| Previous changeset 5:2ec6529e555d (2018-06-02) Next changeset 7:bea8435e1e79 (2021-06-03) |
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Commit message:
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89" |
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modified:
multicov.py probecoverage.xml test-data/coverage.tab test-data/coverage_pysam.tab test-data/graph.pdf test-data/graph_pysam.pdf |
| b |
| 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)] |
| b |
| 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 |
| b |
| @@ -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" /> |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| b'@@ -673,40 +673,40 @@\n chr16\t20361067\t20361208\tuc002dhb.3_exon_9_0_chr16_20361093_r\t0.0\t0.0\t0.0\n chr16\t20361937\t20362204\tuc002dgz.3_exon_9_0_chr16_20361972_r;uc002dha.3_exon_9_0_chr16_20361972_r;uc002dhb.3_exon_10_0_chr16_20361972_r\t0.0\t0.0\t0.0\n chr16\t20363947\t20364103\tuc002dgz.3_exon_10_0_chr16_20364011_r;uc002dha.3_exon_10_0_chr16_20364011_r;uc002dhb.3_exon_11_0_chr16_20364011_r\t0.0\t0.0\t0.0\n-chr19\t3094375\t3094805\tuc002lxd.3_exon_0_0_chr19_3094408_f\t3.96519721578\t0.0\t0.0\n-chr19\t3110125\t3110366\tuc002lxd.3_exon_1_0_chr19_3110147_f\t170.958677686\t0.0\t0.0\n-chr19\t3113305\t3113513\tuc002lxd.3_exon_2_0_chr19_3113328_f\t96.8229665072\t0.0\t0.0\n-chr19\t3114915\t3115090\tuc002lxd.3_exon_3_0_chr19_3114942_f\t18.6022727273\t0.0\t0.0\n-chr19\t3118900\t3119070\tuc002lxd.3_exon_4_0_chr19_3118922_f\t288.304093567\t0.0\t0.0\n-chr19\t3119175\t3119384\tuc002lxd.3_exon_5_0_chr19_3119204_f\t611.423809524\t0.0\t0.0\n-chr19\t3120965\t3121304\tuc002lxd.3_exon_6_0_chr19_3120987_f\t267.808823529\t0.0\t0.0\n-chr19\t3121310\t3121447\tuc002lxd.3_exon_6_0_chr19_3120987_f\t1155.32608696\t0.0\t0.0\n-chr19\t47341397\t47341813\tuc002pft.1_exon_0_0_chr19_47341423_r;uc002pfu.1_exon_0_0_chr19_47341423_r\t287.717026379\t0.0\t0.0\n-chr19\t47341952\t47342086\tuc002pft.1_exon_1_0_chr19_47341997_r;uc002pfu.1_exon_1_0_chr19_47341997_r\t1049.35555556\t0.0\t0.0\n-chr19\t47342697\t47342876\tuc002pft.1_exon_2_0_chr19_47342722_r\t1050.62222222\t0.0\t0.0\n-chr19\t47349227\t47349441\tuc002pft.1_exon_3_0_chr19_47349250_r;uc002pfu.1_exon_2_0_chr19_47349250_r\t712.423255814\t0.0\t0.0\n-chr19\t47353997\t47354239\tuc002pft.1_exon_4_0_chr19_47354021_r;uc002pfu.1_exon_3_0_chr19_47354021_r\t663.609053498\t0.0\t0.0\n-chr20\t52769992\t52770580\tuc002xwu.1_exon_0_0_chr20_52769988_r;uc002xwv.2_exon_0_0_chr20_52769988_r;uc002xww.2_exon_0_0_chr20_52769988_r\t0.0\t1507.49575552\t0.0\n-chr20\t52770622\t52770705\tuc002xwu.1_exon_0_0_chr20_52769988_r;uc002xwv.2_exon_0_0_chr20_52769988_r;uc002xww.2_exon_0_0_chr20_52769988_r\t0.0\t1234.73809524\t0.0\n-chr20\t52770707\t52771336\tuc002xwu.1_exon_0_0_chr20_52769988_r;uc002xwv.2_exon_0_0_chr20_52769988_r;uc002xww.2_exon_0_0_chr20_52769988_r\t0.0\t1783.23650794\t0.0\n-chr20\t52773678\t52773860\tuc002xwu.1_exon_1_0_chr20_52773708_r;uc002xwv.2_exon_1_0_chr20_52773708_r;uc002xww.2_exon_1_0_chr20_52773708_r\t0.0\t1673.20218579\t0.0\n-chr20\t52773898\t52774150\tuc002xwu.1_exon_2_0_chr20_52773927_r;uc002xwv.2_exon_2_0_chr20_52773927_r\t0.0\t1698.91699605\t0.0\n-chr20\t52774593\t52774726\tuc002xwu.1_exon_3_0_chr20_52774625_r;uc002xwv.2_exon_3_0_chr20_52774625_r;uc002xww.2_exon_2_0_chr20_52774625_r\t0.0\t1404.41044776\t0.0\n-chr20\t52775473\t52775682\tuc002xwu.1_exon_4_0_chr20_52775496_r;uc002xwv.2_exon_4_0_chr20_52775496_r;uc002xww.2_exon_3_0_chr20_52775496_r\t0.0\t1817.36190476\t0.0\n-chr20\t52779223\t52779439\tuc002xwu.1_exon_5_0_chr20_52779256_r;uc002xwv.2_exon_5_0_chr20_52779256_r;uc002xww.2_exon_4_0_chr20_52779256_r\t0.0\t1642.65437788\t0.0\n-chr20\t52780968\t52781144\tuc002xwu.1_exon_6_0_chr20_52780991_r;uc002xwv.2_exon_6_0_chr20_52780991_r;uc002xww.2_exon_5_0_chr20_52780991_r\t0.0\t1448.11864407\t0.0\n-chr20\t52782253\t52782397\tuc002xwu.1_exon_7_0_chr20_52782281_r;uc002xwv.2_exon_7_0_chr20_52782281_r;uc002xww.2_exon_6_0_chr20_52782281_r\t0.0\t1498.3862069\t0.0\n-chr20\t52786108\t52786244\tuc002xwu.1_exon_8_0_chr20_52786131_r;uc002xwv.2_exon_8_0_chr20_52786131_r;uc002xww.2_exon_7_0_chr20_52786131_r\t0.0\t1635.86861314\t0.0\n-chr20\t52788093\t52788504\tuc002xwu.1_exon_9_0_chr20_52788116_r;uc002xwv.2_exon_9_0_chr20_52788116_r;uc002xww.2_exon_8_0_chr20_52788116_r\t0.0\t1655.84708738\t0.0\n-chr20\t52789423\t52789663\tuc002xwv.2_exon_10_0_chr20_52789448_r;uc002xww.2_exon_9_0_chr20_52789448_r\t0.0\t166.136929461\t0.0\n-chr20\t52789828\t52790550\tuc002xwv.2_exon_11_0_chr20_52789861_r;uc002xww.2_exon_10_0_chr20_52789861_r\t0.0\t275.312586445\t0.0\n-chr21\t37832893\t37833027\tuc002yvk.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\t0.0\t0.0\t1415.82222222\n-chr21\t37833063'..b'\t1049.3555555555556\t0.0\t0.0\n+chr19\t47342697\t47342876\tuc002pft.1_exon_2_0_chr19_47342722_r\t1050.6222222222223\t0.0\t0.0\n+chr19\t47349227\t47349441\tuc002pft.1_exon_3_0_chr19_47349250_r;uc002pfu.1_exon_2_0_chr19_47349250_r\t712.4232558139535\t0.0\t0.0\n+chr19\t47353997\t47354239\tuc002pft.1_exon_4_0_chr19_47354021_r;uc002pfu.1_exon_3_0_chr19_47354021_r\t663.6090534979423\t0.0\t0.0\n+chr20\t52769992\t52770580\tuc002xwu.1_exon_0_0_chr20_52769988_r;uc002xwv.2_exon_0_0_chr20_52769988_r;uc002xww.2_exon_0_0_chr20_52769988_r\t0.0\t1507.4957555178269\t0.0\n+chr20\t52770622\t52770705\tuc002xwu.1_exon_0_0_chr20_52769988_r;uc002xwv.2_exon_0_0_chr20_52769988_r;uc002xww.2_exon_0_0_chr20_52769988_r\t0.0\t1234.7380952380952\t0.0\n+chr20\t52770707\t52771336\tuc002xwu.1_exon_0_0_chr20_52769988_r;uc002xwv.2_exon_0_0_chr20_52769988_r;uc002xww.2_exon_0_0_chr20_52769988_r\t0.0\t1783.236507936508\t0.0\n+chr20\t52773678\t52773860\tuc002xwu.1_exon_1_0_chr20_52773708_r;uc002xwv.2_exon_1_0_chr20_52773708_r;uc002xww.2_exon_1_0_chr20_52773708_r\t0.0\t1673.2021857923498\t0.0\n+chr20\t52773898\t52774150\tuc002xwu.1_exon_2_0_chr20_52773927_r;uc002xwv.2_exon_2_0_chr20_52773927_r\t0.0\t1698.9169960474308\t0.0\n+chr20\t52774593\t52774726\tuc002xwu.1_exon_3_0_chr20_52774625_r;uc002xwv.2_exon_3_0_chr20_52774625_r;uc002xww.2_exon_2_0_chr20_52774625_r\t0.0\t1404.410447761194\t0.0\n+chr20\t52775473\t52775682\tuc002xwu.1_exon_4_0_chr20_52775496_r;uc002xwv.2_exon_4_0_chr20_52775496_r;uc002xww.2_exon_3_0_chr20_52775496_r\t0.0\t1817.3619047619047\t0.0\n+chr20\t52779223\t52779439\tuc002xwu.1_exon_5_0_chr20_52779256_r;uc002xwv.2_exon_5_0_chr20_52779256_r;uc002xww.2_exon_4_0_chr20_52779256_r\t0.0\t1642.6543778801843\t0.0\n+chr20\t52780968\t52781144\tuc002xwu.1_exon_6_0_chr20_52780991_r;uc002xwv.2_exon_6_0_chr20_52780991_r;uc002xww.2_exon_5_0_chr20_52780991_r\t0.0\t1448.1186440677966\t0.0\n+chr20\t52782253\t52782397\tuc002xwu.1_exon_7_0_chr20_52782281_r;uc002xwv.2_exon_7_0_chr20_52782281_r;uc002xww.2_exon_6_0_chr20_52782281_r\t0.0\t1498.3862068965518\t0.0\n+chr20\t52786108\t52786244\tuc002xwu.1_exon_8_0_chr20_52786131_r;uc002xwv.2_exon_8_0_chr20_52786131_r;uc002xww.2_exon_7_0_chr20_52786131_r\t0.0\t1635.8686131386862\t0.0\n+chr20\t52788093\t52788504\tuc002xwu.1_exon_9_0_chr20_52788116_r;uc002xwv.2_exon_9_0_chr20_52788116_r;uc002xww.2_exon_8_0_chr20_52788116_r\t0.0\t1655.8470873786407\t0.0\n+chr20\t52789423\t52789663\tuc002xwv.2_exon_10_0_chr20_52789448_r;uc002xww.2_exon_9_0_chr20_52789448_r\t0.0\t166.13692946058092\t0.0\n+chr20\t52789828\t52790550\tuc002xwv.2_exon_11_0_chr20_52789861_r;uc002xww.2_exon_10_0_chr20_52789861_r\t0.0\t275.31258644536655\t0.0\n+chr21\t37832893\t37833027\tuc002yvk.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\t0.0\t0.0\t1415.8222222222223\n+chr21\t37833063\t37834107\tuc002yvk.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\t0.0\t0.0\t292.41244019138753\n+chr21\t37849648\t37849906\tuc002yvl.1_exon_1_0_chr21_37849672_r\t0.0\t0.0\t1593.7374517374517\n+chr21\t37851763\t37852430\tuc002yvl.1_exon_2_0_chr21_37851793_r;uc002yvm.1_exon_1_0_chr21_37851793_r\t0.0\t0.0\t989.193113772455\n+chr21\t37882628\t37882821\tuc002yvn.2_exon_1_0_chr21_37882661_r;uc002yvo.1_exon_1_0_chr21_37882661_r\t0.0\t0.0\t1711.3917525773195\n+chr21\t37914828\t37915151\tuc002yvn.2_exon_2_0_chr21_37914863_r\t0.0\t0.0\t64.72839506172839\n+chr21\t37948678\t37948900\tuc002yvo.1_exon_2_0_chr21_37948709_r\t0.0\t0.0\t1027.1569506726457\n chrX\t22050889\t22051274\tuc004dah.3_exon_0_0_chrX_22050921_f;uc011mjr.2_exon_0_0_chrX_22050921_f\t0.0\t0.0\t0.0\n chrX\t22056139\t22056214\tuc004dah.3_exon_1_0_chrX_22056587_f;uc011mjr.2_exon_1_0_chrX_22056587_f;uc011mjs.2_exon_0_0_chrX_22056171_f\t0.0\t0.0\t0.0\n chrX\t22056229\t22056691\tuc004dah.3_exon_1_0_chrX_22056587_f;uc011mjr.2_exon_1_0_chrX_22056587_f;uc011mjs.2_exon_0_0_chrX_22056171_f\t0.0\t0.0\t0.0\n' |
| b |
| diff -r 2ec6529e555d -r 7c4feda2d9c7 test-data/graph.pdf |
| b |
| Binary file test-data/graph.pdf has changed |
| b |
| diff -r 2ec6529e555d -r 7c4feda2d9c7 test-data/graph_pysam.pdf |
| b |
| Binary file test-data/graph_pysam.pdf has changed |