# HG changeset patch
# User artbio
# Date 1578395336 18000
# Node ID 7c4feda2d9c7abd260f5dbdf9bd686231294ac09
# Parent  2ec6529e555d48e051703802ab67f9fcea27a4a0
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"

diff -r 2ec6529e555d -r 7c4feda2d9c7 multicov.py
--- a/multicov.py	Sat Jun 02 07:10:17 2018 -0400
+++ b/multicov.py	Tue Jan 07 06:08:56 2020 -0500
@@ -26,9 +26,9 @@
         chr = fields[0]
         start = fields[1]
         end = fields[2]
-        coverage = bam_object.count_coverage(reference=chr,
+        coverage = bam_object.count_coverage(contig=chr,
                                              start=int(start)-1,
-                                             end=int(end),
+                                             stop=int(end),
                                              quality_threshold=quality)
         """ Add the 4 coverage values """
         coverage = [sum(x) for x in zip(*coverage)]
diff -r 2ec6529e555d -r 7c4feda2d9c7 probecoverage.xml
--- a/probecoverage.xml	Sat Jun 02 07:10:17 2018 -0400
+++ b/probecoverage.xml	Tue Jan 07 06:08:56 2020 -0500
@@ -1,12 +1,12 @@
-<tool id="probecoverage" name="Probe Coverage" version="0.5.0">
+<tool id="probecoverage" name="Probe Coverage" version="0.6.0">
   <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=r3.3.2_0">r-optparse</requirement>
-        <requirement type="package" version="2.2.1=r3.3.2_0">r-ggplot2</requirement>
-        <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
-        <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement>
+        <requirement type="package" version="1.10=h9402c20_2">samtools</requirement>
+        <requirement type="package" version="2.29.2=hc088bd4_0">bedtools</requirement>
+        <requirement type="package" version="1.6.4=r36h6115d3f_0">r-optparse</requirement>
+        <requirement type="package" version="3.2.1=r36h6115d3f_0">r-ggplot2</requirement>
+        <requirement type="package" version="1.17.3=py37h95a1406_0">numpy</requirement>
+        <requirement type="package" version="0.15.3=py37hbcae180_3">pysam</requirement>
   </requirements>
   <stdio>
       <exit_code range="1:" level="fatal" description="Tool exception" />
diff -r 2ec6529e555d -r 7c4feda2d9c7 test-data/coverage.tab
--- a/test-data/coverage.tab	Sat Jun 02 07:10:17 2018 -0400
+++ b/test-data/coverage.tab	Tue Jan 07 06:08:56 2020 -0500
@@ -674,39 +674,39 @@
 chr16	20361937	20362204	uc002dgz.3_exon_9_0_chr16_20361972_r;uc002dha.3_exon_9_0_chr16_20361972_r;uc002dhb.3_exon_10_0_chr16_20361972_r	0	0	0
 chr16	20363947	20364103	uc002dgz.3_exon_10_0_chr16_20364011_r;uc002dha.3_exon_10_0_chr16_20364011_r;uc002dhb.3_exon_11_0_chr16_20364011_r	0	0	0
 chr19	3094375	3094805	uc002lxd.3_exon_0_0_chr19_3094408_f	16	0	0
-chr19	3110125	3110366	uc002lxd.3_exon_1_0_chr19_3110147_f	309	0	0
+chr19	3110125	3110366	uc002lxd.3_exon_1_0_chr19_3110147_f	311	0	0
 chr19	3113305	3113513	uc002lxd.3_exon_2_0_chr19_3113328_f	163	0	0
 chr19	3114915	3115090	uc002lxd.3_exon_3_0_chr19_3114942_f	37	0	0
 chr19	3118900	3119070	uc002lxd.3_exon_4_0_chr19_3118922_f	390	0	0
-chr19	3119175	3119384	uc002lxd.3_exon_5_0_chr19_3119204_f	957	0	0
+chr19	3119175	3119384	uc002lxd.3_exon_5_0_chr19_3119204_f	958	0	0
 chr19	3120965	3121304	uc002lxd.3_exon_6_0_chr19_3120987_f	1112	0	0
-chr19	3121310	3121447	uc002lxd.3_exon_6_0_chr19_3120987_f	1461	0	0
+chr19	3121310	3121447	uc002lxd.3_exon_6_0_chr19_3120987_f	1462	0	0
 chr19	47341397	47341813	uc002pft.1_exon_0_0_chr19_47341423_r;uc002pfu.1_exon_0_0_chr19_47341423_r	1325	0	0
 chr19	47341952	47342086	uc002pft.1_exon_1_0_chr19_47341997_r;uc002pfu.1_exon_1_0_chr19_47341997_r	1462	0	0
-chr19	47342697	47342876	uc002pft.1_exon_2_0_chr19_47342722_r	1655	0	0
+chr19	47342697	47342876	uc002pft.1_exon_2_0_chr19_47342722_r	1664	0	0
 chr19	47349227	47349441	uc002pft.1_exon_3_0_chr19_47349250_r;uc002pfu.1_exon_2_0_chr19_47349250_r	1173	0	0
-chr19	47353997	47354239	uc002pft.1_exon_4_0_chr19_47354021_r;uc002pfu.1_exon_3_0_chr19_47354021_r	1571	0	0
-chr20	52769992	52770580	uc002xwu.1_exon_0_0_chr20_52769988_r;uc002xwv.2_exon_0_0_chr20_52769988_r;uc002xww.2_exon_0_0_chr20_52769988_r	0	6777	0
-chr20	52770622	52770705	uc002xwu.1_exon_0_0_chr20_52769988_r;uc002xwv.2_exon_0_0_chr20_52769988_r;uc002xww.2_exon_0_0_chr20_52769988_r	0	2069	0
-chr20	52770707	52771336	uc002xwu.1_exon_0_0_chr20_52769988_r;uc002xwv.2_exon_0_0_chr20_52769988_r;uc002xww.2_exon_0_0_chr20_52769988_r	0	8386	0
-chr20	52773678	52773860	uc002xwu.1_exon_1_0_chr20_52773708_r;uc002xwv.2_exon_1_0_chr20_52773708_r;uc002xww.2_exon_1_0_chr20_52773708_r	0	3269	0
-chr20	52773898	52774150	uc002xwu.1_exon_2_0_chr20_52773927_r;uc002xwv.2_exon_2_0_chr20_52773927_r	0	4042	0
-chr20	52774593	52774726	uc002xwu.1_exon_3_0_chr20_52774625_r;uc002xwv.2_exon_3_0_chr20_52774625_r;uc002xww.2_exon_2_0_chr20_52774625_r	0	2012	0
-chr20	52775473	52775682	uc002xwu.1_exon_4_0_chr20_52775496_r;uc002xwv.2_exon_4_0_chr20_52775496_r;uc002xww.2_exon_3_0_chr20_52775496_r	0	3586	0
-chr20	52779223	52779439	uc002xwu.1_exon_5_0_chr20_52779256_r;uc002xwv.2_exon_5_0_chr20_52779256_r;uc002xww.2_exon_4_0_chr20_52779256_r	0	3229	0
-chr20	52780968	52781144	uc002xwu.1_exon_6_0_chr20_52780991_r;uc002xwv.2_exon_6_0_chr20_52780991_r;uc002xww.2_exon_5_0_chr20_52780991_r	0	2534	0
-chr20	52782253	52782397	uc002xwu.1_exon_7_0_chr20_52782281_r;uc002xwv.2_exon_7_0_chr20_52782281_r;uc002xww.2_exon_6_0_chr20_52782281_r	0	2232	0
-chr20	52786108	52786244	uc002xwu.1_exon_8_0_chr20_52786131_r;uc002xwv.2_exon_8_0_chr20_52786131_r;uc002xww.2_exon_7_0_chr20_52786131_r	0	2378	0
-chr20	52788093	52788504	uc002xwu.1_exon_9_0_chr20_52788116_r;uc002xwv.2_exon_9_0_chr20_52788116_r;uc002xww.2_exon_8_0_chr20_52788116_r	0	5400	0
+chr19	47353997	47354239	uc002pft.1_exon_4_0_chr19_47354021_r;uc002pfu.1_exon_3_0_chr19_47354021_r	1574	0	0
+chr20	52769992	52770580	uc002xwu.1_exon_0_0_chr20_52769988_r;uc002xwv.2_exon_0_0_chr20_52769988_r;uc002xww.2_exon_0_0_chr20_52769988_r	0	6783	0
+chr20	52770622	52770705	uc002xwu.1_exon_0_0_chr20_52769988_r;uc002xwv.2_exon_0_0_chr20_52769988_r;uc002xww.2_exon_0_0_chr20_52769988_r	0	2070	0
+chr20	52770707	52771336	uc002xwu.1_exon_0_0_chr20_52769988_r;uc002xwv.2_exon_0_0_chr20_52769988_r;uc002xww.2_exon_0_0_chr20_52769988_r	0	8394	0
+chr20	52773678	52773860	uc002xwu.1_exon_1_0_chr20_52773708_r;uc002xwv.2_exon_1_0_chr20_52773708_r;uc002xww.2_exon_1_0_chr20_52773708_r	0	3272	0
+chr20	52773898	52774150	uc002xwu.1_exon_2_0_chr20_52773927_r;uc002xwv.2_exon_2_0_chr20_52773927_r	0	4046	0
+chr20	52774593	52774726	uc002xwu.1_exon_3_0_chr20_52774625_r;uc002xwv.2_exon_3_0_chr20_52774625_r;uc002xww.2_exon_2_0_chr20_52774625_r	0	2017	0
+chr20	52775473	52775682	uc002xwu.1_exon_4_0_chr20_52775496_r;uc002xwv.2_exon_4_0_chr20_52775496_r;uc002xww.2_exon_3_0_chr20_52775496_r	0	3590	0
+chr20	52779223	52779439	uc002xwu.1_exon_5_0_chr20_52779256_r;uc002xwv.2_exon_5_0_chr20_52779256_r;uc002xww.2_exon_4_0_chr20_52779256_r	0	3232	0
+chr20	52780968	52781144	uc002xwu.1_exon_6_0_chr20_52780991_r;uc002xwv.2_exon_6_0_chr20_52780991_r;uc002xww.2_exon_5_0_chr20_52780991_r	0	2537	0
+chr20	52782253	52782397	uc002xwu.1_exon_7_0_chr20_52782281_r;uc002xwv.2_exon_7_0_chr20_52782281_r;uc002xww.2_exon_6_0_chr20_52782281_r	0	2233	0
+chr20	52786108	52786244	uc002xwu.1_exon_8_0_chr20_52786131_r;uc002xwv.2_exon_8_0_chr20_52786131_r;uc002xww.2_exon_7_0_chr20_52786131_r	0	2379	0
+chr20	52788093	52788504	uc002xwu.1_exon_9_0_chr20_52788116_r;uc002xwv.2_exon_9_0_chr20_52788116_r;uc002xww.2_exon_8_0_chr20_52788116_r	0	5404	0
 chr20	52789423	52789663	uc002xwv.2_exon_10_0_chr20_52789448_r;uc002xww.2_exon_9_0_chr20_52789448_r	0	517	0
-chr20	52789828	52790550	uc002xwv.2_exon_11_0_chr20_52789861_r;uc002xww.2_exon_10_0_chr20_52789861_r	0	1557	0
+chr20	52789828	52790550	uc002xwv.2_exon_11_0_chr20_52789861_r;uc002xww.2_exon_10_0_chr20_52789861_r	0	1559	0
 chr21	37832893	37833027	uc002yvk.2_exon_0_0_chr21_37832920_r;uc002yvl.1_exon_0_0_chr21_37832920_r;uc002yvm.1_exon_0_0_chr21_37832920_r;uc002yvn.2_exon_0_0_chr21_37832920_r;uc002yvo.1_exon_0_0_chr21_37832920_r;uc021wja.1_exon_0_0_chr21_37833274_r	0	0	2296
-chr21	37833063	37834107	uc002yvk.2_exon_0_0_chr21_37832920_r;uc002yvl.1_exon_0_0_chr21_37832920_r;uc002yvm.1_exon_0_0_chr21_37832920_r;uc002yvn.2_exon_0_0_chr21_37832920_r;uc002yvo.1_exon_0_0_chr21_37832920_r;uc021wja.1_exon_0_0_chr21_37833274_r	0	0	2903
-chr21	37849648	37849906	uc002yvl.1_exon_1_0_chr21_37849672_r	0	0	3388
-chr21	37851763	37852430	uc002yvl.1_exon_2_0_chr21_37851793_r;uc002yvm.1_exon_1_0_chr21_37851793_r	0	0	5073
-chr21	37882628	37882821	uc002yvn.2_exon_1_0_chr21_37882661_r;uc002yvo.1_exon_1_0_chr21_37882661_r	0	0	3018
+chr21	37833063	37834107	uc002yvk.2_exon_0_0_chr21_37832920_r;uc002yvl.1_exon_0_0_chr21_37832920_r;uc002yvm.1_exon_0_0_chr21_37832920_r;uc002yvn.2_exon_0_0_chr21_37832920_r;uc002yvo.1_exon_0_0_chr21_37832920_r;uc021wja.1_exon_0_0_chr21_37833274_r	0	0	2905
+chr21	37849648	37849906	uc002yvl.1_exon_1_0_chr21_37849672_r	0	0	3389
+chr21	37851763	37852430	uc002yvl.1_exon_2_0_chr21_37851793_r;uc002yvm.1_exon_1_0_chr21_37851793_r	0	0	5082
+chr21	37882628	37882821	uc002yvn.2_exon_1_0_chr21_37882661_r;uc002yvo.1_exon_1_0_chr21_37882661_r	0	0	3019
 chr21	37914828	37915151	uc002yvn.2_exon_2_0_chr21_37914863_r	0	0	323
-chr21	37948678	37948900	uc002yvo.1_exon_2_0_chr21_37948709_r	0	0	1946
+chr21	37948678	37948900	uc002yvo.1_exon_2_0_chr21_37948709_r	0	0	1948
 chrX	22050889	22051274	uc004dah.3_exon_0_0_chrX_22050921_f;uc011mjr.2_exon_0_0_chrX_22050921_f	0	0	0
 chrX	22056139	22056214	uc004dah.3_exon_1_0_chrX_22056587_f;uc011mjr.2_exon_1_0_chrX_22056587_f;uc011mjs.2_exon_0_0_chrX_22056171_f	0	0	0
 chrX	22056229	22056691	uc004dah.3_exon_1_0_chrX_22056587_f;uc011mjr.2_exon_1_0_chrX_22056587_f;uc011mjs.2_exon_0_0_chrX_22056171_f	0	0	0
diff -r 2ec6529e555d -r 7c4feda2d9c7 test-data/coverage_pysam.tab
--- a/test-data/coverage_pysam.tab	Sat Jun 02 07:10:17 2018 -0400
+++ b/test-data/coverage_pysam.tab	Tue Jan 07 06:08:56 2020 -0500
@@ -673,40 +673,40 @@
 chr16	20361067	20361208	uc002dhb.3_exon_9_0_chr16_20361093_r	0.0	0.0	0.0
 chr16	20361937	20362204	uc002dgz.3_exon_9_0_chr16_20361972_r;uc002dha.3_exon_9_0_chr16_20361972_r;uc002dhb.3_exon_10_0_chr16_20361972_r	0.0	0.0	0.0
 chr16	20363947	20364103	uc002dgz.3_exon_10_0_chr16_20364011_r;uc002dha.3_exon_10_0_chr16_20364011_r;uc002dhb.3_exon_11_0_chr16_20364011_r	0.0	0.0	0.0
-chr19	3094375	3094805	uc002lxd.3_exon_0_0_chr19_3094408_f	3.96519721578	0.0	0.0
-chr19	3110125	3110366	uc002lxd.3_exon_1_0_chr19_3110147_f	170.958677686	0.0	0.0
-chr19	3113305	3113513	uc002lxd.3_exon_2_0_chr19_3113328_f	96.8229665072	0.0	0.0
-chr19	3114915	3115090	uc002lxd.3_exon_3_0_chr19_3114942_f	18.6022727273	0.0	0.0
-chr19	3118900	3119070	uc002lxd.3_exon_4_0_chr19_3118922_f	288.304093567	0.0	0.0
-chr19	3119175	3119384	uc002lxd.3_exon_5_0_chr19_3119204_f	611.423809524	0.0	0.0
-chr19	3120965	3121304	uc002lxd.3_exon_6_0_chr19_3120987_f	267.808823529	0.0	0.0
-chr19	3121310	3121447	uc002lxd.3_exon_6_0_chr19_3120987_f	1155.32608696	0.0	0.0
-chr19	47341397	47341813	uc002pft.1_exon_0_0_chr19_47341423_r;uc002pfu.1_exon_0_0_chr19_47341423_r	287.717026379	0.0	0.0
-chr19	47341952	47342086	uc002pft.1_exon_1_0_chr19_47341997_r;uc002pfu.1_exon_1_0_chr19_47341997_r	1049.35555556	0.0	0.0
-chr19	47342697	47342876	uc002pft.1_exon_2_0_chr19_47342722_r	1050.62222222	0.0	0.0
-chr19	47349227	47349441	uc002pft.1_exon_3_0_chr19_47349250_r;uc002pfu.1_exon_2_0_chr19_47349250_r	712.423255814	0.0	0.0
-chr19	47353997	47354239	uc002pft.1_exon_4_0_chr19_47354021_r;uc002pfu.1_exon_3_0_chr19_47354021_r	663.609053498	0.0	0.0
-chr20	52769992	52770580	uc002xwu.1_exon_0_0_chr20_52769988_r;uc002xwv.2_exon_0_0_chr20_52769988_r;uc002xww.2_exon_0_0_chr20_52769988_r	0.0	1507.49575552	0.0
-chr20	52770622	52770705	uc002xwu.1_exon_0_0_chr20_52769988_r;uc002xwv.2_exon_0_0_chr20_52769988_r;uc002xww.2_exon_0_0_chr20_52769988_r	0.0	1234.73809524	0.0
-chr20	52770707	52771336	uc002xwu.1_exon_0_0_chr20_52769988_r;uc002xwv.2_exon_0_0_chr20_52769988_r;uc002xww.2_exon_0_0_chr20_52769988_r	0.0	1783.23650794	0.0
-chr20	52773678	52773860	uc002xwu.1_exon_1_0_chr20_52773708_r;uc002xwv.2_exon_1_0_chr20_52773708_r;uc002xww.2_exon_1_0_chr20_52773708_r	0.0	1673.20218579	0.0
-chr20	52773898	52774150	uc002xwu.1_exon_2_0_chr20_52773927_r;uc002xwv.2_exon_2_0_chr20_52773927_r	0.0	1698.91699605	0.0
-chr20	52774593	52774726	uc002xwu.1_exon_3_0_chr20_52774625_r;uc002xwv.2_exon_3_0_chr20_52774625_r;uc002xww.2_exon_2_0_chr20_52774625_r	0.0	1404.41044776	0.0
-chr20	52775473	52775682	uc002xwu.1_exon_4_0_chr20_52775496_r;uc002xwv.2_exon_4_0_chr20_52775496_r;uc002xww.2_exon_3_0_chr20_52775496_r	0.0	1817.36190476	0.0
-chr20	52779223	52779439	uc002xwu.1_exon_5_0_chr20_52779256_r;uc002xwv.2_exon_5_0_chr20_52779256_r;uc002xww.2_exon_4_0_chr20_52779256_r	0.0	1642.65437788	0.0
-chr20	52780968	52781144	uc002xwu.1_exon_6_0_chr20_52780991_r;uc002xwv.2_exon_6_0_chr20_52780991_r;uc002xww.2_exon_5_0_chr20_52780991_r	0.0	1448.11864407	0.0
-chr20	52782253	52782397	uc002xwu.1_exon_7_0_chr20_52782281_r;uc002xwv.2_exon_7_0_chr20_52782281_r;uc002xww.2_exon_6_0_chr20_52782281_r	0.0	1498.3862069	0.0
-chr20	52786108	52786244	uc002xwu.1_exon_8_0_chr20_52786131_r;uc002xwv.2_exon_8_0_chr20_52786131_r;uc002xww.2_exon_7_0_chr20_52786131_r	0.0	1635.86861314	0.0
-chr20	52788093	52788504	uc002xwu.1_exon_9_0_chr20_52788116_r;uc002xwv.2_exon_9_0_chr20_52788116_r;uc002xww.2_exon_8_0_chr20_52788116_r	0.0	1655.84708738	0.0
-chr20	52789423	52789663	uc002xwv.2_exon_10_0_chr20_52789448_r;uc002xww.2_exon_9_0_chr20_52789448_r	0.0	166.136929461	0.0
-chr20	52789828	52790550	uc002xwv.2_exon_11_0_chr20_52789861_r;uc002xww.2_exon_10_0_chr20_52789861_r	0.0	275.312586445	0.0
-chr21	37832893	37833027	uc002yvk.2_exon_0_0_chr21_37832920_r;uc002yvl.1_exon_0_0_chr21_37832920_r;uc002yvm.1_exon_0_0_chr21_37832920_r;uc002yvn.2_exon_0_0_chr21_37832920_r;uc002yvo.1_exon_0_0_chr21_37832920_r;uc021wja.1_exon_0_0_chr21_37833274_r	0.0	0.0	1415.82222222
-chr21	37833063	37834107	uc002yvk.2_exon_0_0_chr21_37832920_r;uc002yvl.1_exon_0_0_chr21_37832920_r;uc002yvm.1_exon_0_0_chr21_37832920_r;uc002yvn.2_exon_0_0_chr21_37832920_r;uc002yvo.1_exon_0_0_chr21_37832920_r;uc021wja.1_exon_0_0_chr21_37833274_r	0.0	0.0	292.412440191
-chr21	37849648	37849906	uc002yvl.1_exon_1_0_chr21_37849672_r	0.0	0.0	1593.73745174
-chr21	37851763	37852430	uc002yvl.1_exon_2_0_chr21_37851793_r;uc002yvm.1_exon_1_0_chr21_37851793_r	0.0	0.0	989.193113772
-chr21	37882628	37882821	uc002yvn.2_exon_1_0_chr21_37882661_r;uc002yvo.1_exon_1_0_chr21_37882661_r	0.0	0.0	1711.39175258
-chr21	37914828	37915151	uc002yvn.2_exon_2_0_chr21_37914863_r	0.0	0.0	64.7283950617
-chr21	37948678	37948900	uc002yvo.1_exon_2_0_chr21_37948709_r	0.0	0.0	1027.15695067
+chr19	3094375	3094805	uc002lxd.3_exon_0_0_chr19_3094408_f	3.965197215777262	0.0	0.0
+chr19	3110125	3110366	uc002lxd.3_exon_1_0_chr19_3110147_f	170.95867768595042	0.0	0.0
+chr19	3113305	3113513	uc002lxd.3_exon_2_0_chr19_3113328_f	96.82296650717703	0.0	0.0
+chr19	3114915	3115090	uc002lxd.3_exon_3_0_chr19_3114942_f	18.602272727272727	0.0	0.0
+chr19	3118900	3119070	uc002lxd.3_exon_4_0_chr19_3118922_f	288.30409356725147	0.0	0.0
+chr19	3119175	3119384	uc002lxd.3_exon_5_0_chr19_3119204_f	611.4238095238095	0.0	0.0
+chr19	3120965	3121304	uc002lxd.3_exon_6_0_chr19_3120987_f	267.80882352941177	0.0	0.0
+chr19	3121310	3121447	uc002lxd.3_exon_6_0_chr19_3120987_f	1155.3260869565217	0.0	0.0
+chr19	47341397	47341813	uc002pft.1_exon_0_0_chr19_47341423_r;uc002pfu.1_exon_0_0_chr19_47341423_r	287.7170263788969	0.0	0.0
+chr19	47341952	47342086	uc002pft.1_exon_1_0_chr19_47341997_r;uc002pfu.1_exon_1_0_chr19_47341997_r	1049.3555555555556	0.0	0.0
+chr19	47342697	47342876	uc002pft.1_exon_2_0_chr19_47342722_r	1050.6222222222223	0.0	0.0
+chr19	47349227	47349441	uc002pft.1_exon_3_0_chr19_47349250_r;uc002pfu.1_exon_2_0_chr19_47349250_r	712.4232558139535	0.0	0.0
+chr19	47353997	47354239	uc002pft.1_exon_4_0_chr19_47354021_r;uc002pfu.1_exon_3_0_chr19_47354021_r	663.6090534979423	0.0	0.0
+chr20	52769992	52770580	uc002xwu.1_exon_0_0_chr20_52769988_r;uc002xwv.2_exon_0_0_chr20_52769988_r;uc002xww.2_exon_0_0_chr20_52769988_r	0.0	1507.4957555178269	0.0
+chr20	52770622	52770705	uc002xwu.1_exon_0_0_chr20_52769988_r;uc002xwv.2_exon_0_0_chr20_52769988_r;uc002xww.2_exon_0_0_chr20_52769988_r	0.0	1234.7380952380952	0.0
+chr20	52770707	52771336	uc002xwu.1_exon_0_0_chr20_52769988_r;uc002xwv.2_exon_0_0_chr20_52769988_r;uc002xww.2_exon_0_0_chr20_52769988_r	0.0	1783.236507936508	0.0
+chr20	52773678	52773860	uc002xwu.1_exon_1_0_chr20_52773708_r;uc002xwv.2_exon_1_0_chr20_52773708_r;uc002xww.2_exon_1_0_chr20_52773708_r	0.0	1673.2021857923498	0.0
+chr20	52773898	52774150	uc002xwu.1_exon_2_0_chr20_52773927_r;uc002xwv.2_exon_2_0_chr20_52773927_r	0.0	1698.9169960474308	0.0
+chr20	52774593	52774726	uc002xwu.1_exon_3_0_chr20_52774625_r;uc002xwv.2_exon_3_0_chr20_52774625_r;uc002xww.2_exon_2_0_chr20_52774625_r	0.0	1404.410447761194	0.0
+chr20	52775473	52775682	uc002xwu.1_exon_4_0_chr20_52775496_r;uc002xwv.2_exon_4_0_chr20_52775496_r;uc002xww.2_exon_3_0_chr20_52775496_r	0.0	1817.3619047619047	0.0
+chr20	52779223	52779439	uc002xwu.1_exon_5_0_chr20_52779256_r;uc002xwv.2_exon_5_0_chr20_52779256_r;uc002xww.2_exon_4_0_chr20_52779256_r	0.0	1642.6543778801843	0.0
+chr20	52780968	52781144	uc002xwu.1_exon_6_0_chr20_52780991_r;uc002xwv.2_exon_6_0_chr20_52780991_r;uc002xww.2_exon_5_0_chr20_52780991_r	0.0	1448.1186440677966	0.0
+chr20	52782253	52782397	uc002xwu.1_exon_7_0_chr20_52782281_r;uc002xwv.2_exon_7_0_chr20_52782281_r;uc002xww.2_exon_6_0_chr20_52782281_r	0.0	1498.3862068965518	0.0
+chr20	52786108	52786244	uc002xwu.1_exon_8_0_chr20_52786131_r;uc002xwv.2_exon_8_0_chr20_52786131_r;uc002xww.2_exon_7_0_chr20_52786131_r	0.0	1635.8686131386862	0.0
+chr20	52788093	52788504	uc002xwu.1_exon_9_0_chr20_52788116_r;uc002xwv.2_exon_9_0_chr20_52788116_r;uc002xww.2_exon_8_0_chr20_52788116_r	0.0	1655.8470873786407	0.0
+chr20	52789423	52789663	uc002xwv.2_exon_10_0_chr20_52789448_r;uc002xww.2_exon_9_0_chr20_52789448_r	0.0	166.13692946058092	0.0
+chr20	52789828	52790550	uc002xwv.2_exon_11_0_chr20_52789861_r;uc002xww.2_exon_10_0_chr20_52789861_r	0.0	275.31258644536655	0.0
+chr21	37832893	37833027	uc002yvk.2_exon_0_0_chr21_37832920_r;uc002yvl.1_exon_0_0_chr21_37832920_r;uc002yvm.1_exon_0_0_chr21_37832920_r;uc002yvn.2_exon_0_0_chr21_37832920_r;uc002yvo.1_exon_0_0_chr21_37832920_r;uc021wja.1_exon_0_0_chr21_37833274_r	0.0	0.0	1415.8222222222223
+chr21	37833063	37834107	uc002yvk.2_exon_0_0_chr21_37832920_r;uc002yvl.1_exon_0_0_chr21_37832920_r;uc002yvm.1_exon_0_0_chr21_37832920_r;uc002yvn.2_exon_0_0_chr21_37832920_r;uc002yvo.1_exon_0_0_chr21_37832920_r;uc021wja.1_exon_0_0_chr21_37833274_r	0.0	0.0	292.41244019138753
+chr21	37849648	37849906	uc002yvl.1_exon_1_0_chr21_37849672_r	0.0	0.0	1593.7374517374517
+chr21	37851763	37852430	uc002yvl.1_exon_2_0_chr21_37851793_r;uc002yvm.1_exon_1_0_chr21_37851793_r	0.0	0.0	989.193113772455
+chr21	37882628	37882821	uc002yvn.2_exon_1_0_chr21_37882661_r;uc002yvo.1_exon_1_0_chr21_37882661_r	0.0	0.0	1711.3917525773195
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+chr21	37948678	37948900	uc002yvo.1_exon_2_0_chr21_37948709_r	0.0	0.0	1027.1569506726457
 chrX	22050889	22051274	uc004dah.3_exon_0_0_chrX_22050921_f;uc011mjr.2_exon_0_0_chrX_22050921_f	0.0	0.0	0.0
 chrX	22056139	22056214	uc004dah.3_exon_1_0_chrX_22056587_f;uc011mjr.2_exon_1_0_chrX_22056587_f;uc011mjs.2_exon_0_0_chrX_22056171_f	0.0	0.0	0.0
 chrX	22056229	22056691	uc004dah.3_exon_1_0_chrX_22056587_f;uc011mjr.2_exon_1_0_chrX_22056587_f;uc011mjs.2_exon_0_0_chrX_22056171_f	0.0	0.0	0.0
diff -r 2ec6529e555d -r 7c4feda2d9c7 test-data/graph.pdf
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diff -r 2ec6529e555d -r 7c4feda2d9c7 test-data/graph_pysam.pdf
Binary file test-data/graph_pysam.pdf has changed