| Previous changeset 1:db50f51a2952 (2019-08-17) |
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Commit message:
"planemo upload for repository https://github.com/jsh58/Genrich commit 62a6ec655d7743ce084e45ba02b495e8bd2dc06c" |
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modified:
genrich.xml |
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added:
test-data/CTCF_PE_CTRL_chr22_2.bam test-data/CTCF_PE_ChIP_chr22_2.bam test-data/Pool.bed test-data/Pool.encodepeak test-data/Pool1.bedgraph test-data/Pool2.bedgraph |
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| diff -r db50f51a2952 -r 8353f3cc03db genrich.xml --- a/genrich.xml Sat Aug 17 16:24:04 2019 -0400 +++ b/genrich.xml Thu Aug 29 10:42:38 2019 -0400 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="genrich" name="Genrich" version="0.5+galaxy1"> +<tool id="genrich" name="Genrich" version="0.5+galaxy2"> <description>Detecting sites of genomic enrichment</description> <requirements> <requirement type="package" version="0.5">genrich</requirement> @@ -19,7 +19,7 @@ ## Treatment File(s) #if str($treatment.t_multi_select) == "Yes": - -t ${ ' '.join( [ "'%s'" % $x for $x in $treatment.input_treatment_file] ) } + -t ${ ','.join( [ "'%s'" % $x for $x in $treatment.input_treatment_file] ) } #else -t '$treatment.input_treatment_file' #end if @@ -27,7 +27,7 @@ ## Control File(s) #if str($control.c_select) == "Yes": #if str($control.c_multiple.c_multi_select) == "Yes": - -c ${ ' '.join( [ "'%s'" % $x for $x in $control.c_multiple.input_control_file] ) } + -c ${ ','.join( [ "'%s'" % $x for $x in $control.c_multiple.input_control_file] ) } #else -c '$control.c_multiple.input_control_file' #end if @@ -251,6 +251,21 @@ <output name="out_bedgraph2" ftype="bedgraph" file="CTCF2.bedgraph" compare="contains" lines_diff="1" /> <output name="out_bed" ftype="bed" file="CTCF.bed" /> </test> + <!-- ChIP Test Data for Pooled Data (Replicates)--> + <test expect_num_outputs="4"> + <param name="input_treatment_file" ftype="bam" value="CTCF_PE_ChIP_chr22.bam,CTCF_PE_ChIP_chr22_2.bam" /> + <param name="input_control_file" ftype="bam" value="CTCF_PE_CTRL_chr22.bam,CTCF_PE_CTRL_chr22_2.bam" /> + <param name="c_select" value="Yes" /> + <param name="t_multi_select" value="Yes" /> + <param name="c_multi_select" value="Yes" /> + <param name="bedgraph1" value="True" /> + <param name="bedgraph2" value="True" /> + <param name="bed" value="True" /> + <output name="outfile" ftype="encodepeak" file="Pool.encodepeak" /> + <output name="out_bedgraph1" ftype="bedgraph" file="Pool1.bedgraph" /> + <output name="out_bedgraph2" ftype="bedgraph" file="Pool2.bedgraph" compare="contains" lines_diff="2" /> + <output name="out_bed" ftype="bed" file="Pool.bed" /> + </test> </tests> <help><![CDATA[ |
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| diff -r db50f51a2952 -r 8353f3cc03db test-data/CTCF_PE_CTRL_chr22_2.bam |
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| Binary file test-data/CTCF_PE_CTRL_chr22_2.bam has changed |
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| diff -r db50f51a2952 -r 8353f3cc03db test-data/CTCF_PE_ChIP_chr22_2.bam |
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| Binary file test-data/CTCF_PE_ChIP_chr22_2.bam has changed |
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| diff -r db50f51a2952 -r 8353f3cc03db test-data/Pool.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Pool.bed Thu Aug 29 10:42:38 2019 -0400 |
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| b'@@ -0,0 +1,1910 @@\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+chr'..b'C_1\n+chr22\t21265687\t21266111\tMONK:4:1101:2036:162467#ATCACG_1_C_1\n+chr22\t24796223\t24796573\tMONK:4:1101:2041:13081#ATCACG_1_C_1\n+chr22\t20903546\t20903860\tMONK:4:1101:2043:44900#ATCACG_1_C_1\n+chr22\t44947744\t44948083\tMONK:4:1101:2045:136863#ATCACG_1_C_1\n+chr22\t35636457\t35636824\tMONK:4:1101:2047:115492#ATCACG_1_C_1\n+chr22\t44562366\t44562744\tMONK:4:1101:2048:196819#ATCACG_1_C_1\n+chr22\t24582402\t24582746\tMONK:4:1101:2049:58183#ATCACG_1_C_1\n+chr22\t26010455\t26010720\tMONK:4:1101:2050:5906#ATCACG_1_C_1\n+chr22\t45463711\t45464061\tMONK:4:1101:2054:61445#ATCACG_1_C_1\n+chr22\t39339209\t39339568\tMONK:4:1101:2055:47818#ATCACG_1_C_1\n+chr22\t37702677\t37702998\tMONK:4:1101:2056:18419#ATCACG_1_C_1\n+chr22\t37214433\t37214750\tMONK:4:1101:2058:70645#ATCACG_1_C_1\n+chr22\t28314510\t28314866\tMONK:4:1101:2059:89462#ATCACG_1_C_1\n+chr22\t37825262\t37825575\tMONK:4:1101:2059:196988#ATCACG_1_C_1\n+chr22\t18141593\t18141906\tMONK:4:1101:2060:13739#ATCACG_1_C_1\n+chr22\t39925680\t39926050\tMONK:4:1101:2060:57734#ATCACG_1_C_1\n+chr22\t30580500\t30580828\tMONK:4:1101:2061:170858#ATCACG_1_C_1\n+chr22\t23028992\t23029360\tMONK:4:1101:2064:103362#ATCACG_1_C_1\n+chr22\t23528598\t23528875\tMONK:4:1101:2066:182063#ATCACG_1_C_1\n+chr22\t44874800\t44875183\tMONK:4:1101:2068:7662#ATCACG_1_C_1\n+chr22\t39584484\t39584818\tMONK:4:1101:2068:77978#ATCACG_1_C_1\n+chr22\t33797772\t33798061\tMONK:4:1101:2068:100271#ATCACG_1_C_1\n+chr22\t35986252\t35986607\tMONK:4:1101:2070:23404#ATCACG_1_C_1\n+chr22\t27311920\t27312230\tMONK:4:1101:2070:30134#ATCACG_1_C_1\n+chr22\t36963258\t36963578\tMONK:4:1101:2073:141053#ATCACG_1_C_1\n+chr22\t19307238\t19307559\tMONK:4:1101:2073:146945#ATCACG_1_C_1\n+chr22\t31219645\t31219924\tMONK:4:1101:2074:66425#ATCACG_1_C_1\n+chr22\t19541960\t19542242\tMONK:4:1101:2075:118078#ATCACG_1_C_1\n+chr22\t27264361\t27264647\tMONK:4:1101:2077:158799#ATCACG_1_C_1\n+chr22\t42257620\t42257866\tMONK:4:1101:2077:197509#ATCACG_1_C_1\n+chr22\t35098395\t35098663\tMONK:4:1101:2083:101663#ATCACG_1_C_1\n+chr22\t20919441\t20919738\tMONK:4:1101:2089:170479#ATCACG_1_C_1\n+chr22\t51103700\t51104012\tMONK:4:1101:2091:141368#ATCACG_1_C_1\n+chr22\t40869949\t40870251\tMONK:4:1101:2091:200382#ATCACG_1_C_1\n+chr22\t45587887\t45588179\tMONK:4:1101:2092:30754#ATCACG_1_C_1\n+chr22\t30805512\t30805877\tMONK:4:1101:2099:16909#ATCACG_1_C_1\n+chr22\t44033966\t44034285\tMONK:4:1101:2099:32241#ATCACG_1_C_1\n+chr22\t41128651\t41128939\tMONK:4:1101:2103:85862#ATCACG_1_C_1\n+chr22\t28533601\t28533854\tMONK:4:1101:2106:138815#ATCACG_1_C_1\n+chr22\t22154290\t22154577\tMONK:4:1101:2114:80529#ATCACG_1_C_1\n+chr22\t38039414\t38039729\tMONK:4:1101:2120:28549#ATCACG_1_C_1\n+chr22\t39540350\t39540559\tMONK:4:1101:2121:154878#ATCACG_1_C_1\n+chr22\t20884321\t20884672\tMONK:4:1101:2127:115141#ATCACG_1_C_1\n+chr22\t24551823\t24552160\tMONK:4:1101:2130:172811#ATCACG_1_C_1\n+chr22\t18259249\t18259606\tMONK:4:1101:2132:95793#ATCACG_1_C_1\n+chr22\t25373041\t25373209\tMONK:4:1101:2132:128439#ATCACG_1_C_1\n+chr22\t32529163\t32529537\tMONK:4:1101:2132:137046#ATCACG_1_C_1\n+chr22\t38822667\t38823045\tMONK:4:1101:2134:94771#ATCACG_1_C_1\n+chr22\t26159451\t26159615\tMONK:4:1101:2138:27181#ATCACG_1_C_1\n+chr22\t34441238\t34441585\tMONK:4:1101:2139:139454#ATCACG_1_C_1\n+chr22\t45610815\t45611077\tMONK:4:1101:2139:183067#ATCACG_1_C_1\n+chr22\t39671600\t39671996\tMONK:4:1101:2144:33342#ATCACG_1_C_1\n+chr22\t45926669\t45926955\tMONK:4:1101:2145:111087#ATCACG_1_C_1\n+chr22\t42353807\t42353994\tMONK:4:1101:2147:150414#ATCACG_1_C_1\n+chr22\t24153559\t24153892\tMONK:4:1101:2149:92715#ATCACG_1_C_1\n+chr22\t18633120\t18633461\tMONK:4:1101:2149:117901#ATCACG_1_C_1\n+chr22\t28398677\t28398947\tMONK:4:1101:2154:12577#ATCACG_1_C_1\n+chr22\t21293552\t21293918\tMONK:4:1101:2156:25409#ATCACG_1_C_1\n+chr22\t41276700\t41276988\tMONK:4:1101:2159:7211#ATCACG_1_C_1\n+chr22\t48967117\t48967481\tMONK:4:1101:2167:87699#ATCACG_1_C_1\n+chr22\t35225703\t35226036\tMONK:4:1101:2169:189605#ATCACG_1_C_1\n+chr22\t26683772\t26684132\tMONK:4:1101:2170:100928#ATCACG_1_C_1\n+chr22\t43356750\t43357110\tMONK:4:1101:2172:94564#ATCACG_1_C_1\n+chr22\t42949335\t42949675\tMONK:4:1101:2174:117708#ATCACG_1_C_1\n+chr22\t48493138\t48493460\tMONK:4:1101:2178:193175#ATCACG_1_C_1\n' 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| diff -r db50f51a2952 -r 8353f3cc03db test-data/Pool.encodepeak --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Pool.encodepeak Thu Aug 29 10:42:38 2019 -0400 |
| b |
| b'@@ -0,0 +1,421 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|
| b |
| diff -r db50f51a2952 -r 8353f3cc03db test-data/Pool1.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Pool1.bedgraph Thu Aug 29 10:42:38 2019 -0400 |
| b |
| b'@@ -0,0 +1,1935 @@\n+chr\tstart\tend\t-log(p)_0\t-log(p)_1\t-log(p)_comb\t-log(q)\tsignif\n+chr1\t0\t249250621\t0.000000\t0.000000\t0.000000\t0.000000\n+chr2\t0\t243199373\t0.000000\t0.000000\t0.000000\t0.000000\n+chr3\t0\t198022430\t0.000000\t0.000000\t0.000000\t0.000000\n+chr4\t0\t191154276\t0.000000\t0.000000\t0.000000\t0.000000\n+chr5\t0\t180915260\t0.000000\t0.000000\t0.000000\t0.000000\n+chr6\t0\t171115067\t0.000000\t0.000000\t0.000000\t0.000000\n+chr7\t0\t159138663\t0.000000\t0.000000\t0.000000\t0.000000\n+chr8\t0\t146364022\t0.000000\t0.000000\t0.000000\t0.000000\n+chr9\t0\t141213431\t0.000000\t0.000000\t0.000000\t0.000000\n+chr10\t0\t135534747\t0.000000\t0.000000\t0.000000\t0.000000\n+chr11\t0\t135006516\t0.000000\t0.000000\t0.000000\t0.000000\n+chr12\t0\t133851895\t0.000000\t0.000000\t0.000000\t0.000000\n+chr13\t0\t115169878\t0.000000\t0.000000\t0.000000\t0.000000\n+chr14\t0\t107349540\t0.000000\t0.000000\t0.000000\t0.000000\n+chr15\t0\t102531392\t0.000000\t0.000000\t0.000000\t0.000000\n+chr16\t0\t90354753\t0.000000\t0.000000\t0.000000\t0.000000\n+chr17\t0\t81195210\t0.000000\t0.000000\t0.000000\t0.000000\n+chr18\t0\t78077248\t0.000000\t0.000000\t0.000000\t0.000000\n+chr19\t0\t59128983\t0.000000\t0.000000\t0.000000\t0.000000\n+chr20\t0\t63025520\t0.000000\t0.000000\t0.000000\t0.000000\n+chr21\t0\t48129895\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t0\t16874913\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t16874913\t16875110\t28.826399\t28.826399\t55.526501\t49.916557\t*\n+chr22\t16875110\t17213301\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t17213301\t17213528\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t17213528\t17305939\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t17305939\t17306331\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t17306331\t17331220\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t17331220\t17331528\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t17331528\t17333158\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t17333158\t17333474\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t17333474\t17374212\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t17374212\t17374535\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t17374535\t17377196\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t17377196\t17377428\t28.826399\t28.826399\t55.526501\t49.916557\t*\n+chr22\t17377428\t17529435\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t17529435\t17529809\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t17529809\t17555930\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t17555930\t17556245\t28.826399\t28.826399\t55.526501\t49.916557\t*\n+chr22\t17556245\t17574927\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t17574927\t17575208\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t17575208\t17652822\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t17652822\t17652841\t28.826399\t28.826399\t55.526501\t49.916557\t*\n+chr22\t17652841\t17653093\t32.549095\t32.549095\t62.919518\t56.241673\t*\n+chr22\t17653093\t17653159\t28.826399\t28.826399\t55.526501\t49.916557\t*\n+chr22\t17653159\t17686483\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t17686483\t17686744\t28.826399\t28.826399\t55.526501\t49.916557\t*\n+chr22\t17686744\t17697561\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t17697561\t17697877\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t17697877\t17718259\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t17718259\t17718522\t28.826399\t28.826399\t55.526501\t49.916557\t*\n+chr22\t17718522\t17836468\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t17836468\t17836780\t28.826399\t28.826399\t55.526501\t49.916557\t*\n+chr22\t17836780\t17847348\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t17847348\t17847549\t28.826399\t28.826399\t55.526501\t49.916557\t*\n+chr22\t17847549\t17979862\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t17979862\t17980115\t28.826399\t28.826399\t55.526501\t49.916557\t*\n+chr22\t17980115\t17999764\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t17999764\t17999976\t28.826399\t28.826399\t55.526501\t49.916557\t*\n+chr22\t17999976\t18137643\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t18137643\t18137939\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t18137939\t18141593\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t18141593\t18141906\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t18141906\t18178995\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t18178995\t18179198\t28.826399\t28.826399\t55.526501\t49.916557\t*\n+chr22\t18179198\t182015'..b'50338471\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t50338471\t50354362\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t50354362\t50354742\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t50354742\t50418074\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t50418074\t50418305\t28.826399\t28.826399\t55.526501\t49.916557\t*\n+chr22\t50418305\t50451024\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t50451024\t50451324\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t50451324\t50468615\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t50468615\t50468733\t28.826399\t28.826399\t55.526501\t49.916557\t*\n+chr22\t50468733\t50468871\t32.549095\t32.549095\t62.919518\t56.241673\t*\n+chr22\t50468871\t50468928\t28.826399\t28.826399\t55.526501\t49.916557\t*\n+chr22\t50468928\t50472607\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t50472607\t50472929\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t50472929\t50512931\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t50512931\t50513121\t28.826399\t28.826399\t55.526501\t49.916557\t*\n+chr22\t50513121\t50574751\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t50574751\t50575063\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t50575063\t50628501\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t50628501\t50628741\t28.826399\t28.826399\t55.526501\t49.916557\t*\n+chr22\t50628741\t50630995\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t50630995\t50631224\t28.826399\t28.826399\t55.526501\t49.916557\t*\n+chr22\t50631224\t50645170\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t50645170\t50645459\t28.826399\t28.826399\t55.526501\t49.916557\t*\n+chr22\t50645459\t50658290\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t50658290\t50658656\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t50658656\t50716298\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t50716298\t50716549\t28.826399\t28.826399\t55.526501\t49.916557\t*\n+chr22\t50716549\t50728249\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t50728249\t50728594\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t50728594\t50757826\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t50757826\t50758150\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t50758150\t50769460\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t50769460\t50769676\t28.826399\t28.826399\t55.526501\t49.916557\t*\n+chr22\t50769676\t50802506\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t50802506\t50802827\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t50802827\t50911511\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t50911511\t50911831\t28.826399\t28.826399\t55.526501\t49.916557\t*\n+chr22\t50911831\t50936751\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t50936751\t50936936\t28.826399\t28.826399\t55.526501\t49.916557\t*\n+chr22\t50936936\t50965071\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t50965071\t50965340\t28.826399\t28.826399\t55.526501\t49.916557\t*\n+chr22\t50965340\t50972925\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t50972925\t50973062\t28.826399\t28.826399\t55.526501\t49.916557\t*\n+chr22\t50973062\t50982866\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t50982866\t50983075\t28.826399\t28.826399\t55.526501\t49.916557\t*\n+chr22\t50983075\t51058888\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t51058888\t51059217\t28.826399\t28.826399\t55.526501\t49.916557\t*\n+chr22\t51059217\t51066506\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t51066506\t51066791\t28.826399\t28.826399\t55.526501\t49.916557\t*\n+chr22\t51066791\t51102143\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t51102143\t51102471\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t51102471\t51103700\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t51103700\t51104012\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t51104012\t51130088\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t51130088\t51130096\t28.826399\t28.826399\t55.526501\t49.916557\t*\n+chr22\t51130096\t51130313\t32.549095\t32.549095\t62.919518\t56.241673\t*\n+chr22\t51130313\t51130412\t28.826399\t28.826399\t55.526501\t49.916557\t*\n+chr22\t51130412\t51208525\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t51208525\t51208735\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t51208735\t51213606\t0.000000\t0.000000\t0.000000\t0.000000\n+chr22\t51213606\t51213856\t28.826399\t28.826399\t55.526501\t49.916557\t*\n+chr22\t51213856\t51304566\t0.000000\t0.000000\t0.000000\t0.000000\n+chrX\t0\t155270560\t0.000000\t0.000000\t0.000000\t0.000000\n+chrY\t0\t59373566\t0.000000\t0.000000\t0.000000\t0.000000\n' |
| b |
| diff -r db50f51a2952 -r 8353f3cc03db test-data/Pool2.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Pool2.bedgraph Thu Aug 29 10:42:38 2019 -0400 |
| b |
| b'@@ -0,0 +1,3872 @@\n+# experimental file: CTCF_PE_ChIP_chr22.bam; control file: CTCF_PE_CTRL_chr22.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\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' |