r;uc003odc.4_exon_3_0_chr6_33163347_r;uc003odc.4_exon_4_0_chr6_33163684_r;uc003odc.4_exon_5_0_chr6_33164211_r;uc003ode.1_exon_0_0_chr6_33163562_r;uc011dqr.3_exon_3_0_chr6_33163347_r;uc011dqr.3_exon_4_0_chr6_33163684_r;uc011dqr.3_exon_5_0_chr6_33164211_r;uc011dqs.2_exon_0_0_chr6_33163388_r;uc011dqs.2_exon_1_0_chr6_33164211_r;uc011dqt.2_exon_0_0_chr6_33163562_r;uc011dqu.2_exon_0_0_chr6_33163562_r	0.0	0.0	0.0
+chr6	33165506	33165750	uc003odb.4_exon_6_0_chr6_33165539_r;uc003odc.4_exon_6_0_chr6_33165539_r;uc003ode.1_exon_1_0_chr6_33165539_r;uc011dqr.3_exon_6_0_chr6_33165539_r;uc011dqs.2_exon_2_0_chr6_33165539_r;uc011dqt.2_exon_1_0_chr6_33165539_r;uc011dqu.2_exon_1_0_chr6_33165539_r	0.0	0.0	0.0
+chr6	33166051	33166388	uc003odb.4_exon_7_0_chr6_33166085_r;uc003odc.4_exon_7_0_chr6_33166085_r;uc003ode.1_exon_2_0_chr6_33166085_r;uc011dqr.3_exon_7_0_chr6_33166085_r;uc011dqs.2_exon_3_0_chr6_33166085_r;uc011dqt.2_exon_2_0_chr6_33166085_r;uc011dqu.2_exon_2_0_chr6_33166085_r	0.0	0.0	0.0
+chr6	33166911	33167063	uc003odb.4_exon_8_0_chr6_33166946_r;uc003odc.4_exon_8_0_chr6_33166946_r;uc011dqt.2_exon_3_0_chr6_33166946_r	0.0	0.0	0.0
+chr6	33167071	33167209	uc003odb.4_exon_8_0_chr6_33166946_r;uc003odc.4_exon_8_0_chr6_33166946_r;uc011dqt.2_exon_3_0_chr6_33166946_r	0.0	0.0	0.0
+chr6	33167986	33168096	uc003odb.4_exon_9_0_chr6_33168019_r;uc003odc.4_exon_9_0_chr6_33168019_r;uc011dqs.2_exon_4_0_chr6_33168019_r;uc011dqt.2_exon_4_0_chr6_33168019_r;uc011dqu.2_exon_3_0_chr6_33168019_r	0.0	0.0	0.0
+chr6	33168111	33168490	uc003odb.4_exon_9_0_chr6_33168019_r;uc003odc.4_exon_9_0_chr6_33168019_r;uc011dqs.2_exon_4_0_chr6_33168019_r;uc011dqt.2_exon_4_0_chr6_33168019_r;uc011dqu.2_exon_3_0_chr6_33168019_r	0.0	0.0	0.0
+chr6	33168506	33168646	uc011dqr.3_exon_8_0_chr6_33168544_r	0.0	0.0	0.0
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+chr6	132190486	132190668	uc003qcy.3_exon_4_0_chr6_132190498_f;uc011ecf.2_exon_12_0_chr6_132190498_f	0.0	0.0	0.0
+chr6	132193151	132193281	uc003qcy.3_exon_5_0_chr6_132193210_f;uc011ecf.2_exon_13_0_chr6_132193210_f	0.0	0.0	0.0
+chr6	132194041	132194215	uc003qcy.3_exon_6_0_chr6_132194063_f;uc011ecf.2_exon_14_0_chr6_132194063_f	0.0	0.0	0.0
+chr6	132195371	132195508	uc003qcy.3_exon_7_0_chr6_132195408_f;uc011ecf.2_exon_15_0_chr6_132195408_f	0.0	0.0	0.0
+chr6	132196881	132197023	uc003qcy.3_exon_8_0_chr6_132196916_f;uc011ecf.2_exon_16_0_chr6_132196916_f	0.0	0.0	0.0
+chr6	132198106	132198847	uc003qcy.3_exon_9_0_chr6_132198132_f;uc011ecf.2_exon_17_0_chr6_132198132_f	0.0	0.0	0.0
+chr6	132199636	132199778	uc011ecf.2_exon_18_0_chr6_132199682_f	0.0	0.0	0.0
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+chr6	132212351	132212894	uc011ecf.2_exon_24_0_chr6_132211481_f	0.0	0.0	0.0
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+chr6	132215691	132216320	uc011ecf.2_exon_24_0_chr6_132211481_f	0.0	0.0	0.0
+chr6_cox_hap2	4605164	4605706	uc011fpt.3_exon_0_0_chr6_cox_hap2_4605198_r;uc011fpu.3_exon_0_0_chr6_cox_hap2_4605198_r;uc011fpw.3_exon_0_0_chr6_cox_hap2_4605198_r	0.0	0.0	0.0
+chr6_cox_hap2	4605724	4606454	uc011fpt.3_exon_0_0_chr6_cox_hap2_4605198_r;uc011fpu.3_exon_0_0_chr6_cox_hap2_4605198_r;uc011fpw.3_exon_0_0_chr6_cox_hap2_4605198_r	0.0	0.0	0.0
+chr6_cox_hap2	4606534	4606674	uc011fpt.3_exon_1_0_chr6_cox_hap2_4606558_r;uc011fpu.3_exon_1_0_chr6_cox_hap2_4606558_r;uc011fpw.3_exon_1_0_chr6_cox_hap2_4606558_r	0.0	0.0	0.0
+chr6_cox_hap2	4606949	4607102	uc011fpt.3_exon_2_0_chr6_cox_hap2_4606976_r;uc011fpu.3_exon_2_0_chr6_cox_hap2_4606976_r;uc011fpw.3_exon_2_0_chr6_cox_hap2_4606976_r	0.0	0.0	0.0
+chr6_cox_hap2	4607149	4608104	uc011fpt.3_exon_3_0_chr6_cox_hap2_4607183_r;uc011fpt.3_exon_4_0_chr6_cox_hap2_4607520_r;uc011fpt.3_exon_5_0_chr6_cox_hap2_4608047_r;uc011fpu.3_exon_3_0_chr6_cox_hap2_4607183_r;uc011fpu.3_exon_4_0_chr6_cox_hap2_4607520_r;uc011fpu.3_exon_5_0_chr6_cox_hap2_4608047_r;uc011fpw.3_exon_3_0_chr6_cox_hap2_4607183_r;uc011fpw.3_exon_4_0_chr6_cox_hap2_4607520_r;uc011fpw.3_exon_5_0_chr6_cox_hap2_4608047_r;uc011fpx.2_exon_0_0_chr6_cox_hap2_4607224_r;uc011fpx.2_exon_1_0_chr6_cox_hap2_4608047_r;uc011fpy.1_exon_0_0_chr6_cox_hap2_4607398_r;uc011fpz.2_exon_0_0_chr6_cox_hap2_4607398_r;uc011fqa.2_exon_0_0_chr6_cox_hap2_4607398_r	0.0	0.0	0.0
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+chr6_cox_hap2	4612344	4612480	uc011fpw.3_exon_8_0_chr6_cox_hap2_4612378_r	0.0	0.0	0.0
+chr6_dbb_hap3	4442634	4443175	uc011gly.3_exon_0_0_chr6_dbb_hap3_4442669_r;uc011glz.3_exon_0_0_chr6_dbb_hap3_4442669_r;uc011gmb.3_exon_0_0_chr6_dbb_hap3_4442669_r	0.0	0.0	0.0
+chr6_dbb_hap3	4443194	4443924	uc011gly.3_exon_0_0_chr6_dbb_hap3_4442669_r;uc011glz.3_exon_0_0_chr6_dbb_hap3_4442669_r;uc011gmb.3_exon_0_0_chr6_dbb_hap3_4442669_r	0.0	0.0	0.0
+chr6_dbb_hap3	4444004	4444175	uc011gly.3_exon_1_0_chr6_dbb_hap3_4444029_r;uc011glz.3_exon_1_0_chr6_dbb_hap3_4444029_r;uc011gmb.3_exon_1_0_chr6_dbb_hap3_4444029_r	0.0	0.0	0.0
+chr6_dbb_hap3	4444424	4444567	uc011gly.3_exon_2_0_chr6_dbb_hap3_4444447_r;uc011glz.3_exon_2_0_chr6_dbb_hap3_4444447_r;uc011gmb.3_exon_2_0_chr6_dbb_hap3_4444447_r	0.0	0.0	0.0
+chr6_dbb_hap3	4444619	4445581	uc011gly.3_exon_3_0_chr6_dbb_hap3_4444654_r;uc011gly.3_exon_4_0_chr6_dbb_hap3_4444991_r;uc011gly.3_exon_5_0_chr6_dbb_hap3_4445518_r;uc011glz.3_exon_3_0_chr6_dbb_hap3_4444654_r;uc011glz.3_exon_4_0_chr6_dbb_hap3_4444991_r;uc011glz.3_exon_5_0_chr6_dbb_hap3_4445518_r;uc011gmb.3_exon_3_0_chr6_dbb_hap3_4444654_r;uc011gmb.3_exon_4_0_chr6_dbb_hap3_4444991_r;uc011gmb.3_exon_5_0_chr6_dbb_hap3_4445518_r;uc011gmc.2_exon_0_0_chr6_dbb_hap3_4444695_r;uc011gmc.2_exon_1_0_chr6_dbb_hap3_4445518_r;uc011gmd.1_exon_0_0_chr6_dbb_hap3_4444869_r;uc011gme.2_exon_0_0_chr6_dbb_hap3_4444869_r;uc011gmf.2_exon_0_0_chr6_dbb_hap3_4444869_r	0.0	0.0	0.0
+chr6_dbb_hap3	4445594	4445722	uc011gly.3_exon_3_0_chr6_dbb_hap3_4444654_r;uc011gly.3_exon_4_0_chr6_dbb_hap3_4444991_r;uc011gly.3_exon_5_0_chr6_dbb_hap3_4445518_r;uc011glz.3_exon_3_0_chr6_dbb_hap3_4444654_r;uc011glz.3_exon_4_0_chr6_dbb_hap3_4444991_r;uc011glz.3_exon_5_0_chr6_dbb_hap3_4445518_r;uc011gmb.3_exon_3_0_chr6_dbb_hap3_4444654_r;uc011gmb.3_exon_4_0_chr6_dbb_hap3_4444991_r;uc011gmb.3_exon_5_0_chr6_dbb_hap3_4445518_r;uc011gmc.2_exon_0_0_chr6_dbb_hap3_4444695_r;uc011gmc.2_exon_1_0_chr6_dbb_hap3_4445518_r;uc011gmd.1_exon_0_0_chr6_dbb_hap3_4444869_r;uc011gme.2_exon_0_0_chr6_dbb_hap3_4444869_r;uc011gmf.2_exon_0_0_chr6_dbb_hap3_4444869_r	0.0	0.0	0.0
+chr6_dbb_hap3	4446814	4447061	uc011gly.3_exon_6_0_chr6_dbb_hap3_4446846_r;uc011glz.3_exon_6_0_chr6_dbb_hap3_4446846_r;uc011gmb.3_exon_6_0_chr6_dbb_hap3_4446846_r;uc011gmc.2_exon_2_0_chr6_dbb_hap3_4446846_r;uc011gmd.1_exon_1_0_chr6_dbb_hap3_4446846_r;uc011gme.2_exon_1_0_chr6_dbb_hap3_4446846_r;uc011gmf.2_exon_1_0_chr6_dbb_hap3_4446846_r	0.0	0.0	0.0
+chr6_dbb_hap3	4447359	4447695	uc011gly.3_exon_7_0_chr6_dbb_hap3_4447392_r;uc011glz.3_exon_7_0_chr6_dbb_hap3_4447392_r;uc011gmb.3_exon_7_0_chr6_dbb_hap3_4447392_r;uc011gmc.2_exon_3_0_chr6_dbb_hap3_4447392_r;uc011gmd.1_exon_2_0_chr6_dbb_hap3_4447392_r;uc011gme.2_exon_2_0_chr6_dbb_hap3_4447392_r;uc011gmf.2_exon_2_0_chr6_dbb_hap3_4447392_r	0.0	0.0	0.0
+chr6_dbb_hap3	4448224	4448371	uc011gly.3_exon_8_0_chr6_dbb_hap3_4448253_r;uc011glz.3_exon_8_0_chr6_dbb_hap3_4448253_r;uc011gme.2_exon_3_0_chr6_dbb_hap3_4448253_r	0.0	0.0	0.0
+chr6_dbb_hap3	4448374	4448511	uc011gly.3_exon_8_0_chr6_dbb_hap3_4448253_r;uc011glz.3_exon_8_0_chr6_dbb_hap3_4448253_r;uc011gme.2_exon_3_0_chr6_dbb_hap3_4448253_r	0.0	0.0	0.0
+chr6_dbb_hap3	4449294	4449404	uc011gly.3_exon_9_0_chr6_dbb_hap3_4449326_r;uc011glz.3_exon_9_0_chr6_dbb_hap3_4449326_r;uc011gmc.2_exon_4_0_chr6_dbb_hap3_4449326_r;uc011gme.2_exon_4_0_chr6_dbb_hap3_4449326_r;uc011gmf.2_exon_3_0_chr6_dbb_hap3_4449326_r	0.0	0.0	0.0
+chr6_dbb_hap3	4449419	4449798	uc011gly.3_exon_9_0_chr6_dbb_hap3_4449326_r;uc011glz.3_exon_9_0_chr6_dbb_hap3_4449326_r;uc011gmc.2_exon_4_0_chr6_dbb_hap3_4449326_r;uc011gme.2_exon_4_0_chr6_dbb_hap3_4449326_r;uc011gmf.2_exon_3_0_chr6_dbb_hap3_4449326_r	0.0	0.0	0.0
+chr6_dbb_hap3	4449814	4449954	uc011gmb.3_exon_8_0_chr6_dbb_hap3_4449851_r	0.0	0.0	0.0
+chr6_mann_hap4	4618646	4619934	uc011hgn.3_exon_0_0_chr6_mann_hap4_4618677_r;uc011hgo.3_exon_0_0_chr6_mann_hap4_4618677_r;uc011hgq.3_exon_0_0_chr6_mann_hap4_4618677_r	0.0	0.0	0.0
+chr6_mann_hap4	4620016	4620159	uc011hgn.3_exon_1_0_chr6_mann_hap4_4620038_r;uc011hgo.3_exon_1_0_chr6_mann_hap4_4620038_r;uc011hgq.3_exon_1_0_chr6_mann_hap4_4620038_r	0.0	0.0	0.0
+chr6_mann_hap4	4620426	4620577	uc011hgn.3_exon_2_0_chr6_mann_hap4_4620456_r;uc011hgo.3_exon_2_0_chr6_mann_hap4_4620456_r;uc011hgq.3_exon_2_0_chr6_mann_hap4_4620456_r	0.0	0.0	0.0
+chr6_mann_hap4	4620636	4621588	uc011hgn.3_exon_3_0_chr6_mann_hap4_4620663_r;uc011hgn.3_exon_4_0_chr6_mann_hap4_4621000_r;uc011hgn.3_exon_5_0_chr6_mann_hap4_4621527_r;uc011hgo.3_exon_3_0_chr6_mann_hap4_4620663_r;uc011hgo.3_exon_4_0_chr6_mann_hap4_4621000_r;uc011hgo.3_exon_5_0_chr6_mann_hap4_4621527_r;uc011hgq.3_exon_3_0_chr6_mann_hap4_4620663_r;uc011hgq.3_exon_4_0_chr6_mann_hap4_4621000_r;uc011hgq.3_exon_5_0_chr6_mann_hap4_4621527_r;uc011hgr.2_exon_0_0_chr6_mann_hap4_4620704_r;uc011hgr.2_exon_1_0_chr6_mann_hap4_4621527_r;uc011hgs.1_exon_0_0_chr6_mann_hap4_4620878_r;uc011hgt.2_exon_0_0_chr6_mann_hap4_4620878_r;uc011hgu.2_exon_0_0_chr6_mann_hap4_4620878_r	0.0	0.0	0.0
+chr6_mann_hap4	4621591	4621730	uc011hgn.3_exon_3_0_chr6_mann_hap4_4620663_r;uc011hgn.3_exon_4_0_chr6_mann_hap4_4621000_r;uc011hgn.3_exon_5_0_chr6_mann_hap4_4621527_r;uc011hgo.3_exon_3_0_chr6_mann_hap4_4620663_r;uc011hgo.3_exon_4_0_chr6_mann_hap4_4621000_r;uc011hgo.3_exon_5_0_chr6_mann_hap4_4621527_r;uc011hgq.3_exon_3_0_chr6_mann_hap4_4620663_r;uc011hgq.3_exon_4_0_chr6_mann_hap4_4621000_r;uc011hgq.3_exon_5_0_chr6_mann_hap4_4621527_r;uc011hgr.2_exon_0_0_chr6_mann_hap4_4620704_r;uc011hgr.2_exon_1_0_chr6_mann_hap4_4621527_r;uc011hgs.1_exon_0_0_chr6_mann_hap4_4620878_r;uc011hgt.2_exon_0_0_chr6_mann_hap4_4620878_r;uc011hgu.2_exon_0_0_chr6_mann_hap4_4620878_r	0.0	0.0	0.0
+chr6_mann_hap4	4622826	4623065	uc011hgn.3_exon_6_0_chr6_mann_hap4_4622855_r;uc011hgo.3_exon_6_0_chr6_mann_hap4_4622855_r;uc011hgq.3_exon_6_0_chr6_mann_hap4_4622855_r;uc011hgr.2_exon_2_0_chr6_mann_hap4_4622855_r;uc011hgs.1_exon_1_0_chr6_mann_hap4_4622855_r;uc011hgt.2_exon_1_0_chr6_mann_hap4_4622855_r;uc011hgu.2_exon_1_0_chr6_mann_hap4_4622855_r	0.0	0.0	0.0
+chr6_mann_hap4	4623366	4623703	uc011hgn.3_exon_7_0_chr6_mann_hap4_4623401_r;uc011hgo.3_exon_7_0_chr6_mann_hap4_4623401_r;uc011hgq.3_exon_7_0_chr6_mann_hap4_4623401_r;uc011hgr.2_exon_3_0_chr6_mann_hap4_4623401_r;uc011hgs.1_exon_2_0_chr6_mann_hap4_4623401_r;uc011hgt.2_exon_2_0_chr6_mann_hap4_4623401_r;uc011hgu.2_exon_2_0_chr6_mann_hap4_4623401_r	0.0	0.0	0.0
+chr6_mann_hap4	4624226	4624378	uc011hgn.3_exon_8_0_chr6_mann_hap4_4624262_r;uc011hgo.3_exon_8_0_chr6_mann_hap4_4624262_r;uc011hgt.2_exon_3_0_chr6_mann_hap4_4624262_r	0.0	0.0	0.0
+chr6_mann_hap4	4624386	4624523	uc011hgn.3_exon_8_0_chr6_mann_hap4_4624262_r;uc011hgo.3_exon_8_0_chr6_mann_hap4_4624262_r;uc011hgt.2_exon_3_0_chr6_mann_hap4_4624262_r	0.0	0.0	0.0
+chr6_mann_hap4	4625301	4625412	uc011hgn.3_exon_9_0_chr6_mann_hap4_4625335_r;uc011hgo.3_exon_9_0_chr6_mann_hap4_4625335_r;uc011hgr.2_exon_4_0_chr6_mann_hap4_4625335_r;uc011hgt.2_exon_4_0_chr6_mann_hap4_4625335_r;uc011hgu.2_exon_3_0_chr6_mann_hap4_4625335_r	0.0	0.0	0.0
+chr6_mann_hap4	4625426	4625809	uc011hgn.3_exon_9_0_chr6_mann_hap4_4625335_r;uc011hgo.3_exon_9_0_chr6_mann_hap4_4625335_r;uc011hgr.2_exon_4_0_chr6_mann_hap4_4625335_r;uc011hgt.2_exon_4_0_chr6_mann_hap4_4625335_r;uc011hgu.2_exon_3_0_chr6_mann_hap4_4625335_r	0.0	0.0	0.0
+chr6_mann_hap4	4625826	4625962	uc011hgq.3_exon_8_0_chr6_mann_hap4_4625860_r	0.0	0.0	0.0
+chr6_mcf_hap5	4635098	4635635	uc011ibu.3_exon_0_0_chr6_mcf_hap5_4635126_r;uc011ibv.3_exon_0_0_chr6_mcf_hap5_4635126_r;uc011ibx.3_exon_0_0_chr6_mcf_hap5_4635126_r	0.0	0.0	0.0
+chr6_mcf_hap5	4635653	4636382	uc011ibu.3_exon_0_0_chr6_mcf_hap5_4635126_r;uc011ibv.3_exon_0_0_chr6_mcf_hap5_4635126_r;uc011ibx.3_exon_0_0_chr6_mcf_hap5_4635126_r	0.0	0.0	0.0
+chr6_mcf_hap5	4636463	4636602	uc011ibu.3_exon_1_0_chr6_mcf_hap5_4636486_r;uc011ibv.3_exon_1_0_chr6_mcf_hap5_4636486_r;uc011ibx.3_exon_1_0_chr6_mcf_hap5_4636486_r	0.0	0.0	0.0
+chr6_mcf_hap5	4636873	4637025	uc011ibu.3_exon_2_0_chr6_mcf_hap5_4636904_r;uc011ibv.3_exon_2_0_chr6_mcf_hap5_4636904_r;uc011ibx.3_exon_2_0_chr6_mcf_hap5_4636904_r	0.0	0.0	0.0
+chr6_mcf_hap5	4637088	4637237	uc011ibu.3_exon_3_0_chr6_mcf_hap5_4637111_r;uc011ibu.3_exon_4_0_chr6_mcf_hap5_4637446_r;uc011ibu.3_exon_5_0_chr6_mcf_hap5_4637973_r;uc011ibv.3_exon_3_0_chr6_mcf_hap5_4637111_r;uc011ibv.3_exon_4_0_chr6_mcf_hap5_4637446_r;uc011ibv.3_exon_5_0_chr6_mcf_hap5_4637973_r;uc011ibx.3_exon_3_0_chr6_mcf_hap5_4637111_r;uc011ibx.3_exon_4_0_chr6_mcf_hap5_4637446_r;uc011ibx.3_exon_5_0_chr6_mcf_hap5_4637973_r;uc011iby.2_exon_0_0_chr6_mcf_hap5_4637152_r;uc011iby.2_exon_1_0_chr6_mcf_hap5_4637973_r;uc011ibz.1_exon_0_0_chr6_mcf_hap5_4637326_r;uc011ica.2_exon_0_0_chr6_mcf_hap5_4637326_r;uc011icb.2_exon_0_0_chr6_mcf_hap5_4637326_r	0.0	0.0	0.0
+chr6_mcf_hap5	4637238	4638034	uc011ibu.3_exon_3_0_chr6_mcf_hap5_4637111_r;uc011ibu.3_exon_4_0_chr6_mcf_hap5_4637446_r;uc011ibu.3_exon_5_0_chr6_mcf_hap5_4637973_r;uc011ibv.3_exon_3_0_chr6_mcf_hap5_4637111_r;uc011ibv.3_exon_4_0_chr6_mcf_hap5_4637446_r;uc011ibv.3_exon_5_0_chr6_mcf_hap5_4637973_r;uc011ibx.3_exon_3_0_chr6_mcf_hap5_4637111_r;uc011ibx.3_exon_4_0_chr6_mcf_hap5_4637446_r;uc011ibx.3_exon_5_0_chr6_mcf_hap5_4637973_r;uc011iby.2_exon_0_0_chr6_mcf_hap5_4637152_r;uc011iby.2_exon_1_0_chr6_mcf_hap5_4637973_r;uc011ibz.1_exon_0_0_chr6_mcf_hap5_4637326_r;uc011ica.2_exon_0_0_chr6_mcf_hap5_4637326_r;uc011icb.2_exon_0_0_chr6_mcf_hap5_4637326_r	0.0	0.0	0.0
+chr6_mcf_hap5	4638038	4638177	uc011ibu.3_exon_3_0_chr6_mcf_hap5_4637111_r;uc011ibu.3_exon_4_0_chr6_mcf_hap5_4637446_r;uc011ibu.3_exon_5_0_chr6_mcf_hap5_4637973_r;uc011ibv.3_exon_3_0_chr6_mcf_hap5_4637111_r;uc011ibv.3_exon_4_0_chr6_mcf_hap5_4637446_r;uc011ibv.3_exon_5_0_chr6_mcf_hap5_4637973_r;uc011ibx.3_exon_3_0_chr6_mcf_hap5_4637111_r;uc011ibx.3_exon_4_0_chr6_mcf_hap5_4637446_r;uc011ibx.3_exon_5_0_chr6_mcf_hap5_4637973_r;uc011iby.2_exon_0_0_chr6_mcf_hap5_4637152_r;uc011iby.2_exon_1_0_chr6_mcf_hap5_4637973_r;uc011ibz.1_exon_0_0_chr6_mcf_hap5_4637326_r;uc011ica.2_exon_0_0_chr6_mcf_hap5_4637326_r;uc011icb.2_exon_0_0_chr6_mcf_hap5_4637326_r	0.0	0.0	0.0
+chr6_mcf_hap5	4639268	4639512	uc011ibu.3_exon_6_0_chr6_mcf_hap5_4639301_r;uc011ibv.3_exon_6_0_chr6_mcf_hap5_4639301_r;uc011ibx.3_exon_6_0_chr6_mcf_hap5_4639301_r;uc011iby.2_exon_2_0_chr6_mcf_hap5_4639301_r;uc011ibz.1_exon_1_0_chr6_mcf_hap5_4639301_r;uc011ica.2_exon_1_0_chr6_mcf_hap5_4639301_r;uc011icb.2_exon_1_0_chr6_mcf_hap5_4639301_r	0.0	0.0	0.0
+chr6_mcf_hap5	4639813	4640150	uc011ibu.3_exon_7_0_chr6_mcf_hap5_4639847_r;uc011ibv.3_exon_7_0_chr6_mcf_hap5_4639847_r;uc011ibx.3_exon_7_0_chr6_mcf_hap5_4639847_r;uc011iby.2_exon_3_0_chr6_mcf_hap5_4639847_r;uc011ibz.1_exon_2_0_chr6_mcf_hap5_4639847_r;uc011ica.2_exon_2_0_chr6_mcf_hap5_4639847_r;uc011icb.2_exon_2_0_chr6_mcf_hap5_4639847_r	0.0	0.0	0.0
+chr6_mcf_hap5	4640678	4640825	uc011ibu.3_exon_8_0_chr6_mcf_hap5_4640707_r;uc011ibv.3_exon_8_0_chr6_mcf_hap5_4640707_r;uc011ica.2_exon_3_0_chr6_mcf_hap5_4640707_r	0.0	0.0	0.0
+chr6_mcf_hap5	4640828	4640965	uc011ibu.3_exon_8_0_chr6_mcf_hap5_4640707_r;uc011ibv.3_exon_8_0_chr6_mcf_hap5_4640707_r;uc011ica.2_exon_3_0_chr6_mcf_hap5_4640707_r	0.0	0.0	0.0
+chr6_mcf_hap5	4641748	4641858	uc011ibu.3_exon_9_0_chr6_mcf_hap5_4641780_r;uc011ibv.3_exon_9_0_chr6_mcf_hap5_4641780_r;uc011iby.2_exon_4_0_chr6_mcf_hap5_4641780_r;uc011ica.2_exon_4_0_chr6_mcf_hap5_4641780_r;uc011icb.2_exon_3_0_chr6_mcf_hap5_4641780_r	0.0	0.0	0.0
+chr6_mcf_hap5	4641873	4642252	uc011ibu.3_exon_9_0_chr6_mcf_hap5_4641780_r;uc011ibv.3_exon_9_0_chr6_mcf_hap5_4641780_r;uc011iby.2_exon_4_0_chr6_mcf_hap5_4641780_r;uc011ica.2_exon_4_0_chr6_mcf_hap5_4641780_r;uc011icb.2_exon_3_0_chr6_mcf_hap5_4641780_r	0.0	0.0	0.0
+chr6_mcf_hap5	4642268	4642408	uc011ibx.3_exon_8_0_chr6_mcf_hap5_4642305_r	0.0	0.0	0.0
+chr6_qbl_hap6	4393556	4394093	uc011izg.3_exon_0_0_chr6_qbl_hap6_4393584_r;uc011izh.3_exon_0_0_chr6_qbl_hap6_4393584_r;uc011izj.3_exon_0_0_chr6_qbl_hap6_4393584_r	0.0	0.0	0.0
+chr6_qbl_hap6	4394111	4394841	uc011izg.3_exon_0_0_chr6_qbl_hap6_4393584_r;uc011izh.3_exon_0_0_chr6_qbl_hap6_4393584_r;uc011izj.3_exon_0_0_chr6_qbl_hap6_4393584_r	0.0	0.0	0.0
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+chr7	107423390	107423572	uc003ver.2_exon_11_0_chr7_107423425_r;uc003ves.2_exon_10_0_chr7_107423425_r	0.0	0.0	0.0
+chr7	107423620	107423833	uc003ver.2_exon_12_0_chr7_107423650_r;uc003ves.2_exon_11_0_chr7_107423650_r	0.0	0.0	0.0
+chr7	107427240	107427385	uc003ver.2_exon_13_0_chr7_107427272_r;uc003ves.2_exon_12_0_chr7_107427272_r	0.0	0.0	0.0
+chr7	107427770	107427982	uc003ver.2_exon_14_0_chr7_107427802_r;uc003ves.2_exon_13_0_chr7_107427802_r	0.0	0.0	0.0
+chr7	107429945	107430150	uc003ver.2_exon_15_0_chr7_107429969_r;uc003ves.2_exon_14_0_chr7_107429969_r	0.0	0.0	0.0
+chr7	107431460	107431716	uc003ver.2_exon_16_0_chr7_107431493_r;uc003ves.2_exon_15_0_chr7_107431493_r	0.0	0.0	0.0
+chr7	107432250	107432426	uc003ver.2_exon_17_0_chr7_107432275_r;uc003ves.2_exon_16_0_chr7_107432275_r	0.0	0.0	0.0
+chr7	107434165	107434339	uc003ver.2_exon_18_0_chr7_107434187_r;uc003ves.2_exon_17_0_chr7_107434187_r	0.0	0.0	0.0
+chr7	107434795	107435073	uc003ver.2_exon_19_0_chr7_107434824_r;uc003ves.2_exon_18_0_chr7_107434824_r	0.0	0.0	0.0
+chr7	107443530	107443722	uc003ver.2_exon_20_0_chr7_107443556_r;uc003ves.2_exon_19_0_chr7_107443556_r	0.0	0.0	0.0
+chr7	142568932	142569393	uc003wbw.1_exon_0_0_chr7_142568960_r;uc003wbx.2_exon_0_0_chr7_142568960_r;uc010lou.1_exon_0_0_chr7_142568960_r	0.0	0.0	0.0
+chr7	142569397	142569786	uc003wbw.1_exon_0_0_chr7_142568960_r;uc003wbx.2_exon_0_0_chr7_142568960_r;uc010lou.1_exon_0_0_chr7_142568960_r	0.0	0.0	0.0
+chr7	142570097	142570248	uc003wbw.1_exon_1_0_chr7_142570125_r;uc003wbx.2_exon_1_0_chr7_142570125_r;uc010lou.1_exon_1_0_chr7_142570125_r	0.0	0.0	0.0
+chr7	142571177	142571486	uc003wbw.1_exon_2_0_chr7_142571201_r;uc003wbx.2_exon_2_0_chr7_142571201_r;uc010lou.1_exon_2_0_chr7_142571201_r	0.0	0.0	0.0
+chr7	142571777	142571935	uc003wbw.1_exon_3_0_chr7_142571829_r;uc003wbx.2_exon_3_0_chr7_142571829_r;uc010lou.1_exon_3_0_chr7_142571829_r	0.0	0.0	0.0
+chr7	142572212	142572438	uc003wbw.1_exon_4_0_chr7_142572244_r;uc003wbx.2_exon_4_0_chr7_142572244_r;uc010lou.1_exon_4_0_chr7_142572244_r	0.0	0.0	0.0
+chr7	142572622	142572758	uc003wbw.1_exon_5_0_chr7_142572657_r;uc003wbx.2_exon_5_0_chr7_142572657_r;uc010lou.1_exon_5_0_chr7_142572657_r	0.0	0.0	0.0
+chr7	142572792	142572942	uc003wbw.1_exon_6_0_chr7_142572831_r;uc003wbx.2_exon_6_0_chr7_142572831_r;uc010lou.1_exon_6_0_chr7_142572831_r	0.0	0.0	0.0
+chr7	142573197	142573475	uc003wbw.1_exon_7_0_chr7_142573221_r;uc003wbx.2_exon_7_0_chr7_142573221_r;uc010lou.1_exon_7_0_chr7_142573221_r	0.0	0.0	0.0
+chr7	142573487	142573697	uc003wbw.1_exon_8_0_chr7_142573511_r;uc003wbx.2_exon_8_0_chr7_142573511_r;uc010lou.1_exon_8_0_chr7_142573511_r	0.0	0.0	0.0
+chr7	142574127	142574384	uc003wbw.1_exon_9_0_chr7_142574161_r;uc003wbx.2_exon_9_0_chr7_142574161_r;uc010lou.1_exon_9_0_chr7_142574161_r	0.0	0.0	0.0
+chr7	142574467	142574617	uc003wbx.2_exon_10_0_chr7_142574492_r;uc010lou.1_exon_10_0_chr7_142574492_r	0.0	0.0	0.0
+chr7	142574867	142575816	uc003wbx.2_exon_11_0_chr7_142574895_r;uc003wbx.2_exon_12_0_chr7_142575404_r;uc003wbx.2_exon_13_0_chr7_142575682_r;uc010lou.1_exon_11_0_chr7_142574895_r	0.0	0.0	0.0
+chr7	142583107	142583536	uc003wbx.2_exon_14_0_chr7_142583134_r	0.0	0.0	0.0
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+chr7	142611762	142611916	uc003wby.1_exon_3_0_chr7_142611810_r	0.0	0.0	0.0
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+chr7	142612612	142612772	uc003wby.1_exon_6_0_chr7_142612652_r	0.0	0.0	0.0
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+chr7	142625752	142625972	uc003wby.1_exon_9_0_chr7_142625786_r;uc003wbz.3_exon_2_0_chr7_142625786_r	0.0	0.0	0.0
+chr7	142626092	142626236	uc003wby.1_exon_10_0_chr7_142626117_r;uc003wbz.3_exon_3_0_chr7_142626117_r	0.0	0.0	0.0
+chr7	142626487	142626686	uc003wby.1_exon_11_0_chr7_142626523_r;uc003wbz.3_exon_4_0_chr7_142626523_r	0.0	0.0	0.0
+chr7	142627117	142627313	uc003wby.1_exon_12_0_chr7_142627153_r;uc003wbz.3_exon_5_0_chr7_142627153_r	0.0	0.0	0.0
+chr7	142627417	142627551	uc003wby.1_exon_13_0_chr7_142627444_r;uc003wbz.3_exon_6_0_chr7_142627444_r	0.0	0.0	0.0
+chr7	142630402	142630694	uc003wby.1_exon_14_0_chr7_142630429_r;uc003wbz.3_exon_7_0_chr7_142630429_r	0.0	0.0	0.0
+chr7	142630727	142630864	uc003wby.1_exon_14_0_chr7_142630429_r;uc003wbz.3_exon_7_0_chr7_142630429_r	0.0	0.0	0.0
+chr8	38268623	38269612	uc003xlp.3_exon_0_0_chr8_38268656_r;uc010lwf.3_exon_0_0_chr8_38268656_r;uc010lwk.3_exon_0_0_chr8_38268656_r;uc011lbu.2_exon_0_0_chr8_38268656_r;uc011lbv.2_exon_0_0_chr8_38268656_r;uc011lbw.2_exon_0_0_chr8_38268656_r;uc022aua.1_exon_0_0_chr8_38268656_r;uc022aub.1_exon_0_0_chr8_38268656_r;uc022auc.1_exon_0_0_chr8_38268656_r;uc022aud.1_exon_0_0_chr8_38268656_r	0.0	0.0	0.0
+chr8	38269843	38270303	uc003xlp.3_exon_0_0_chr8_38268656_r;uc010lwf.3_exon_0_0_chr8_38268656_r;uc010lwk.3_exon_0_0_chr8_38268656_r;uc011lbu.2_exon_0_0_chr8_38268656_r;uc011lbv.2_exon_0_0_chr8_38268656_r;uc011lbw.2_exon_0_0_chr8_38268656_r;uc022aua.1_exon_0_0_chr8_38268656_r;uc022aub.1_exon_0_0_chr8_38268656_r;uc022auc.1_exon_0_0_chr8_38268656_r;uc022aud.1_exon_0_0_chr8_38268656_r	0.0	0.0	0.0
+chr8	38270373	38270723	uc003xlp.3_exon_0_0_chr8_38268656_r;uc010lwf.3_exon_0_0_chr8_38268656_r;uc010lwk.3_exon_0_0_chr8_38268656_r;uc011lbu.2_exon_0_0_chr8_38268656_r;uc011lbv.2_exon_0_0_chr8_38268656_r;uc011lbw.2_exon_0_0_chr8_38268656_r;uc022aua.1_exon_0_0_chr8_38268656_r;uc022aub.1_exon_0_0_chr8_38268656_r;uc022auc.1_exon_0_0_chr8_38268656_r;uc022aud.1_exon_0_0_chr8_38268656_r	0.0	0.0	0.0
+chr8	38270743	38271350	uc003xlp.3_exon_0_0_chr8_38268656_r;uc010lwf.3_exon_0_0_chr8_38268656_r;uc010lwk.3_exon_0_0_chr8_38268656_r;uc011lbu.2_exon_0_0_chr8_38268656_r;uc011lbv.2_exon_0_0_chr8_38268656_r;uc011lbw.2_exon_0_0_chr8_38268656_r;uc022aua.1_exon_0_0_chr8_38268656_r;uc022aub.1_exon_0_0_chr8_38268656_r;uc022auc.1_exon_0_0_chr8_38268656_r;uc022aud.1_exon_0_0_chr8_38268656_r	0.0	0.0	0.0
+chr8	38271413	38271567	uc003xlp.3_exon_1_0_chr8_38271436_r;uc010lwf.3_exon_1_0_chr8_38271436_r;uc010lwk.3_exon_1_0_chr8_38271436_r;uc011lbu.2_exon_1_0_chr8_38271436_r;uc011lbv.2_exon_1_0_chr8_38271436_r;uc011lbw.2_exon_1_0_chr8_38271436_r;uc022aua.1_exon_1_0_chr8_38271436_r;uc022aub.1_exon_1_0_chr8_38271436_r;uc022auc.1_exon_1_0_chr8_38271436_r;uc022aud.1_exon_1_0_chr8_38271436_r	0.0	0.0	0.0
+chr8	38271638	38271830	uc003xlp.3_exon_2_0_chr8_38271670_r;uc010lwf.3_exon_2_0_chr8_38271670_r;uc010lwk.3_exon_2_0_chr8_38271670_r;uc011lbu.2_exon_2_0_chr8_38271670_r;uc011lbv.2_exon_2_0_chr8_38271670_r;uc011lbw.2_exon_2_0_chr8_38271670_r;uc022aua.1_exon_2_0_chr8_38271670_r;uc022aub.1_exon_2_0_chr8_38271670_r;uc022auc.1_exon_2_0_chr8_38271670_r;uc022aud.1_exon_2_0_chr8_38271670_r	0.0	0.0	0.0
+chr8	38272033	38272174	uc003xlp.3_exon_3_0_chr8_38272077_r;uc010lwf.3_exon_3_0_chr8_38272077_r;uc010lwk.3_exon_3_0_chr8_38272077_r;uc011lbu.2_exon_3_0_chr8_38272077_r;uc011lbv.2_exon_3_0_chr8_38272077_r;uc011lbw.2_exon_3_0_chr8_38272077_r;uc022aua.1_exon_3_0_chr8_38272077_r;uc022aub.1_exon_3_0_chr8_38272077_r;uc022auc.1_exon_3_0_chr8_38272077_r;uc022aud.1_exon_3_0_chr8_38272077_r	0.0	0.0	0.0
+chr8	38272268	38272446	uc003xlp.3_exon_4_0_chr8_38272297_r;uc010lwf.3_exon_4_0_chr8_38272297_r;uc010lwk.3_exon_4_0_chr8_38272297_r;uc011lbu.2_exon_4_0_chr8_38272297_r;uc011lbv.2_exon_4_0_chr8_38272297_r;uc011lbw.2_exon_4_0_chr8_38272297_r;uc022aua.1_exon_4_0_chr8_38272297_r;uc022aub.1_exon_4_0_chr8_38272297_r;uc022auc.1_exon_4_0_chr8_38272297_r;uc022aud.1_exon_4_0_chr8_38272297_r	0.0	0.0	0.0
+chr8	38273338	38273621	uc003xlp.3_exon_5_0_chr8_38273388_r;uc010lwf.3_exon_5_0_chr8_38273363_r;uc010lwk.3_exon_5_0_chr8_38273388_r;uc011lbu.2_exon_5_0_chr8_38273388_r;uc011lbv.2_exon_5_0_chr8_38273388_r;uc011lbw.2_exon_5_0_chr8_38273388_r;uc022aua.1_exon_5_0_chr8_38273388_r;uc022aub.1_exon_5_0_chr8_38273388_r;uc022auc.1_exon_5_0_chr8_38273388_r;uc022aud.1_exon_5_0_chr8_38273388_r	0.0	0.0	0.0
+chr8	38274798	38274969	uc003xlp.3_exon_6_0_chr8_38274824_r;uc010lwf.3_exon_6_0_chr8_38274824_r;uc010lwk.3_exon_6_0_chr8_38274824_r;uc011lbu.2_exon_6_0_chr8_38274824_r;uc011lbv.2_exon_6_0_chr8_38274824_r;uc011lbw.2_exon_6_0_chr8_38274824_r;uc022aua.1_exon_6_0_chr8_38274824_r;uc022aub.1_exon_6_0_chr8_38274824_r;uc022auc.1_exon_6_0_chr8_38274824_r;uc022aud.1_exon_6_0_chr8_38274824_r	0.0	0.0	0.0
+chr8	38275353	38275526	uc003xlp.3_exon_7_0_chr8_38275388_r;uc010lwf.3_exon_7_0_chr8_38275388_r;uc010lwk.3_exon_7_0_chr8_38275388_r;uc011lbu.2_exon_7_0_chr8_38275388_r;uc011lbv.2_exon_7_0_chr8_38275388_r;uc011lbw.2_exon_7_0_chr8_38275388_r;uc022aua.1_exon_7_0_chr8_38275388_r;uc022aub.1_exon_7_0_chr8_38275388_r;uc022auc.1_exon_7_0_chr8_38275388_r;uc022aud.1_exon_7_0_chr8_38275388_r	0.0	0.0	0.0
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+chr8	38277018	38277278	uc003xlp.3_exon_9_0_chr8_38277057_r;uc010lwk.3_exon_9_0_chr8_38277057_r;uc011lbr.2_exon_0_0_chr8_38277051_r;uc011lbs.2_exon_0_0_chr8_38277051_r;uc011lbt.1_exon_0_0_chr8_38277057_r;uc011lbu.2_exon_9_0_chr8_38277051_r;uc011lbv.2_exon_9_0_chr8_38277051_r;uc011lbw.2_exon_9_0_chr8_38277051_r;uc022aua.1_exon_9_0_chr8_38277051_r;uc022aub.1_exon_9_0_chr8_38277051_r;uc022auc.1_exon_9_0_chr8_38277051_r;uc022aud.1_exon_9_0_chr8_38277051_r	0.0	0.0	0.0
+chr8	38279133	38279489	uc003xlp.3_exon_10_0_chr8_38279315_r;uc010lwk.3_exon_10_0_chr8_38279315_r;uc011lbr.2_exon_1_0_chr8_38279315_r;uc011lbs.2_exon_1_0_chr8_38279315_r;uc011lbu.2_exon_10_0_chr8_38279315_r;uc011lbv.2_exon_10_0_chr8_38279315_r;uc011lbw.2_exon_10_0_chr8_38279315_r;uc011lbx.1_exon_0_0_chr8_38279166_r;uc022aua.1_exon_10_0_chr8_38279315_r;uc022aub.1_exon_10_0_chr8_38279315_r;uc022auc.1_exon_10_0_chr8_38279315_r;uc022aud.1_exon_10_0_chr8_38279315_r	0.0	0.0	0.0
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+chr8	38281193	38282237	uc003xlp.3_exon_11_0_chr8_38282027_r;uc003xlu.3_exon_0_0_chr8_38280851_r;uc003xlv.3_exon_0_0_chr8_38280851_r;uc010lwk.3_exon_11_0_chr8_38282027_r;uc011lbr.2_exon_3_0_chr8_38282027_r;uc011lbs.2_exon_2_0_chr8_38282027_r;uc011lbt.1_exon_1_0_chr8_38282027_r;uc011lbu.2_exon_11_0_chr8_38282027_r;uc011lbv.2_exon_11_0_chr8_38282027_r;uc011lbw.2_exon_11_0_chr8_38282027_r;uc011lbx.1_exon_1_0_chr8_38282027_r;uc022aua.1_exon_11_0_chr8_38282027_r;uc022aub.1_exon_11_0_chr8_38282027_r;uc022auc.1_exon_11_0_chr8_38282027_r;uc022aud.1_exon_11_0_chr8_38282027_r	0.0	0.0	0.0
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+chrX	128710269	128710542	uc004euq.3_exon_17_0_chrX_128710294_f;uc004eur.3_exon_17_0_chrX_128710294_f	0.0	0.0	0.0
+chrX	128718259	128718394	uc004euq.3_exon_18_0_chrX_128718321_f	0.0	0.0	0.0
+chrX	128720954	128721127	uc004euq.3_exon_19_0_chrX_128720979_f;uc004eur.3_exon_18_0_chrX_128720979_f	0.0	0.0	0.0
+chrX	128722114	128722271	uc004euq.3_exon_20_0_chrX_128722156_f;uc004eur.3_exon_19_0_chrX_128722156_f	0.0	0.0	0.0
+chrX	128722829	128723018	uc004euq.3_exon_21_0_chrX_128722863_f;uc004eur.3_exon_20_0_chrX_128722863_f;uc010nrb.3_exon_0_0_chrX_128722863_f	0.0	0.0	0.0
+chrX	128723789	128723974	uc004euq.3_exon_22_0_chrX_128723822_f;uc004eur.3_exon_21_0_chrX_128723822_f	0.0	0.0	0.0
+chrX	128724099	128725469	uc004euq.3_exon_23_0_chrX_128724123_f;uc004eur.3_exon_22_0_chrX_128724123_f;uc010nrb.3_exon_1_0_chrX_128724123_f	0.0	0.0	0.0
+chrX	128725474	128726564	uc004euq.3_exon_23_0_chrX_128724123_f;uc004eur.3_exon_22_0_chrX_128724123_f;uc010nrb.3_exon_1_0_chrX_128724123_f	0.0	0.0	0.0
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Binary file test-data/graph_pysam.pdf has changed