| Next changeset 1:a538bbdae31b (2016-02-18) |
|
Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/metilene commit 090bc9bb5c775600f4727d8729a032b52e78bd05-dirty |
|
added:
metilene.xml test-data/example_S1.bedgraph test-data/example_S2.bedgraph test-data/example_S3.bedgraph test-data/example_S4.bedgraph test-data/example_S5.bedgraph test-data/example_S6.bedgraph test-data/example_S7.bedgraph test-data/example_S8.bedgraph test-data/metilene.out tool_dependencies.xml |
| b |
| diff -r 000000000000 -r 0d988a56e332 metilene.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/metilene.xml Thu Dec 17 17:10:08 2015 -0500 |
| [ |
| @@ -0,0 +1,127 @@ +<?xml version="1.0" encoding="utf-8"?> +<tool id="metilene" name="metilene" version="0.2-4.0"> + <description> + calling differentially methylated regions from bisulfite sequencing data + </description> + <requirements> + <requirement type="package" version="0.2-4">metilene</requirement> + <requirement type="package" version="5.18.1">perl</requirement> + <requirement type="package" version="3.2.1">R</requirement> + <requirement type="package" version="0.9.3">r_ggplot2</requirement> + <requirement type="package" version="2.24">bedtools</requirement> + <requirement type="package" version="8.22">gnu_coreutils</requirement> + </requirements> + <stdio> + <exit_code range=":-1"/> + <exit_code range="1:" /> + </stdio> + <version_command>echo "0.2-4"</version_command> + <command><![CDATA[ + ## preprocessing + ## generate metilene_g1_g2.input from multiple bedgraph files + metilene_input.pl + --in1 $opt_in1 + --in2 $opt_in2 + >/dev/null 2>/dev/null + && + ## metilene main program + metilene + -M $Options.opt_M + -m $Options.opt_m + -d $Options.opt_d + -t 1 + -f 1 + -v $Options.opt_v + metilene_g1_g2.input + >$output_bedlike + 2>/dev/null + && + ## postprocessing + cut -f1-4 $output_bedlike > $output_bedgraph 2>/dev/null + && + ## write to job directory + metilene_output.pl + -q $output_bedlike + -p 0.05 + -o ./metilene >/dev/null 2>/dev/null + ]]></command> + <inputs> + <!-- input bedgraph files 1 --> + <param name="opt_in1" type="data" format="bed,bedgraph" multiple="true" + label="Input group 1" + help="set of sorted bedgraph input profiles of group 1" /> + <!-- input bedgraph files 2 --> + <param name="opt_in2" type="data" format="bed,bedgraph" multiple="true" + label="Input group 2" + help="set of sorted bedgraph input profiles of group 2" /> + + <!-- Advanced parameters (folded) --> + <section name="Options" title="Advanced Options" expanded="False"> + <param name="opt_M" type="integer" value="300" + label="The allowed nt distance between two CpGs within a DMR" + help="-M, --maxdist"/> + + <param name="opt_m" type="integer" value="10" + label="The minimum # of CpGs in a DMR" + help="-m, --mincpgs"/> + + <param name="opt_d" type="float" value="0.1" + label="The minimum mean methylation difference for calling DMRs" + help="-d, --minMethDiff"/> + + <param name="opt_v" type="float" value="0.7" label="Stringency of the valley filter (0.0 - 1.0)" + help="-v, --valley"> + <validator type="in_range" min="0.0" max="1.0" message="Valley filter value must be in [0,1]." /> + </param> + </section> + </inputs> + <outputs> + <!-- finally: for bed-like use format=tabular --> + <data format="tabular" name="output_bedlike" + label="${tool.name} on ${on_string}" /> + <data format="bedgraph" name="output_bedgraph" + label="${tool.name} bedgraph on ${on_string}" /> + <data format="bedgraph" name="output_qval_bedgraph" + label="${tool.name} qval<0.05 bedgraph on ${on_string}" + from_work_dir="metilene_qval.0.05.bedgraph" /> + <data format="pdf" name="output_qval_pdf" + label="${tool.name} qval<0.05 plots on ${on_string}" + from_work_dir="metilene_qval.0.05.pdf" /> + <data format="bedgraph" name="output_qval_out" + label="${tool.name} qval<0.05 out on ${on_string}" + from_work_dir="metilene_qval.0.05.out" /> + </outputs> + <tests> + <test> + <param name="opt_in1" value="example_S1.bedgraph,example_S2.bedgraph,example_S3.bedgraph,example_S4.bedgraph" /> + <param name="opt_in2" value="example_S5.bedgraph,example_S6.bedgraph,example_S7.bedgraph,example_S8.bedgraph" /> + <output name="output_bedlike" file="metilene.out" /> + </test> + </tests> + <help><![CDATA[ +**Fast and sensitive calling of differentially methylated regions +from bisulfite sequencing data** + +Detailed documentation of the stand-alone tool metilene is available at +.. __: http://www.bioinf.uni-leipzig.de/Software/metilene/manual.pdf + +The software metilene is available for download at +.. __: http://www.bioinf.uni-leipzig.de/Software/metilene/ + ]]></help> + + <citations> + <citation type="bibtex">@Article{Juhling_Kretzmer_Bernhart-metil_Fast_and-2015, + author = {Juhling, Frank and Kretzmer, Helene and Bernhart, Stephan + H. and Otto, Christian and Stadler, Peter F. and Hoffmann, + Steve}, + title = {metilene: {Fast} and sensitive calling of differentially + methylated regions from bisulfite sequencing data}, + page = {[Epub ahead of print]}, + journal = {Genome Res}, + year = {2015}, + pmid = {26631489}, + doi = {10.1101/gr.196394.115}, + issn = {1088-9051}, + issn = {1549-5469}}</citation> + </citations> +</tool> |
| b |
| diff -r 000000000000 -r 0d988a56e332 test-data/example_S1.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example_S1.bedgraph Thu Dec 17 17:10:08 2015 -0500 |
| b |
| b'@@ -0,0 +1,10699 @@\n+#chrom\tstart\tend\tS1\n+chr19\t9294488\t9294489\t0.91\n+chr19\t9294489\t9294490\t0.78\n+chr19\t9294492\t9294493\t0.95\n+chr19\t9294493\t9294494\t0.81\n+chr19\t9294500\t9294501\t0.93\n+chr19\t9294501\t9294502\t0.85\n+chr19\t9294505\t9294506\t0.93\n+chr19\t9294582\t9294583\t0.81\n+chr19\t9294589\t9294590\t0.93\n+chr19\t9294590\t9294591\t0.94\n+chr19\t10616344\t10616345\t0.00\n+chr19\t10616373\t10616374\t0.05\n+chr19\t10616385\t10616386\t0.00\n+chr19\t10616399\t10616400\t0.00\n+chr19\t10616400\t10616401\t0.20\n+chr19\t10616420\t10616421\t0.00\n+chr19\t10616421\t10616422\t0.08\n+chr19\t10616457\t10616458\t0.00\n+chr19\t10616471\t10616472\t0.00\n+chr19\t10616479\t10616480\t0.06\n+chr19\t10616490\t10616491\t0.00\n+chr19\t10616505\t10616506\t0.00\n+chr19\t10616518\t10616519\t0.00\n+chr19\t10616610\t10616611\t0.07\n+chr19\t10617230\t10617231\t1.00\n+chr19\t10617839\t10617840\t1.00\n+chr19\t10617867\t10617868\t0.94\n+chr19\t10617872\t10617873\t0.89\n+chr19\t10617899\t10617900\t0.89\n+chr19\t10617930\t10617931\t0.91\n+chr19\t10618135\t10618136\t1.00\n+chr19\t10618148\t10618149\t0.83\n+chr19\t10618207\t10618208\t0.80\n+chr19\t10618794\t10618795\t0.87\n+chr19\t10618815\t10618816\t0.91\n+chr19\t10618836\t10618837\t1.00\n+chr19\t10618843\t10618844\t1.00\n+chr19\t10619205\t10619206\t0.55\n+chr19\t10619225\t10619226\t0.60\n+chr19\t10619248\t10619249\t0.82\n+chr19\t10620129\t10620130\t1.00\n+chr19\t10620161\t10620162\t0.93\n+chr19\t10620219\t10620220\t0.82\n+chr19\t10620220\t10620221\t0.82\n+chr19\t10620268\t10620269\t0.80\n+chr19\t10620723\t10620724\t1.00\n+chr19\t10620731\t10620732\t0.94\n+chr19\t10620743\t10620744\t0.74\n+chr19\t10620770\t10620771\t0.77\n+chr19\t10620956\t10620957\t0.00\n+chr19\t10620986\t10620987\t0.00\n+chr19\t10621042\t10621043\t0.00\n+chr19\t10621079\t10621080\t0.00\n+chr19\t10621091\t10621092\t0.00\n+chr19\t10621106\t10621107\t0.00\n+chr19\t10621107\t10621108\t0.00\n+chr19\t10621116\t10621117\t0.00\n+chr19\t10621117\t10621118\t0.00\n+chr19\t10621128\t10621129\t0.00\n+chr19\t10621129\t10621130\t0.00\n+chr19\t10621150\t10621151\t0.00\n+chr19\t10621168\t10621169\t0.00\n+chr19\t10621169\t10621170\t0.00\n+chr19\t10621184\t10621185\t0.00\n+chr19\t10621202\t10621203\t0.00\n+chr19\t10621228\t10621229\t0.04\n+chr19\t10621231\t10621232\t0.04\n+chr19\t10621242\t10621243\t0.05\n+chr19\t10621525\t10621526\t0.67\n+chr19\t10621846\t10621847\t1.00\n+chr19\t10621884\t10621885\t0.79\n+chr19\t10622139\t10622140\t0.53\n+chr19\t10622140\t10622141\t0.69\n+chr19\t10622179\t10622180\t0.79\n+chr19\t10622183\t10622184\t0.79\n+chr19\t10622242\t10622243\t0.56\n+chr19\t10623789\t10623790\t0.64\n+chr19\t10623970\t10623971\t0.95\n+chr19\t10624001\t10624002\t0.91\n+chr19\t10624047\t10624048\t0.83\n+chr19\t10624073\t10624074\t0.94\n+chr19\t10624122\t10624123\t0.89\n+chr19\t10624246\t10624247\t0.50\n+chr19\t10624282\t10624283\t0.88\n+chr19\t10624311\t10624312\t0.41\n+chr19\t10624322\t10624323\t0.44\n+chr19\t10624476\t10624477\t0.23\n+chr19\t10624483\t10624484\t0.25\n+chr19\t10624503\t10624504\t0.23\n+chr19\t10624521\t10624522\t0.17\n+chr19\t10624525\t10624526\t0.29\n+chr19\t10624526\t10624527\t0.53\n+chr19\t10624540\t10624541\t0.28\n+chr19\t10624541\t10624542\t0.62\n+chr19\t10624558\t10624559\t0.22\n+chr19\t10624559\t10624560\t0.06\n+chr19\t10624573\t10624574\t0.06\n+chr19\t10624574\t10624575\t0.31\n+chr19\t10624576\t10624577\t0.50\n+chr19\t10624578\t10624579\t0.26\n+chr19\t10624586\t10624587\t0.30\n+chr19\t10624587\t10624588\t0.50\n+chr19\t10624593\t10624594\t0.16\n+chr19\t10624594\t10624595\t0.35\n+chr19\t10624598\t10624599\t0.10\n+chr19\t10624599\t10624600\t0.22\n+chr19\t10624603\t10624604\t0.10\n+chr19\t10624604\t10624605\t0.35\n+chr19\t10624625\t10624626\t0.06\n+chr19\t10624626\t10624627\t0.14\n+chr19\t10624638\t10624639\t0.00\n+chr19\t10624641\t10624642\t0.11\n+chr19\t10624642\t10624643\t0.09\n+chr19\t10624651\t10624652\t0.14\n+chr19\t10624664\t10624665\t0.00\n+chr19\t10624666\t10624667\t0.00\n+chr19\t10624670\t10624671\t0.12\n+chr19\t10624673\t10624674\t0.20\n+chr19\t10624691\t10624692\t0.04\n+chr19\t10624702\t10624703\t0.18\n+chr19\t10624713\t10624714\t0.09\n+chr19\t10624717\t10624718\t0.15\n+chr19\t10624731\t10624732\t0.23\n+chr19\t10624739\t10624740\t0.17\n+chr19\t10624741\t10624742\t0.15\n+chr19\t10624746\t10624747\t0.53\n+chr19\t10624753\t10624754\t0.32\n+chr19\t10624755\t10624756\t0.21\n+chr19\t10624766\t10624767\t0.11\n+chr19\t10624822\t10624823\t0.04\n+chr19\t10624848\t10624849\t0.03\n+chr19\t10624850\t10624851\t0.03\n+chr19\t10624853\t10'..b'326\t1.00\n+chr19\t11622676\t11622677\t1.00\n+chr19\t11622772\t11622773\t1.00\n+chr19\t11622803\t11622804\t1.00\n+chr19\t11622824\t11622825\t1.00\n+chr19\t11622832\t11622833\t0.92\n+chr19\t11623375\t11623376\t0.67\n+chr19\t11623514\t11623515\t0.94\n+chr19\t11623863\t11623864\t1.00\n+chr19\t11623913\t11623914\t1.00\n+chr19\t11623914\t11623915\t0.92\n+chr19\t11623958\t11623959\t0.94\n+chr19\t11623980\t11623981\t0.88\n+chr19\t11623991\t11623992\t0.88\n+chr19\t11624012\t11624013\t1.00\n+chr19\t11624042\t11624043\t0.95\n+chr19\t11624071\t11624072\t0.90\n+chr19\t11624506\t11624507\t0.95\n+chr19\t11624521\t11624522\t0.91\n+chr19\t11624598\t11624599\t1.00\n+chr19\t11624618\t11624619\t1.00\n+chr19\t11624762\t11624763\t0.94\n+chr19\t11624766\t11624767\t1.00\n+chr19\t11624780\t11624781\t1.00\n+chr19\t11624788\t11624789\t1.00\n+chr19\t11624789\t11624790\t0.95\n+chr19\t11624821\t11624822\t0.95\n+chr19\t11624822\t11624823\t1.00\n+chr19\t11624827\t11624828\t1.00\n+chr19\t11624828\t11624829\t1.00\n+chr19\t11624831\t11624832\t1.00\n+chr19\t11624832\t11624833\t1.00\n+chr19\t11624841\t11624842\t0.95\n+chr19\t11624842\t11624843\t1.00\n+chr19\t11624856\t11624857\t0.71\n+chr19\t11624857\t11624858\t1.00\n+chr19\t11624871\t11624872\t1.00\n+chr19\t11624872\t11624873\t1.00\n+chr19\t11624881\t11624882\t0.83\n+chr19\t11624882\t11624883\t1.00\n+chr19\t11624895\t11624896\t1.00\n+chr19\t11624896\t11624897\t0.85\n+chr19\t11624947\t11624948\t1.00\n+chr19\t11624948\t11624949\t1.00\n+chr19\t11624955\t11624956\t1.00\n+chr19\t11624999\t11625000\t1.00\n+chr19\t11625016\t11625017\t0.95\n+chr19\t11625025\t11625026\t1.00\n+chr19\t11625091\t11625092\t1.00\n+chr19\t11625525\t11625526\t0.92\n+chr19\t11625532\t11625533\t0.92\n+chr19\t11625986\t11625987\t0.79\n+chr19\t11626010\t11626011\t0.64\n+chr19\t11626018\t11626019\t0.81\n+chr19\t11626062\t11626063\t0.94\n+chr19\t11626074\t11626075\t1.00\n+chr19\t11626107\t11626108\t0.95\n+chr19\t11626138\t11626139\t0.92\n+chr19\t11626152\t11626153\t0.96\n+chr19\t11626159\t11626160\t0.96\n+chr19\t11626163\t11626164\t0.89\n+chr19\t11626307\t11626308\t1.00\n+chr19\t11626310\t11626311\t1.00\n+chr19\t11626510\t11626511\t1.00\n+chr19\t11626688\t11626689\t1.00\n+chr19\t11626697\t11626698\t0.88\n+chr19\t11626801\t11626802\t0.88\n+chr19\t11626802\t11626803\t1.00\n+chr19\t11626831\t11626832\t0.94\n+chr19\t11626890\t11626891\t0.80\n+chr19\t11626891\t11626892\t0.93\n+chr19\t11628279\t11628280\t0.92\n+chr19\t11629051\t11629052\t0.80\n+chr19\t12557735\t12557736\t0.97\n+chr19\t12557743\t12557744\t0.93\n+chr19\t12557780\t12557781\t0.92\n+chr19\t12557797\t12557798\t0.98\n+chr19\t12557813\t12557814\t0.83\n+chr19\t12557837\t12557838\t0.85\n+chr19\t12557857\t12557858\t0.93\n+chr19\t12557860\t12557861\t0.84\n+chr19\t12557861\t12557862\t0.95\n+chr19\t12557868\t12557869\t0.79\n+chr19\t12557869\t12557870\t0.93\n+chr19\t12557872\t12557873\t0.73\n+chr19\t12886714\t12886715\t0.96\n+chr19\t12886722\t12886723\t0.93\n+chr19\t12886839\t12886840\t0.84\n+chr19\t12886847\t12886848\t0.78\n+chr19\t12886851\t12886852\t0.75\n+chr19\t12886881\t12886882\t0.95\n+chr19\t20249178\t20249179\t0.71\n+chr19\t20980035\t20980036\t0.97\n+chr19\t20980043\t20980044\t0.93\n+chr19\t20980160\t20980161\t0.85\n+chr19\t20980168\t20980169\t0.78\n+chr19\t20980172\t20980173\t0.73\n+chr19\t20980202\t20980203\t0.95\n+chr19\t32808847\t32808848\t1.00\n+chr19\t32808851\t32808852\t1.00\n+chr19\t32808858\t32808859\t1.00\n+chr19\t32808872\t32808873\t0.83\n+chr19\t32808892\t32808893\t0.84\n+chr19\t32808903\t32808904\t0.84\n+chr19\t34949320\t34949321\t0.93\n+chr19\t34949324\t34949325\t0.94\n+chr19\t34949325\t34949326\t0.81\n+chr19\t34949333\t34949334\t0.85\n+chr19\t34949337\t34949338\t0.94\n+chr19\t34949414\t34949415\t0.81\n+chr19\t34949421\t34949422\t0.93\n+chr19\t34949422\t34949423\t0.94\n+chr19\t37284441\t37284442\t0.94\n+chr19\t37284471\t37284472\t0.76\n+chr19\t37284475\t37284476\t0.78\n+chr19\t37284483\t37284484\t0.85\n+chr19\t37284600\t37284601\t0.90\n+chr19\t37284608\t37284609\t0.97\n+chr19\t38614049\t38614050\t0.92\n+chr19\t38614057\t38614058\t0.78\n+chr19\t38678212\t38678213\t0.91\n+chr19\t38678216\t38678217\t0.94\n+chr19\t38678224\t38678225\t0.93\n+chr19\t38678228\t38678229\t1.00\n+chr19\t38678248\t38678249\t0.89\n+chr19\t38678272\t38678273\t0.78\n+chr19\t38678273\t38678274\t0.85\n+chr19\t38678288\t38678289\t0.97\n+chr19\t38678289\t38678290\t0.90\n+chr19\t53096176\t53096177\t0.92\n+chr19\t53096184\t53096185\t0.79\n+chr19\t53180250\t53180251\t0.91\n+chr19\t55510145\t55510146\t0.92\n+chr19\t58036654\t58036655\t0.53\n' |
| b |
| diff -r 000000000000 -r 0d988a56e332 test-data/example_S2.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example_S2.bedgraph Thu Dec 17 17:10:08 2015 -0500 |
| b |
| b'@@ -0,0 +1,10699 @@\n+#chrom\tstart\tend\tS2\n+chr19\t9294488\t9294489\t0.92\n+chr19\t9294489\t9294490\t0.82\n+chr19\t9294492\t9294493\t0.91\n+chr19\t9294493\t9294494\t0.71\n+chr19\t9294500\t9294501\t0.96\n+chr19\t9294501\t9294502\t0.78\n+chr19\t9294505\t9294506\t0.90\n+chr19\t9294582\t9294583\t0.84\n+chr19\t9294589\t9294590\t0.90\n+chr19\t9294590\t9294591\t0.91\n+chr19\t10616344\t10616345\t0.00\n+chr19\t10616373\t10616374\t0.04\n+chr19\t10616385\t10616386\t0.00\n+chr19\t10616399\t10616400\t0.00\n+chr19\t10616400\t10616401\t0.06\n+chr19\t10616420\t10616421\t0.00\n+chr19\t10616421\t10616422\t0.00\n+chr19\t10616457\t10616458\t0.00\n+chr19\t10616471\t10616472\t0.00\n+chr19\t10616479\t10616480\t0.06\n+chr19\t10616490\t10616491\t0.00\n+chr19\t10616505\t10616506\t0.00\n+chr19\t10616518\t10616519\t0.00\n+chr19\t10616610\t10616611\t0.05\n+chr19\t10617230\t10617231\t0.94\n+chr19\t10617839\t10617840\t1.00\n+chr19\t10617867\t10617868\t0.92\n+chr19\t10617872\t10617873\t0.85\n+chr19\t10617899\t10617900\t0.79\n+chr19\t10617930\t10617931\t0.92\n+chr19\t10618135\t10618136\t1.00\n+chr19\t10618148\t10618149\t0.94\n+chr19\t10618207\t10618208\t0.88\n+chr19\t10618794\t10618795\t0.80\n+chr19\t10618815\t10618816\t1.00\n+chr19\t10618836\t10618837\t1.00\n+chr19\t10618843\t10618844\t1.00\n+chr19\t10619205\t10619206\t0.58\n+chr19\t10619225\t10619226\t0.24\n+chr19\t10619248\t10619249\t0.82\n+chr19\t10620129\t10620130\t0.90\n+chr19\t10620161\t10620162\t0.85\n+chr19\t10620219\t10620220\t0.93\n+chr19\t10620220\t10620221\t0.70\n+chr19\t10620268\t10620269\t0.67\n+chr19\t10620723\t10620724\t0.80\n+chr19\t10620731\t10620732\t0.67\n+chr19\t10620743\t10620744\t0.60\n+chr19\t10620770\t10620771\t0.75\n+chr19\t10620956\t10620957\t0.00\n+chr19\t10620986\t10620987\t0.00\n+chr19\t10621042\t10621043\t0.00\n+chr19\t10621079\t10621080\t0.00\n+chr19\t10621091\t10621092\t0.00\n+chr19\t10621106\t10621107\t0.00\n+chr19\t10621107\t10621108\t0.00\n+chr19\t10621116\t10621117\t0.00\n+chr19\t10621117\t10621118\t0.00\n+chr19\t10621128\t10621129\t0.00\n+chr19\t10621129\t10621130\t0.00\n+chr19\t10621150\t10621151\t0.00\n+chr19\t10621168\t10621169\t0.00\n+chr19\t10621169\t10621170\t0.00\n+chr19\t10621184\t10621185\t0.00\n+chr19\t10621202\t10621203\t0.00\n+chr19\t10621228\t10621229\t0.15\n+chr19\t10621231\t10621232\t0.00\n+chr19\t10621242\t10621243\t0.00\n+chr19\t10621525\t10621526\t0.36\n+chr19\t10621846\t10621847\t0.87\n+chr19\t10621884\t10621885\t0.72\n+chr19\t10622139\t10622140\t0.43\n+chr19\t10622140\t10622141\t0.76\n+chr19\t10622179\t10622180\t0.79\n+chr19\t10622183\t10622184\t0.89\n+chr19\t10622242\t10622243\t0.25\n+chr19\t10623789\t10623790\t0.39\n+chr19\t10623970\t10623971\t0.79\n+chr19\t10624001\t10624002\t0.92\n+chr19\t10624047\t10624048\t0.94\n+chr19\t10624073\t10624074\t0.90\n+chr19\t10624122\t10624123\t0.96\n+chr19\t10624246\t10624247\t0.39\n+chr19\t10624282\t10624283\t0.79\n+chr19\t10624311\t10624312\t0.52\n+chr19\t10624322\t10624323\t0.35\n+chr19\t10624476\t10624477\t0.23\n+chr19\t10624483\t10624484\t0.29\n+chr19\t10624503\t10624504\t0.20\n+chr19\t10624521\t10624522\t0.31\n+chr19\t10624525\t10624526\t0.35\n+chr19\t10624526\t10624527\t0.41\n+chr19\t10624540\t10624541\t0.35\n+chr19\t10624541\t10624542\t0.41\n+chr19\t10624558\t10624559\t0.50\n+chr19\t10624559\t10624560\t0.21\n+chr19\t10624573\t10624574\t0.08\n+chr19\t10624574\t10624575\t0.24\n+chr19\t10624576\t10624577\t0.46\n+chr19\t10624578\t10624579\t0.24\n+chr19\t10624586\t10624587\t0.46\n+chr19\t10624587\t10624588\t0.36\n+chr19\t10624593\t10624594\t0.35\n+chr19\t10624594\t10624595\t0.21\n+chr19\t10624598\t10624599\t0.21\n+chr19\t10624599\t10624600\t0.50\n+chr19\t10624603\t10624604\t0.39\n+chr19\t10624604\t10624605\t0.43\n+chr19\t10624625\t10624626\t0.28\n+chr19\t10624626\t10624627\t0.08\n+chr19\t10624638\t10624639\t0.15\n+chr19\t10624641\t10624642\t0.18\n+chr19\t10624642\t10624643\t0.00\n+chr19\t10624651\t10624652\t0.13\n+chr19\t10624664\t10624665\t0.00\n+chr19\t10624666\t10624667\t0.00\n+chr19\t10624670\t10624671\t0.17\n+chr19\t10624673\t10624674\t0.17\n+chr19\t10624691\t10624692\t0.04\n+chr19\t10624702\t10624703\t0.26\n+chr19\t10624713\t10624714\t0.16\n+chr19\t10624717\t10624718\t0.20\n+chr19\t10624731\t10624732\t0.26\n+chr19\t10624739\t10624740\t0.09\n+chr19\t10624741\t10624742\t0.10\n+chr19\t10624746\t10624747\t0.33\n+chr19\t10624753\t10624754\t0.26\n+chr19\t10624755\t10624756\t0.06\n+chr19\t10624766\t10624767\t0.15\n+chr19\t10624822\t10624823\t0.14\n+chr19\t10624848\t10624849\t0.05\n+chr19\t10624850\t10624851\t0.05\n+chr19\t10624853\t10'..b'326\t0.94\n+chr19\t11622676\t11622677\t1.00\n+chr19\t11622772\t11622773\t0.93\n+chr19\t11622803\t11622804\t1.00\n+chr19\t11622824\t11622825\t1.00\n+chr19\t11622832\t11622833\t1.00\n+chr19\t11623375\t11623376\t0.53\n+chr19\t11623514\t11623515\t0.95\n+chr19\t11623863\t11623864\t0.94\n+chr19\t11623913\t11623914\t1.00\n+chr19\t11623914\t11623915\t1.00\n+chr19\t11623958\t11623959\t0.93\n+chr19\t11623980\t11623981\t0.90\n+chr19\t11623991\t11623992\t0.91\n+chr19\t11624012\t11624013\t0.95\n+chr19\t11624042\t11624043\t0.95\n+chr19\t11624071\t11624072\t1.00\n+chr19\t11624506\t11624507\t0.87\n+chr19\t11624521\t11624522\t0.94\n+chr19\t11624598\t11624599\t0.93\n+chr19\t11624618\t11624619\t0.87\n+chr19\t11624762\t11624763\t0.92\n+chr19\t11624766\t11624767\t1.00\n+chr19\t11624780\t11624781\t1.00\n+chr19\t11624788\t11624789\t1.00\n+chr19\t11624789\t11624790\t0.94\n+chr19\t11624821\t11624822\t0.94\n+chr19\t11624822\t11624823\t1.00\n+chr19\t11624827\t11624828\t1.00\n+chr19\t11624828\t11624829\t1.00\n+chr19\t11624831\t11624832\t1.00\n+chr19\t11624832\t11624833\t1.00\n+chr19\t11624841\t11624842\t0.94\n+chr19\t11624842\t11624843\t1.00\n+chr19\t11624856\t11624857\t0.69\n+chr19\t11624857\t11624858\t1.00\n+chr19\t11624871\t11624872\t0.93\n+chr19\t11624872\t11624873\t0.89\n+chr19\t11624881\t11624882\t0.79\n+chr19\t11624882\t11624883\t0.95\n+chr19\t11624895\t11624896\t1.00\n+chr19\t11624896\t11624897\t0.88\n+chr19\t11624947\t11624948\t1.00\n+chr19\t11624948\t11624949\t1.00\n+chr19\t11624955\t11624956\t1.00\n+chr19\t11624999\t11625000\t0.95\n+chr19\t11625016\t11625017\t0.95\n+chr19\t11625025\t11625026\t1.00\n+chr19\t11625091\t11625092\t0.89\n+chr19\t11625525\t11625526\t0.92\n+chr19\t11625532\t11625533\t0.90\n+chr19\t11625986\t11625987\t0.67\n+chr19\t11626010\t11626011\t0.63\n+chr19\t11626018\t11626019\t0.70\n+chr19\t11626062\t11626063\t0.85\n+chr19\t11626074\t11626075\t0.79\n+chr19\t11626107\t11626108\t1.00\n+chr19\t11626138\t11626139\t0.89\n+chr19\t11626152\t11626153\t1.00\n+chr19\t11626159\t11626160\t1.00\n+chr19\t11626163\t11626164\t0.88\n+chr19\t11626307\t11626308\t1.00\n+chr19\t11626310\t11626311\t1.00\n+chr19\t11626510\t11626511\t0.91\n+chr19\t11626688\t11626689\t0.85\n+chr19\t11626697\t11626698\t0.79\n+chr19\t11626801\t11626802\t1.00\n+chr19\t11626802\t11626803\t1.00\n+chr19\t11626831\t11626832\t0.94\n+chr19\t11626890\t11626891\t0.93\n+chr19\t11626891\t11626892\t0.86\n+chr19\t11628279\t11628280\t1.00\n+chr19\t11629051\t11629052\t0.92\n+chr19\t12557735\t12557736\t0.92\n+chr19\t12557743\t12557744\t0.92\n+chr19\t12557780\t12557781\t0.88\n+chr19\t12557797\t12557798\t0.98\n+chr19\t12557813\t12557814\t0.87\n+chr19\t12557837\t12557838\t0.80\n+chr19\t12557857\t12557858\t0.93\n+chr19\t12557860\t12557861\t0.83\n+chr19\t12557861\t12557862\t0.98\n+chr19\t12557868\t12557869\t0.68\n+chr19\t12557869\t12557870\t0.90\n+chr19\t12557872\t12557873\t0.82\n+chr19\t12886714\t12886715\t0.90\n+chr19\t12886722\t12886723\t0.90\n+chr19\t12886839\t12886840\t0.82\n+chr19\t12886847\t12886848\t0.68\n+chr19\t12886851\t12886852\t0.81\n+chr19\t12886881\t12886882\t1.00\n+chr19\t20249178\t20249179\t0.74\n+chr19\t20980035\t20980036\t0.92\n+chr19\t20980043\t20980044\t0.92\n+chr19\t20980160\t20980161\t0.84\n+chr19\t20980168\t20980169\t0.70\n+chr19\t20980172\t20980173\t0.80\n+chr19\t20980202\t20980203\t1.00\n+chr19\t32808847\t32808848\t1.00\n+chr19\t32808851\t32808852\t0.82\n+chr19\t32808858\t32808859\t0.89\n+chr19\t32808872\t32808873\t0.88\n+chr19\t32808892\t32808893\t0.83\n+chr19\t32808903\t32808904\t0.90\n+chr19\t34949320\t34949321\t0.93\n+chr19\t34949324\t34949325\t0.91\n+chr19\t34949325\t34949326\t0.68\n+chr19\t34949333\t34949334\t0.78\n+chr19\t34949337\t34949338\t0.93\n+chr19\t34949414\t34949415\t0.84\n+chr19\t34949421\t34949422\t0.90\n+chr19\t34949422\t34949423\t0.91\n+chr19\t37284441\t37284442\t1.00\n+chr19\t37284471\t37284472\t0.81\n+chr19\t37284475\t37284476\t0.68\n+chr19\t37284483\t37284484\t0.83\n+chr19\t37284600\t37284601\t0.91\n+chr19\t37284608\t37284609\t0.93\n+chr19\t38614049\t38614050\t0.88\n+chr19\t38614057\t38614058\t0.82\n+chr19\t38678212\t38678213\t0.89\n+chr19\t38678216\t38678217\t0.92\n+chr19\t38678224\t38678225\t0.95\n+chr19\t38678228\t38678229\t1.00\n+chr19\t38678248\t38678249\t0.84\n+chr19\t38678272\t38678273\t0.92\n+chr19\t38678273\t38678274\t0.83\n+chr19\t38678288\t38678289\t0.92\n+chr19\t38678289\t38678290\t0.81\n+chr19\t53096176\t53096177\t0.88\n+chr19\t53096184\t53096185\t0.82\n+chr19\t53180250\t53180251\t0.85\n+chr19\t55510145\t55510146\t0.87\n+chr19\t58036654\t58036655\t0.54\n' |
| b |
| diff -r 000000000000 -r 0d988a56e332 test-data/example_S3.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example_S3.bedgraph Thu Dec 17 17:10:08 2015 -0500 |
| b |
| b'@@ -0,0 +1,10699 @@\n+#chrom\tstart\tend\tS3\n+chr19\t9294488\t9294489\t0.86\n+chr19\t9294489\t9294490\t0.86\n+chr19\t9294492\t9294493\t0.92\n+chr19\t9294493\t9294494\t0.78\n+chr19\t9294500\t9294501\t0.92\n+chr19\t9294501\t9294502\t0.90\n+chr19\t9294505\t9294506\t0.95\n+chr19\t9294582\t9294583\t0.93\n+chr19\t9294589\t9294590\t0.90\n+chr19\t9294590\t9294591\t0.99\n+chr19\t10616344\t10616345\t0.00\n+chr19\t10616373\t10616374\t0.05\n+chr19\t10616385\t10616386\t0.00\n+chr19\t10616399\t10616400\t0.00\n+chr19\t10616400\t10616401\t0.00\n+chr19\t10616420\t10616421\t0.00\n+chr19\t10616421\t10616422\t0.07\n+chr19\t10616457\t10616458\t0.00\n+chr19\t10616471\t10616472\t0.00\n+chr19\t10616479\t10616480\t0.05\n+chr19\t10616490\t10616491\t0.00\n+chr19\t10616505\t10616506\t0.00\n+chr19\t10616518\t10616519\t0.00\n+chr19\t10616610\t10616611\t0.09\n+chr19\t10617230\t10617231\t1.00\n+chr19\t10617839\t10617840\t1.00\n+chr19\t10617867\t10617868\t0.92\n+chr19\t10617872\t10617873\t0.85\n+chr19\t10617899\t10617900\t0.85\n+chr19\t10617930\t10617931\t1.00\n+chr19\t10618135\t10618136\t1.00\n+chr19\t10618148\t10618149\t1.00\n+chr19\t10618207\t10618208\t0.93\n+chr19\t10618794\t10618795\t0.83\n+chr19\t10618815\t10618816\t1.00\n+chr19\t10618836\t10618837\t1.00\n+chr19\t10618843\t10618844\t1.00\n+chr19\t10619205\t10619206\t0.50\n+chr19\t10619225\t10619226\t0.46\n+chr19\t10619248\t10619249\t0.64\n+chr19\t10620129\t10620130\t1.00\n+chr19\t10620161\t10620162\t0.92\n+chr19\t10620219\t10620220\t0.92\n+chr19\t10620220\t10620221\t0.80\n+chr19\t10620268\t10620269\t0.88\n+chr19\t10620723\t10620724\t0.93\n+chr19\t10620731\t10620732\t0.86\n+chr19\t10620743\t10620744\t0.71\n+chr19\t10620770\t10620771\t0.62\n+chr19\t10620956\t10620957\t0.00\n+chr19\t10620986\t10620987\t0.00\n+chr19\t10621042\t10621043\t0.00\n+chr19\t10621079\t10621080\t0.00\n+chr19\t10621091\t10621092\t0.00\n+chr19\t10621106\t10621107\t0.00\n+chr19\t10621107\t10621108\t0.00\n+chr19\t10621116\t10621117\t0.00\n+chr19\t10621117\t10621118\t0.00\n+chr19\t10621128\t10621129\t0.00\n+chr19\t10621129\t10621130\t0.00\n+chr19\t10621150\t10621151\t0.00\n+chr19\t10621168\t10621169\t0.00\n+chr19\t10621169\t10621170\t0.00\n+chr19\t10621184\t10621185\t0.00\n+chr19\t10621202\t10621203\t0.00\n+chr19\t10621228\t10621229\t0.07\n+chr19\t10621231\t10621232\t0.08\n+chr19\t10621242\t10621243\t0.08\n+chr19\t10621525\t10621526\t0.64\n+chr19\t10621846\t10621847\t0.80\n+chr19\t10621884\t10621885\t0.77\n+chr19\t10622139\t10622140\t0.44\n+chr19\t10622140\t10622141\t0.76\n+chr19\t10622179\t10622180\t0.67\n+chr19\t10622183\t10622184\t0.83\n+chr19\t10622242\t10622243\t0.38\n+chr19\t10623789\t10623790\t0.29\n+chr19\t10623970\t10623971\t0.93\n+chr19\t10624001\t10624002\t0.83\n+chr19\t10624047\t10624048\t0.62\n+chr19\t10624073\t10624074\t0.87\n+chr19\t10624122\t10624123\t1.00\n+chr19\t10624246\t10624247\t0.31\n+chr19\t10624282\t10624283\t1.00\n+chr19\t10624311\t10624312\t0.75\n+chr19\t10624322\t10624323\t0.44\n+chr19\t10624476\t10624477\t0.54\n+chr19\t10624483\t10624484\t0.42\n+chr19\t10624503\t10624504\t0.25\n+chr19\t10624521\t10624522\t0.46\n+chr19\t10624525\t10624526\t0.47\n+chr19\t10624526\t10624527\t0.47\n+chr19\t10624540\t10624541\t0.42\n+chr19\t10624541\t10624542\t0.62\n+chr19\t10624558\t10624559\t0.33\n+chr19\t10624559\t10624560\t0.20\n+chr19\t10624573\t10624574\t0.15\n+chr19\t10624574\t10624575\t0.31\n+chr19\t10624576\t10624577\t0.45\n+chr19\t10624578\t10624579\t0.30\n+chr19\t10624586\t10624587\t0.33\n+chr19\t10624587\t10624588\t0.44\n+chr19\t10624593\t10624594\t0.24\n+chr19\t10624594\t10624595\t0.16\n+chr19\t10624598\t10624599\t0.29\n+chr19\t10624599\t10624600\t0.59\n+chr19\t10624603\t10624604\t0.29\n+chr19\t10624604\t10624605\t0.28\n+chr19\t10624625\t10624626\t0.20\n+chr19\t10624626\t10624627\t0.07\n+chr19\t10624638\t10624639\t0.07\n+chr19\t10624641\t10624642\t0.24\n+chr19\t10624642\t10624643\t0.08\n+chr19\t10624651\t10624652\t0.19\n+chr19\t10624664\t10624665\t0.00\n+chr19\t10624666\t10624667\t0.00\n+chr19\t10624670\t10624671\t0.12\n+chr19\t10624673\t10624674\t0.12\n+chr19\t10624691\t10624692\t0.04\n+chr19\t10624702\t10624703\t0.18\n+chr19\t10624713\t10624714\t0.07\n+chr19\t10624717\t10624718\t0.11\n+chr19\t10624731\t10624732\t0.25\n+chr19\t10624739\t10624740\t0.13\n+chr19\t10624741\t10624742\t0.19\n+chr19\t10624746\t10624747\t0.36\n+chr19\t10624753\t10624754\t0.30\n+chr19\t10624755\t10624756\t0.26\n+chr19\t10624766\t10624767\t0.11\n+chr19\t10624822\t10624823\t0.05\n+chr19\t10624848\t10624849\t0.04\n+chr19\t10624850\t10624851\t0.04\n+chr19\t10624853\t10'..b'326\t1.00\n+chr19\t11622676\t11622677\t1.00\n+chr19\t11622772\t11622773\t1.00\n+chr19\t11622803\t11622804\t1.00\n+chr19\t11622824\t11622825\t1.00\n+chr19\t11622832\t11622833\t1.00\n+chr19\t11623375\t11623376\t0.75\n+chr19\t11623514\t11623515\t0.80\n+chr19\t11623863\t11623864\t1.00\n+chr19\t11623913\t11623914\t1.00\n+chr19\t11623914\t11623915\t1.00\n+chr19\t11623958\t11623959\t0.95\n+chr19\t11623980\t11623981\t0.95\n+chr19\t11623991\t11623992\t0.95\n+chr19\t11624012\t11624013\t1.00\n+chr19\t11624042\t11624043\t0.94\n+chr19\t11624071\t11624072\t0.95\n+chr19\t11624506\t11624507\t0.93\n+chr19\t11624521\t11624522\t1.00\n+chr19\t11624598\t11624599\t0.86\n+chr19\t11624618\t11624619\t0.92\n+chr19\t11624762\t11624763\t0.90\n+chr19\t11624766\t11624767\t1.00\n+chr19\t11624780\t11624781\t1.00\n+chr19\t11624788\t11624789\t1.00\n+chr19\t11624789\t11624790\t0.77\n+chr19\t11624821\t11624822\t0.93\n+chr19\t11624822\t11624823\t1.00\n+chr19\t11624827\t11624828\t1.00\n+chr19\t11624828\t11624829\t1.00\n+chr19\t11624831\t11624832\t1.00\n+chr19\t11624832\t11624833\t0.94\n+chr19\t11624841\t11624842\t0.90\n+chr19\t11624842\t11624843\t1.00\n+chr19\t11624856\t11624857\t0.78\n+chr19\t11624857\t11624858\t0.94\n+chr19\t11624871\t11624872\t0.95\n+chr19\t11624872\t11624873\t1.00\n+chr19\t11624881\t11624882\t0.80\n+chr19\t11624882\t11624883\t1.00\n+chr19\t11624895\t11624896\t0.95\n+chr19\t11624896\t11624897\t0.86\n+chr19\t11624947\t11624948\t1.00\n+chr19\t11624948\t11624949\t1.00\n+chr19\t11624955\t11624956\t1.00\n+chr19\t11624999\t11625000\t1.00\n+chr19\t11625016\t11625017\t0.94\n+chr19\t11625025\t11625026\t1.00\n+chr19\t11625091\t11625092\t0.90\n+chr19\t11625525\t11625526\t0.79\n+chr19\t11625532\t11625533\t0.93\n+chr19\t11625986\t11625987\t0.75\n+chr19\t11626010\t11626011\t0.72\n+chr19\t11626018\t11626019\t0.76\n+chr19\t11626062\t11626063\t0.70\n+chr19\t11626074\t11626075\t0.92\n+chr19\t11626107\t11626108\t1.00\n+chr19\t11626138\t11626139\t1.00\n+chr19\t11626152\t11626153\t0.89\n+chr19\t11626159\t11626160\t0.94\n+chr19\t11626163\t11626164\t0.94\n+chr19\t11626307\t11626308\t1.00\n+chr19\t11626310\t11626311\t1.00\n+chr19\t11626510\t11626511\t1.00\n+chr19\t11626688\t11626689\t0.86\n+chr19\t11626697\t11626698\t0.79\n+chr19\t11626801\t11626802\t0.92\n+chr19\t11626802\t11626803\t0.92\n+chr19\t11626831\t11626832\t0.88\n+chr19\t11626890\t11626891\t0.92\n+chr19\t11626891\t11626892\t1.00\n+chr19\t11628279\t11628280\t1.00\n+chr19\t11629051\t11629052\t0.91\n+chr19\t12557735\t12557736\t0.95\n+chr19\t12557743\t12557744\t0.93\n+chr19\t12557780\t12557781\t0.92\n+chr19\t12557797\t12557798\t0.94\n+chr19\t12557813\t12557814\t0.94\n+chr19\t12557837\t12557838\t0.86\n+chr19\t12557857\t12557858\t0.96\n+chr19\t12557860\t12557861\t0.88\n+chr19\t12557861\t12557862\t0.94\n+chr19\t12557868\t12557869\t0.76\n+chr19\t12557869\t12557870\t0.88\n+chr19\t12557872\t12557873\t0.83\n+chr19\t12886714\t12886715\t0.95\n+chr19\t12886722\t12886723\t0.93\n+chr19\t12886839\t12886840\t0.88\n+chr19\t12886847\t12886848\t0.75\n+chr19\t12886851\t12886852\t0.80\n+chr19\t12886881\t12886882\t0.87\n+chr19\t20249178\t20249179\t0.71\n+chr19\t20980035\t20980036\t0.95\n+chr19\t20980043\t20980044\t0.93\n+chr19\t20980160\t20980161\t0.89\n+chr19\t20980168\t20980169\t0.76\n+chr19\t20980172\t20980173\t0.83\n+chr19\t20980202\t20980203\t0.87\n+chr19\t32808847\t32808848\t1.00\n+chr19\t32808851\t32808852\t0.86\n+chr19\t32808858\t32808859\t0.80\n+chr19\t32808872\t32808873\t0.87\n+chr19\t32808892\t32808893\t0.87\n+chr19\t32808903\t32808904\t0.70\n+chr19\t34949320\t34949321\t0.88\n+chr19\t34949324\t34949325\t0.89\n+chr19\t34949325\t34949326\t0.78\n+chr19\t34949333\t34949334\t0.90\n+chr19\t34949337\t34949338\t0.96\n+chr19\t34949414\t34949415\t0.93\n+chr19\t34949421\t34949422\t0.90\n+chr19\t34949422\t34949423\t0.99\n+chr19\t37284441\t37284442\t0.86\n+chr19\t37284471\t37284472\t0.84\n+chr19\t37284475\t37284476\t0.77\n+chr19\t37284483\t37284484\t0.89\n+chr19\t37284600\t37284601\t0.93\n+chr19\t37284608\t37284609\t0.95\n+chr19\t38614049\t38614050\t0.94\n+chr19\t38614057\t38614058\t0.83\n+chr19\t38678212\t38678213\t0.87\n+chr19\t38678216\t38678217\t0.89\n+chr19\t38678224\t38678225\t0.91\n+chr19\t38678228\t38678229\t0.96\n+chr19\t38678248\t38678249\t0.85\n+chr19\t38678272\t38678273\t0.85\n+chr19\t38678273\t38678274\t0.89\n+chr19\t38678288\t38678289\t0.90\n+chr19\t38678289\t38678290\t0.92\n+chr19\t53096176\t53096177\t0.89\n+chr19\t53096184\t53096185\t0.79\n+chr19\t53180250\t53180251\t0.93\n+chr19\t55510145\t55510146\t0.88\n+chr19\t58036654\t58036655\t0.49\n' |
| b |
| diff -r 000000000000 -r 0d988a56e332 test-data/example_S4.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example_S4.bedgraph Thu Dec 17 17:10:08 2015 -0500 |
| b |
| b'@@ -0,0 +1,10699 @@\n+#chrom\tstart\tend\tS4\n+chr19\t9294488\t9294489\t0.94\n+chr19\t9294489\t9294490\t0.80\n+chr19\t9294492\t9294493\t0.89\n+chr19\t9294493\t9294494\t0.84\n+chr19\t9294500\t9294501\t0.95\n+chr19\t9294501\t9294502\t0.84\n+chr19\t9294505\t9294506\t0.92\n+chr19\t9294582\t9294583\t0.90\n+chr19\t9294589\t9294590\t0.94\n+chr19\t9294590\t9294591\t0.94\n+chr19\t10616344\t10616345\t0.00\n+chr19\t10616373\t10616374\t0.07\n+chr19\t10616385\t10616386\t0.00\n+chr19\t10616399\t10616400\t0.04\n+chr19\t10616400\t10616401\t0.00\n+chr19\t10616420\t10616421\t0.00\n+chr19\t10616421\t10616422\t0.00\n+chr19\t10616457\t10616458\t0.00\n+chr19\t10616471\t10616472\t0.00\n+chr19\t10616479\t10616480\t0.04\n+chr19\t10616490\t10616491\t0.00\n+chr19\t10616505\t10616506\t0.00\n+chr19\t10616518\t10616519\t0.00\n+chr19\t10616610\t10616611\t0.06\n+chr19\t10617230\t10617231\t1.00\n+chr19\t10617839\t10617840\t0.90\n+chr19\t10617867\t10617868\t0.87\n+chr19\t10617872\t10617873\t0.86\n+chr19\t10617899\t10617900\t0.76\n+chr19\t10617930\t10617931\t0.83\n+chr19\t10618135\t10618136\t1.00\n+chr19\t10618148\t10618149\t0.90\n+chr19\t10618207\t10618208\t0.89\n+chr19\t10618794\t10618795\t0.78\n+chr19\t10618815\t10618816\t1.00\n+chr19\t10618836\t10618837\t0.93\n+chr19\t10618843\t10618844\t0.94\n+chr19\t10619205\t10619206\t0.36\n+chr19\t10619225\t10619226\t0.54\n+chr19\t10619248\t10619249\t0.87\n+chr19\t10620129\t10620130\t0.75\n+chr19\t10620161\t10620162\t0.94\n+chr19\t10620219\t10620220\t0.92\n+chr19\t10620220\t10620221\t0.75\n+chr19\t10620268\t10620269\t0.67\n+chr19\t10620723\t10620724\t0.89\n+chr19\t10620731\t10620732\t0.75\n+chr19\t10620743\t10620744\t0.53\n+chr19\t10620770\t10620771\t0.62\n+chr19\t10620956\t10620957\t0.00\n+chr19\t10620986\t10620987\t0.00\n+chr19\t10621042\t10621043\t0.16\n+chr19\t10621079\t10621080\t0.00\n+chr19\t10621091\t10621092\t0.00\n+chr19\t10621106\t10621107\t0.00\n+chr19\t10621107\t10621108\t0.00\n+chr19\t10621116\t10621117\t0.00\n+chr19\t10621117\t10621118\t0.00\n+chr19\t10621128\t10621129\t0.00\n+chr19\t10621129\t10621130\t0.00\n+chr19\t10621150\t10621151\t0.00\n+chr19\t10621168\t10621169\t0.05\n+chr19\t10621169\t10621170\t0.00\n+chr19\t10621184\t10621185\t0.00\n+chr19\t10621202\t10621203\t0.00\n+chr19\t10621228\t10621229\t0.05\n+chr19\t10621231\t10621232\t0.00\n+chr19\t10621242\t10621243\t0.00\n+chr19\t10621525\t10621526\t0.64\n+chr19\t10621846\t10621847\t0.92\n+chr19\t10621884\t10621885\t0.77\n+chr19\t10622139\t10622140\t0.47\n+chr19\t10622140\t10622141\t0.75\n+chr19\t10622179\t10622180\t0.79\n+chr19\t10622183\t10622184\t0.74\n+chr19\t10622242\t10622243\t0.44\n+chr19\t10623789\t10623790\t0.55\n+chr19\t10623970\t10623971\t0.82\n+chr19\t10624001\t10624002\t0.90\n+chr19\t10624047\t10624048\t0.75\n+chr19\t10624073\t10624074\t0.92\n+chr19\t10624122\t10624123\t0.90\n+chr19\t10624246\t10624247\t0.33\n+chr19\t10624282\t10624283\t0.91\n+chr19\t10624311\t10624312\t0.47\n+chr19\t10624322\t10624323\t0.60\n+chr19\t10624476\t10624477\t0.33\n+chr19\t10624483\t10624484\t0.14\n+chr19\t10624503\t10624504\t0.33\n+chr19\t10624521\t10624522\t0.44\n+chr19\t10624525\t10624526\t0.47\n+chr19\t10624526\t10624527\t0.29\n+chr19\t10624540\t10624541\t0.42\n+chr19\t10624541\t10624542\t0.69\n+chr19\t10624558\t10624559\t0.38\n+chr19\t10624559\t10624560\t0.50\n+chr19\t10624573\t10624574\t0.36\n+chr19\t10624574\t10624575\t0.20\n+chr19\t10624576\t10624577\t0.57\n+chr19\t10624578\t10624579\t0.41\n+chr19\t10624586\t10624587\t0.35\n+chr19\t10624587\t10624588\t0.38\n+chr19\t10624593\t10624594\t0.24\n+chr19\t10624594\t10624595\t0.29\n+chr19\t10624598\t10624599\t0.23\n+chr19\t10624599\t10624600\t0.43\n+chr19\t10624603\t10624604\t0.35\n+chr19\t10624604\t10624605\t0.36\n+chr19\t10624625\t10624626\t0.27\n+chr19\t10624626\t10624627\t0.17\n+chr19\t10624638\t10624639\t0.10\n+chr19\t10624641\t10624642\t0.33\n+chr19\t10624642\t10624643\t0.08\n+chr19\t10624651\t10624652\t0.28\n+chr19\t10624664\t10624665\t0.20\n+chr19\t10624666\t10624667\t0.12\n+chr19\t10624670\t10624671\t0.22\n+chr19\t10624673\t10624674\t0.19\n+chr19\t10624691\t10624692\t0.18\n+chr19\t10624702\t10624703\t0.32\n+chr19\t10624713\t10624714\t0.26\n+chr19\t10624717\t10624718\t0.33\n+chr19\t10624731\t10624732\t0.32\n+chr19\t10624739\t10624740\t0.19\n+chr19\t10624741\t10624742\t0.28\n+chr19\t10624746\t10624747\t0.37\n+chr19\t10624753\t10624754\t0.27\n+chr19\t10624755\t10624756\t0.20\n+chr19\t10624766\t10624767\t0.32\n+chr19\t10624822\t10624823\t0.09\n+chr19\t10624848\t10624849\t0.10\n+chr19\t10624850\t10624851\t0.10\n+chr19\t10624853\t10'..b'326\t1.00\n+chr19\t11622676\t11622677\t0.79\n+chr19\t11622772\t11622773\t1.00\n+chr19\t11622803\t11622804\t1.00\n+chr19\t11622824\t11622825\t0.93\n+chr19\t11622832\t11622833\t1.00\n+chr19\t11623375\t11623376\t0.75\n+chr19\t11623514\t11623515\t0.80\n+chr19\t11623863\t11623864\t1.00\n+chr19\t11623913\t11623914\t1.00\n+chr19\t11623914\t11623915\t1.00\n+chr19\t11623958\t11623959\t0.92\n+chr19\t11623980\t11623981\t0.82\n+chr19\t11623991\t11623992\t0.92\n+chr19\t11624012\t11624013\t1.00\n+chr19\t11624042\t11624043\t0.94\n+chr19\t11624071\t11624072\t1.00\n+chr19\t11624506\t11624507\t0.92\n+chr19\t11624521\t11624522\t1.00\n+chr19\t11624598\t11624599\t1.00\n+chr19\t11624618\t11624619\t1.00\n+chr19\t11624762\t11624763\t0.86\n+chr19\t11624766\t11624767\t1.00\n+chr19\t11624780\t11624781\t0.94\n+chr19\t11624788\t11624789\t1.00\n+chr19\t11624789\t11624790\t0.89\n+chr19\t11624821\t11624822\t0.90\n+chr19\t11624822\t11624823\t1.00\n+chr19\t11624827\t11624828\t1.00\n+chr19\t11624828\t11624829\t0.96\n+chr19\t11624831\t11624832\t1.00\n+chr19\t11624832\t11624833\t1.00\n+chr19\t11624841\t11624842\t0.91\n+chr19\t11624842\t11624843\t0.96\n+chr19\t11624856\t11624857\t0.71\n+chr19\t11624857\t11624858\t0.92\n+chr19\t11624871\t11624872\t1.00\n+chr19\t11624872\t11624873\t1.00\n+chr19\t11624881\t11624882\t0.83\n+chr19\t11624882\t11624883\t1.00\n+chr19\t11624895\t11624896\t0.96\n+chr19\t11624896\t11624897\t0.91\n+chr19\t11624947\t11624948\t0.92\n+chr19\t11624948\t11624949\t1.00\n+chr19\t11624955\t11624956\t1.00\n+chr19\t11624999\t11625000\t0.96\n+chr19\t11625016\t11625017\t0.96\n+chr19\t11625025\t11625026\t1.00\n+chr19\t11625091\t11625092\t0.95\n+chr19\t11625525\t11625526\t0.80\n+chr19\t11625532\t11625533\t0.89\n+chr19\t11625986\t11625987\t0.85\n+chr19\t11626010\t11626011\t0.54\n+chr19\t11626018\t11626019\t0.85\n+chr19\t11626062\t11626063\t0.80\n+chr19\t11626074\t11626075\t0.92\n+chr19\t11626107\t11626108\t1.00\n+chr19\t11626138\t11626139\t1.00\n+chr19\t11626152\t11626153\t1.00\n+chr19\t11626159\t11626160\t0.94\n+chr19\t11626163\t11626164\t0.94\n+chr19\t11626307\t11626308\t0.82\n+chr19\t11626310\t11626311\t1.00\n+chr19\t11626510\t11626511\t1.00\n+chr19\t11626688\t11626689\t1.00\n+chr19\t11626697\t11626698\t0.89\n+chr19\t11626801\t11626802\t0.90\n+chr19\t11626802\t11626803\t0.80\n+chr19\t11626831\t11626832\t0.96\n+chr19\t11626890\t11626891\t0.96\n+chr19\t11626891\t11626892\t0.88\n+chr19\t11628279\t11628280\t0.95\n+chr19\t11629051\t11629052\t0.85\n+chr19\t12557735\t12557736\t0.98\n+chr19\t12557743\t12557744\t0.92\n+chr19\t12557780\t12557781\t0.97\n+chr19\t12557797\t12557798\t0.91\n+chr19\t12557813\t12557814\t0.90\n+chr19\t12557837\t12557838\t0.86\n+chr19\t12557857\t12557858\t0.92\n+chr19\t12557860\t12557861\t0.86\n+chr19\t12557861\t12557862\t0.96\n+chr19\t12557868\t12557869\t0.73\n+chr19\t12557869\t12557870\t0.93\n+chr19\t12557872\t12557873\t0.71\n+chr19\t12886714\t12886715\t0.98\n+chr19\t12886722\t12886723\t0.92\n+chr19\t12886839\t12886840\t0.86\n+chr19\t12886847\t12886848\t0.72\n+chr19\t12886851\t12886852\t0.68\n+chr19\t12886881\t12886882\t0.94\n+chr19\t20249178\t20249179\t0.74\n+chr19\t20980035\t20980036\t0.98\n+chr19\t20980043\t20980044\t0.92\n+chr19\t20980160\t20980161\t0.88\n+chr19\t20980168\t20980169\t0.75\n+chr19\t20980172\t20980173\t0.69\n+chr19\t20980202\t20980203\t0.93\n+chr19\t32808847\t32808848\t1.00\n+chr19\t32808851\t32808852\t1.00\n+chr19\t32808858\t32808859\t0.88\n+chr19\t32808872\t32808873\t0.88\n+chr19\t32808892\t32808893\t0.71\n+chr19\t32808903\t32808904\t0.67\n+chr19\t34949320\t34949321\t0.92\n+chr19\t34949324\t34949325\t0.89\n+chr19\t34949325\t34949326\t0.82\n+chr19\t34949333\t34949334\t0.84\n+chr19\t34949337\t34949338\t0.94\n+chr19\t34949414\t34949415\t0.90\n+chr19\t34949421\t34949422\t0.94\n+chr19\t34949422\t34949423\t0.94\n+chr19\t37284441\t37284442\t0.93\n+chr19\t37284471\t37284472\t0.67\n+chr19\t37284475\t37284476\t0.71\n+chr19\t37284483\t37284484\t0.89\n+chr19\t37284600\t37284601\t0.92\n+chr19\t37284608\t37284609\t0.98\n+chr19\t38614049\t38614050\t0.87\n+chr19\t38614057\t38614058\t0.89\n+chr19\t38678212\t38678213\t0.88\n+chr19\t38678216\t38678217\t0.86\n+chr19\t38678224\t38678225\t0.88\n+chr19\t38678228\t38678229\t0.96\n+chr19\t38678248\t38678249\t0.86\n+chr19\t38678272\t38678273\t0.84\n+chr19\t38678273\t38678274\t0.81\n+chr19\t38678288\t38678289\t0.90\n+chr19\t38678289\t38678290\t0.85\n+chr19\t53096176\t53096177\t0.84\n+chr19\t53096184\t53096185\t0.86\n+chr19\t53180250\t53180251\t0.88\n+chr19\t55510145\t55510146\t0.86\n+chr19\t58036654\t58036655\t0.61\n' |
| b |
| diff -r 000000000000 -r 0d988a56e332 test-data/example_S5.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example_S5.bedgraph Thu Dec 17 17:10:08 2015 -0500 |
| b |
| b'@@ -0,0 +1,10699 @@\n+#chrom\tstart\tend\tS5\n+chr19\t9294488\t9294489\t0.93\n+chr19\t9294489\t9294490\t0.79\n+chr19\t9294492\t9294493\t0.97\n+chr19\t9294493\t9294494\t0.62\n+chr19\t9294500\t9294501\t0.94\n+chr19\t9294501\t9294502\t0.75\n+chr19\t9294505\t9294506\t0.90\n+chr19\t9294582\t9294583\t0.84\n+chr19\t9294589\t9294590\t0.79\n+chr19\t9294590\t9294591\t0.91\n+chr19\t10616344\t10616345\t0.00\n+chr19\t10616373\t10616374\t0.00\n+chr19\t10616385\t10616386\t0.09\n+chr19\t10616399\t10616400\t0.15\n+chr19\t10616400\t10616401\t0.00\n+chr19\t10616420\t10616421\t0.08\n+chr19\t10616421\t10616422\t0.07\n+chr19\t10616457\t10616458\t0.00\n+chr19\t10616471\t10616472\t0.00\n+chr19\t10616479\t10616480\t0.00\n+chr19\t10616490\t10616491\t0.00\n+chr19\t10616505\t10616506\t0.00\n+chr19\t10616518\t10616519\t0.00\n+chr19\t10616610\t10616611\t0.00\n+chr19\t10617230\t10617231\t0.94\n+chr19\t10617839\t10617840\t0.64\n+chr19\t10617867\t10617868\t0.47\n+chr19\t10617872\t10617873\t0.67\n+chr19\t10617899\t10617900\t0.31\n+chr19\t10617930\t10617931\t0.14\n+chr19\t10618135\t10618136\t0.53\n+chr19\t10618148\t10618149\t0.68\n+chr19\t10618207\t10618208\t0.95\n+chr19\t10618794\t10618795\t0.67\n+chr19\t10618815\t10618816\t0.94\n+chr19\t10618836\t10618837\t0.93\n+chr19\t10618843\t10618844\t0.71\n+chr19\t10619205\t10619206\t0.08\n+chr19\t10619225\t10619226\t0.15\n+chr19\t10619248\t10619249\t1.00\n+chr19\t10620129\t10620130\t0.27\n+chr19\t10620161\t10620162\t0.27\n+chr19\t10620219\t10620220\t0.50\n+chr19\t10620220\t10620221\t0.60\n+chr19\t10620268\t10620269\t0.92\n+chr19\t10620723\t10620724\t0.36\n+chr19\t10620731\t10620732\t0.17\n+chr19\t10620743\t10620744\t0.12\n+chr19\t10620770\t10620771\t0.00\n+chr19\t10620956\t10620957\t0.00\n+chr19\t10620986\t10620987\t0.00\n+chr19\t10621042\t10621043\t0.08\n+chr19\t10621079\t10621080\t0.00\n+chr19\t10621091\t10621092\t0.00\n+chr19\t10621106\t10621107\t0.00\n+chr19\t10621107\t10621108\t0.00\n+chr19\t10621116\t10621117\t0.00\n+chr19\t10621117\t10621118\t0.00\n+chr19\t10621128\t10621129\t0.00\n+chr19\t10621129\t10621130\t0.00\n+chr19\t10621150\t10621151\t0.00\n+chr19\t10621168\t10621169\t0.00\n+chr19\t10621169\t10621170\t0.00\n+chr19\t10621184\t10621185\t0.04\n+chr19\t10621202\t10621203\t0.00\n+chr19\t10621228\t10621229\t0.00\n+chr19\t10621231\t10621232\t0.05\n+chr19\t10621242\t10621243\t0.06\n+chr19\t10621525\t10621526\t0.12\n+chr19\t10621846\t10621847\t0.89\n+chr19\t10621884\t10621885\t0.22\n+chr19\t10622139\t10622140\t0.15\n+chr19\t10622140\t10622141\t0.11\n+chr19\t10622179\t10622180\t0.38\n+chr19\t10622183\t10622184\t0.73\n+chr19\t10622242\t10622243\t0.00\n+chr19\t10623789\t10623790\t0.00\n+chr19\t10623970\t10623971\t0.90\n+chr19\t10624001\t10624002\t0.88\n+chr19\t10624047\t10624048\t0.62\n+chr19\t10624073\t10624074\t0.95\n+chr19\t10624122\t10624123\t0.96\n+chr19\t10624246\t10624247\t0.20\n+chr19\t10624282\t10624283\t0.70\n+chr19\t10624311\t10624312\t0.23\n+chr19\t10624322\t10624323\t0.26\n+chr19\t10624476\t10624477\t0.50\n+chr19\t10624483\t10624484\t0.27\n+chr19\t10624503\t10624504\t0.87\n+chr19\t10624521\t10624522\t0.92\n+chr19\t10624525\t10624526\t0.92\n+chr19\t10624526\t10624527\t0.87\n+chr19\t10624540\t10624541\t0.80\n+chr19\t10624541\t10624542\t0.88\n+chr19\t10624558\t10624559\t0.93\n+chr19\t10624559\t10624560\t0.94\n+chr19\t10624573\t10624574\t1.00\n+chr19\t10624574\t10624575\t0.93\n+chr19\t10624576\t10624577\t1.00\n+chr19\t10624578\t10624579\t0.93\n+chr19\t10624586\t10624587\t1.00\n+chr19\t10624587\t10624588\t1.00\n+chr19\t10624593\t10624594\t1.00\n+chr19\t10624594\t10624595\t0.86\n+chr19\t10624598\t10624599\t0.81\n+chr19\t10624599\t10624600\t0.93\n+chr19\t10624603\t10624604\t1.00\n+chr19\t10624604\t10624605\t0.69\n+chr19\t10624625\t10624626\t0.83\n+chr19\t10624626\t10624627\t0.62\n+chr19\t10624638\t10624639\t0.88\n+chr19\t10624641\t10624642\t0.87\n+chr19\t10624642\t10624643\t0.55\n+chr19\t10624651\t10624652\t0.67\n+chr19\t10624664\t10624665\t0.87\n+chr19\t10624666\t10624667\t0.53\n+chr19\t10624670\t10624671\t0.88\n+chr19\t10624673\t10624674\t0.81\n+chr19\t10624691\t10624692\t0.38\n+chr19\t10624702\t10624703\t0.82\n+chr19\t10624713\t10624714\t0.64\n+chr19\t10624717\t10624718\t0.69\n+chr19\t10624731\t10624732\t0.56\n+chr19\t10624739\t10624740\t0.60\n+chr19\t10624741\t10624742\t0.60\n+chr19\t10624746\t10624747\t0.62\n+chr19\t10624753\t10624754\t0.50\n+chr19\t10624755\t10624756\t0.33\n+chr19\t10624766\t10624767\t0.45\n+chr19\t10624822\t10624823\t0.04\n+chr19\t10624848\t10624849\t0.05\n+chr19\t10624850\t10624851\t0.13\n+chr19\t10624853\t10'..b'326\t0.87\n+chr19\t11622676\t11622677\t0.67\n+chr19\t11622772\t11622773\t0.83\n+chr19\t11622803\t11622804\t1.00\n+chr19\t11622824\t11622825\t0.86\n+chr19\t11622832\t11622833\t1.00\n+chr19\t11623375\t11623376\t0.69\n+chr19\t11623514\t11623515\t0.73\n+chr19\t11623863\t11623864\t0.95\n+chr19\t11623913\t11623914\t0.86\n+chr19\t11623914\t11623915\t0.87\n+chr19\t11623958\t11623959\t0.95\n+chr19\t11623980\t11623981\t0.94\n+chr19\t11623991\t11623992\t0.96\n+chr19\t11624012\t11624013\t0.95\n+chr19\t11624042\t11624043\t0.84\n+chr19\t11624071\t11624072\t0.96\n+chr19\t11624506\t11624507\t0.88\n+chr19\t11624521\t11624522\t0.55\n+chr19\t11624598\t11624599\t0.92\n+chr19\t11624618\t11624619\t1.00\n+chr19\t11624762\t11624763\t0.92\n+chr19\t11624766\t11624767\t1.00\n+chr19\t11624780\t11624781\t1.00\n+chr19\t11624788\t11624789\t1.00\n+chr19\t11624789\t11624790\t1.00\n+chr19\t11624821\t11624822\t0.95\n+chr19\t11624822\t11624823\t1.00\n+chr19\t11624827\t11624828\t0.89\n+chr19\t11624828\t11624829\t1.00\n+chr19\t11624831\t11624832\t0.67\n+chr19\t11624832\t11624833\t0.50\n+chr19\t11624841\t11624842\t0.82\n+chr19\t11624842\t11624843\t1.00\n+chr19\t11624856\t11624857\t0.94\n+chr19\t11624857\t11624858\t0.85\n+chr19\t11624871\t11624872\t1.00\n+chr19\t11624872\t11624873\t0.88\n+chr19\t11624881\t11624882\t1.00\n+chr19\t11624882\t11624883\t0.88\n+chr19\t11624895\t11624896\t0.87\n+chr19\t11624896\t11624897\t1.00\n+chr19\t11624947\t11624948\t1.00\n+chr19\t11624948\t11624949\t1.00\n+chr19\t11624955\t11624956\t1.00\n+chr19\t11624999\t11625000\t0.93\n+chr19\t11625016\t11625017\t0.91\n+chr19\t11625025\t11625026\t1.00\n+chr19\t11625091\t11625092\t1.00\n+chr19\t11625525\t11625526\t0.88\n+chr19\t11625532\t11625533\t0.88\n+chr19\t11625986\t11625987\t0.75\n+chr19\t11626010\t11626011\t0.86\n+chr19\t11626018\t11626019\t0.76\n+chr19\t11626062\t11626063\t0.90\n+chr19\t11626074\t11626075\t0.95\n+chr19\t11626107\t11626108\t1.00\n+chr19\t11626138\t11626139\t1.00\n+chr19\t11626152\t11626153\t1.00\n+chr19\t11626159\t11626160\t1.00\n+chr19\t11626163\t11626164\t1.00\n+chr19\t11626307\t11626308\t0.85\n+chr19\t11626310\t11626311\t1.00\n+chr19\t11626510\t11626511\t0.42\n+chr19\t11626688\t11626689\t0.93\n+chr19\t11626697\t11626698\t0.79\n+chr19\t11626801\t11626802\t0.88\n+chr19\t11626802\t11626803\t0.88\n+chr19\t11626831\t11626832\t0.92\n+chr19\t11626890\t11626891\t0.56\n+chr19\t11626891\t11626892\t0.50\n+chr19\t11628279\t11628280\t0.89\n+chr19\t11629051\t11629052\t0.90\n+chr19\t12557735\t12557736\t1.00\n+chr19\t12557743\t12557744\t0.90\n+chr19\t12557780\t12557781\t0.93\n+chr19\t12557797\t12557798\t0.91\n+chr19\t12557813\t12557814\t0.73\n+chr19\t12557837\t12557838\t0.65\n+chr19\t12557857\t12557858\t0.91\n+chr19\t12557860\t12557861\t0.76\n+chr19\t12557861\t12557862\t0.91\n+chr19\t12557868\t12557869\t0.66\n+chr19\t12557869\t12557870\t0.96\n+chr19\t12557872\t12557873\t0.72\n+chr19\t12886714\t12886715\t1.00\n+chr19\t12886722\t12886723\t0.90\n+chr19\t12886839\t12886840\t0.76\n+chr19\t12886847\t12886848\t0.64\n+chr19\t12886851\t12886852\t0.74\n+chr19\t12886881\t12886882\t0.82\n+chr19\t20249178\t20249179\t0.89\n+chr19\t20980035\t20980036\t1.00\n+chr19\t20980043\t20980044\t0.90\n+chr19\t20980160\t20980161\t0.77\n+chr19\t20980168\t20980169\t0.63\n+chr19\t20980172\t20980173\t0.72\n+chr19\t20980202\t20980203\t0.82\n+chr19\t32808847\t32808848\t1.00\n+chr19\t32808851\t32808852\t0.95\n+chr19\t32808858\t32808859\t0.88\n+chr19\t32808872\t32808873\t0.96\n+chr19\t32808892\t32808893\t0.71\n+chr19\t32808903\t32808904\t0.88\n+chr19\t34949320\t34949321\t0.93\n+chr19\t34949324\t34949325\t0.98\n+chr19\t34949325\t34949326\t0.61\n+chr19\t34949333\t34949334\t0.74\n+chr19\t34949337\t34949338\t0.88\n+chr19\t34949414\t34949415\t0.84\n+chr19\t34949421\t34949422\t0.81\n+chr19\t34949422\t34949423\t0.91\n+chr19\t37284441\t37284442\t0.79\n+chr19\t37284471\t37284472\t0.78\n+chr19\t37284475\t37284476\t0.65\n+chr19\t37284483\t37284484\t0.79\n+chr19\t37284600\t37284601\t0.89\n+chr19\t37284608\t37284609\t1.00\n+chr19\t38614049\t38614050\t0.86\n+chr19\t38614057\t38614058\t0.67\n+chr19\t38678212\t38678213\t0.89\n+chr19\t38678216\t38678217\t0.94\n+chr19\t38678224\t38678225\t0.91\n+chr19\t38678228\t38678229\t0.94\n+chr19\t38678248\t38678249\t0.74\n+chr19\t38678272\t38678273\t0.74\n+chr19\t38678273\t38678274\t0.65\n+chr19\t38678288\t38678289\t0.89\n+chr19\t38678289\t38678290\t0.85\n+chr19\t53096176\t53096177\t0.88\n+chr19\t53096184\t53096185\t0.71\n+chr19\t53180250\t53180251\t0.87\n+chr19\t55510145\t55510146\t0.87\n+chr19\t58036654\t58036655\t0.68\n' |
| b |
| diff -r 000000000000 -r 0d988a56e332 test-data/example_S6.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example_S6.bedgraph Thu Dec 17 17:10:08 2015 -0500 |
| b |
| b'@@ -0,0 +1,10699 @@\n+#chrom\tstart\tend\tS6\n+chr19\t9294488\t9294489\t0.89\n+chr19\t9294489\t9294490\t0.77\n+chr19\t9294492\t9294493\t1.00\n+chr19\t9294493\t9294494\t0.67\n+chr19\t9294500\t9294501\t0.97\n+chr19\t9294501\t9294502\t0.88\n+chr19\t9294505\t9294506\t0.85\n+chr19\t9294582\t9294583\t0.85\n+chr19\t9294589\t9294590\t0.88\n+chr19\t9294590\t9294591\t0.95\n+chr19\t10616344\t10616345\t0.00\n+chr19\t10616373\t10616374\t0.00\n+chr19\t10616385\t10616386\t0.15\n+chr19\t10616399\t10616400\t0.00\n+chr19\t10616400\t10616401\t0.09\n+chr19\t10616420\t10616421\t0.05\n+chr19\t10616421\t10616422\t0.08\n+chr19\t10616457\t10616458\t0.00\n+chr19\t10616471\t10616472\t0.00\n+chr19\t10616479\t10616480\t0.00\n+chr19\t10616490\t10616491\t0.00\n+chr19\t10616505\t10616506\t0.00\n+chr19\t10616518\t10616519\t0.00\n+chr19\t10616610\t10616611\t0.20\n+chr19\t10617230\t10617231\t0.88\n+chr19\t10617839\t10617840\t0.78\n+chr19\t10617867\t10617868\t0.86\n+chr19\t10617872\t10617873\t0.79\n+chr19\t10617899\t10617900\t0.53\n+chr19\t10617930\t10617931\t0.45\n+chr19\t10618135\t10618136\t0.83\n+chr19\t10618148\t10618149\t0.88\n+chr19\t10618207\t10618208\t0.94\n+chr19\t10618794\t10618795\t0.90\n+chr19\t10618815\t10618816\t0.96\n+chr19\t10618836\t10618837\t1.00\n+chr19\t10618843\t10618844\t0.96\n+chr19\t10619205\t10619206\t0.06\n+chr19\t10619225\t10619226\t0.82\n+chr19\t10619248\t10619249\t1.00\n+chr19\t10620129\t10620130\t0.55\n+chr19\t10620161\t10620162\t0.92\n+chr19\t10620219\t10620220\t1.00\n+chr19\t10620220\t10620221\t0.87\n+chr19\t10620268\t10620269\t0.83\n+chr19\t10620723\t10620724\t0.65\n+chr19\t10620731\t10620732\t0.69\n+chr19\t10620743\t10620744\t0.22\n+chr19\t10620770\t10620771\t0.21\n+chr19\t10620956\t10620957\t0.00\n+chr19\t10620986\t10620987\t0.00\n+chr19\t10621042\t10621043\t0.04\n+chr19\t10621079\t10621080\t0.00\n+chr19\t10621091\t10621092\t0.00\n+chr19\t10621106\t10621107\t0.00\n+chr19\t10621107\t10621108\t0.00\n+chr19\t10621116\t10621117\t0.00\n+chr19\t10621117\t10621118\t0.00\n+chr19\t10621128\t10621129\t0.00\n+chr19\t10621129\t10621130\t0.00\n+chr19\t10621150\t10621151\t0.00\n+chr19\t10621168\t10621169\t0.00\n+chr19\t10621169\t10621170\t0.00\n+chr19\t10621184\t10621185\t0.04\n+chr19\t10621202\t10621203\t0.00\n+chr19\t10621228\t10621229\t0.00\n+chr19\t10621231\t10621232\t0.05\n+chr19\t10621242\t10621243\t0.17\n+chr19\t10621525\t10621526\t0.53\n+chr19\t10621846\t10621847\t0.94\n+chr19\t10621884\t10621885\t0.62\n+chr19\t10622139\t10622140\t0.30\n+chr19\t10622140\t10622141\t0.33\n+chr19\t10622179\t10622180\t0.47\n+chr19\t10622183\t10622184\t0.67\n+chr19\t10622242\t10622243\t0.12\n+chr19\t10623789\t10623790\t0.07\n+chr19\t10623970\t10623971\t0.83\n+chr19\t10624001\t10624002\t0.90\n+chr19\t10624047\t10624048\t0.84\n+chr19\t10624073\t10624074\t1.00\n+chr19\t10624122\t10624123\t0.95\n+chr19\t10624246\t10624247\t0.76\n+chr19\t10624282\t10624283\t1.00\n+chr19\t10624311\t10624312\t0.78\n+chr19\t10624322\t10624323\t0.47\n+chr19\t10624476\t10624477\t0.53\n+chr19\t10624483\t10624484\t0.13\n+chr19\t10624503\t10624504\t0.47\n+chr19\t10624521\t10624522\t0.78\n+chr19\t10624525\t10624526\t0.82\n+chr19\t10624526\t10624527\t0.87\n+chr19\t10624540\t10624541\t0.50\n+chr19\t10624541\t10624542\t0.87\n+chr19\t10624558\t10624559\t0.88\n+chr19\t10624559\t10624560\t0.81\n+chr19\t10624573\t10624574\t0.95\n+chr19\t10624574\t10624575\t0.94\n+chr19\t10624576\t10624577\t1.00\n+chr19\t10624578\t10624579\t0.95\n+chr19\t10624586\t10624587\t1.00\n+chr19\t10624587\t10624588\t0.93\n+chr19\t10624593\t10624594\t0.95\n+chr19\t10624594\t10624595\t0.87\n+chr19\t10624598\t10624599\t0.83\n+chr19\t10624599\t10624600\t0.93\n+chr19\t10624603\t10624604\t1.00\n+chr19\t10624604\t10624605\t0.81\n+chr19\t10624625\t10624626\t0.78\n+chr19\t10624626\t10624627\t0.79\n+chr19\t10624638\t10624639\t0.59\n+chr19\t10624641\t10624642\t0.44\n+chr19\t10624642\t10624643\t0.18\n+chr19\t10624651\t10624652\t0.68\n+chr19\t10624664\t10624665\t0.88\n+chr19\t10624666\t10624667\t0.60\n+chr19\t10624670\t10624671\t0.71\n+chr19\t10624673\t10624674\t0.75\n+chr19\t10624691\t10624692\t0.32\n+chr19\t10624702\t10624703\t0.58\n+chr19\t10624713\t10624714\t0.28\n+chr19\t10624717\t10624718\t0.85\n+chr19\t10624731\t10624732\t0.33\n+chr19\t10624739\t10624740\t0.20\n+chr19\t10624741\t10624742\t0.76\n+chr19\t10624746\t10624747\t0.62\n+chr19\t10624753\t10624754\t0.22\n+chr19\t10624755\t10624756\t0.08\n+chr19\t10624766\t10624767\t0.19\n+chr19\t10624822\t10624823\t0.03\n+chr19\t10624848\t10624849\t0.00\n+chr19\t10624850\t10624851\t0.00\n+chr19\t10624853\t10'..b'326\t0.59\n+chr19\t11622676\t11622677\t0.83\n+chr19\t11622772\t11622773\t1.00\n+chr19\t11622803\t11622804\t1.00\n+chr19\t11622824\t11622825\t0.87\n+chr19\t11622832\t11622833\t0.77\n+chr19\t11623375\t11623376\t0.45\n+chr19\t11623514\t11623515\t0.55\n+chr19\t11623863\t11623864\t0.95\n+chr19\t11623913\t11623914\t0.95\n+chr19\t11623914\t11623915\t0.95\n+chr19\t11623958\t11623959\t1.00\n+chr19\t11623980\t11623981\t1.00\n+chr19\t11623991\t11623992\t0.96\n+chr19\t11624012\t11624013\t1.00\n+chr19\t11624042\t11624043\t0.38\n+chr19\t11624071\t11624072\t0.93\n+chr19\t11624506\t11624507\t0.95\n+chr19\t11624521\t11624522\t0.71\n+chr19\t11624598\t11624599\t1.00\n+chr19\t11624618\t11624619\t1.00\n+chr19\t11624762\t11624763\t1.00\n+chr19\t11624766\t11624767\t1.00\n+chr19\t11624780\t11624781\t1.00\n+chr19\t11624788\t11624789\t0.88\n+chr19\t11624789\t11624790\t0.96\n+chr19\t11624821\t11624822\t0.94\n+chr19\t11624822\t11624823\t1.00\n+chr19\t11624827\t11624828\t0.94\n+chr19\t11624828\t11624829\t0.96\n+chr19\t11624831\t11624832\t0.94\n+chr19\t11624832\t11624833\t0.96\n+chr19\t11624841\t11624842\t0.94\n+chr19\t11624842\t11624843\t1.00\n+chr19\t11624856\t11624857\t1.00\n+chr19\t11624857\t11624858\t0.93\n+chr19\t11624871\t11624872\t0.94\n+chr19\t11624872\t11624873\t0.96\n+chr19\t11624881\t11624882\t1.00\n+chr19\t11624882\t11624883\t0.96\n+chr19\t11624895\t11624896\t0.81\n+chr19\t11624896\t11624897\t0.96\n+chr19\t11624947\t11624948\t1.00\n+chr19\t11624948\t11624949\t1.00\n+chr19\t11624955\t11624956\t1.00\n+chr19\t11624999\t11625000\t0.67\n+chr19\t11625016\t11625017\t0.50\n+chr19\t11625025\t11625026\t0.95\n+chr19\t11625091\t11625092\t0.96\n+chr19\t11625525\t11625526\t1.00\n+chr19\t11625532\t11625533\t0.88\n+chr19\t11625986\t11625987\t0.75\n+chr19\t11626010\t11626011\t0.72\n+chr19\t11626018\t11626019\t0.53\n+chr19\t11626062\t11626063\t0.74\n+chr19\t11626074\t11626075\t0.83\n+chr19\t11626107\t11626108\t0.86\n+chr19\t11626138\t11626139\t0.94\n+chr19\t11626152\t11626153\t0.86\n+chr19\t11626159\t11626160\t1.00\n+chr19\t11626163\t11626164\t1.00\n+chr19\t11626307\t11626308\t0.96\n+chr19\t11626310\t11626311\t1.00\n+chr19\t11626510\t11626511\t0.36\n+chr19\t11626688\t11626689\t1.00\n+chr19\t11626697\t11626698\t0.93\n+chr19\t11626801\t11626802\t0.85\n+chr19\t11626802\t11626803\t0.93\n+chr19\t11626831\t11626832\t0.85\n+chr19\t11626890\t11626891\t0.55\n+chr19\t11626891\t11626892\t0.48\n+chr19\t11628279\t11628280\t0.92\n+chr19\t11629051\t11629052\t0.86\n+chr19\t12557735\t12557736\t1.00\n+chr19\t12557743\t12557744\t0.92\n+chr19\t12557780\t12557781\t0.81\n+chr19\t12557797\t12557798\t0.94\n+chr19\t12557813\t12557814\t0.66\n+chr19\t12557837\t12557838\t0.76\n+chr19\t12557857\t12557858\t0.95\n+chr19\t12557860\t12557861\t0.87\n+chr19\t12557861\t12557862\t0.95\n+chr19\t12557868\t12557869\t0.73\n+chr19\t12557869\t12557870\t0.96\n+chr19\t12557872\t12557873\t0.77\n+chr19\t12886714\t12886715\t1.00\n+chr19\t12886722\t12886723\t0.92\n+chr19\t12886839\t12886840\t0.86\n+chr19\t12886847\t12886848\t0.74\n+chr19\t12886851\t12886852\t0.77\n+chr19\t12886881\t12886882\t0.91\n+chr19\t20249178\t20249179\t0.74\n+chr19\t20980035\t20980036\t1.00\n+chr19\t20980043\t20980044\t0.92\n+chr19\t20980160\t20980161\t0.87\n+chr19\t20980168\t20980169\t0.73\n+chr19\t20980172\t20980173\t0.79\n+chr19\t20980202\t20980203\t0.91\n+chr19\t32808847\t32808848\t1.00\n+chr19\t32808851\t32808852\t0.97\n+chr19\t32808858\t32808859\t0.75\n+chr19\t32808872\t32808873\t0.83\n+chr19\t32808892\t32808893\t0.67\n+chr19\t32808903\t32808904\t0.70\n+chr19\t34949320\t34949321\t0.88\n+chr19\t34949324\t34949325\t1.00\n+chr19\t34949325\t34949326\t0.71\n+chr19\t34949333\t34949334\t0.83\n+chr19\t34949337\t34949338\t0.83\n+chr19\t34949414\t34949415\t0.85\n+chr19\t34949421\t34949422\t0.87\n+chr19\t34949422\t34949423\t0.95\n+chr19\t37284441\t37284442\t0.91\n+chr19\t37284471\t37284472\t0.78\n+chr19\t37284475\t37284476\t0.75\n+chr19\t37284483\t37284484\t0.89\n+chr19\t37284600\t37284601\t0.93\n+chr19\t37284608\t37284609\t1.00\n+chr19\t38614049\t38614050\t0.71\n+chr19\t38614057\t38614058\t0.75\n+chr19\t38678212\t38678213\t0.96\n+chr19\t38678216\t38678217\t0.93\n+chr19\t38678224\t38678225\t0.96\n+chr19\t38678228\t38678229\t0.96\n+chr19\t38678248\t38678249\t0.93\n+chr19\t38678272\t38678273\t0.92\n+chr19\t38678273\t38678274\t0.64\n+chr19\t38678288\t38678289\t1.00\n+chr19\t38678289\t38678290\t0.76\n+chr19\t53096176\t53096177\t0.74\n+chr19\t53096184\t53096185\t0.71\n+chr19\t53180250\t53180251\t0.69\n+chr19\t55510145\t55510146\t0.73\n+chr19\t58036654\t58036655\t0.53\n' |
| b |
| diff -r 000000000000 -r 0d988a56e332 test-data/example_S7.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example_S7.bedgraph Thu Dec 17 17:10:08 2015 -0500 |
| b |
| b'@@ -0,0 +1,10699 @@\n+#chrom\tstart\tend\tS7\n+chr19\t9294488\t9294489\t0.93\n+chr19\t9294489\t9294490\t0.78\n+chr19\t9294492\t9294493\t1.00\n+chr19\t9294493\t9294494\t0.71\n+chr19\t9294500\t9294501\t0.93\n+chr19\t9294501\t9294502\t0.93\n+chr19\t9294505\t9294506\t0.83\n+chr19\t9294582\t9294583\t0.86\n+chr19\t9294589\t9294590\t0.82\n+chr19\t9294590\t9294591\t0.93\n+chr19\t10616344\t10616345\t0.00\n+chr19\t10616373\t10616374\t0.00\n+chr19\t10616385\t10616386\t0.05\n+chr19\t10616399\t10616400\t0.00\n+chr19\t10616400\t10616401\t0.00\n+chr19\t10616420\t10616421\t0.05\n+chr19\t10616421\t10616422\t0.14\n+chr19\t10616457\t10616458\t0.00\n+chr19\t10616471\t10616472\t0.00\n+chr19\t10616479\t10616480\t0.00\n+chr19\t10616490\t10616491\t0.00\n+chr19\t10616505\t10616506\t0.00\n+chr19\t10616518\t10616519\t0.00\n+chr19\t10616610\t10616611\t0.00\n+chr19\t10617230\t10617231\t1.00\n+chr19\t10617839\t10617840\t0.47\n+chr19\t10617867\t10617868\t0.46\n+chr19\t10617872\t10617873\t0.93\n+chr19\t10617899\t10617900\t0.69\n+chr19\t10617930\t10617931\t0.45\n+chr19\t10618135\t10618136\t0.62\n+chr19\t10618148\t10618149\t0.64\n+chr19\t10618207\t10618208\t0.80\n+chr19\t10618794\t10618795\t0.86\n+chr19\t10618815\t10618816\t0.93\n+chr19\t10618836\t10618837\t0.75\n+chr19\t10618843\t10618844\t0.92\n+chr19\t10619205\t10619206\t0.36\n+chr19\t10619225\t10619226\t0.83\n+chr19\t10619248\t10619249\t0.93\n+chr19\t10620129\t10620130\t0.85\n+chr19\t10620161\t10620162\t0.92\n+chr19\t10620219\t10620220\t0.90\n+chr19\t10620220\t10620221\t0.89\n+chr19\t10620268\t10620269\t0.92\n+chr19\t10620723\t10620724\t0.79\n+chr19\t10620731\t10620732\t0.86\n+chr19\t10620743\t10620744\t0.07\n+chr19\t10620770\t10620771\t0.23\n+chr19\t10620956\t10620957\t0.00\n+chr19\t10620986\t10620987\t0.00\n+chr19\t10621042\t10621043\t0.04\n+chr19\t10621079\t10621080\t0.00\n+chr19\t10621091\t10621092\t0.00\n+chr19\t10621106\t10621107\t0.00\n+chr19\t10621107\t10621108\t0.00\n+chr19\t10621116\t10621117\t0.00\n+chr19\t10621117\t10621118\t0.00\n+chr19\t10621128\t10621129\t0.00\n+chr19\t10621129\t10621130\t0.00\n+chr19\t10621150\t10621151\t0.00\n+chr19\t10621168\t10621169\t0.00\n+chr19\t10621169\t10621170\t0.00\n+chr19\t10621184\t10621185\t0.00\n+chr19\t10621202\t10621203\t0.05\n+chr19\t10621228\t10621229\t0.00\n+chr19\t10621231\t10621232\t0.07\n+chr19\t10621242\t10621243\t0.06\n+chr19\t10621525\t10621526\t0.25\n+chr19\t10621846\t10621847\t0.92\n+chr19\t10621884\t10621885\t0.70\n+chr19\t10622139\t10622140\t0.21\n+chr19\t10622140\t10622141\t0.08\n+chr19\t10622179\t10622180\t0.62\n+chr19\t10622183\t10622184\t0.60\n+chr19\t10622242\t10622243\t0.25\n+chr19\t10623789\t10623790\t0.10\n+chr19\t10623970\t10623971\t0.92\n+chr19\t10624001\t10624002\t0.68\n+chr19\t10624047\t10624048\t0.76\n+chr19\t10624073\t10624074\t1.00\n+chr19\t10624122\t10624123\t0.95\n+chr19\t10624246\t10624247\t0.26\n+chr19\t10624282\t10624283\t0.95\n+chr19\t10624311\t10624312\t0.38\n+chr19\t10624322\t10624323\t0.55\n+chr19\t10624476\t10624477\t0.46\n+chr19\t10624483\t10624484\t0.38\n+chr19\t10624503\t10624504\t0.60\n+chr19\t10624521\t10624522\t0.58\n+chr19\t10624525\t10624526\t0.50\n+chr19\t10624526\t10624527\t0.53\n+chr19\t10624540\t10624541\t0.43\n+chr19\t10624541\t10624542\t0.62\n+chr19\t10624558\t10624559\t0.43\n+chr19\t10624559\t10624560\t0.69\n+chr19\t10624573\t10624574\t0.62\n+chr19\t10624574\t10624575\t0.57\n+chr19\t10624576\t10624577\t1.00\n+chr19\t10624578\t10624579\t0.73\n+chr19\t10624586\t10624587\t1.00\n+chr19\t10624587\t10624588\t1.00\n+chr19\t10624593\t10624594\t0.86\n+chr19\t10624594\t10624595\t0.71\n+chr19\t10624598\t10624599\t0.47\n+chr19\t10624599\t10624600\t0.62\n+chr19\t10624603\t10624604\t0.60\n+chr19\t10624604\t10624605\t0.46\n+chr19\t10624625\t10624626\t0.23\n+chr19\t10624626\t10624627\t0.00\n+chr19\t10624638\t10624639\t0.31\n+chr19\t10624641\t10624642\t0.40\n+chr19\t10624642\t10624643\t0.10\n+chr19\t10624651\t10624652\t0.20\n+chr19\t10624664\t10624665\t0.19\n+chr19\t10624666\t10624667\t0.19\n+chr19\t10624670\t10624671\t0.18\n+chr19\t10624673\t10624674\t0.39\n+chr19\t10624691\t10624692\t0.20\n+chr19\t10624702\t10624703\t0.26\n+chr19\t10624713\t10624714\t0.14\n+chr19\t10624717\t10624718\t0.33\n+chr19\t10624731\t10624732\t0.44\n+chr19\t10624739\t10624740\t0.46\n+chr19\t10624741\t10624742\t0.29\n+chr19\t10624746\t10624747\t0.54\n+chr19\t10624753\t10624754\t0.14\n+chr19\t10624755\t10624756\t0.14\n+chr19\t10624766\t10624767\t0.13\n+chr19\t10624822\t10624823\t0.08\n+chr19\t10624848\t10624849\t0.03\n+chr19\t10624850\t10624851\t0.03\n+chr19\t10624853\t10'..b'326\t0.90\n+chr19\t11622676\t11622677\t0.60\n+chr19\t11622772\t11622773\t0.88\n+chr19\t11622803\t11622804\t1.00\n+chr19\t11622824\t11622825\t0.93\n+chr19\t11622832\t11622833\t1.00\n+chr19\t11623375\t11623376\t0.58\n+chr19\t11623514\t11623515\t1.00\n+chr19\t11623863\t11623864\t1.00\n+chr19\t11623913\t11623914\t0.95\n+chr19\t11623914\t11623915\t0.93\n+chr19\t11623958\t11623959\t1.00\n+chr19\t11623980\t11623981\t0.88\n+chr19\t11623991\t11623992\t0.91\n+chr19\t11624012\t11624013\t0.95\n+chr19\t11624042\t11624043\t0.86\n+chr19\t11624071\t11624072\t0.96\n+chr19\t11624506\t11624507\t0.95\n+chr19\t11624521\t11624522\t0.75\n+chr19\t11624598\t11624599\t1.00\n+chr19\t11624618\t11624619\t0.88\n+chr19\t11624762\t11624763\t0.92\n+chr19\t11624766\t11624767\t0.92\n+chr19\t11624780\t11624781\t1.00\n+chr19\t11624788\t11624789\t0.93\n+chr19\t11624789\t11624790\t1.00\n+chr19\t11624821\t11624822\t0.94\n+chr19\t11624822\t11624823\t1.00\n+chr19\t11624827\t11624828\t0.94\n+chr19\t11624828\t11624829\t0.94\n+chr19\t11624831\t11624832\t0.94\n+chr19\t11624832\t11624833\t0.94\n+chr19\t11624841\t11624842\t0.89\n+chr19\t11624842\t11624843\t1.00\n+chr19\t11624856\t11624857\t0.76\n+chr19\t11624857\t11624858\t1.00\n+chr19\t11624871\t11624872\t1.00\n+chr19\t11624872\t11624873\t1.00\n+chr19\t11624881\t11624882\t1.00\n+chr19\t11624882\t11624883\t1.00\n+chr19\t11624895\t11624896\t0.93\n+chr19\t11624896\t11624897\t1.00\n+chr19\t11624947\t11624948\t1.00\n+chr19\t11624948\t11624949\t0.92\n+chr19\t11624955\t11624956\t1.00\n+chr19\t11624999\t11625000\t0.94\n+chr19\t11625016\t11625017\t0.86\n+chr19\t11625025\t11625026\t0.92\n+chr19\t11625091\t11625092\t0.82\n+chr19\t11625525\t11625526\t1.00\n+chr19\t11625532\t11625533\t0.92\n+chr19\t11625986\t11625987\t0.62\n+chr19\t11626010\t11626011\t0.76\n+chr19\t11626018\t11626019\t0.65\n+chr19\t11626062\t11626063\t0.62\n+chr19\t11626074\t11626075\t0.82\n+chr19\t11626107\t11626108\t0.94\n+chr19\t11626138\t11626139\t0.94\n+chr19\t11626152\t11626153\t0.93\n+chr19\t11626159\t11626160\t0.93\n+chr19\t11626163\t11626164\t1.00\n+chr19\t11626307\t11626308\t0.72\n+chr19\t11626310\t11626311\t0.88\n+chr19\t11626510\t11626511\t0.57\n+chr19\t11626688\t11626689\t1.00\n+chr19\t11626697\t11626698\t0.90\n+chr19\t11626801\t11626802\t0.85\n+chr19\t11626802\t11626803\t0.58\n+chr19\t11626831\t11626832\t0.95\n+chr19\t11626890\t11626891\t0.74\n+chr19\t11626891\t11626892\t0.85\n+chr19\t11628279\t11628280\t0.85\n+chr19\t11629051\t11629052\t1.00\n+chr19\t12557735\t12557736\t1.00\n+chr19\t12557743\t12557744\t0.93\n+chr19\t12557780\t12557781\t0.92\n+chr19\t12557797\t12557798\t0.93\n+chr19\t12557813\t12557814\t0.57\n+chr19\t12557837\t12557838\t0.73\n+chr19\t12557857\t12557858\t0.87\n+chr19\t12557860\t12557861\t0.87\n+chr19\t12557861\t12557862\t0.87\n+chr19\t12557868\t12557869\t0.68\n+chr19\t12557869\t12557870\t1.00\n+chr19\t12557872\t12557873\t0.81\n+chr19\t12886714\t12886715\t1.00\n+chr19\t12886722\t12886723\t0.94\n+chr19\t12886839\t12886840\t0.86\n+chr19\t12886847\t12886848\t0.71\n+chr19\t12886851\t12886852\t0.80\n+chr19\t12886881\t12886882\t0.90\n+chr19\t20249178\t20249179\t0.84\n+chr19\t20980035\t20980036\t1.00\n+chr19\t20980043\t20980044\t0.94\n+chr19\t20980160\t20980161\t0.86\n+chr19\t20980168\t20980169\t0.74\n+chr19\t20980172\t20980173\t0.86\n+chr19\t20980202\t20980203\t0.89\n+chr19\t32808847\t32808848\t0.83\n+chr19\t32808851\t32808852\t0.92\n+chr19\t32808858\t32808859\t0.92\n+chr19\t32808872\t32808873\t0.77\n+chr19\t32808892\t32808893\t0.73\n+chr19\t32808903\t32808904\t0.79\n+chr19\t34949320\t34949321\t0.92\n+chr19\t34949324\t34949325\t1.00\n+chr19\t34949325\t34949326\t0.75\n+chr19\t34949333\t34949334\t0.86\n+chr19\t34949337\t34949338\t0.82\n+chr19\t34949414\t34949415\t0.86\n+chr19\t34949421\t34949422\t0.82\n+chr19\t34949422\t34949423\t0.94\n+chr19\t37284441\t37284442\t0.90\n+chr19\t37284471\t37284472\t0.80\n+chr19\t37284475\t37284476\t0.71\n+chr19\t37284483\t37284484\t0.89\n+chr19\t37284600\t37284601\t0.94\n+chr19\t37284608\t37284609\t1.00\n+chr19\t38614049\t38614050\t0.80\n+chr19\t38614057\t38614058\t0.80\n+chr19\t38678212\t38678213\t1.00\n+chr19\t38678216\t38678217\t1.00\n+chr19\t38678224\t38678225\t0.89\n+chr19\t38678228\t38678229\t1.00\n+chr19\t38678248\t38678249\t0.83\n+chr19\t38678272\t38678273\t0.88\n+chr19\t38678273\t38678274\t0.73\n+chr19\t38678288\t38678289\t1.00\n+chr19\t38678289\t38678290\t0.82\n+chr19\t53096176\t53096177\t0.75\n+chr19\t53096184\t53096185\t0.82\n+chr19\t53180250\t53180251\t0.80\n+chr19\t55510145\t55510146\t0.70\n+chr19\t58036654\t58036655\t0.58\n' |
| b |
| diff -r 000000000000 -r 0d988a56e332 test-data/example_S8.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example_S8.bedgraph Thu Dec 17 17:10:08 2015 -0500 |
| b |
| b'@@ -0,0 +1,10699 @@\n+#chrom\tstart\tend\tS8\n+chr19\t9294488\t9294489\t0.96\n+chr19\t9294489\t9294490\t0.75\n+chr19\t9294492\t9294493\t1.00\n+chr19\t9294493\t9294494\t0.51\n+chr19\t9294500\t9294501\t0.96\n+chr19\t9294501\t9294502\t0.83\n+chr19\t9294505\t9294506\t0.73\n+chr19\t9294582\t9294583\t0.90\n+chr19\t9294589\t9294590\t0.84\n+chr19\t9294590\t9294591\t0.94\n+chr19\t10616344\t10616345\t0.00\n+chr19\t10616373\t10616374\t0.00\n+chr19\t10616385\t10616386\t0.12\n+chr19\t10616399\t10616400\t0.00\n+chr19\t10616400\t10616401\t0.18\n+chr19\t10616420\t10616421\t0.07\n+chr19\t10616421\t10616422\t0.07\n+chr19\t10616457\t10616458\t0.00\n+chr19\t10616471\t10616472\t0.00\n+chr19\t10616479\t10616480\t0.00\n+chr19\t10616490\t10616491\t0.00\n+chr19\t10616505\t10616506\t0.00\n+chr19\t10616518\t10616519\t0.00\n+chr19\t10616610\t10616611\t0.06\n+chr19\t10617230\t10617231\t1.00\n+chr19\t10617839\t10617840\t0.71\n+chr19\t10617867\t10617868\t0.81\n+chr19\t10617872\t10617873\t0.94\n+chr19\t10617899\t10617900\t0.71\n+chr19\t10617930\t10617931\t0.38\n+chr19\t10618135\t10618136\t0.60\n+chr19\t10618148\t10618149\t0.67\n+chr19\t10618207\t10618208\t0.95\n+chr19\t10618794\t10618795\t0.64\n+chr19\t10618815\t10618816\t0.83\n+chr19\t10618836\t10618837\t1.00\n+chr19\t10618843\t10618844\t0.95\n+chr19\t10619205\t10619206\t0.30\n+chr19\t10619225\t10619226\t0.45\n+chr19\t10619248\t10619249\t1.00\n+chr19\t10620129\t10620130\t0.29\n+chr19\t10620161\t10620162\t0.72\n+chr19\t10620219\t10620220\t0.67\n+chr19\t10620220\t10620221\t0.50\n+chr19\t10620268\t10620269\t0.50\n+chr19\t10620723\t10620724\t0.12\n+chr19\t10620731\t10620732\t0.17\n+chr19\t10620743\t10620744\t0.06\n+chr19\t10620770\t10620771\t0.06\n+chr19\t10620956\t10620957\t0.06\n+chr19\t10620986\t10620987\t0.07\n+chr19\t10621042\t10621043\t0.10\n+chr19\t10621079\t10621080\t0.00\n+chr19\t10621091\t10621092\t0.00\n+chr19\t10621106\t10621107\t0.00\n+chr19\t10621107\t10621108\t0.00\n+chr19\t10621116\t10621117\t0.00\n+chr19\t10621117\t10621118\t0.00\n+chr19\t10621128\t10621129\t0.00\n+chr19\t10621129\t10621130\t0.00\n+chr19\t10621150\t10621151\t0.00\n+chr19\t10621168\t10621169\t0.00\n+chr19\t10621169\t10621170\t0.00\n+chr19\t10621184\t10621185\t0.00\n+chr19\t10621202\t10621203\t0.00\n+chr19\t10621228\t10621229\t0.00\n+chr19\t10621231\t10621232\t0.11\n+chr19\t10621242\t10621243\t0.26\n+chr19\t10621525\t10621526\t0.11\n+chr19\t10621846\t10621847\t0.86\n+chr19\t10621884\t10621885\t0.43\n+chr19\t10622139\t10622140\t0.15\n+chr19\t10622140\t10622141\t0.08\n+chr19\t10622179\t10622180\t0.38\n+chr19\t10622183\t10622184\t0.73\n+chr19\t10622242\t10622243\t0.18\n+chr19\t10623789\t10623790\t0.15\n+chr19\t10623970\t10623971\t0.72\n+chr19\t10624001\t10624002\t0.80\n+chr19\t10624047\t10624048\t0.78\n+chr19\t10624073\t10624074\t0.48\n+chr19\t10624122\t10624123\t1.00\n+chr19\t10624246\t10624247\t0.27\n+chr19\t10624282\t10624283\t1.00\n+chr19\t10624311\t10624312\t0.62\n+chr19\t10624322\t10624323\t0.83\n+chr19\t10624476\t10624477\t0.50\n+chr19\t10624483\t10624484\t0.50\n+chr19\t10624503\t10624504\t0.73\n+chr19\t10624521\t10624522\t0.75\n+chr19\t10624525\t10624526\t0.67\n+chr19\t10624526\t10624527\t0.70\n+chr19\t10624540\t10624541\t0.57\n+chr19\t10624541\t10624542\t0.55\n+chr19\t10624558\t10624559\t0.83\n+chr19\t10624559\t10624560\t0.75\n+chr19\t10624573\t10624574\t0.63\n+chr19\t10624574\t10624575\t0.50\n+chr19\t10624576\t10624577\t0.94\n+chr19\t10624578\t10624579\t0.88\n+chr19\t10624586\t10624587\t0.88\n+chr19\t10624587\t10624588\t0.73\n+chr19\t10624593\t10624594\t0.87\n+chr19\t10624594\t10624595\t0.57\n+chr19\t10624598\t10624599\t0.53\n+chr19\t10624599\t10624600\t0.31\n+chr19\t10624603\t10624604\t0.87\n+chr19\t10624604\t10624605\t0.42\n+chr19\t10624625\t10624626\t0.46\n+chr19\t10624626\t10624627\t0.00\n+chr19\t10624638\t10624639\t0.73\n+chr19\t10624641\t10624642\t0.71\n+chr19\t10624642\t10624643\t0.30\n+chr19\t10624651\t10624652\t0.58\n+chr19\t10624664\t10624665\t0.42\n+chr19\t10624666\t10624667\t0.36\n+chr19\t10624670\t10624671\t0.50\n+chr19\t10624673\t10624674\t0.46\n+chr19\t10624691\t10624692\t0.27\n+chr19\t10624702\t10624703\t0.12\n+chr19\t10624713\t10624714\t0.06\n+chr19\t10624717\t10624718\t0.25\n+chr19\t10624731\t10624732\t0.12\n+chr19\t10624739\t10624740\t0.29\n+chr19\t10624741\t10624742\t0.29\n+chr19\t10624746\t10624747\t0.37\n+chr19\t10624753\t10624754\t0.22\n+chr19\t10624755\t10624756\t0.00\n+chr19\t10624766\t10624767\t0.21\n+chr19\t10624822\t10624823\t0.23\n+chr19\t10624848\t10624849\t0.04\n+chr19\t10624850\t10624851\t0.00\n+chr19\t10624853\t10'..b'326\t0.74\n+chr19\t11622676\t11622677\t0.91\n+chr19\t11622772\t11622773\t0.40\n+chr19\t11622803\t11622804\t0.94\n+chr19\t11622824\t11622825\t0.93\n+chr19\t11622832\t11622833\t1.00\n+chr19\t11623375\t11623376\t0.29\n+chr19\t11623514\t11623515\t0.92\n+chr19\t11623863\t11623864\t0.89\n+chr19\t11623913\t11623914\t0.90\n+chr19\t11623914\t11623915\t0.94\n+chr19\t11623958\t11623959\t1.00\n+chr19\t11623980\t11623981\t0.94\n+chr19\t11623991\t11623992\t0.94\n+chr19\t11624012\t11624013\t1.00\n+chr19\t11624042\t11624043\t0.86\n+chr19\t11624071\t11624072\t0.67\n+chr19\t11624506\t11624507\t0.95\n+chr19\t11624521\t11624522\t0.55\n+chr19\t11624598\t11624599\t1.00\n+chr19\t11624618\t11624619\t1.00\n+chr19\t11624762\t11624763\t0.92\n+chr19\t11624766\t11624767\t1.00\n+chr19\t11624780\t11624781\t1.00\n+chr19\t11624788\t11624789\t0.90\n+chr19\t11624789\t11624790\t1.00\n+chr19\t11624821\t11624822\t0.91\n+chr19\t11624822\t11624823\t1.00\n+chr19\t11624827\t11624828\t1.00\n+chr19\t11624828\t11624829\t0.93\n+chr19\t11624831\t11624832\t1.00\n+chr19\t11624832\t11624833\t0.94\n+chr19\t11624841\t11624842\t0.92\n+chr19\t11624842\t11624843\t1.00\n+chr19\t11624856\t11624857\t1.00\n+chr19\t11624857\t11624858\t1.00\n+chr19\t11624871\t11624872\t1.00\n+chr19\t11624872\t11624873\t0.92\n+chr19\t11624881\t11624882\t1.00\n+chr19\t11624882\t11624883\t1.00\n+chr19\t11624895\t11624896\t0.90\n+chr19\t11624896\t11624897\t1.00\n+chr19\t11624947\t11624948\t1.00\n+chr19\t11624948\t11624949\t1.00\n+chr19\t11624955\t11624956\t1.00\n+chr19\t11624999\t11625000\t0.93\n+chr19\t11625016\t11625017\t0.92\n+chr19\t11625025\t11625026\t1.00\n+chr19\t11625091\t11625092\t0.85\n+chr19\t11625525\t11625526\t1.00\n+chr19\t11625532\t11625533\t0.85\n+chr19\t11625986\t11625987\t0.61\n+chr19\t11626010\t11626011\t0.62\n+chr19\t11626018\t11626019\t0.62\n+chr19\t11626062\t11626063\t0.68\n+chr19\t11626074\t11626075\t0.89\n+chr19\t11626107\t11626108\t0.93\n+chr19\t11626138\t11626139\t1.00\n+chr19\t11626152\t11626153\t0.87\n+chr19\t11626159\t11626160\t1.00\n+chr19\t11626163\t11626164\t0.93\n+chr19\t11626307\t11626308\t1.00\n+chr19\t11626310\t11626311\t1.00\n+chr19\t11626510\t11626511\t0.65\n+chr19\t11626688\t11626689\t0.94\n+chr19\t11626697\t11626698\t0.83\n+chr19\t11626801\t11626802\t0.81\n+chr19\t11626802\t11626803\t0.83\n+chr19\t11626831\t11626832\t0.95\n+chr19\t11626890\t11626891\t0.80\n+chr19\t11626891\t11626892\t0.83\n+chr19\t11628279\t11628280\t0.86\n+chr19\t11629051\t11629052\t1.00\n+chr19\t12557735\t12557736\t0.95\n+chr19\t12557743\t12557744\t0.88\n+chr19\t12557780\t12557781\t0.97\n+chr19\t12557797\t12557798\t0.97\n+chr19\t12557813\t12557814\t0.79\n+chr19\t12557837\t12557838\t0.71\n+chr19\t12557857\t12557858\t0.93\n+chr19\t12557860\t12557861\t0.85\n+chr19\t12557861\t12557862\t0.98\n+chr19\t12557868\t12557869\t0.67\n+chr19\t12557869\t12557870\t1.00\n+chr19\t12557872\t12557873\t0.68\n+chr19\t12886714\t12886715\t0.95\n+chr19\t12886722\t12886723\t0.88\n+chr19\t12886839\t12886840\t0.84\n+chr19\t12886847\t12886848\t0.66\n+chr19\t12886851\t12886852\t0.73\n+chr19\t12886881\t12886882\t0.88\n+chr19\t20249178\t20249179\t0.71\n+chr19\t20980035\t20980036\t0.95\n+chr19\t20980043\t20980044\t0.89\n+chr19\t20980160\t20980161\t0.85\n+chr19\t20980168\t20980169\t0.67\n+chr19\t20980172\t20980173\t0.76\n+chr19\t20980202\t20980203\t0.87\n+chr19\t32808847\t32808848\t0.81\n+chr19\t32808851\t32808852\t0.68\n+chr19\t32808858\t32808859\t0.87\n+chr19\t32808872\t32808873\t0.83\n+chr19\t32808892\t32808893\t0.78\n+chr19\t32808903\t32808904\t0.58\n+chr19\t34949320\t34949321\t0.97\n+chr19\t34949324\t34949325\t0.98\n+chr19\t34949325\t34949326\t0.56\n+chr19\t34949333\t34949334\t0.81\n+chr19\t34949337\t34949338\t0.74\n+chr19\t34949414\t34949415\t0.90\n+chr19\t34949421\t34949422\t0.85\n+chr19\t34949422\t34949423\t0.92\n+chr19\t37284441\t37284442\t0.87\n+chr19\t37284471\t37284472\t0.73\n+chr19\t37284475\t37284476\t0.65\n+chr19\t37284483\t37284484\t0.83\n+chr19\t37284600\t37284601\t0.89\n+chr19\t37284608\t37284609\t0.95\n+chr19\t38614049\t38614050\t0.75\n+chr19\t38614057\t38614058\t0.80\n+chr19\t38678212\t38678213\t1.00\n+chr19\t38678216\t38678217\t0.97\n+chr19\t38678224\t38678225\t0.94\n+chr19\t38678228\t38678229\t0.94\n+chr19\t38678248\t38678249\t0.81\n+chr19\t38678272\t38678273\t0.76\n+chr19\t38678273\t38678274\t0.68\n+chr19\t38678288\t38678289\t1.00\n+chr19\t38678289\t38678290\t0.86\n+chr19\t53096176\t53096177\t0.78\n+chr19\t53096184\t53096185\t0.85\n+chr19\t53180250\t53180251\t0.79\n+chr19\t55510145\t55510146\t0.76\n+chr19\t58036654\t58036655\t0.69\n' |
| b |
| diff -r 000000000000 -r 0d988a56e332 test-data/metilene.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/metilene.out Thu Dec 17 17:10:08 2015 -0500 |
| b |
| @@ -0,0 +1,102 @@ +chr19 10624503 10624742 3.3e-16 -0.383986 37 4.3e-14 1.5e-19 0.25041 0.63439 +chr19 10625238 10625388 6.9e-07 -0.194231 26 4.9e-14 3.1e-10 0.09375 0.28798 +chr19 10625393 10625445 9.1e-06 -0.334423 13 4.6e-12 4.1e-09 0.14346 0.47788 +chr19 10625445 10625501 0.34 -0.176750 10 1.4e-06 0.00015 0.15125 0.328 +chr19 10625503 10625568 0.13 -0.340000 10 1.4e-08 5.6e-05 0.215 0.555 +chr19 10627955 10628104 1 -0.224500 10 8e-06 0.00089 0.13125 0.35575 +chr19 10649471 10649797 1 -0.169306 18 0.00027 0.007 0.32014 0.48944 +chr19 10651269 10651840 1 0.160500 10 0.028 0.039 0.6095 0.449 +chr19 10665280 10665739 1 0.262679 14 5.3e-07 0.0009 0.85804 0.59536 +chr19 10677825 10678072 1 0.150714 14 0.00012 0.00086 0.38786 0.23714 +chr19 10692028 10692359 1 0.105000 10 0.011 0.09 0.4575 0.3525 +chr19 10694970 10695148 1 0.132250 10 0.11 0.057 0.799 0.66675 +chr19 10753659 10754249 1 0.165682 11 0.0006 0.015 0.85364 0.68795 +chr19 10787206 10787584 0.46 0.177292 12 1.7e-07 0.0002 0.92875 0.75146 +chr19 10793898 10794095 0.019 -0.116000 10 3.9e-06 8.4e-06 0.84 0.956 +chr19 10802720 10803193 1 0.169167 12 0.0014 0.013 0.87292 0.70375 +chr19 10804610 10805885 0.42 0.200417 24 1.2e-06 0.00019 0.66938 0.46896 +chr19 10806085 10806355 1 -0.241500 10 3.2e-05 0.011 0.181 0.4225 +chr19 10840168 10840312 1 0.147250 10 4.7e-05 0.00087 0.90425 0.757 +chr19 10853391 10854047 0.13 0.124750 10 1.2e-06 6e-05 0.94625 0.8215 +chr19 10855021 10855854 1 0.121000 10 0.0041 0.016 0.8515 0.7305 +chr19 10858170 10858760 6.3e-05 0.324250 10 5.3e-11 2.8e-08 0.8915 0.56725 +chr19 10860309 10861011 1 0.117500 10 0.00097 0.0059 0.92475 0.80725 +chr19 10866650 10867448 1 0.171429 14 5.9e-05 0.0028 0.85446 0.68304 +chr19 10876049 10876672 1 0.140500 10 0.0023 0.012 0.89625 0.75575 +chr19 10877682 10878531 1 0.124167 12 0.0014 0.00091 0.91625 0.79208 +chr19 10887402 10887846 1 0.170833 12 0.011 0.076 0.58625 0.41542 +chr19 10928642 10928813 0.0071 0.101250 10 1.4e-07 3.2e-06 0.94825 0.847 +chr19 10939890 10940634 0.05 0.192143 14 9.8e-06 2.2e-05 0.89375 0.70161 +chr19 10947344 10947483 7.8e-08 -0.356731 13 6.1e-12 3.5e-11 0.46096 0.81769 +chr19 10997976 10998526 2.5e-07 0.498500 10 8e-13 1.1e-10 0.87275 0.37425 +chr19 11006467 11007609 0.0098 0.278158 19 4.3e-10 4.4e-06 0.86132 0.58316 +chr19 11030428 11030907 1 0.101000 10 0.023 0.014 0.89425 0.79325 +chr19 11036051 11036440 0.12 0.243750 10 1.9e-07 5.4e-05 0.85275 0.609 +chr19 11040212 11040659 0.00042 0.204028 18 1.1e-10 1.9e-07 0.30056 0.096528 +chr19 11056417 11056540 0.014 0.266500 10 3.7e-06 6.4e-06 0.59825 0.33175 +chr19 11072934 11073838 1.2e-12 0.535000 20 4.6e-14 5.6e-16 0.68088 0.14588 +chr19 11077326 11077585 1.1e-14 0.706406 16 4.3e-14 5e-18 0.80234 0.095938 +chr19 11081481 11081743 0.0069 0.236250 10 2.9e-09 3.1e-06 0.945 0.70875 +chr19 11084338 11084493 0.0094 0.256000 10 1.6e-08 4.2e-06 0.749 0.493 +chr19 11084524 11084841 2.2e-16 0.806111 18 4.6e-14 1e-19 0.91222 0.10611 +chr19 11086226 11086876 1.1e-11 0.634464 14 4.3e-14 4.8e-15 0.91518 0.28071 +chr19 11087248 11088068 5.2e-26 0.801932 22 3.7e-14 2.3e-29 0.84307 0.041136 +chr19 11090548 11091241 1.4e-31 0.476983 29 3.6e-14 6.3e-35 0.54034 0.063362 +chr19 11094281 11094942 0.013 0.174853 17 4.8e-08 5.8e-06 0.91015 0.73529 +chr19 11096356 11096687 1 0.181000 10 0.0019 0.03 0.88225 0.70125 +chr19 11128754 11129461 0.59 0.127361 18 1.8e-05 0.00027 0.90667 0.77931 +chr19 11131338 11132185 1 0.210227 11 2e-05 0.00061 0.89727 0.68705 +chr19 11134067 11134983 1 0.183158 19 2.5e-06 0.0014 0.89895 0.71579 +chr19 11135098 11135203 1 0.101250 10 0.0011 0.00085 0.9645 0.86325 +chr19 11139238 11139692 0.36 0.249250 10 9.8e-08 0.00016 0.917 0.66775 +chr19 11140854 11141413 0.54 0.149500 10 4.9e-06 0.00024 0.94425 0.79475 +chr19 11142536 11143257 6.1e-09 0.360469 16 5.1e-14 2.7e-12 0.86687 0.50641 +chr19 11144943 11145419 1.9e-09 0.587917 12 4.8e-14 8.7e-13 0.84875 0.26083 +chr19 11145469 11145536 0.05 0.157000 10 1.3e-08 2.2e-05 0.95575 0.79875 +chr19 11155522 11155974 0.87 0.130750 10 2.4e-05 0.00039 0.871 0.74025 +chr19 11159207 11159488 1.3e-10 0.618077 13 4.4e-14 6e-14 0.66673 0.048654 +chr19 11160325 11161217 7.1e-22 0.688125 24 4.5e-14 3.2e-25 0.77823 0.090104 +chr19 11162322 11162686 0.24 0.222308 13 1.3e-05 0.00011 0.39904 0.17673 +chr19 11163813 11163975 0.13 0.213000 10 1.2e-06 5.8e-05 0.89725 0.68425 +chr19 11165765 11166307 1 0.153250 10 0.0014 0.011 0.93825 0.785 +chr19 11171065 11171571 1 0.147500 13 1.9e-05 0.0013 0.92654 0.77904 +chr19 11179685 11180777 1 0.163333 12 0.002 0.018 0.93583 0.7725 +chr19 11245060 11245680 1 0.123000 10 0.012 0.19 0.887 0.764 +chr19 11278922 11279785 1 -0.285000 10 0.00015 0.0029 0.496 0.781 +chr19 11288389 11288853 1 0.185000 10 0.015 0.0036 0.6565 0.4715 +chr19 11289761 11289923 1 0.183500 10 1.5e-05 0.00089 0.3535 0.17 +chr19 11301235 11301809 5.3e-08 0.623500 10 1.2e-12 2.4e-11 0.808 0.1845 +chr19 11304033 11304225 1 0.104500 10 6.4e-06 0.00053 0.95025 0.84575 +chr19 11311059 11311457 1 0.130962 13 3.1e-06 0.0019 0.91712 0.78615 +chr19 11341001 11341680 1 0.180000 13 0.021 0.044 0.7275 0.5475 +chr19 11354131 11354402 0.84 -0.130750 10 0.00028 0.00038 0.09275 0.2235 +chr19 11362795 11363368 1 0.116250 10 0.01 0.091 0.86925 0.753 +chr19 11371724 11372385 1 0.181250 14 0.0031 0.029 0.69804 0.51679 +chr19 11375151 11375626 0.43 0.276000 10 0.00017 0.00019 0.65625 0.38025 +chr19 11376137 11376795 0.99 0.232292 12 0.00016 0.00044 0.57729 0.345 +chr19 11410378 11410837 1 0.181000 10 0.058 0.011 0.777 0.596 +chr19 11430046 11430647 1 0.132935 23 3.4e-06 0.0014 0.89043 0.7575 +chr19 11446834 11447358 0.33 0.176750 10 0.0002 0.00015 0.8785 0.70175 +chr19 11447904 11448133 1 -0.134000 10 0.026 0.28 0.24 0.374 +chr19 11449349 11449851 1 0.229615 13 9.6e-05 0.0019 0.55519 0.32558 +chr19 11467267 11467765 0.039 0.301750 10 1.5e-07 1.8e-05 0.7625 0.46075 +chr19 11484502 11484870 1 -0.150250 10 0.00066 0.021 0.1155 0.26575 +chr19 11493199 11493422 1 -0.200208 12 7.1e-05 0.0052 0.52667 0.72688 +chr19 11507504 11507858 1 0.156500 10 0.0048 0.022 0.78175 0.62525 +chr19 11509495 11509884 1 0.117143 14 0.0015 0.074 0.85964 0.7425 +chr19 11510358 11510564 0.47 0.247000 10 5.1e-07 0.00021 0.856 0.609 +chr19 11516916 11517167 4.9e-13 0.260250 20 4.3e-14 2.2e-16 0.33687 0.076625 +chr19 11532291 11532486 0.02 -0.222250 10 8.3e-10 9.1e-06 0.052 0.27425 +chr19 11546948 11547287 0.096 0.270750 10 6.5e-05 4.3e-05 0.586 0.31525 +chr19 11547298 11548086 1 0.206000 10 0.00029 0.008 0.81975 0.61375 +chr19 11555765 11556289 0.34 0.181750 10 3.1e-07 0.00015 0.93675 0.755 +chr19 11557459 11557835 0.0036 0.417727 11 6.3e-10 1.6e-06 0.66455 0.24682 +chr19 11558631 11558874 1 -0.155250 10 0.00059 0.012 0.59875 0.754 +chr19 11564167 11564498 1 0.188250 10 0.0099 0.004 0.694 0.50575 +chr19 11574129 11574509 0.0029 0.287333 15 2.4e-08 1.3e-06 0.64283 0.3555 +chr19 11577217 11577526 1 0.118250 10 0.0089 0.0096 0.8635 0.74525 +chr19 11590469 11591012 4e-12 -0.228359 32 4.1e-14 1.8e-15 0.088906 0.31727 +chr19 11591538 11591910 0.00029 -0.332500 15 4.5e-12 1.3e-07 0.3535 0.686 +chr19 11591912 11592067 0.39 -0.217105 19 5.5e-08 0.00017 0.23039 0.4475 +chr19 11605792 11605902 1.5e-05 0.412500 14 5.6e-14 6.8e-09 0.8875 0.475 +chr19 11606965 11607349 1 0.169318 11 0.031 0.078 0.69523 0.52591 |
| b |
| diff -r 000000000000 -r 0d988a56e332 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Dec 17 17:10:08 2015 -0500 |
| b |
| @@ -0,0 +1,50 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="perl" version="5.18.1"> + <repository changeset_revision="8b3509930a44" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="R" version="3.2.1"> + <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="bedtools" version="2.24"> + <repository changeset_revision="39b86c1e267d" name="package_bedtools_2_24" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="gnu_coreutils" version="8.22"> + <repository changeset_revision="ac64dfe4b1fb" name="package_gnu_coreutils_8_22" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="ggplot2" version="0.9.3"> + <repository changeset_revision="07de191649b4" name="package_r_ggplot2_0_9_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="metilene" version="0.2-4"> + <install version="1.0"> + <actions> + <action sha256sum="7430b4c2af4f43d389ad690dfe42c9ce7a63b2bff4ff0ac59afc0f1ec7e600f2" type="download_by_url"> + https://depot.galaxyproject.org/software/metilene/metilene_0.2-4_src_all.tar.gz + </action> + <action type="shell_command">make</action> + <!-- move binary and scripts to installation bin directory --> + <action type="move_file"> + <source>metilene</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>metilene_input.pl</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>metilene_output.pl</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>metilene_output.R</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme>Metilene is precompiled for Linux</readme> + </package> +</tool_dependency> |