| Next changeset 1:db50f51a2952 (2019-08-17) |
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Commit message:
planemo upload for repository https://github.com/jsh58/Genrich commit 38aa99ebf650c22a1c4965f6f008882aea7033ba |
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added:
genrich.xml test-data/CTCF.bed test-data/CTCF.encodepeak test-data/CTCF1.bedgraph test-data/CTCF2.bedgraph test-data/CTCF_PE_CTRL_chr22.bam test-data/CTCF_PE_ChIP_chr22.bam test-data/atac_out.encodepeak test-data/atac_out2.bedgraph test-data/atac_out3.bedgraph test-data/atac_out4.bed test-data/atac_test.bam |
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| diff -r 000000000000 -r a41d96fc0b20 genrich.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/genrich.xml Mon Jul 15 09:43:27 2019 -0400 |
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| b'@@ -0,0 +1,373 @@\n+<tool id="genrich" name="Genrich" version="0.5">\n+ <description>Detecting sites of genomic enrichment</description>\n+ <requirements>\n+ <requirement type="package" version="0.5">genrich</requirement>\n+ <requirement type="package" version="1.9">samtools</requirement>\n+ </requirements>\n+\n+ <version_command>Genrich --version</version_command>\n+\n+ <command detect_errors="exit_code"><![CDATA[\n+\n+#set $file_stderr = \'genrich_stderr\'\n+\n+Genrich\n+\n+###########\n+## Input ##\n+###########\n+\n+## Treatment File(s)\n+#if str($treatment.t_multi_select) == "Yes":\n+ -t ${ \' \'.join( [ "\'%s\'" % $x for $x in $treatment.input_treatment_file] ) }\n+#else\n+ -t \'$treatment.input_treatment_file\'\n+#end if\n+\n+## Control File(s)\n+#if str($control.c_select) == "Yes":\n+ #if str($control.c_multiple.c_multi_select) == "Yes":\n+ -c ${ \' \'.join( [ "\'%s\'" % $x for $x in $control.c_multiple.input_control_file] ) }\n+ #else\n+ -c \'$control.c_multiple.input_control_file\'\n+ #end if\n+#end if\n+\n+####################\n+## Filter Options ##\n+####################\n+\n+#if $filter_options.duplicates:\n+ \'$filter_options.duplicates\' \'${out_dups}\'\n+#end if\n+\n+#if $filter_options.exclude_chr:\n+ -e \'$filter_options.exclude_chr\'\n+#end if\n+\n+#if str($cond_exclude.exclude_select) == "Yes":\n+ -E $cond_exclude.erf\n+#end if\n+\n+-m $filter_options.min_mapq\n+-s $filter_options.alignment_score\n+$filter_options.unpaired\n+\n+#if $filter_options.alignment_lengths:\n+ -w $filter_options.alignment_lengths\n+#end if\n+\n+$filter_options.alignment_lengths2\n+\n+##################\n+## ATAC Options ##\n+##################\n+\n+$atac_options.atac\n+-d $atac_options.expand_sites\n+\n+#########################\n+## Peakcalling Options ##\n+#########################\n+\n+-q $peakcalling_options.max_q\n+\n+#if $peakcalling_options.max_p:\n+ -p $peakcalling_options.max_p\n+#end if\n+\n+-a $peakcalling_options.min_auc\n+-l $peakcalling_options.min_peak_length\n+-g $peakcalling_options.max_dist\n+\n+###################\n+## Other Options ##\n+###################\n+\n+$other_options.skip_peak_calling\n+-v\n+\n+####################\n+## Output Options ##\n+####################\n+\n+#if $output_options.bedgraph1:\n+ -f \'${out_bedgraph1}\'\n+#end if\n+\n+#if $output_options.bedgraph2:\n+ -k \'${out_bedgraph2}\'\n+#end if\n+\n+#if $output_options.bed:\n+ -b \'${out_bed}\'\n+#end if\n+\n+-o \'${outfile}\'\n+\n+2>&1 > $file_stderr &&\n+exit_code_for_galaxy=\\$? &&\n+cat $file_stderr 2>&1 &&\n+exit \\$exit_code_for_galaxy\n+\n+ ]]></command>\n+ <inputs>\n+ <conditional name="treatment">\n+ <param name="t_multi_select" type="select" label="Are you pooling Treatment Files?" help="For more information, see Help section below" >\n+ <option value="No" selected="True">No</option>\n+ <option value="Yes">Yes</option>\n+ </param>\n+ <when value="No" >\n+ <param name="input_treatment_file" argument="-t" type="data" format="qname_sorted.bam" label="Treatment File(s)" />\n+ </when>\n+ <when value="Yes">\n+ <param name="input_treatment_file" argument="-t" type="data" format="qname_sorted.bam" multiple="true" label="Treatment Files" />\n+ </when>\n+ </conditional>\n+\n+ <conditional name="control">\n+ <param name="c_select" type="select" label="Do you have a Control File?" >\n+ <option value="Yes">Yes</option>\n+ <option value="No" selected="True">No</option>\n+ </param>\n+ <when value="Yes">\n+ <conditional name="c_multiple">\n+ <param name="c_multi_select" type="select" label="Are you pooling Control Files?" help="For more information, see Help section below" >\n+ <option value="No" selected="True">No</option>\n+ <option value="Yes">Yes</option>\n+ </param>\n+ <when value="No" >\n+ '..b'e (the longest interval in case of ties)\n+\n+Example:\n+chr1 894446 894988 peak_10 402 . 217.824936 4.344683 1.946031 317\n+chr1 895834 896167 peak_11 343 . 114.331093 4.344683 1.946031 90\n+\n+Optional files\n+\n+ -c Input SAM/BAM file(s) for control sample(s)\n+\n+Alignment files for control samples (e.g. input DNA) can be specified, although this is not strictly required.\n+SAM/BAM files for multiple replicates can be listed, comma-separated (or space-separated, in quotes) and in the same order as the experimental files. Missing control files should be indicated with null.\n+\n+ -f Output bedgraph-ish file for p/q values\n+\n+With a single replicate, this log file lists experimental/control pileup values, p- and q-values, and significance (*) for each interval.\n+\n+Example:\n+chr1 894435 894436 33.000000 2.477916 3.183460 1.208321\n+chr1 894436 894442 34.000000 2.477916 3.231466 1.241843\n+chr1 894442 894446 35.000000 2.477916 3.278469 1.274561\n+chr1 894446 894447 36.000000 2.477916 3.324516 1.306471 *\n+chr1 894447 894450 39.000000 2.477916 3.457329 1.398035 *\n+chr1 894450 894451 40.000000 2.477916 3.499948 1.427253 *\n+chr1 894451 894460 41.000000 2.477916 3.541798 1.455938 *\n+\n+With multiple replicates, this log file lists p-values of each replicate, combined p-value, q-value, and significance for each interval.\n+Note that this file (as well as the -k file, below) is called "bedgraph-ish" because it contains multiple dataValue fields, which isn\'t strictly allowed in the bedGraph format. However, a simple application of awk can produce the desired bedgraph files for visualization purposes (see this awk reference for a guide to printing specific fields of input records).\n+When peak-calling is skipped (-X), the significance column is not produced.\n+\n+ -k Output bedgraph-ish file for pileups and p-values\n+\n+For each replicate, sequentially, this file lists a header line (# experimental file: <name>; control file: <name>), followed by experimental/control pileups and a p-value for each interval. This is the way to examine pileup values with multiple replicates, since the -f log file does not supply them in that case.\n+\n+ -b Output BED file for reads/fragments/intervals\n+\n+This is an unsorted BED file of the reads/fragments/intervals analyzed. The 4th column gives the read name, number of valid alignments, \'E\'xperimental or \'C\'ontrol, and sample number (0-based), e.g. SRR5427886.59_2_E_0.\n+\n+ -R Output file for PCR duplicates (only with -r)\n+\n+This log file lists the header of each read/fragment classified as a PCR duplicate, followed by the alignment, the header of the read/fragment it matched, and the alignment type.\n+\n+Example:\n+SRR5427886.5958 chr4:185201876-185201975 SRR5427886.4688 paired\n+SRR5427886.1826 chr12:34372610,+;chr1:91852878,- SRR5427886.2040 discordant\n+SRR5427886.10866 chr14:53438632,+ SRR5427886.4746 single\n+\n+The duplicates from multiple input files are separated by a comment line listing the next filename, such as # experimental file #0: SRR5427886.bam.\n+This file can be used to filter the original SAM/BAM file, using a simple script such as getReads.py, for example.\n+\n+\n+--------------------\n+\n+**More Information**\n+\n+--------------------\n+\n+See the excellent `Genrich documentation`_\n+\n+.. _`Genrich documentation`: https://github.com/jsh58/Genrich\n+\n+\n+--------------------\n+\n+**Galaxy Wrapper Development**\n+\n+--------------------\n+\n+Author: Florian Heyl <heylf@informatik.uni-freiburg.de>\n+\n+\n+ ]]></help>\n+ <citations>\n+ <citation type="bibtex">\n+@misc{genrich,\n+ title = {Genrich},\n+ url = {https://github.com/jsh58/Genrich},\n+ urldate = {2019-07-15},\n+ author = {John M. Gaspar},\n+ year = {2018},\n+}\n+ </citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r a41d96fc0b20 test-data/CTCF.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CTCF.bed Mon Jul 15 09:43:27 2019 -0400 |
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| b'@@ -0,0 +1,955 @@\n+chr22\t39268661\t39268882\tDG7PMJN1:313:C1579ACXX:4:1101:1327:21682_1_E_0\n+chr22\t47158056\t47158376\tDG7PMJN1:313:C1579ACXX:4:1101:1332:42537_1_E_0\n+chr22\t47089504\t47089698\tDG7PMJN1:313:C1579ACXX:4:1101:1332:87995_1_E_0\n+chr22\t32061696\t32062004\tDG7PMJN1:313:C1579ACXX:4:1101:1334:64870_1_E_0\n+chr22\t27129531\t27129743\tDG7PMJN1:313:C1579ACXX:4:1101:1335:62201_1_E_0\n+chr22\t36462290\t36462537\tDG7PMJN1:313:C1579ACXX:4:1101:1337:68808_1_E_0\n+chr22\t21306063\t21306268\tDG7PMJN1:313:C1579ACXX:4:1101:1338:175510_1_E_0\n+chr22\t18379432\t18379662\tDG7PMJN1:313:C1579ACXX:4:1101:1353:6398_1_E_0\n+chr22\t39492880\t39493165\tDG7PMJN1:313:C1579ACXX:4:1101:1353:95885_1_E_0\n+chr22\t31316312\t31316530\tDG7PMJN1:313:C1579ACXX:4:1101:1355:14336_1_E_0\n+chr22\t46432623\t46432839\tDG7PMJN1:313:C1579ACXX:4:1101:1361:86288_1_E_0\n+chr22\t22776990\t22777208\tDG7PMJN1:313:C1579ACXX:4:1101:1362:161018_1_E_0\n+chr22\t34319847\t34320073\tDG7PMJN1:313:C1579ACXX:4:1101:1366:139084_1_E_0\n+chr22\t39566735\t39566961\tDG7PMJN1:313:C1579ACXX:4:1101:1368:93380_1_E_0\n+chr22\t39378468\t39378802\tDG7PMJN1:313:C1579ACXX:4:1101:1371:153735_1_E_0\n+chr22\t29223458\t29223749\tDG7PMJN1:313:C1579ACXX:4:1101:1372:19426_1_E_0\n+chr22\t42494019\t42494222\tDG7PMJN1:313:C1579ACXX:4:1101:1373:92078_1_E_0\n+chr22\t50982866\t50983075\tDG7PMJN1:313:C1579ACXX:4:1101:1375:74927_1_E_0\n+chr22\t22511297\t22511510\tDG7PMJN1:313:C1579ACXX:4:1101:1376:42382_1_E_0\n+chr22\t47154865\t47155113\tDG7PMJN1:313:C1579ACXX:4:1101:1376:172509_1_E_0\n+chr22\t22193635\t22193984\tDG7PMJN1:313:C1579ACXX:4:1101:1378:70470_1_E_0\n+chr22\t28275318\t28275639\tDG7PMJN1:313:C1579ACXX:4:1101:1380:66504_1_E_0\n+chr22\t51130096\t51130412\tDG7PMJN1:313:C1579ACXX:4:1101:1381:101381_1_E_0\n+chr22\t43151700\t43151988\tDG7PMJN1:313:C1579ACXX:4:1101:1383:80388_1_E_0\n+chr22\t29550297\t29550637\tDG7PMJN1:313:C1579ACXX:4:1101:1384:159425_1_E_0\n+chr22\t45335869\t45336069\tDG7PMJN1:313:C1579ACXX:4:1101:1392:62140_1_E_0\n+chr22\t39706894\t39707144\tDG7PMJN1:313:C1579ACXX:4:1101:1392:148796_1_E_0\n+chr22\t42142707\t42142909\tDG7PMJN1:313:C1579ACXX:4:1101:1399:93401_1_E_0\n+chr22\t25348098\t25348291\tDG7PMJN1:313:C1579ACXX:4:1101:1402:183382_1_E_0\n+chr22\t22556130\t22556393\tDG7PMJN1:313:C1579ACXX:4:1101:1407:106599_1_E_0\n+chr22\t32838053\t32838399\tDG7PMJN1:313:C1579ACXX:4:1101:1407:121847_1_E_0\n+chr22\t43810586\t43810909\tDG7PMJN1:313:C1579ACXX:4:1101:1408:49267_1_E_0\n+chr22\t42891122\t42891345\tDG7PMJN1:313:C1579ACXX:4:1101:1409:4177_1_E_0\n+chr22\t39369729\t39369947\tDG7PMJN1:313:C1579ACXX:4:1101:1415:139393_1_E_0\n+chr22\t19617529\t19617717\tDG7PMJN1:313:C1579ACXX:4:1101:1419:25150_1_E_0\n+chr22\t40328883\t40329177\tDG7PMJN1:313:C1579ACXX:4:1101:1423:200331_1_E_0\n+chr22\t34235089\t34235273\tDG7PMJN1:313:C1579ACXX:4:1101:1424:184511_1_E_0\n+chr22\t24858022\t24858247\tDG7PMJN1:313:C1579ACXX:4:1101:1427:27081_1_E_0\n+chr22\t18558818\t18559099\tDG7PMJN1:313:C1579ACXX:4:1101:1430:24038_1_E_0\n+chr22\t17686483\t17686744\tDG7PMJN1:313:C1579ACXX:4:1101:1432:97957_1_E_0\n+chr22\t41079231\t41079417\tDG7PMJN1:313:C1579ACXX:4:1101:1436:124107_1_E_0\n+chr22\t22080951\t22081225\tDG7PMJN1:313:C1579ACXX:4:1101:1439:75078_1_E_0\n+chr22\t31139935\t31140165\tDG7PMJN1:313:C1579ACXX:4:1101:1443:142841_1_E_0\n+chr22\t33604108\t33604336\tDG7PMJN1:313:C1579ACXX:4:1101:1449:139381_1_E_0\n+chr22\t46722697\t46722886\tDG7PMJN1:313:C1579ACXX:4:1101:1458:34809_1_E_0\n+chr22\t50628501\t50628741\tDG7PMJN1:313:C1579ACXX:4:1101:1461:72100_1_E_0\n+chr22\t46390070\t46390323\tDG7PMJN1:313:C1579ACXX:4:1101:1463:30273_1_E_0\n+chr22\t38658003\t38658270\tDG7PMJN1:313:C1579ACXX:4:1101:1464:91394_1_E_0\n+chr22\t39095780\t39095980\tDG7PMJN1:313:C1579ACXX:4:1101:1471:24845_1_E_0\n+chr22\t37365109\t37365446\tDG7PMJN1:313:C1579ACXX:4:1101:1473:158755_1_E_0\n+chr22\t35469732\t35470060\tDG7PMJN1:313:C1579ACXX:4:1101:1475:36510_1_E_0\n+chr22\t30651861\t30652069\tDG7PMJN1:313:C1579ACXX:4:1101:1479:167893_1_E_0\n+chr22\t46969895\t46970107\tDG7PMJN1:313:C1579ACXX:4:1101:1484:74796_1_E_0\n+chr22\t39267843\t39268143\tDG7PMJN1:313:C1579ACXX:4:1101:1487:87484_1_E_0\n+chr22\t41295036\t41295322\tDG7PMJN1:313:C1579ACXX:4:1101:1489:7496_1_E_0\n+chr2'..b'C_0\n+chr22\t21265687\t21266111\tMONK:4:1101:2036:162467#ATCACG_1_C_0\n+chr22\t24796223\t24796573\tMONK:4:1101:2041:13081#ATCACG_1_C_0\n+chr22\t20903546\t20903860\tMONK:4:1101:2043:44900#ATCACG_1_C_0\n+chr22\t44947744\t44948083\tMONK:4:1101:2045:136863#ATCACG_1_C_0\n+chr22\t35636457\t35636824\tMONK:4:1101:2047:115492#ATCACG_1_C_0\n+chr22\t44562366\t44562744\tMONK:4:1101:2048:196819#ATCACG_1_C_0\n+chr22\t24582402\t24582746\tMONK:4:1101:2049:58183#ATCACG_1_C_0\n+chr22\t26010455\t26010720\tMONK:4:1101:2050:5906#ATCACG_1_C_0\n+chr22\t45463711\t45464061\tMONK:4:1101:2054:61445#ATCACG_1_C_0\n+chr22\t39339209\t39339568\tMONK:4:1101:2055:47818#ATCACG_1_C_0\n+chr22\t37702677\t37702998\tMONK:4:1101:2056:18419#ATCACG_1_C_0\n+chr22\t37214433\t37214750\tMONK:4:1101:2058:70645#ATCACG_1_C_0\n+chr22\t28314510\t28314866\tMONK:4:1101:2059:89462#ATCACG_1_C_0\n+chr22\t37825262\t37825575\tMONK:4:1101:2059:196988#ATCACG_1_C_0\n+chr22\t18141593\t18141906\tMONK:4:1101:2060:13739#ATCACG_1_C_0\n+chr22\t39925680\t39926050\tMONK:4:1101:2060:57734#ATCACG_1_C_0\n+chr22\t30580500\t30580828\tMONK:4:1101:2061:170858#ATCACG_1_C_0\n+chr22\t23028992\t23029360\tMONK:4:1101:2064:103362#ATCACG_1_C_0\n+chr22\t23528598\t23528875\tMONK:4:1101:2066:182063#ATCACG_1_C_0\n+chr22\t44874800\t44875183\tMONK:4:1101:2068:7662#ATCACG_1_C_0\n+chr22\t39584484\t39584818\tMONK:4:1101:2068:77978#ATCACG_1_C_0\n+chr22\t33797772\t33798061\tMONK:4:1101:2068:100271#ATCACG_1_C_0\n+chr22\t35986252\t35986607\tMONK:4:1101:2070:23404#ATCACG_1_C_0\n+chr22\t27311920\t27312230\tMONK:4:1101:2070:30134#ATCACG_1_C_0\n+chr22\t36963258\t36963578\tMONK:4:1101:2073:141053#ATCACG_1_C_0\n+chr22\t19307238\t19307559\tMONK:4:1101:2073:146945#ATCACG_1_C_0\n+chr22\t31219645\t31219924\tMONK:4:1101:2074:66425#ATCACG_1_C_0\n+chr22\t19541960\t19542242\tMONK:4:1101:2075:118078#ATCACG_1_C_0\n+chr22\t27264361\t27264647\tMONK:4:1101:2077:158799#ATCACG_1_C_0\n+chr22\t42257620\t42257866\tMONK:4:1101:2077:197509#ATCACG_1_C_0\n+chr22\t35098395\t35098663\tMONK:4:1101:2083:101663#ATCACG_1_C_0\n+chr22\t20919441\t20919738\tMONK:4:1101:2089:170479#ATCACG_1_C_0\n+chr22\t51103700\t51104012\tMONK:4:1101:2091:141368#ATCACG_1_C_0\n+chr22\t40869949\t40870251\tMONK:4:1101:2091:200382#ATCACG_1_C_0\n+chr22\t45587887\t45588179\tMONK:4:1101:2092:30754#ATCACG_1_C_0\n+chr22\t30805512\t30805877\tMONK:4:1101:2099:16909#ATCACG_1_C_0\n+chr22\t44033966\t44034285\tMONK:4:1101:2099:32241#ATCACG_1_C_0\n+chr22\t41128651\t41128939\tMONK:4:1101:2103:85862#ATCACG_1_C_0\n+chr22\t28533601\t28533854\tMONK:4:1101:2106:138815#ATCACG_1_C_0\n+chr22\t22154290\t22154577\tMONK:4:1101:2114:80529#ATCACG_1_C_0\n+chr22\t38039414\t38039729\tMONK:4:1101:2120:28549#ATCACG_1_C_0\n+chr22\t39540350\t39540559\tMONK:4:1101:2121:154878#ATCACG_1_C_0\n+chr22\t20884321\t20884672\tMONK:4:1101:2127:115141#ATCACG_1_C_0\n+chr22\t24551823\t24552160\tMONK:4:1101:2130:172811#ATCACG_1_C_0\n+chr22\t18259249\t18259606\tMONK:4:1101:2132:95793#ATCACG_1_C_0\n+chr22\t25373041\t25373209\tMONK:4:1101:2132:128439#ATCACG_1_C_0\n+chr22\t32529163\t32529537\tMONK:4:1101:2132:137046#ATCACG_1_C_0\n+chr22\t38822667\t38823045\tMONK:4:1101:2134:94771#ATCACG_1_C_0\n+chr22\t26159451\t26159615\tMONK:4:1101:2138:27181#ATCACG_1_C_0\n+chr22\t34441238\t34441585\tMONK:4:1101:2139:139454#ATCACG_1_C_0\n+chr22\t45610815\t45611077\tMONK:4:1101:2139:183067#ATCACG_1_C_0\n+chr22\t39671600\t39671996\tMONK:4:1101:2144:33342#ATCACG_1_C_0\n+chr22\t45926669\t45926955\tMONK:4:1101:2145:111087#ATCACG_1_C_0\n+chr22\t42353807\t42353994\tMONK:4:1101:2147:150414#ATCACG_1_C_0\n+chr22\t24153559\t24153892\tMONK:4:1101:2149:92715#ATCACG_1_C_0\n+chr22\t18633120\t18633461\tMONK:4:1101:2149:117901#ATCACG_1_C_0\n+chr22\t28398677\t28398947\tMONK:4:1101:2154:12577#ATCACG_1_C_0\n+chr22\t21293552\t21293918\tMONK:4:1101:2156:25409#ATCACG_1_C_0\n+chr22\t41276700\t41276988\tMONK:4:1101:2159:7211#ATCACG_1_C_0\n+chr22\t48967117\t48967481\tMONK:4:1101:2167:87699#ATCACG_1_C_0\n+chr22\t35225703\t35226036\tMONK:4:1101:2169:189605#ATCACG_1_C_0\n+chr22\t26683772\t26684132\tMONK:4:1101:2170:100928#ATCACG_1_C_0\n+chr22\t43356750\t43357110\tMONK:4:1101:2172:94564#ATCACG_1_C_0\n+chr22\t42949335\t42949675\tMONK:4:1101:2174:117708#ATCACG_1_C_0\n+chr22\t48493138\t48493460\tMONK:4:1101:2178:193175#ATCACG_1_C_0\n' |
| b |
| diff -r 000000000000 -r a41d96fc0b20 test-data/CTCF.encodepeak --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CTCF.encodepeak Mon Jul 15 09:43:27 2019 -0400 |
| b |
| b'@@ -0,0 +1,421 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|
| b |
| diff -r 000000000000 -r a41d96fc0b20 test-data/CTCF1.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CTCF1.bedgraph Mon Jul 15 09:43:27 2019 -0400 |
| b |
| b'@@ -0,0 +1,1935 @@\n+chr\tstart\tend\texperimental\tcontrol\t-log(p)\t-log(q)\tsignif\n+chr1\t0\t249250621\t0.000000\t0.000039\t0.000000\t0.000000\n+chr2\t0\t243199373\t0.000000\t0.000039\t0.000000\t0.000000\n+chr3\t0\t198022430\t0.000000\t0.000039\t0.000000\t0.000000\n+chr4\t0\t191154276\t0.000000\t0.000039\t0.000000\t0.000000\n+chr5\t0\t180915260\t0.000000\t0.000039\t0.000000\t0.000000\n+chr6\t0\t171115067\t0.000000\t0.000039\t0.000000\t0.000000\n+chr7\t0\t159138663\t0.000000\t0.000039\t0.000000\t0.000000\n+chr8\t0\t146364022\t0.000000\t0.000039\t0.000000\t0.000000\n+chr9\t0\t141213431\t0.000000\t0.000039\t0.000000\t0.000000\n+chr10\t0\t135534747\t0.000000\t0.000039\t0.000000\t0.000000\n+chr11\t0\t135006516\t0.000000\t0.000039\t0.000000\t0.000000\n+chr12\t0\t133851895\t0.000000\t0.000039\t0.000000\t0.000000\n+chr13\t0\t115169878\t0.000000\t0.000039\t0.000000\t0.000000\n+chr14\t0\t107349540\t0.000000\t0.000039\t0.000000\t0.000000\n+chr15\t0\t102531392\t0.000000\t0.000039\t0.000000\t0.000000\n+chr16\t0\t90354753\t0.000000\t0.000039\t0.000000\t0.000000\n+chr17\t0\t81195210\t0.000000\t0.000039\t0.000000\t0.000000\n+chr18\t0\t78077248\t0.000000\t0.000039\t0.000000\t0.000000\n+chr19\t0\t59128983\t0.000000\t0.000039\t0.000000\t0.000000\n+chr20\t0\t63025520\t0.000000\t0.000039\t0.000000\t0.000000\n+chr21\t0\t48129895\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t0\t16874913\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t16874913\t16875110\t1.000000\t0.000039\t28.826399\t23.216457\t*\n+chr22\t16875110\t17213301\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t17213301\t17213528\t0.000000\t0.793817\t0.000000\t0.000000\n+chr22\t17213528\t17305939\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t17305939\t17306331\t0.000000\t0.793817\t0.000000\t0.000000\n+chr22\t17306331\t17331220\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t17331220\t17331528\t0.000000\t0.793817\t0.000000\t0.000000\n+chr22\t17331528\t17333158\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t17333158\t17333474\t0.000000\t0.793817\t0.000000\t0.000000\n+chr22\t17333474\t17374212\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t17374212\t17374535\t0.000000\t0.793817\t0.000000\t0.000000\n+chr22\t17374535\t17377196\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t17377196\t17377428\t1.000000\t0.000039\t28.826399\t23.216457\t*\n+chr22\t17377428\t17529435\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t17529435\t17529809\t0.000000\t0.793817\t0.000000\t0.000000\n+chr22\t17529809\t17555930\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t17555930\t17556245\t1.000000\t0.000039\t28.826399\t23.216457\t*\n+chr22\t17556245\t17574927\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t17574927\t17575208\t0.000000\t0.793817\t0.000000\t0.000000\n+chr22\t17575208\t17652822\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t17652822\t17652841\t1.000000\t0.000039\t28.826399\t23.216457\t*\n+chr22\t17652841\t17653093\t2.000000\t0.000039\t32.549095\t25.871252\t*\n+chr22\t17653093\t17653159\t1.000000\t0.000039\t28.826399\t23.216457\t*\n+chr22\t17653159\t17686483\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t17686483\t17686744\t1.000000\t0.000039\t28.826399\t23.216457\t*\n+chr22\t17686744\t17697561\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t17697561\t17697877\t0.000000\t0.793817\t0.000000\t0.000000\n+chr22\t17697877\t17718259\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t17718259\t17718522\t1.000000\t0.000039\t28.826399\t23.216457\t*\n+chr22\t17718522\t17836468\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t17836468\t17836780\t1.000000\t0.000039\t28.826399\t23.216457\t*\n+chr22\t17836780\t17847348\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t17847348\t17847549\t1.000000\t0.000039\t28.826399\t23.216457\t*\n+chr22\t17847549\t17979862\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t17979862\t17980115\t1.000000\t0.000039\t28.826399\t23.216457\t*\n+chr22\t17980115\t17999764\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t17999764\t17999976\t1.000000\t0.000039\t28.826399\t23.216457\t*\n+chr22\t17999976\t18137643\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t18137643\t18137939\t0.000000\t0.793817\t0.000000\t0.000000\n+chr22\t18137939\t18141593\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t18141593\t18141906\t0.000000\t0.793817\t0.000000\t0.000000\n+chr22\t18141906\t18178995\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t18178995\t18179198\t1.000000\t0.000039\t28.826399\t23.216457\t*\n+chr22\t18179198\t18201532\t0.000000\t0.000039\t0.000000\t'..b'.000039\t0.000000\t0.000000\n+chr22\t50338193\t50338471\t0.000000\t0.793817\t0.000000\t0.000000\n+chr22\t50338471\t50354362\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t50354362\t50354742\t0.000000\t0.793817\t0.000000\t0.000000\n+chr22\t50354742\t50418074\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t50418074\t50418305\t1.000000\t0.000039\t28.826399\t23.216457\t*\n+chr22\t50418305\t50451024\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t50451024\t50451324\t0.000000\t0.793817\t0.000000\t0.000000\n+chr22\t50451324\t50468615\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t50468615\t50468733\t1.000000\t0.000039\t28.826399\t23.216457\t*\n+chr22\t50468733\t50468871\t2.000000\t0.000039\t32.549095\t25.871252\t*\n+chr22\t50468871\t50468928\t1.000000\t0.000039\t28.826399\t23.216457\t*\n+chr22\t50468928\t50472607\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t50472607\t50472929\t0.000000\t0.793817\t0.000000\t0.000000\n+chr22\t50472929\t50512931\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t50512931\t50513121\t1.000000\t0.000039\t28.826399\t23.216457\t*\n+chr22\t50513121\t50574751\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t50574751\t50575063\t0.000000\t0.793817\t0.000000\t0.000000\n+chr22\t50575063\t50628501\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t50628501\t50628741\t1.000000\t0.000039\t28.826399\t23.216457\t*\n+chr22\t50628741\t50630995\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t50630995\t50631224\t1.000000\t0.000039\t28.826399\t23.216457\t*\n+chr22\t50631224\t50645170\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t50645170\t50645459\t1.000000\t0.000039\t28.826399\t23.216457\t*\n+chr22\t50645459\t50658290\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t50658290\t50658656\t0.000000\t0.793817\t0.000000\t0.000000\n+chr22\t50658656\t50716298\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t50716298\t50716549\t1.000000\t0.000039\t28.826399\t23.216457\t*\n+chr22\t50716549\t50728249\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t50728249\t50728594\t0.000000\t0.793817\t0.000000\t0.000000\n+chr22\t50728594\t50757826\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t50757826\t50758150\t0.000000\t0.793817\t0.000000\t0.000000\n+chr22\t50758150\t50769460\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t50769460\t50769676\t1.000000\t0.000039\t28.826399\t23.216457\t*\n+chr22\t50769676\t50802506\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t50802506\t50802827\t0.000000\t0.793817\t0.000000\t0.000000\n+chr22\t50802827\t50911511\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t50911511\t50911831\t1.000000\t0.000039\t28.826399\t23.216457\t*\n+chr22\t50911831\t50936751\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t50936751\t50936936\t1.000000\t0.000039\t28.826399\t23.216457\t*\n+chr22\t50936936\t50965071\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t50965071\t50965340\t1.000000\t0.000039\t28.826399\t23.216457\t*\n+chr22\t50965340\t50972925\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t50972925\t50973062\t1.000000\t0.000039\t28.826399\t23.216457\t*\n+chr22\t50973062\t50982866\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t50982866\t50983075\t1.000000\t0.000039\t28.826399\t23.216457\t*\n+chr22\t50983075\t51058888\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t51058888\t51059217\t1.000000\t0.000039\t28.826399\t23.216457\t*\n+chr22\t51059217\t51066506\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t51066506\t51066791\t1.000000\t0.000039\t28.826399\t23.216457\t*\n+chr22\t51066791\t51102143\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t51102143\t51102471\t0.000000\t0.793817\t0.000000\t0.000000\n+chr22\t51102471\t51103700\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t51103700\t51104012\t0.000000\t0.793817\t0.000000\t0.000000\n+chr22\t51104012\t51130088\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t51130088\t51130096\t1.000000\t0.000039\t28.826399\t23.216457\t*\n+chr22\t51130096\t51130313\t2.000000\t0.000039\t32.549095\t25.871252\t*\n+chr22\t51130313\t51130412\t1.000000\t0.000039\t28.826399\t23.216457\t*\n+chr22\t51130412\t51208525\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t51208525\t51208735\t0.000000\t0.793817\t0.000000\t0.000000\n+chr22\t51208735\t51213606\t0.000000\t0.000039\t0.000000\t0.000000\n+chr22\t51213606\t51213856\t1.000000\t0.000039\t28.826399\t23.216457\t*\n+chr22\t51213856\t51304566\t0.000000\t0.000039\t0.000000\t0.000000\n+chrX\t0\t155270560\t0.000000\t0.000039\t0.000000\t0.000000\n+chrY\t0\t59373566\t0.000000\t0.000039\t0.000000\t0.000000\n' |
| b |
| diff -r 000000000000 -r a41d96fc0b20 test-data/CTCF2.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CTCF2.bedgraph Mon Jul 15 09:43:27 2019 -0400 |
| b |
| b'@@ -0,0 +1,1936 @@\n+# experimental file: CTCF1.bam; control file: CTCF2.bam\n+chr\tstart\tend\texperimental\tcontrol\t-log(p)\n+chr1\t0\t249250621\t0.000000\t0.000039\t0.000000\n+chr2\t0\t243199373\t0.000000\t0.000039\t0.000000\n+chr3\t0\t198022430\t0.000000\t0.000039\t0.000000\n+chr4\t0\t191154276\t0.000000\t0.000039\t0.000000\n+chr5\t0\t180915260\t0.000000\t0.000039\t0.000000\n+chr6\t0\t171115067\t0.000000\t0.000039\t0.000000\n+chr7\t0\t159138663\t0.000000\t0.000039\t0.000000\n+chr8\t0\t146364022\t0.000000\t0.000039\t0.000000\n+chr9\t0\t141213431\t0.000000\t0.000039\t0.000000\n+chr10\t0\t135534747\t0.000000\t0.000039\t0.000000\n+chr11\t0\t135006516\t0.000000\t0.000039\t0.000000\n+chr12\t0\t133851895\t0.000000\t0.000039\t0.000000\n+chr13\t0\t115169878\t0.000000\t0.000039\t0.000000\n+chr14\t0\t107349540\t0.000000\t0.000039\t0.000000\n+chr15\t0\t102531392\t0.000000\t0.000039\t0.000000\n+chr16\t0\t90354753\t0.000000\t0.000039\t0.000000\n+chr17\t0\t81195210\t0.000000\t0.000039\t0.000000\n+chr18\t0\t78077248\t0.000000\t0.000039\t0.000000\n+chr19\t0\t59128983\t0.000000\t0.000039\t0.000000\n+chr20\t0\t63025520\t0.000000\t0.000039\t0.000000\n+chr21\t0\t48129895\t0.000000\t0.000039\t0.000000\n+chr22\t0\t16874913\t0.000000\t0.000039\t0.000000\n+chr22\t16874913\t16875110\t1.000000\t0.000039\t28.826399\n+chr22\t16875110\t17213301\t0.000000\t0.000039\t0.000000\n+chr22\t17213301\t17213528\t0.000000\t0.793817\t0.000000\n+chr22\t17213528\t17305939\t0.000000\t0.000039\t0.000000\n+chr22\t17305939\t17306331\t0.000000\t0.793817\t0.000000\n+chr22\t17306331\t17331220\t0.000000\t0.000039\t0.000000\n+chr22\t17331220\t17331528\t0.000000\t0.793817\t0.000000\n+chr22\t17331528\t17333158\t0.000000\t0.000039\t0.000000\n+chr22\t17333158\t17333474\t0.000000\t0.793817\t0.000000\n+chr22\t17333474\t17374212\t0.000000\t0.000039\t0.000000\n+chr22\t17374212\t17374535\t0.000000\t0.793817\t0.000000\n+chr22\t17374535\t17377196\t0.000000\t0.000039\t0.000000\n+chr22\t17377196\t17377428\t1.000000\t0.000039\t28.826399\n+chr22\t17377428\t17529435\t0.000000\t0.000039\t0.000000\n+chr22\t17529435\t17529809\t0.000000\t0.793817\t0.000000\n+chr22\t17529809\t17555930\t0.000000\t0.000039\t0.000000\n+chr22\t17555930\t17556245\t1.000000\t0.000039\t28.826399\n+chr22\t17556245\t17574927\t0.000000\t0.000039\t0.000000\n+chr22\t17574927\t17575208\t0.000000\t0.793817\t0.000000\n+chr22\t17575208\t17652822\t0.000000\t0.000039\t0.000000\n+chr22\t17652822\t17652841\t1.000000\t0.000039\t28.826399\n+chr22\t17652841\t17653093\t2.000000\t0.000039\t32.549095\n+chr22\t17653093\t17653159\t1.000000\t0.000039\t28.826399\n+chr22\t17653159\t17686483\t0.000000\t0.000039\t0.000000\n+chr22\t17686483\t17686744\t1.000000\t0.000039\t28.826399\n+chr22\t17686744\t17697561\t0.000000\t0.000039\t0.000000\n+chr22\t17697561\t17697877\t0.000000\t0.793817\t0.000000\n+chr22\t17697877\t17718259\t0.000000\t0.000039\t0.000000\n+chr22\t17718259\t17718522\t1.000000\t0.000039\t28.826399\n+chr22\t17718522\t17836468\t0.000000\t0.000039\t0.000000\n+chr22\t17836468\t17836780\t1.000000\t0.000039\t28.826399\n+chr22\t17836780\t17847348\t0.000000\t0.000039\t0.000000\n+chr22\t17847348\t17847549\t1.000000\t0.000039\t28.826399\n+chr22\t17847549\t17979862\t0.000000\t0.000039\t0.000000\n+chr22\t17979862\t17980115\t1.000000\t0.000039\t28.826399\n+chr22\t17980115\t17999764\t0.000000\t0.000039\t0.000000\n+chr22\t17999764\t17999976\t1.000000\t0.000039\t28.826399\n+chr22\t17999976\t18137643\t0.000000\t0.000039\t0.000000\n+chr22\t18137643\t18137939\t0.000000\t0.793817\t0.000000\n+chr22\t18137939\t18141593\t0.000000\t0.000039\t0.000000\n+chr22\t18141593\t18141906\t0.000000\t0.793817\t0.000000\n+chr22\t18141906\t18178995\t0.000000\t0.000039\t0.000000\n+chr22\t18178995\t18179198\t1.000000\t0.000039\t28.826399\n+chr22\t18179198\t18201532\t0.000000\t0.000039\t0.000000\n+chr22\t18201532\t18201830\t0.000000\t0.793817\t0.000000\n+chr22\t18201830\t18225329\t0.000000\t0.000039\t0.000000\n+chr22\t18225329\t18225542\t1.000000\t0.000039\t28.826399\n+chr22\t18225542\t18259249\t0.000000\t0.000039\t0.000000\n+chr22\t18259249\t18259606\t0.000000\t0.793817\t0.000000\n+chr22\t18259606\t18263815\t0.000000\t0.000039\t0.000000\n+chr22\t18263815\t18264099\t0.000000\t0.793817\t0.000000\n+chr22\t18264099\t18267916\t0.000000\t0.000039\t0.000000\n+chr22\t18267916\t18268161\t1.000000\t0.000039\t28.826399\n+chr22\t18268161\t18281979\t0.000000\t0.000039\t0.000000\n+chr22\t18281979\t18282182\t1.000000\t0.000039\t28.826399\n+chr22\t'..b'8885\t50049313\t0.000000\t0.000039\t0.000000\n+chr22\t50049313\t50049602\t0.000000\t0.793817\t0.000000\n+chr22\t50049602\t50059030\t0.000000\t0.000039\t0.000000\n+chr22\t50059030\t50059315\t0.000000\t0.793817\t0.000000\n+chr22\t50059315\t50125688\t0.000000\t0.000039\t0.000000\n+chr22\t50125688\t50125865\t0.000000\t0.793817\t0.000000\n+chr22\t50125865\t50214174\t0.000000\t0.000039\t0.000000\n+chr22\t50214174\t50214574\t0.000000\t0.793817\t0.000000\n+chr22\t50214574\t50233496\t0.000000\t0.000039\t0.000000\n+chr22\t50233496\t50233928\t0.000000\t0.793817\t0.000000\n+chr22\t50233928\t50234415\t0.000000\t0.000039\t0.000000\n+chr22\t50234415\t50234797\t0.000000\t0.793817\t0.000000\n+chr22\t50234797\t50338193\t0.000000\t0.000039\t0.000000\n+chr22\t50338193\t50338471\t0.000000\t0.793817\t0.000000\n+chr22\t50338471\t50354362\t0.000000\t0.000039\t0.000000\n+chr22\t50354362\t50354742\t0.000000\t0.793817\t0.000000\n+chr22\t50354742\t50418074\t0.000000\t0.000039\t0.000000\n+chr22\t50418074\t50418305\t1.000000\t0.000039\t28.826399\n+chr22\t50418305\t50451024\t0.000000\t0.000039\t0.000000\n+chr22\t50451024\t50451324\t0.000000\t0.793817\t0.000000\n+chr22\t50451324\t50468615\t0.000000\t0.000039\t0.000000\n+chr22\t50468615\t50468733\t1.000000\t0.000039\t28.826399\n+chr22\t50468733\t50468871\t2.000000\t0.000039\t32.549095\n+chr22\t50468871\t50468928\t1.000000\t0.000039\t28.826399\n+chr22\t50468928\t50472607\t0.000000\t0.000039\t0.000000\n+chr22\t50472607\t50472929\t0.000000\t0.793817\t0.000000\n+chr22\t50472929\t50512931\t0.000000\t0.000039\t0.000000\n+chr22\t50512931\t50513121\t1.000000\t0.000039\t28.826399\n+chr22\t50513121\t50574751\t0.000000\t0.000039\t0.000000\n+chr22\t50574751\t50575063\t0.000000\t0.793817\t0.000000\n+chr22\t50575063\t50628501\t0.000000\t0.000039\t0.000000\n+chr22\t50628501\t50628741\t1.000000\t0.000039\t28.826399\n+chr22\t50628741\t50630995\t0.000000\t0.000039\t0.000000\n+chr22\t50630995\t50631224\t1.000000\t0.000039\t28.826399\n+chr22\t50631224\t50645170\t0.000000\t0.000039\t0.000000\n+chr22\t50645170\t50645459\t1.000000\t0.000039\t28.826399\n+chr22\t50645459\t50658290\t0.000000\t0.000039\t0.000000\n+chr22\t50658290\t50658656\t0.000000\t0.793817\t0.000000\n+chr22\t50658656\t50716298\t0.000000\t0.000039\t0.000000\n+chr22\t50716298\t50716549\t1.000000\t0.000039\t28.826399\n+chr22\t50716549\t50728249\t0.000000\t0.000039\t0.000000\n+chr22\t50728249\t50728594\t0.000000\t0.793817\t0.000000\n+chr22\t50728594\t50757826\t0.000000\t0.000039\t0.000000\n+chr22\t50757826\t50758150\t0.000000\t0.793817\t0.000000\n+chr22\t50758150\t50769460\t0.000000\t0.000039\t0.000000\n+chr22\t50769460\t50769676\t1.000000\t0.000039\t28.826399\n+chr22\t50769676\t50802506\t0.000000\t0.000039\t0.000000\n+chr22\t50802506\t50802827\t0.000000\t0.793817\t0.000000\n+chr22\t50802827\t50911511\t0.000000\t0.000039\t0.000000\n+chr22\t50911511\t50911831\t1.000000\t0.000039\t28.826399\n+chr22\t50911831\t50936751\t0.000000\t0.000039\t0.000000\n+chr22\t50936751\t50936936\t1.000000\t0.000039\t28.826399\n+chr22\t50936936\t50965071\t0.000000\t0.000039\t0.000000\n+chr22\t50965071\t50965340\t1.000000\t0.000039\t28.826399\n+chr22\t50965340\t50972925\t0.000000\t0.000039\t0.000000\n+chr22\t50972925\t50973062\t1.000000\t0.000039\t28.826399\n+chr22\t50973062\t50982866\t0.000000\t0.000039\t0.000000\n+chr22\t50982866\t50983075\t1.000000\t0.000039\t28.826399\n+chr22\t50983075\t51058888\t0.000000\t0.000039\t0.000000\n+chr22\t51058888\t51059217\t1.000000\t0.000039\t28.826399\n+chr22\t51059217\t51066506\t0.000000\t0.000039\t0.000000\n+chr22\t51066506\t51066791\t1.000000\t0.000039\t28.826399\n+chr22\t51066791\t51102143\t0.000000\t0.000039\t0.000000\n+chr22\t51102143\t51102471\t0.000000\t0.793817\t0.000000\n+chr22\t51102471\t51103700\t0.000000\t0.000039\t0.000000\n+chr22\t51103700\t51104012\t0.000000\t0.793817\t0.000000\n+chr22\t51104012\t51130088\t0.000000\t0.000039\t0.000000\n+chr22\t51130088\t51130096\t1.000000\t0.000039\t28.826399\n+chr22\t51130096\t51130313\t2.000000\t0.000039\t32.549095\n+chr22\t51130313\t51130412\t1.000000\t0.000039\t28.826399\n+chr22\t51130412\t51208525\t0.000000\t0.000039\t0.000000\n+chr22\t51208525\t51208735\t0.000000\t0.793817\t0.000000\n+chr22\t51208735\t51213606\t0.000000\t0.000039\t0.000000\n+chr22\t51213606\t51213856\t1.000000\t0.000039\t28.826399\n+chr22\t51213856\t51304566\t0.000000\t0.000039\t0.000000\n+chrX\t0\t155270560\t0.000000\t0.000039\t0.000000\n+chrY\t0\t59373566\t0.000000\t0.000039\t0.000000\n' |
| b |
| diff -r 000000000000 -r a41d96fc0b20 test-data/CTCF_PE_CTRL_chr22.bam |
| b |
| Binary file test-data/CTCF_PE_CTRL_chr22.bam has changed |
| b |
| diff -r 000000000000 -r a41d96fc0b20 test-data/CTCF_PE_ChIP_chr22.bam |
| b |
| Binary file test-data/CTCF_PE_ChIP_chr22.bam has changed |
| b |
| diff -r 000000000000 -r a41d96fc0b20 test-data/atac_out.encodepeak --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/atac_out.encodepeak Mon Jul 15 09:43:27 2019 -0400 |
| b |
| b'@@ -0,0 +1,1720 @@\n+chr22\t10741211\t10741383\tpeak_0\t1000\t.\t3104.551270\t25.087999\t19.350746\t86\n+chr22\t10783762\t10783951\tpeak_1\t1000\t.\t3411.396484\t25.087999\t19.350746\t94\n+chr22\t10941132\t10941358\tpeak_2\t1000\t.\t3609.943359\t25.087999\t19.350746\t50\n+chr22\t11288260\t11288400\tpeak_3\t1000\t.\t2526.960449\t25.087999\t19.350746\t70\n+chr22\t11294541\t11294778\tpeak_4\t1000\t.\t3609.943359\t25.087999\t19.350746\t50\n+chr22\t11308120\t11308390\tpeak_5\t1000\t.\t3609.943359\t25.087999\t19.350746\t50\n+chr22\t11353133\t11353270\tpeak_6\t1000\t.\t2472.811279\t25.087999\t19.350746\t68\n+chr22\t11552745\t11552929\tpeak_7\t1000\t.\t3321.147949\t25.087999\t19.350746\t92\n+chr22\t11968830\t11968965\tpeak_8\t1000\t.\t2436.711670\t25.087999\t19.350746\t67\n+chr22\t12368335\t12368524\tpeak_9\t1000\t.\t3411.396484\t25.087999\t19.350746\t94\n+chr22\t12602352\t12602487\tpeak_10\t1000\t.\t2436.711670\t25.087999\t19.350746\t67\n+chr22\t12604334\t12604434\tpeak_11\t1000\t.\t1804.971680\t25.087999\t19.350746\t50\n+chr22\t12604536\t12604636\tpeak_12\t1000\t.\t1804.971680\t25.087999\t19.350746\t50\n+chr22\t12636264\t12636400\tpeak_13\t1000\t.\t2454.761475\t25.087999\t19.350746\t68\n+chr22\t12721963\t12722241\tpeak_14\t1000\t.\t3609.943359\t25.087999\t19.350746\t50\n+chr22\t16099521\t16099665\tpeak_15\t1000\t.\t2599.159180\t25.087999\t19.350746\t72\n+chr22\t16415232\t16415332\tpeak_16\t1000\t.\t1804.971680\t25.087999\t19.350746\t50\n+chr22\t16415515\t16415615\tpeak_17\t1000\t.\t1804.971680\t25.087999\t19.350746\t50\n+chr22\t16582465\t16582684\tpeak_18\t1000\t.\t3609.943359\t25.087999\t19.350746\t50\n+chr22\t16597062\t16597205\tpeak_19\t1000\t.\t2581.109619\t25.087999\t19.350746\t71\n+chr22\t16609678\t16609874\tpeak_20\t1000\t.\t3537.744629\t25.087999\t19.350746\t98\n+chr22\t16670291\t16670391\tpeak_21\t1000\t.\t1804.971680\t25.087999\t19.350746\t50\n+chr22\t16670516\t16670616\tpeak_22\t1000\t.\t1804.971680\t25.087999\t19.350746\t50\n+chr22\t16806452\t16806683\tpeak_23\t1000\t.\t3609.943359\t25.087999\t19.350746\t50\n+chr22\t16922061\t16922193\tpeak_24\t1000\t.\t2382.562744\t25.087999\t19.350746\t66\n+chr22\t17075614\t17075761\tpeak_25\t1000\t.\t2653.308350\t25.087999\t19.350746\t73\n+chr22\t17085376\t17085722\tpeak_26\t1000\t.\t5269.096680\t28.561464\t21.684465\t117\n+chr22\t17107363\t17107637\tpeak_27\t1000\t.\t3609.943359\t25.087999\t19.350746\t50\n+chr22\t17121710\t17121897\tpeak_28\t1000\t.\t3375.297119\t25.087999\t19.350746\t93\n+chr22\t17158863\t17158963\tpeak_29\t1000\t.\t1804.971680\t25.087999\t19.350746\t50\n+chr22\t17159194\t17159294\tpeak_30\t1000\t.\t1804.971680\t25.087999\t19.350746\t50\n+chr22\t17166346\t17166446\tpeak_31\t1000\t.\t1804.971680\t25.087999\t19.350746\t50\n+chr22\t17166596\t17166696\tpeak_32\t1000\t.\t1804.971680\t25.087999\t19.350746\t50\n+chr22\t17243742\t17244031\tpeak_33\t1000\t.\t3609.943359\t25.087999\t19.350746\t50\n+chr22\t17260757\t17260999\tpeak_34\t1000\t.\t3609.943359\t25.087999\t19.350746\t50\n+chr22\t17368675\t17368775\tpeak_35\t1000\t.\t1804.971680\t25.087999\t19.350746\t50\n+chr22\t17368902\t17369002\tpeak_36\t1000\t.\t1804.971680\t25.087999\t19.350746\t50\n+chr22\t17375500\t17375635\tpeak_37\t1000\t.\t2436.711670\t25.087999\t19.350746\t67\n+chr22\t17397311\t17397475\tpeak_38\t1000\t.\t2960.153564\t25.087999\t19.350746\t82\n+chr22\t17433017\t17433233\tpeak_39\t1000\t.\t3609.943359\t25.087999\t19.350746\t50\n+chr22\t17474600\t17474734\tpeak_40\t1000\t.\t2418.662109\t25.087999\t19.350746\t67\n+chr22\t17541883\t17542069\tpeak_41\t1000\t.\t3357.247314\t25.087999\t19.350746\t93\n+chr22\t17549638\t17549819\tpeak_42\t1000\t.\t3266.998779\t25.087999\t19.350746\t90\n+chr22\t17552085\t17552185\tpeak_43\t1000\t.\t1804.971680\t25.087999\t19.350746\t50\n+chr22\t17552287\t17552387\tpeak_44\t1000\t.\t1804.971680\t25.087999\t19.350746\t50\n+chr22\t17570180\t17570409\tpeak_45\t1000\t.\t3609.943359\t25.087999\t19.350746\t50\n+chr22\t17576283\t17576527\tpeak_46\t1000\t.\t4422.439453\t28.561464\t21.684465\t52\n+chr22\t17595913\t17596013\tpeak_47\t1000\t.\t1804.971680\t25.087999\t19.350746\t50\n+chr22\t17596134\t17596234\tpeak_48\t1000\t.\t1804.971680\t25.087999\t19.350746\t50\n+chr22\t17628693\t17628793\tpeak_49\t1000\t.\t1804.971680\t25.087999\t19.350746\t50\n+chr22\t17629351\t17629451\tpeak_50\t1000\t.\t1804.971680\t25.087999\t19.350746\t50\n+chr22\t17649951\t17650157\tpeak_51\t1000\t.\t3609.943359\t25.087999\t19.350746\t50\n+chr22\t17672156\t17672298\tpeak_52\t1000\t.\t2563.059814\t25.087999\t19.350746\t71\n+chr22\t1770656'..b'50072210\t50072310\tpeak_1668\t1000\t.\t1804.971680\t25.087999\t19.350746\t50\n+chr22\t50084579\t50084845\tpeak_1669\t1000\t.\t3609.943359\t25.087999\t19.350746\t50\n+chr22\t50123816\t50123971\tpeak_1670\t1000\t.\t2797.706055\t25.087999\t19.350746\t77\n+chr22\t50148961\t50149227\tpeak_1671\t1000\t.\t3609.943359\t25.087999\t19.350746\t50\n+chr22\t50162685\t50162981\tpeak_1672\t1000\t.\t3609.943359\t25.087999\t19.350746\t50\n+chr22\t50180371\t50180715\tpeak_1673\t1000\t.\t5394.204102\t28.561464\t21.684465\t225\n+chr22\t50188468\t50188671\tpeak_1674\t1000\t.\t3609.943359\t25.087999\t19.350746\t50\n+chr22\t50195987\t50196254\tpeak_1675\t1000\t.\t3609.943359\t25.087999\t19.350746\t50\n+chr22\t50198372\t50198543\tpeak_1676\t1000\t.\t3086.501709\t25.087999\t19.350746\t85\n+chr22\t50200587\t50200687\tpeak_1677\t1000\t.\t1804.971680\t25.087999\t19.350746\t50\n+chr22\t50200811\t50200911\tpeak_1678\t1000\t.\t1804.971680\t25.087999\t19.350746\t50\n+chr22\t50241171\t50241359\tpeak_1679\t1000\t.\t3393.346680\t25.087999\t19.350746\t94\n+chr22\t50245040\t50245192\tpeak_1680\t1000\t.\t2743.556885\t25.087999\t19.350746\t76\n+chr22\t50251526\t50251660\tpeak_1681\t1000\t.\t2418.662109\t25.087999\t19.350746\t67\n+chr22\t50263591\t50263781\tpeak_1682\t1000\t.\t3429.446289\t25.087999\t19.350746\t95\n+chr22\t50266922\t50267177\tpeak_1683\t1000\t.\t3609.943359\t25.087999\t19.350746\t50\n+chr22\t50272115\t50272388\tpeak_1684\t1000\t.\t3609.943359\t25.087999\t19.350746\t50\n+chr22\t50282450\t50282622\tpeak_1685\t1000\t.\t3104.551270\t25.087999\t19.350746\t86\n+chr22\t50283563\t50283663\tpeak_1686\t1000\t.\t1804.971680\t25.087999\t19.350746\t50\n+chr22\t50283876\t50283976\tpeak_1687\t1000\t.\t1804.971680\t25.087999\t19.350746\t50\n+chr22\t50304431\t50304531\tpeak_1688\t1000\t.\t1804.971680\t25.087999\t19.350746\t50\n+chr22\t50304998\t50305320\tpeak_1689\t1000\t.\t4458.280273\t25.087999\t19.350746\t73\n+chr22\t50318869\t50319079\tpeak_1690\t1000\t.\t3609.943359\t25.087999\t19.350746\t50\n+chr22\t50341592\t50341766\tpeak_1691\t1000\t.\t3140.650635\t25.087999\t19.350746\t87\n+chr22\t50355118\t50355273\tpeak_1692\t1000\t.\t2797.706055\t25.087999\t19.350746\t77\n+chr22\t50387086\t50387362\tpeak_1693\t1000\t.\t3609.943359\t25.087999\t19.350746\t50\n+chr22\t50428784\t50429021\tpeak_1694\t1000\t.\t3609.943359\t25.087999\t19.350746\t50\n+chr22\t50482515\t50482652\tpeak_1695\t1000\t.\t2472.811279\t25.087999\t19.350746\t68\n+chr22\t50506123\t50506339\tpeak_1696\t1000\t.\t3609.943359\t25.087999\t19.350746\t50\n+chr22\t50507808\t50507944\tpeak_1697\t1000\t.\t2454.761475\t25.087999\t19.350746\t68\n+chr22\t50508105\t50508293\tpeak_1698\t1000\t.\t3393.346680\t25.087999\t19.350746\t94\n+chr22\t50525767\t50525976\tpeak_1699\t1000\t.\t3609.943359\t25.087999\t19.350746\t50\n+chr22\t50562570\t50562711\tpeak_1700\t1000\t.\t2545.010010\t25.087999\t19.350746\t70\n+chr22\t50562977\t50563259\tpeak_1701\t1000\t.\t3609.943359\t25.087999\t19.350746\t50\n+chr22\t50570532\t50570675\tpeak_1702\t1000\t.\t2581.109619\t25.087999\t19.350746\t71\n+chr22\t50582639\t50583150\tpeak_1703\t1000\t.\t8841.138672\t30.700907\t22.760651\t407\n+chr22\t50596834\t50596934\tpeak_1704\t1000\t.\t1804.971680\t25.087999\t19.350746\t50\n+chr22\t50597090\t50597190\tpeak_1705\t1000\t.\t1804.971680\t25.087999\t19.350746\t50\n+chr22\t50609140\t50609240\tpeak_1706\t1000\t.\t1804.971680\t25.087999\t19.350746\t50\n+chr22\t50609362\t50609462\tpeak_1707\t1000\t.\t1804.971680\t25.087999\t19.350746\t50\n+chr22\t50610464\t50610564\tpeak_1708\t1000\t.\t1804.971680\t25.087999\t19.350746\t50\n+chr22\t50610671\t50610771\tpeak_1709\t1000\t.\t1804.971680\t25.087999\t19.350746\t50\n+chr22\t50621779\t50622067\tpeak_1710\t1000\t.\t3609.943359\t25.087999\t19.350746\t50\n+chr22\t50622844\t50623203\tpeak_1711\t1000\t.\t5414.915039\t25.087999\t19.350746\t50\n+chr22\t50623435\t50623535\tpeak_1712\t1000\t.\t1804.971680\t25.087999\t19.350746\t50\n+chr22\t50628191\t50628334\tpeak_1713\t1000\t.\t2581.109619\t25.087999\t19.350746\t71\n+chr22\t50675198\t50675298\tpeak_1714\t1000\t.\t1804.971680\t25.087999\t19.350746\t50\n+chr22\t50675430\t50675530\tpeak_1715\t1000\t.\t1804.971680\t25.087999\t19.350746\t50\n+chr22\t50708813\t50709078\tpeak_1716\t1000\t.\t3609.943359\t25.087999\t19.350746\t50\n+chr22\t50722110\t50722384\tpeak_1717\t1000\t.\t3609.943359\t25.087999\t19.350746\t50\n+chr22\t50724764\t50725016\tpeak_1718\t1000\t.\t3609.943359\t25.087999\t19.350746\t50\n+chr22\t50754667\t50754811\tpeak_1719\t1000\t.\t2599.159180\t25.087999\t19.350746\t72\n' |
| b |
| diff -r 000000000000 -r a41d96fc0b20 test-data/atac_out2.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/atac_out2.bedgraph Mon Jul 15 09:43:27 2019 -0400 |
| b |
| b'@@ -0,0 +1,4769 @@\n+chr\tstart\tend\texperimental\tcontrol\t-log(p)\t-log(q)\tsignif\n+chr1\t0\t248956422\t0.000000\t0.000082\t0.000000\t0.000000\n+chr10\t0\t133797422\t0.000000\t0.000082\t0.000000\t0.000000\n+chr11\t0\t135086622\t0.000000\t0.000082\t0.000000\t0.000000\n+chr11_KI270721v1_random\t0\t100316\t0.000000\t0.000082\t0.000000\t0.000000\n+chr12\t0\t133275309\t0.000000\t0.000082\t0.000000\t0.000000\n+chr13\t0\t114364328\t0.000000\t0.000082\t0.000000\t0.000000\n+chr14\t0\t107043718\t0.000000\t0.000082\t0.000000\t0.000000\n+chr14_GL000009v2_random\t0\t201709\t0.000000\t0.000082\t0.000000\t0.000000\n+chr14_GL000225v1_random\t0\t211173\t0.000000\t0.000082\t0.000000\t0.000000\n+chr14_KI270722v1_random\t0\t194050\t0.000000\t0.000082\t0.000000\t0.000000\n+chr14_GL000194v1_random\t0\t191469\t0.000000\t0.000082\t0.000000\t0.000000\n+chr14_KI270723v1_random\t0\t38115\t0.000000\t0.000082\t0.000000\t0.000000\n+chr14_KI270724v1_random\t0\t39555\t0.000000\t0.000082\t0.000000\t0.000000\n+chr14_KI270725v1_random\t0\t172810\t0.000000\t0.000082\t0.000000\t0.000000\n+chr14_KI270726v1_random\t0\t43739\t0.000000\t0.000082\t0.000000\t0.000000\n+chr15\t0\t101991189\t0.000000\t0.000082\t0.000000\t0.000000\n+chr15_KI270727v1_random\t0\t448248\t0.000000\t0.000082\t0.000000\t0.000000\n+chr16\t0\t90338345\t0.000000\t0.000082\t0.000000\t0.000000\n+chr16_KI270728v1_random\t0\t1872759\t0.000000\t0.000082\t0.000000\t0.000000\n+chr17\t0\t83257441\t0.000000\t0.000082\t0.000000\t0.000000\n+chr17_GL000205v2_random\t0\t185591\t0.000000\t0.000082\t0.000000\t0.000000\n+chr17_KI270729v1_random\t0\t280839\t0.000000\t0.000082\t0.000000\t0.000000\n+chr17_KI270730v1_random\t0\t112551\t0.000000\t0.000082\t0.000000\t0.000000\n+chr18\t0\t80373285\t0.000000\t0.000082\t0.000000\t0.000000\n+chr19\t0\t58617616\t0.000000\t0.000082\t0.000000\t0.000000\n+chr1_KI270706v1_random\t0\t175055\t0.000000\t0.000082\t0.000000\t0.000000\n+chr1_KI270707v1_random\t0\t32032\t0.000000\t0.000082\t0.000000\t0.000000\n+chr1_KI270708v1_random\t0\t127682\t0.000000\t0.000082\t0.000000\t0.000000\n+chr1_KI270709v1_random\t0\t66860\t0.000000\t0.000082\t0.000000\t0.000000\n+chr1_KI270710v1_random\t0\t40176\t0.000000\t0.000082\t0.000000\t0.000000\n+chr1_KI270711v1_random\t0\t42210\t0.000000\t0.000082\t0.000000\t0.000000\n+chr1_KI270712v1_random\t0\t176043\t0.000000\t0.000082\t0.000000\t0.000000\n+chr1_KI270713v1_random\t0\t40745\t0.000000\t0.000082\t0.000000\t0.000000\n+chr1_KI270714v1_random\t0\t41717\t0.000000\t0.000082\t0.000000\t0.000000\n+chr2\t0\t242193529\t0.000000\t0.000082\t0.000000\t0.000000\n+chr20\t0\t64444167\t0.000000\t0.000082\t0.000000\t0.000000\n+chr21\t0\t46709983\t0.000000\t0.000082\t0.000000\t0.000000\n+chr22\t0\t10741211\t0.000000\t0.000082\t0.000000\t0.000000\n+chr22\t10741211\t10741383\t1.000000\t0.000082\t25.087999\t19.350746\t*\n+chr22\t10741383\t10783762\t0.000000\t0.000082\t0.000000\t0.000000\n+chr22\t10783762\t10783951\t1.000000\t0.000082\t25.087999\t19.350746\t*\n+chr22\t10783951\t10941132\t0.000000\t0.000082\t0.000000\t0.000000\n+chr22\t10941132\t10941232\t1.000000\t0.000082\t25.087999\t19.350746\t*\n+chr22\t10941232\t10941258\t0.000000\t0.000082\t0.000000\t0.000000\n+chr22\t10941258\t10941358\t1.000000\t0.000082\t25.087999\t19.350746\t*\n+chr22\t10941358\t11288260\t0.000000\t0.000082\t0.000000\t0.000000\n+chr22\t11288260\t11288400\t1.000000\t0.000082\t25.087999\t19.350746\t*\n+chr22\t11288400\t11294541\t0.000000\t0.000082\t0.000000\t0.000000\n+chr22\t11294541\t11294641\t1.000000\t0.000082\t25.087999\t19.350746\t*\n+chr22\t11294641\t11294678\t0.000000\t0.000082\t0.000000\t0.000000\n+chr22\t11294678\t11294778\t1.000000\t0.000082\t25.087999\t19.350746\t*\n+chr22\t11294778\t11308120\t0.000000\t0.000082\t0.000000\t0.000000\n+chr22\t11308120\t11308220\t1.000000\t0.000082\t25.087999\t19.350746\t*\n+chr22\t11308220\t11308290\t0.000000\t0.000082\t0.000000\t0.000000\n+chr22\t11308290\t11308390\t1.000000\t0.000082\t25.087999\t19.350746\t*\n+chr22\t11308390\t11353133\t0.000000\t0.000082\t0.000000\t0.000000\n+chr22\t11353133\t11353270\t1.000000\t0.000082\t25.087999\t19.350746\t*\n+chr22\t11353270\t11552745\t0.000000\t0.000082\t0.000000\t0.000000\n+chr22\t11552745\t11552929\t1.000000\t0.000082\t25.087999\t19.350746\t*\n+chr22\t11552929\t11968830\t0.000000\t0.000082\t0.000000\t0.000000\n+chr22\t11968830\t11968965\t1.000000\t0.000082\t25.087999\t19.350746\t*\n+chr22\t11968965\t12368335\t0.000000\t0.000082\t0.000000\t0.000000\n'..b'00\n+chrUn_KI270333v1\t0\t2699\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270335v1\t0\t1048\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270338v1\t0\t1428\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270340v1\t0\t1428\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270336v1\t0\t1026\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270337v1\t0\t1121\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270363v1\t0\t1803\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270364v1\t0\t2855\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270362v1\t0\t3530\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270366v1\t0\t8320\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270378v1\t0\t1048\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270379v1\t0\t1045\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270389v1\t0\t1298\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270390v1\t0\t2387\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270387v1\t0\t1537\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270395v1\t0\t1143\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270396v1\t0\t1880\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270388v1\t0\t1216\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270394v1\t0\t970\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270386v1\t0\t1788\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270391v1\t0\t1484\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270383v1\t0\t1750\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270393v1\t0\t1308\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270384v1\t0\t1658\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270392v1\t0\t971\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270381v1\t0\t1930\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270385v1\t0\t990\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270382v1\t0\t4215\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270376v1\t0\t1136\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270374v1\t0\t2656\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270372v1\t0\t1650\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270373v1\t0\t1451\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270375v1\t0\t2378\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270371v1\t0\t2805\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270448v1\t0\t7992\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270521v1\t0\t7642\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_GL000195v1\t0\t182896\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_GL000219v1\t0\t179198\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_GL000220v1\t0\t161802\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_GL000224v1\t0\t179693\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270741v1\t0\t157432\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_GL000226v1\t0\t15008\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_GL000213v1\t0\t164239\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270743v1\t0\t210658\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270744v1\t0\t168472\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270745v1\t0\t41891\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270746v1\t0\t66486\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270747v1\t0\t198735\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270748v1\t0\t93321\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270749v1\t0\t158759\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270750v1\t0\t148850\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270751v1\t0\t150742\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270752v1\t0\t27745\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270753v1\t0\t62944\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270754v1\t0\t40191\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270755v1\t0\t36723\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270756v1\t0\t79590\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270757v1\t0\t71251\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_GL000214v1\t0\t137718\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_KI270742v1\t0\t186739\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_GL000216v2\t0\t176608\t0.000000\t0.000082\t0.000000\t0.000000\n+chrUn_GL000218v1\t0\t161147\t0.000000\t0.000082\t0.000000\t0.000000\n+chrX\t0\t156040895\t0.000000\t0.000082\t0.000000\t0.000000\n+chrY\t0\t57227415\t0.000000\t0.000082\t0.000000\t0.000000\n+chrY_KI270740v1_random\t0\t37240\t0.000000\t0.000082\t0.000000\t0.000000\n' |
| b |
| diff -r 000000000000 -r a41d96fc0b20 test-data/atac_out3.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/atac_out3.bedgraph Mon Jul 15 09:43:27 2019 -0400 |
| b |
| b'@@ -0,0 +1,4770 @@\n+# experimental file: atac_test.bam; control file: NA\n+chr\tstart\tend\texperimental\tcontrol\t-log(p)\n+chr1\t0\t248956422\t0.000000\t0.000082\t0.000000\n+chr10\t0\t133797422\t0.000000\t0.000082\t0.000000\n+chr11\t0\t135086622\t0.000000\t0.000082\t0.000000\n+chr11_KI270721v1_random\t0\t100316\t0.000000\t0.000082\t0.000000\n+chr12\t0\t133275309\t0.000000\t0.000082\t0.000000\n+chr13\t0\t114364328\t0.000000\t0.000082\t0.000000\n+chr14\t0\t107043718\t0.000000\t0.000082\t0.000000\n+chr14_GL000009v2_random\t0\t201709\t0.000000\t0.000082\t0.000000\n+chr14_GL000225v1_random\t0\t211173\t0.000000\t0.000082\t0.000000\n+chr14_KI270722v1_random\t0\t194050\t0.000000\t0.000082\t0.000000\n+chr14_GL000194v1_random\t0\t191469\t0.000000\t0.000082\t0.000000\n+chr14_KI270723v1_random\t0\t38115\t0.000000\t0.000082\t0.000000\n+chr14_KI270724v1_random\t0\t39555\t0.000000\t0.000082\t0.000000\n+chr14_KI270725v1_random\t0\t172810\t0.000000\t0.000082\t0.000000\n+chr14_KI270726v1_random\t0\t43739\t0.000000\t0.000082\t0.000000\n+chr15\t0\t101991189\t0.000000\t0.000082\t0.000000\n+chr15_KI270727v1_random\t0\t448248\t0.000000\t0.000082\t0.000000\n+chr16\t0\t90338345\t0.000000\t0.000082\t0.000000\n+chr16_KI270728v1_random\t0\t1872759\t0.000000\t0.000082\t0.000000\n+chr17\t0\t83257441\t0.000000\t0.000082\t0.000000\n+chr17_GL000205v2_random\t0\t185591\t0.000000\t0.000082\t0.000000\n+chr17_KI270729v1_random\t0\t280839\t0.000000\t0.000082\t0.000000\n+chr17_KI270730v1_random\t0\t112551\t0.000000\t0.000082\t0.000000\n+chr18\t0\t80373285\t0.000000\t0.000082\t0.000000\n+chr19\t0\t58617616\t0.000000\t0.000082\t0.000000\n+chr1_KI270706v1_random\t0\t175055\t0.000000\t0.000082\t0.000000\n+chr1_KI270707v1_random\t0\t32032\t0.000000\t0.000082\t0.000000\n+chr1_KI270708v1_random\t0\t127682\t0.000000\t0.000082\t0.000000\n+chr1_KI270709v1_random\t0\t66860\t0.000000\t0.000082\t0.000000\n+chr1_KI270710v1_random\t0\t40176\t0.000000\t0.000082\t0.000000\n+chr1_KI270711v1_random\t0\t42210\t0.000000\t0.000082\t0.000000\n+chr1_KI270712v1_random\t0\t176043\t0.000000\t0.000082\t0.000000\n+chr1_KI270713v1_random\t0\t40745\t0.000000\t0.000082\t0.000000\n+chr1_KI270714v1_random\t0\t41717\t0.000000\t0.000082\t0.000000\n+chr2\t0\t242193529\t0.000000\t0.000082\t0.000000\n+chr20\t0\t64444167\t0.000000\t0.000082\t0.000000\n+chr21\t0\t46709983\t0.000000\t0.000082\t0.000000\n+chr22\t0\t10741211\t0.000000\t0.000082\t0.000000\n+chr22\t10741211\t10741383\t1.000000\t0.000082\t25.087999\n+chr22\t10741383\t10783762\t0.000000\t0.000082\t0.000000\n+chr22\t10783762\t10783951\t1.000000\t0.000082\t25.087999\n+chr22\t10783951\t10941132\t0.000000\t0.000082\t0.000000\n+chr22\t10941132\t10941232\t1.000000\t0.000082\t25.087999\n+chr22\t10941232\t10941258\t0.000000\t0.000082\t0.000000\n+chr22\t10941258\t10941358\t1.000000\t0.000082\t25.087999\n+chr22\t10941358\t11288260\t0.000000\t0.000082\t0.000000\n+chr22\t11288260\t11288400\t1.000000\t0.000082\t25.087999\n+chr22\t11288400\t11294541\t0.000000\t0.000082\t0.000000\n+chr22\t11294541\t11294641\t1.000000\t0.000082\t25.087999\n+chr22\t11294641\t11294678\t0.000000\t0.000082\t0.000000\n+chr22\t11294678\t11294778\t1.000000\t0.000082\t25.087999\n+chr22\t11294778\t11308120\t0.000000\t0.000082\t0.000000\n+chr22\t11308120\t11308220\t1.000000\t0.000082\t25.087999\n+chr22\t11308220\t11308290\t0.000000\t0.000082\t0.000000\n+chr22\t11308290\t11308390\t1.000000\t0.000082\t25.087999\n+chr22\t11308390\t11353133\t0.000000\t0.000082\t0.000000\n+chr22\t11353133\t11353270\t1.000000\t0.000082\t25.087999\n+chr22\t11353270\t11552745\t0.000000\t0.000082\t0.000000\n+chr22\t11552745\t11552929\t1.000000\t0.000082\t25.087999\n+chr22\t11552929\t11968830\t0.000000\t0.000082\t0.000000\n+chr22\t11968830\t11968965\t1.000000\t0.000082\t25.087999\n+chr22\t11968965\t12368335\t0.000000\t0.000082\t0.000000\n+chr22\t12368335\t12368524\t1.000000\t0.000082\t25.087999\n+chr22\t12368524\t12602352\t0.000000\t0.000082\t0.000000\n+chr22\t12602352\t12602487\t1.000000\t0.000082\t25.087999\n+chr22\t12602487\t12604334\t0.000000\t0.000082\t0.000000\n+chr22\t12604334\t12604434\t1.000000\t0.000082\t25.087999\n+chr22\t12604434\t12604536\t0.000000\t0.000082\t0.000000\n+chr22\t12604536\t12604636\t1.000000\t0.000082\t25.087999\n+chr22\t12604636\t12636264\t0.000000\t0.000082\t0.000000\n+chr22\t12636264\t12636400\t1.000000\t0.000082\t25.087999\n+chr22\t12636400\t12721963\t0.000000\t0.000082\t0.000000\n+chr22\t12721963\t12722063\t1.000'..b'0082\t0.000000\n+chrUn_KI270579v1\t0\t31033\t0.000000\t0.000082\t0.000000\n+chrUn_KI270589v1\t0\t44474\t0.000000\t0.000082\t0.000000\n+chrUn_KI270590v1\t0\t4685\t0.000000\t0.000082\t0.000000\n+chrUn_KI270584v1\t0\t4513\t0.000000\t0.000082\t0.000000\n+chrUn_KI270582v1\t0\t6504\t0.000000\t0.000082\t0.000000\n+chrUn_KI270588v1\t0\t6158\t0.000000\t0.000082\t0.000000\n+chrUn_KI270593v1\t0\t3041\t0.000000\t0.000082\t0.000000\n+chrUn_KI270591v1\t0\t5796\t0.000000\t0.000082\t0.000000\n+chrUn_KI270330v1\t0\t1652\t0.000000\t0.000082\t0.000000\n+chrUn_KI270329v1\t0\t1040\t0.000000\t0.000082\t0.000000\n+chrUn_KI270334v1\t0\t1368\t0.000000\t0.000082\t0.000000\n+chrUn_KI270333v1\t0\t2699\t0.000000\t0.000082\t0.000000\n+chrUn_KI270335v1\t0\t1048\t0.000000\t0.000082\t0.000000\n+chrUn_KI270338v1\t0\t1428\t0.000000\t0.000082\t0.000000\n+chrUn_KI270340v1\t0\t1428\t0.000000\t0.000082\t0.000000\n+chrUn_KI270336v1\t0\t1026\t0.000000\t0.000082\t0.000000\n+chrUn_KI270337v1\t0\t1121\t0.000000\t0.000082\t0.000000\n+chrUn_KI270363v1\t0\t1803\t0.000000\t0.000082\t0.000000\n+chrUn_KI270364v1\t0\t2855\t0.000000\t0.000082\t0.000000\n+chrUn_KI270362v1\t0\t3530\t0.000000\t0.000082\t0.000000\n+chrUn_KI270366v1\t0\t8320\t0.000000\t0.000082\t0.000000\n+chrUn_KI270378v1\t0\t1048\t0.000000\t0.000082\t0.000000\n+chrUn_KI270379v1\t0\t1045\t0.000000\t0.000082\t0.000000\n+chrUn_KI270389v1\t0\t1298\t0.000000\t0.000082\t0.000000\n+chrUn_KI270390v1\t0\t2387\t0.000000\t0.000082\t0.000000\n+chrUn_KI270387v1\t0\t1537\t0.000000\t0.000082\t0.000000\n+chrUn_KI270395v1\t0\t1143\t0.000000\t0.000082\t0.000000\n+chrUn_KI270396v1\t0\t1880\t0.000000\t0.000082\t0.000000\n+chrUn_KI270388v1\t0\t1216\t0.000000\t0.000082\t0.000000\n+chrUn_KI270394v1\t0\t970\t0.000000\t0.000082\t0.000000\n+chrUn_KI270386v1\t0\t1788\t0.000000\t0.000082\t0.000000\n+chrUn_KI270391v1\t0\t1484\t0.000000\t0.000082\t0.000000\n+chrUn_KI270383v1\t0\t1750\t0.000000\t0.000082\t0.000000\n+chrUn_KI270393v1\t0\t1308\t0.000000\t0.000082\t0.000000\n+chrUn_KI270384v1\t0\t1658\t0.000000\t0.000082\t0.000000\n+chrUn_KI270392v1\t0\t971\t0.000000\t0.000082\t0.000000\n+chrUn_KI270381v1\t0\t1930\t0.000000\t0.000082\t0.000000\n+chrUn_KI270385v1\t0\t990\t0.000000\t0.000082\t0.000000\n+chrUn_KI270382v1\t0\t4215\t0.000000\t0.000082\t0.000000\n+chrUn_KI270376v1\t0\t1136\t0.000000\t0.000082\t0.000000\n+chrUn_KI270374v1\t0\t2656\t0.000000\t0.000082\t0.000000\n+chrUn_KI270372v1\t0\t1650\t0.000000\t0.000082\t0.000000\n+chrUn_KI270373v1\t0\t1451\t0.000000\t0.000082\t0.000000\n+chrUn_KI270375v1\t0\t2378\t0.000000\t0.000082\t0.000000\n+chrUn_KI270371v1\t0\t2805\t0.000000\t0.000082\t0.000000\n+chrUn_KI270448v1\t0\t7992\t0.000000\t0.000082\t0.000000\n+chrUn_KI270521v1\t0\t7642\t0.000000\t0.000082\t0.000000\n+chrUn_GL000195v1\t0\t182896\t0.000000\t0.000082\t0.000000\n+chrUn_GL000219v1\t0\t179198\t0.000000\t0.000082\t0.000000\n+chrUn_GL000220v1\t0\t161802\t0.000000\t0.000082\t0.000000\n+chrUn_GL000224v1\t0\t179693\t0.000000\t0.000082\t0.000000\n+chrUn_KI270741v1\t0\t157432\t0.000000\t0.000082\t0.000000\n+chrUn_GL000226v1\t0\t15008\t0.000000\t0.000082\t0.000000\n+chrUn_GL000213v1\t0\t164239\t0.000000\t0.000082\t0.000000\n+chrUn_KI270743v1\t0\t210658\t0.000000\t0.000082\t0.000000\n+chrUn_KI270744v1\t0\t168472\t0.000000\t0.000082\t0.000000\n+chrUn_KI270745v1\t0\t41891\t0.000000\t0.000082\t0.000000\n+chrUn_KI270746v1\t0\t66486\t0.000000\t0.000082\t0.000000\n+chrUn_KI270747v1\t0\t198735\t0.000000\t0.000082\t0.000000\n+chrUn_KI270748v1\t0\t93321\t0.000000\t0.000082\t0.000000\n+chrUn_KI270749v1\t0\t158759\t0.000000\t0.000082\t0.000000\n+chrUn_KI270750v1\t0\t148850\t0.000000\t0.000082\t0.000000\n+chrUn_KI270751v1\t0\t150742\t0.000000\t0.000082\t0.000000\n+chrUn_KI270752v1\t0\t27745\t0.000000\t0.000082\t0.000000\n+chrUn_KI270753v1\t0\t62944\t0.000000\t0.000082\t0.000000\n+chrUn_KI270754v1\t0\t40191\t0.000000\t0.000082\t0.000000\n+chrUn_KI270755v1\t0\t36723\t0.000000\t0.000082\t0.000000\n+chrUn_KI270756v1\t0\t79590\t0.000000\t0.000082\t0.000000\n+chrUn_KI270757v1\t0\t71251\t0.000000\t0.000082\t0.000000\n+chrUn_GL000214v1\t0\t137718\t0.000000\t0.000082\t0.000000\n+chrUn_KI270742v1\t0\t186739\t0.000000\t0.000082\t0.000000\n+chrUn_GL000216v2\t0\t176608\t0.000000\t0.000082\t0.000000\n+chrUn_GL000218v1\t0\t161147\t0.000000\t0.000082\t0.000000\n+chrX\t0\t156040895\t0.000000\t0.000082\t0.000000\n+chrY\t0\t57227415\t0.000000\t0.000082\t0.000000\n+chrY_KI270740v1_random\t0\t37240\t0.000000\t0.000082\t0.000000\n' |
| b |
| diff -r 000000000000 -r a41d96fc0b20 test-data/atac_out4.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/atac_out4.bed Mon Jul 15 09:43:27 2019 -0400 |
| b |
| b'@@ -0,0 +1,2160 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BXX:8:2218:2666:9139_1_E_0\n+chr22\t46519094\t46519285\tJ00118:161:H3MCTBBXX:8:2219:2331:10633_1_E_0\n+chr22\t19962007\t19962142\tJ00118:161:H3MCTBBXX:8:2219:7994:4725_1_E_0\n+chr22\t20186208\t20186392\tJ00118:161:H3MCTBBXX:8:2219:18913:2721_1_E_0\n+chr22\t27287282\t27287429\tJ00118:161:H3MCTBBXX:8:2220:1712:37484_1_E_0\n+chr22\t40714541\t40714641\tJ00118:161:H3MCTBBXX:8:2220:4371:9420_1_E_0\n+chr22\t40714689\t40714789\tJ00118:161:H3MCTBBXX:8:2220:4371:9420_1_E_0\n+chr22\t50304431\t50304531\tJ00118:161:H3MCTBBXX:8:2220:6035:14871_1_E_0\n+chr22\t50305220\t50305320\tJ00118:161:H3MCTBBXX:8:2220:6035:14871_1_E_0\n+chr22\t20426024\t20426124\tJ00118:161:H3MCTBBXX:8:2220:10236:5974_1_E_0\n+chr22\t20426269\t20426369\tJ00118:161:H3MCTBBXX:8:2220:10236:5974_1_E_0\n+chr22\t33648515\t33648662\tJ00118:161:H3MCTBBXX:8:2221:7628:4479_1_E_0\n+chr22\t32020254\t32020394\tJ00118:161:H3MCTBBXX:8:2221:12002:42548_1_E_0\n+chr22\t31660982\t31661137\tJ00118:161:H3MCTBBXX:8:2221:14549:1103_1_E_0\n+chr22\t48571099\t48571284\tJ00118:161:H3MCTBBXX:8:2221:16457:45449_1_E_0\n+chr22\t49501144\t49501338\tJ00118:161:H3MCTBBXX:8:2221:28422:1859_1_E_0\n+chr22\t24952506\t24952649\tJ00118:161:H3MCTBBXX:8:2222:8562:27197_1_E_0\n+chr22\t48078533\t48078672\tJ00118:161:H3MCTBBXX:8:2222:8623:18757_1_E_0\n+chr22\t27354151\t27354288\tJ00118:161:H3MCTBBXX:8:2222:27225:18493_1_E_0\n+chr22\t30742301\t30742450\tJ00118:161:H3MCTBBXX:8:2223:17959:2053_1_E_0\n+chr22\t35311931\t35312031\tJ00118:161:H3MCTBBXX:8:2223:19512:40965_1_E_0\n+chr22\t35312135\t35312235\tJ00118:161:H3MCTBBXX:8:2223:19512:40965_1_E_0\n+chr22\t21926565\t21926711\tJ00118:161:H3MCTBBXX:8:2223:22364:4585_1_E_0\n+chr22\t21630025\t21630125\tJ00118:161:H3MCTBBXX:8:2224:20070:28885_1_E_0\n+chr22\t21630166\t21630266\tJ00118:161:H3MCTBBXX:8:2224:20070:28885_1_E_0\n+chr22\t22322145\t22322281\tJ00118:161:H3MCTBBXX:8:2224:20537:47243_1_E_0\n+chr22\t48585839\t48585939\tJ00118:161:H3MCTBBXX:8:2225:4391:12023_1_E_0\n+chr22\t48585966\t48586066\tJ00118:161:H3MCTBBXX:8:2225:4391:12023_1_E_0\n+chr22\t29913948\t29914048\tJ00118:161:H3MCTBBXX:8:2225:26220:16964_1_E_0\n+chr22\t29914235\t29914335\tJ00118:161:H3MCTBBXX:8:2225:26220:16964_1_E_0\n+chr22\t38007101\t38007201\tJ00118:161:H3MCTBBXX:8:2225:26798:30169_1_E_0\n+chr22\t38007275\t38007375\tJ00118:161:H3MCTBBXX:8:2225:26798:30169_1_E_0\n+chr22\t43274079\t43274179\tJ00118:161:H3MCTBBXX:8:2226:7659:5270_1_E_0\n+chr22\t43274612\t43274712\tJ00118:161:H3MCTBBXX:8:2226:7659:5270_1_E_0\n+chr22\t23225902\t23226101\tJ00118:161:H3MCTBBXX:8:2226:9394:4233_1_E_0\n+chr22\t37197882\t37197982\tJ00118:161:H3MCTBBXX:8:2226:13717:11548_1_E_0\n+chr22\t37198069\t37198169\tJ00118:161:H3MCTBBXX:8:2226:13717:11548_1_E_0\n+chr22\t45814291\t45814435\tJ00118:161:H3MCTBBXX:8:2226:18030:3582_1_E_0\n+chr22\t48565077\t48565216\tJ00118:161:H3MCTBBXX:8:2226:18538:16137_1_E_0\n+chr22\t45526915\t45527062\tJ00118:161:H3MCTBBXX:8:2226:27438:4233_1_E_0\n+chr22\t46528099\t46528238\tJ00118:161:H3MCTBBXX:8:2226:31355:18441_1_E_0\n+chr22\t40366267\t40366417\tJ00118:161:H3MCTBBXX:8:2227:3549:30784_1_E_0\n+chr22\t32561322\t32561473\tJ00118:161:H3MCTBBXX:8:2227:11708:48368_1_E_0\n+chr22\t46007935\t46008035\tJ00118:161:H3MCTBBXX:8:2227:11779:2703_1_E_0\n+chr22\t46008092\t46008192\tJ00118:161:H3MCTBBXX:8:2227:11779:2703_1_E_0\n+chr22\t20865972\t20866102\tJ00118:161:H3MCTBBXX:8:2227:13677:8945_1_E_0\n+chr22\t39075096\t39075246\tJ00118:161:H3MCTBBXX:8:2228:12814:32279_1_E_0\n' |
| b |
| diff -r 000000000000 -r a41d96fc0b20 test-data/atac_test.bam |
| b |
| Binary file test-data/atac_test.bam has changed |