Repository 'footprint'
hg clone https://toolshed.g2.bx.psu.edu/repos/rnateam/footprint

Changeset 0:4bff424dfa47 (2017-05-02)
Next changeset 1:0d94a529f925 (2017-11-20)
Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 3a110c632920d1ed94b78053184978040df3edaf
added:
footprint.xml
test-data/input_ATAC_HEK293_hg19_chr1.bam
test-data/input_CTCF_HEK293_chip_hg19_chr1.bed
test-data/input_CTCF_motifs_hg19_chr1.bed
test-data/input_SeqBias_ATAC.txt
test-data/input_hg19.chr1.chrom.size
test-data/input_hg19_chr1.fa
test-data/output.PARAM
test-data/output.RESULTS
test-data/output_plot1.png
test-data/output_plot2.png
tool-data/sam_fa_indices.loc.sample
tool_data_table_conf.xml.sample
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diff -r 000000000000 -r 4bff424dfa47 footprint.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/footprint.xml Tue May 02 15:05:59 2017 -0400
[
b'@@ -0,0 +1,212 @@\n+<?xml version="1.0" encoding="UTF-8"?>\n+<tool id="footprint" name="footprint" version="1.0.0">\n+    <requirements>\n+        <requirement type="package" version="1.0.0">footprint</requirement>\n+    </requirements>\n+    <stdio>\n+        <exit_code range="1:" />\n+    </stdio>\n+    <command><![CDATA[\n+            ln -s \'$bam_file\' ./bam_file.bam\n+\n+            &&\n+\n+            find_footprints.sh\n+\n+            ./bam_file.bam\n+\n+            \'$chrom_sizes\'\n+\n+            \'$motif_coords\'\n+\n+            ## genome source\n+            #if $refGenomeSource.genomeSource == "history":\n+                \'$refGenomeSource.ownFile\'\n+            #else\n+                \'$refGenomeSource.builtin.fields.path\'\n+            #end if\n+\n+            $factor_name\n+\n+            \'$bias_file\'\n+\n+            \'$peak_file\'\n+\n+            $no_of_components\n+\n+            $background\n+\n+            $fixed_bg\n+\n+            &&\n+            mv *.PARAM PARAM\n+            &&\n+            mv *.RESULTS RESULTS\n+            &&\n+            mv *.plot2.png plot2.png\n+            &&\n+            mv *.plot1.png plot1.png\n+]]>\n+    </command>\n+    <inputs>\n+        <param name="bam_file" type="data" format="BAM" label="alignment bam file" help="" />\n+        <param name="chrom_sizes" type="data" format="tablular" label="chromosome length" help="" />\n+        <param name="motif_coords" type="data" format="BED" label="coordinates of motif" help="" />\n+        <conditional name="refGenomeSource">\n+            <param name="genomeSource" type="select"\n+                label="Will you select a reference genome from your\n+                history or use a built-in genome?"\n+                help="The version of genome against which the reads were aligned.">\n+                <option value="fai" selected="True">\n+                    Use a built-in genome</option>\n+                <option value="history">\n+                    Use a genome from my current history</option>\n+            </param>\n+            <when value="fai">\n+            <param name="builtin" type="select"\n+                label="Select a reference genome">\n+                <options from_data_table="sam_fa_indices">\n+                    <filter type="sort_by" column="1" />\n+                    <validator type="no_options"\n+                    message="A built-in reference genome is not available\n+                    for the build associated with the selected input file"/>\n+                </options>\n+            </param>\n+            </when>\n+            <when value="history">\n+                <param name="ownFile" type="data" format="fasta"\n+                label="Select the reference genome"  help="Genome sequences in FASTA format" />\n+            </when>\n+        </conditional>\n+        <param name="factor_name" type="text" label="transcription factor" help="e.g. CTCF" />\n+        <param name="bias_file" type="data"  format="tabular,txt" label="cleavage/transposition bias" help="" />\n+        <param name="peak_file" type="data" format="tabular" label="coordinates of ChIP-seq peaks" help="" />\n+        <param name="no_of_components" type="select" label="number of components">\n+            <option value="2" selected="true">2</option>\n+            <option value="3">3</option>\n+        </param>\n+        <param name="background" type="select" label="background components">\n+            <option value="Seq" selected="true">Seq</option>\n+            <option value="Flat">Flat</option>\n+        </param>\n+        <param name="fixed_bg" type="select" label="fixed background component">\n+            <option value="TRUE" selected="true">TRUE</option>\n+            <option value="FALSE">FALSE</option>\n+        </param>\n+    </inputs>\n+    <outputs>\n+        <data name="RESULTS" format="tabular" from_work_dir="RESULTS" label="${tool.name} on ${on_string}: results" />\n+        <data name="PARAM" format="txt" from_work_dir="PARAM" label="${tool.name} on ${on_string}: parameters" />\n+        <data name="plot1" for'..b'name="plot1" file="output_plot1.png" ftype="png" compare="sim_size" delta="15000" />\n+            <output name="plot2" file="output_plot2.png" ftype="png" compare="sim_size" delta="15000" />\n+        </test>\n+    </tests>\n+    <help><![CDATA[.. class:: infomark\n+\n+**Purpose**\n+\n+This is a pipeline to find transcription factor footprints in ATAC-seq or DNase-seq data.\n+\n+\n+-----\n+\n+.. class:: infomark\n+\n+**Inputs**\n+\n+alignment bam file\n+ * A bam file from the ATAC-seq or DNase-seq experiment.\n+\n+chromosome length\n+ * A tab delimited file with 2 columns.\n+ * The first column is the chromosome name and the second column is the chromosome length for the appropriate organism and genome build.\n+ * Example: chr1    10000000\n+\n+coordinates of motif\n+ * A 6-column bed file with the coordinates of motif matches (eg resulting from scanning the genome with a PWM) for the transcription factor of interest.\n+ * The 6 columns should contain chromosome, start coordinate, end coordinate, name, score and strand information in this order. The coordinates should be closed (1-based).\n+ * Example: chr1    24782   24800   .       11.60   -\n+\n+transcription factor\n+ * The name of the transcription factor of interest supplied by the user, e.g. CTCF.\n+\n+cleavage/transposition bias\n+ * The cleavage/transposition bias of the different protocols, for all 6-mers.\n+ * Provided `options`_: ATAC, DNase double hit or DNase single hit protocols.\n+\n+ .. _options: https://ohlerlab.mdc-berlin.de/software/Reproducible_footprinting_139/\n+\n+coordinates of ChIP-seq peaks\n+ * A file with the coordinates of the ChIP-seq peaks for the transcription factor of interest.\n+ * The format is flexible as long as the first 3 columns (chromosome, start coordinate, end coordinate) are present.\n+ * Example: chr1    237622  237882\n+\n+number of components\n+ * Total number of footprint and background components that should be learned from the data.\n+ * Options are 2 (1 fp and 1 bg) and 3 (2 fp and 1 bg) components.\n+\n+background components\n+ * The mode of initialization for the background component. Options are "Flat" or "Seq".\n+ * Choosing "Flat" initializes this component as a uniform distribution.\n+ * Choosing "Seq" initializes it as the signal profile that would be expected solely due to the protocol bias (given by the cleavage/transposition bias file).\n+\n+fixed background component\n+ * Whether the background component should be kept fixed.\n+ * Options are TRUE or FALSE.\n+ * Setting "TRUE" keeps this component fixed, whereas setting "FALSE" lets it be reestimated during training.\n+\n+-----\n+\n+.. class:: infomark\n+\n+**Outputs**\n+\n+results\n+ * The results of the footprinting analysis.\n+ * The first 6 columns harbor the motif information (identical to the \'coordinates of motif\').\n+ * The 7th column has the footprint score (log-odds of footprint versus background) for each motif instance.\n+ * The following columns show the probabilities for the individual footprint and background components.\n+\n+parameters\n+ * Gives the trained parameters for the footprint and background components.\n+ * It includes as many lines as components (eg the first line has the parameters for the first component).\n+\n+plot 1\n+ * A plot with two panels, showing the initial components above and the final trained components below.\n+ * The plotted values for the final components are given in the \'parameters\' output file explained above.\n+\n+plot 2\n+ * A plot only with the final trained components.\n+ * In a model where 2 components are used, this plot is identical to the bottom panel in plot1.\n+ * When 3 components are used, this plot shows the weighted average of the 2 footprint components as the final footprint profile.\n+\n+]]></help>\n+    <citations>\n+        <citation type="bibtex">@ARTICLE{footprint,\n+        author = {Aslihan Karabacak and Uwe Ohler},\n+        title = {To submit},\n+        journal = {},\n+        year = {},\n+        volume = {},\n+        pages = {}\n+        }</citation>\n+    </citations>\n+</tool>\n'
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diff -r 000000000000 -r 4bff424dfa47 test-data/input_ATAC_HEK293_hg19_chr1.bam
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Binary file test-data/input_ATAC_HEK293_hg19_chr1.bam has changed
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diff -r 000000000000 -r 4bff424dfa47 test-data/input_CTCF_HEK293_chip_hg19_chr1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_CTCF_HEK293_chip_hg19_chr1.bed Tue May 02 15:05:59 2017 -0400
b
b'@@ -0,0 +1,298 @@\n+chr1\t237622\t237882\t.\t251\t.\t39.3372136282643\t-1\t4.09257328230016\t130\n+chr1\t521451\t521711\t.\t188\t.\t29.4653911390088\t-1\t4.16687395085795\t130\n+chr1\t714030\t714290\t.\t121\t.\t19.03863214098\t-1\t4.26636812747811\t130\n+chr1\t805239\t805367\t.\t602\t.\t94.2292831486416\t-1\t4.70166294960891\t62\n+chr1\t840149\t840222\t.\t534\t.\t83.58819019977\t-1\t4.70166294960891\t7\n+chr1\t848265\t848525\t.\t152\t.\t23.8477636726331\t-1\t4.21543133693962\t130\n+chr1\t856446\t856706\t.\t207\t.\t32.4794759581864\t-1\t4.14338332549748\t130\n+chr1\t858440\t858700\t.\t188\t.\t29.4851613052607\t-1\t4.16670830476076\t130\n+chr1\t860970\t861230\t.\t128\t.\t20.1113292263552\t-1\t4.25411767794489\t130\n+chr1\t866999\t867259\t.\t214\t.\t33.5103262128396\t-1\t4.13532986855253\t130\n+chr1\t873508\t873768\t.\t289\t.\t45.2387205908942\t-1\t4.05428357047268\t130\n+chr1\t886824\t887084\t.\t510\t.\t79.8861811021046\t-1\t4.70166294960891\t130\n+chr1\t911513\t911678\t.\t689\t.\t107.847519897553\t-1\t4.70166294960891\t89\n+chr1\t919618\t919795\t.\t845\t.\t132.369252345027\t-1\t4.70166294960891\t83\n+chr1\t937319\t937452\t.\t748\t.\t117.114652592866\t-1\t4.70166294960891\t73\n+chr1\t950809\t951069\t.\t463\t.\t72.5405578909692\t-1\t4.70166294960891\t130\n+chr1\t954656\t954916\t.\t292\t.\t45.7358653753978\t-1\t4.05131462879512\t130\n+chr1\t968380\t968640\t.\t130\t.\t20.4976290985147\t-1\t4.25003433376609\t130\n+chr1\t994636\t994896\t.\t130\t.\t20.3680056919533\t-1\t4.25131207302333\t130\n+chr1\t999288\t999464\t.\t955\t.\t149.626770577348\t-1\t4.70166294960891\t79\n+chr1\t1057574\t1057753\t.\t906\t.\t141.813097699228\t-1\t4.70166294960891\t64\n+chr1\t1166087\t1166347\t.\t118\t.\t18.5490550747838\t-1\t4.27200414624258\t130\n+chr1\t1200451\t1200711\t.\t535\t.\t83.7415377279029\t-1\t4.70166294960891\t130\n+chr1\t1225638\t1225785\t.\t679\t.\t106.325339928315\t-1\t4.70166294960891\t85\n+chr1\t1227309\t1227479\t.\t921\t.\t144.208733477738\t-1\t4.70166294960891\t86\n+chr1\t1235456\t1235716\t.\t603\t.\t94.4024652018722\t-1\t4.70166294960891\t130\n+chr1\t1237363\t1237623\t.\t619\t.\t97.0285460159987\t-1\t4.70166294960891\t130\n+chr1\t1245750\t1246010\t.\t119\t.\t18.655650294742\t-1\t4.2707673160862\t130\n+chr1\t1280110\t1280269\t.\t775\t.\t121.413652365475\t-1\t4.70166294960891\t60\n+chr1\t1285194\t1285454\t.\t274\t.\t43.0086645203508\t-1\t4.0678813777041\t130\n+chr1\t1307509\t1307726\t.\t1000\t.\t171.992836438191\t-1\t4.70166294960891\t107\n+chr1\t1310526\t1310786\t.\t189\t.\t29.6986099222773\t-1\t4.16519088947637\t130\n+chr1\t1311758\t1312018\t.\t164\t.\t25.8209279235507\t-1\t4.19769397508306\t130\n+chr1\t1334823\t1335083\t.\t445\t.\t69.7250464568292\t-1\t4.70166294960891\t130\n+chr1\t1337440\t1337652\t.\t957\t.\t149.829641936127\t-1\t4.70166294960891\t105\n+chr1\t1376351\t1376589\t.\t1000\t.\t226.433834114974\t-1\t4.70166294960891\t116\n+chr1\t1440332\t1440592\t.\t323\t.\t50.6341706866749\t-1\t4.24443381798293\t130\n+chr1\t1440937\t1441197\t.\t140\t.\t22.0517905650777\t-1\t4.2336305801636\t130\n+chr1\t1486621\t1486881\t.\t186\t.\t29.237703150745\t-1\t4.1688685671706\t130\n+chr1\t1533087\t1533347\t.\t373\t.\t58.4724193146654\t-1\t4.70166294960891\t130\n+chr1\t1555508\t1555768\t.\t474\t.\t74.2815232999171\t-1\t4.70166294960891\t130\n+chr1\t1590703\t1590963\t.\t168\t.\t26.4269798580874\t-1\t4.19221608463264\t130\n+chr1\t1597222\t1597361\t.\t796\t.\t124.728586457261\t-1\t4.70166294960891\t87\n+chr1\t1656000\t1656260\t.\t188\t.\t29.4917183043797\t-1\t4.16666096569766\t130\n+chr1\t1710404\t1710664\t.\t264\t.\t41.4688176076288\t-1\t4.07772391714127\t130\n+chr1\t1720526\t1720786\t.\t539\t.\t84.3975708725038\t-1\t4.70166294960891\t130\n+chr1\t1727965\t1728225\t.\t180\t.\t28.2101392093569\t-1\t4.17696475958262\t130\n+chr1\t1790072\t1790332\t.\t459\t.\t71.8610423443221\t-1\t4.70166294960891\t130\n+chr1\t1830681\t1830941\t.\t149\t.\t23.4128553132653\t-1\t4.21957928740638\t130\n+chr1\t1837739\t1837962\t.\t1000\t.\t185.052392146614\t-1\t4.70166294960891\t112\n+chr1\t1840438\t1840698\t.\t397\t.\t62.1621574425913\t-1\t4.70166294960891\t130\n+chr1\t1875487\t1875696\t.\t1000\t.\t165.323985071588\t-1\t4.70166294960891\t122\n+chr1\t1886319\t1886579\t.\t348\t.\t54.494355557585\t-1\t4.70166294960891\t130\n+chr1\t1891560\t1891760\t.\t1000\t.\t159.402915506789\t-1\t4.70166294960891\t101\n+chr1\t1976406\t1976510\t.\t498\t.\t78.0232572941538\t-1\t4.70166294960891\t40\n+chr1\t1978001\t1978192\t.\t974\t.\t152.550529150405\t-1\t4.70166294960891\t95\n+chr1\t1980914\t1981174\t.\t529\t.\t82.8619944304513\t-1\t4.7016629496089'..b'487\t-1\t4.16059456927689\t130\n+chr1\t8499583\t8499843\t.\t511\t.\t80.0245797492564\t-1\t4.70166294960891\t130\n+chr1\t8503614\t8503874\t.\t136\t.\t21.3409038909194\t-1\t4.2411329071092\t130\n+chr1\t8621145\t8621405\t.\t410\t.\t64.2036467575091\t-1\t4.70166294960891\t130\n+chr1\t8658137\t8658397\t.\t261\t.\t40.9386364433157\t-1\t4.08100867099317\t130\n+chr1\t8731478\t8731587\t.\t622\t.\t97.3849807247921\t-1\t4.7016629496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b
diff -r 000000000000 -r 4bff424dfa47 test-data/input_CTCF_motifs_hg19_chr1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_CTCF_motifs_hg19_chr1.bed Tue May 02 15:05:59 2017 -0400
b
b'@@ -0,0 +1,264 @@\n+chr1\t24782\t24800\t.\t11.60\t-\n+chr1\t91420\t91438\t.\t8.57\t+\n+chr1\t135612\t135630\t.\t8.74\t+\n+chr1\t138971\t138989\t.\t8.35\t+\n+chr1\t325146\t325164\t.\t8.34\t-\n+chr1\t327724\t327742\t.\t9.00\t-\n+chr1\t369529\t369547\t.\t10.88\t-\n+chr1\t383613\t383631\t.\t8.58\t+\n+chr1\t423194\t423212\t.\t8.21\t-\n+chr1\t437646\t437664\t.\t8.76\t-\n+chr1\t438122\t438140\t.\t8.16\t-\n+chr1\t441994\t442012\t.\t9.05\t-\n+chr1\t461938\t461956\t.\t9.32\t-\n+chr1\t521533\t521551\t.\t8.98\t+\n+chr1\t544763\t544781\t.\t8.25\t+\n+chr1\t561393\t561411\t.\t8.49\t+\n+chr1\t606065\t606083\t.\t8.20\t-\n+chr1\t620146\t620164\t.\t10.88\t+\n+chr1\t621450\t621468\t.\t8.33\t+\n+chr1\t661978\t661996\t.\t8.70\t+\n+chr1\t664459\t664477\t.\t8.36\t+\n+chr1\t730231\t730249\t.\t9.43\t+\n+chr1\t739162\t739180\t.\t8.40\t+\n+chr1\t793459\t793477\t.\t8.76\t-\n+chr1\t793464\t793482\t.\t8.87\t+\n+chr1\t805298\t805316\t.\t8.37\t+\n+chr1\t919697\t919715\t.\t13.09\t+\n+chr1\t967961\t967979\t.\t9.19\t+\n+chr1\t999344\t999362\t.\t12.46\t-\n+chr1\t1153543\t1153561\t.\t8.12\t-\n+chr1\t1237496\t1237514\t.\t10.75\t+\n+chr1\t1248359\t1248377\t.\t10.31\t+\n+chr1\t1285330\t1285348\t.\t10.67\t+\n+chr1\t1337539\t1337557\t.\t13.03\t-\n+chr1\t1365952\t1365970\t.\t10.14\t+\n+chr1\t1376447\t1376465\t.\t9.24\t-\n+chr1\t1483562\t1483580\t.\t12.35\t+\n+chr1\t1542346\t1542364\t.\t8.26\t-\n+chr1\t1565745\t1565763\t.\t11.98\t+\n+chr1\t1580425\t1580443\t.\t9.60\t+\n+chr1\t1597305\t1597323\t.\t8.19\t-\n+chr1\t1624393\t1624411\t.\t8.82\t-\n+chr1\t1643641\t1643659\t.\t9.60\t+\n+chr1\t1720652\t1720670\t.\t9.53\t+\n+chr1\t1840568\t1840586\t.\t8.29\t-\n+chr1\t1905883\t1905901\t.\t8.62\t-\n+chr1\t1961688\t1961706\t.\t9.26\t-\n+chr1\t1978075\t1978093\t.\t11.00\t-\n+chr1\t1986280\t1986298\t.\t8.54\t+\n+chr1\t2024648\t2024666\t.\t8.63\t-\n+chr1\t2040690\t2040708\t.\t9.00\t-\n+chr1\t2046245\t2046263\t.\t8.48\t+\n+chr1\t2057549\t2057567\t.\t8.78\t-\n+chr1\t2105895\t2105913\t.\t13.21\t-\n+chr1\t2126788\t2126806\t.\t9.04\t+\n+chr1\t2262537\t2262555\t.\t8.41\t-\n+chr1\t2313354\t2313372\t.\t8.78\t-\n+chr1\t2345207\t2345225\t.\t8.11\t-\n+chr1\t2345992\t2346010\t.\t11.43\t+\n+chr1\t2361669\t2361687\t.\t8.34\t+\n+chr1\t2407816\t2407834\t.\t8.91\t+\n+chr1\t2445478\t2445496\t.\t8.49\t-\n+chr1\t2479625\t2479643\t.\t12.60\t-\n+chr1\t2486269\t2486287\t.\t9.03\t+\n+chr1\t2486885\t2486903\t.\t8.77\t+\n+chr1\t2633376\t2633394\t.\t8.97\t-\n+chr1\t2703363\t2703381\t.\t13.82\t-\n+chr1\t2738726\t2738744\t.\t8.75\t+\n+chr1\t2792669\t2792687\t.\t9.89\t+\n+chr1\t2849286\t2849304\t.\t8.82\t-\n+chr1\t2933594\t2933612\t.\t8.09\t+\n+chr1\t3052547\t3052565\t.\t8.43\t+\n+chr1\t3140947\t3140965\t.\t8.99\t-\n+chr1\t3246365\t3246383\t.\t10.74\t-\n+chr1\t3267550\t3267568\t.\t9.26\t+\n+chr1\t3273880\t3273898\t.\t9.70\t-\n+chr1\t3296917\t3296935\t.\t8.87\t+\n+chr1\t3320102\t3320120\t.\t10.52\t+\n+chr1\t3333855\t3333873\t.\t9.18\t+\n+chr1\t3341433\t3341451\t.\t8.61\t-\n+chr1\t3347998\t3348016\t.\t9.54\t+\n+chr1\t3349663\t3349681\t.\t8.67\t+\n+chr1\t3376357\t3376375\t.\t9.87\t-\n+chr1\t3382584\t3382602\t.\t10.07\t-\n+chr1\t3407953\t3407971\t.\t11.86\t+\n+chr1\t3408442\t3408460\t.\t8.53\t+\n+chr1\t3423109\t3423127\t.\t10.46\t-\n+chr1\t3434938\t3434956\t.\t8.55\t+\n+chr1\t3436684\t3436702\t.\t8.29\t-\n+chr1\t3452621\t3452639\t.\t9.39\t-\n+chr1\t3481967\t3481985\t.\t9.22\t+\n+chr1\t3531884\t3531902\t.\t8.50\t-\n+chr1\t3535747\t3535765\t.\t9.34\t-\n+chr1\t3542367\t3542385\t.\t8.58\t+\n+chr1\t3641147\t3641165\t.\t14.34\t-\n+chr1\t3727627\t3727645\t.\t8.64\t-\n+chr1\t3751468\t3751486\t.\t8.16\t+\n+chr1\t3799933\t3799951\t.\t9.25\t+\n+chr1\t3807877\t3807895\t.\t11.43\t-\n+chr1\t3818910\t3818928\t.\t8.26\t+\n+chr1\t3821548\t3821566\t.\t8.42\t+\n+chr1\t4043603\t4043621\t.\t8.28\t+\n+chr1\t4061703\t4061721\t.\t8.37\t+\n+chr1\t4104872\t4104890\t.\t9.05\t+\n+chr1\t4107885\t4107903\t.\t8.42\t+\n+chr1\t4194096\t4194114\t.\t8.25\t-\n+chr1\t4238871\t4238889\t.\t12.03\t-\n+chr1\t4335823\t4335841\t.\t8.35\t-\n+chr1\t4488503\t4488521\t.\t8.51\t-\n+chr1\t4623941\t4623959\t.\t8.18\t+\n+chr1\t4712805\t4712823\t.\t10.14\t+\n+chr1\t4751697\t4751715\t.\t8.53\t+\n+chr1\t4828777\t4828795\t.\t9.21\t-\n+chr1\t4838049\t4838067\t.\t10.99\t-\n+chr1\t4876312\t4876330\t.\t8.65\t-\n+chr1\t4886318\t4886336\t.\t8.85\t-\n+chr1\t4897900\t4897918\t.\t8.61\t+\n+chr1\t4990007\t4990025\t.\t8.75\t+\n+chr1\t5074536\t5074554\t.\t8.19\t-\n+chr1\t5322193\t5322211\t.\t9.59\t-\n+chr1\t5335410\t5335428\t.\t10.31\t-\n+chr1\t5335709\t5335727\t.\t9.13\t-\n+chr1\t5346504\t5346522\t.\t8.24\t+\n+chr1\t5352116\t5352134\t.\t9.03\t+\n+chr1\t5373579\t5373597\t.\t11.07\t-\n+chr1\t5396186\t5396204\t.\t10.44\t-\n+chr1\t5411648\t5411666\t.\t9.94\t-\n+chr1\t5454376\t5454394\t.\t8.34\t+\n+chr1\t5482012\t5482030\t.\t10.80\t-\n+chr1\t5507520'..b'7\t.\t8.73\t+\n+chr1\t5924843\t5924861\t.\t8.68\t+\n+chr1\t5968279\t5968297\t.\t8.20\t+\n+chr1\t5973713\t5973731\t.\t8.38\t+\n+chr1\t5976224\t5976242\t.\t13.41\t-\n+chr1\t5987361\t5987379\t.\t8.68\t+\n+chr1\t6007123\t6007141\t.\t9.03\t+\n+chr1\t6088817\t6088835\t.\t10.76\t-\n+chr1\t6101685\t6101703\t.\t12.09\t+\n+chr1\t6113156\t6113174\t.\t8.36\t+\n+chr1\t6170165\t6170183\t.\t10.58\t-\n+chr1\t6228344\t6228362\t.\t8.16\t+\n+chr1\t6228766\t6228784\t.\t9.00\t+\n+chr1\t6231762\t6231780\t.\t9.23\t-\n+chr1\t6246031\t6246049\t.\t10.23\t-\n+chr1\t6298871\t6298889\t.\t11.80\t+\n+chr1\t6306947\t6306965\t.\t11.53\t+\n+chr1\t6337252\t6337270\t.\t8.27\t-\n+chr1\t6403664\t6403682\t.\t9.10\t-\n+chr1\t6408167\t6408185\t.\t10.01\t+\n+chr1\t6417490\t6417508\t.\t10.56\t-\n+chr1\t6454270\t6454288\t.\t8.77\t+\n+chr1\t6464896\t6464914\t.\t10.13\t-\n+chr1\t6483678\t6483696\t.\t11.45\t+\n+chr1\t6498252\t6498270\t.\t9.56\t-\n+chr1\t6515763\t6515781\t.\t9.34\t-\n+chr1\t6532644\t6532662\t.\t10.17\t-\n+chr1\t6535733\t6535751\t.\t12.17\t-\n+chr1\t6546696\t6546714\t.\t8.99\t+\n+chr1\t6550098\t6550116\t.\t9.27\t-\n+chr1\t6583856\t6583874\t.\t10.98\t-\n+chr1\t6614661\t6614679\t.\t10.39\t-\n+chr1\t6645858\t6645876\t.\t8.28\t+\n+chr1\t6669839\t6669857\t.\t9.27\t-\n+chr1\t6694836\t6694854\t.\t10.35\t-\n+chr1\t6700263\t6700281\t.\t8.12\t-\n+chr1\t6718908\t6718926\t.\t10.06\t+\n+chr1\t6724881\t6724899\t.\t8.90\t-\n+chr1\t6780225\t6780243\t.\t12.26\t+\n+chr1\t6838445\t6838463\t.\t9.81\t+\n+chr1\t6854393\t6854411\t.\t10.13\t+\n+chr1\t6950120\t6950138\t.\t14.72\t-\n+chr1\t6967421\t6967439\t.\t8.95\t-\n+chr1\t6998929\t6998947\t.\t9.60\t+\n+chr1\t7022270\t7022288\t.\t8.38\t+\n+chr1\t7046703\t7046721\t.\t10.01\t-\n+chr1\t7102954\t7102972\t.\t12.60\t+\n+chr1\t7130636\t7130654\t.\t13.02\t-\n+chr1\t7179512\t7179530\t.\t8.89\t+\n+chr1\t7181107\t7181125\t.\t8.75\t-\n+chr1\t7187579\t7187597\t.\t9.61\t-\n+chr1\t7253092\t7253110\t.\t8.50\t-\n+chr1\t7284985\t7285003\t.\t10.57\t+\n+chr1\t7292255\t7292273\t.\t8.94\t+\n+chr1\t7318945\t7318963\t.\t8.98\t+\n+chr1\t7323254\t7323272\t.\t8.57\t+\n+chr1\t7345093\t7345111\t.\t8.60\t-\n+chr1\t7361183\t7361201\t.\t8.16\t+\n+chr1\t7402836\t7402854\t.\t9.21\t-\n+chr1\t7465950\t7465968\t.\t8.88\t+\n+chr1\t7468737\t7468755\t.\t8.72\t-\n+chr1\t7510669\t7510687\t.\t8.28\t-\n+chr1\t7514304\t7514322\t.\t8.71\t+\n+chr1\t7521017\t7521035\t.\t8.26\t-\n+chr1\t7530829\t7530847\t.\t8.19\t-\n+chr1\t7532562\t7532580\t.\t8.15\t+\n+chr1\t7535066\t7535084\t.\t8.48\t-\n+chr1\t7570434\t7570452\t.\t8.57\t-\n+chr1\t7707466\t7707484\t.\t16.00\t-\n+chr1\t7727766\t7727784\t.\t10.49\t+\n+chr1\t7729700\t7729718\t.\t9.95\t+\n+chr1\t7736018\t7736036\t.\t8.17\t+\n+chr1\t7741894\t7741912\t.\t8.26\t-\n+chr1\t7754629\t7754647\t.\t8.96\t+\n+chr1\t7778242\t7778260\t.\t8.35\t+\n+chr1\t7813055\t7813073\t.\t15.10\t-\n+chr1\t7815693\t7815711\t.\t9.14\t-\n+chr1\t7829513\t7829531\t.\t9.78\t+\n+chr1\t7858535\t7858553\t.\t9.58\t+\n+chr1\t7962994\t7963012\t.\t12.78\t-\n+chr1\t8035503\t8035521\t.\t8.15\t+\n+chr1\t8042535\t8042553\t.\t15.12\t+\n+chr1\t8075231\t8075249\t.\t12.07\t+\n+chr1\t8091437\t8091455\t.\t11.63\t+\n+chr1\t8374532\t8374550\t.\t9.51\t-\n+chr1\t8399473\t8399491\t.\t8.64\t+\n+chr1\t8409222\t8409240\t.\t13.01\t-\n+chr1\t8508197\t8508215\t.\t8.26\t-\n+chr1\t8520421\t8520439\t.\t8.31\t+\n+chr1\t8566289\t8566307\t.\t11.73\t+\n+chr1\t8583818\t8583836\t.\t8.21\t+\n+chr1\t8631369\t8631387\t.\t15.23\t-\n+chr1\t8676561\t8676579\t.\t10.15\t+\n+chr1\t8676966\t8676984\t.\t8.93\t+\n+chr1\t8709844\t8709862\t.\t9.84\t+\n+chr1\t8731548\t8731566\t.\t9.33\t-\n+chr1\t8786649\t8786667\t.\t8.55\t-\n+chr1\t8786753\t8786771\t.\t8.70\t-\n+chr1\t8875129\t8875147\t.\t11.06\t+\n+chr1\t8909134\t8909152\t.\t9.68\t-\n+chr1\t8919644\t8919662\t.\t9.30\t+\n+chr1\t8922695\t8922713\t.\t9.69\t+\n+chr1\t8931786\t8931804\t.\t9.64\t+\n+chr1\t9023141\t9023159\t.\t11.44\t+\n+chr1\t9048276\t9048294\t.\t9.35\t-\n+chr1\t9070258\t9070276\t.\t8.32\t+\n+chr1\t9084921\t9084939\t.\t9.61\t-\n+chr1\t9170987\t9171005\t.\t12.18\t+\n+chr1\t9202479\t9202497\t.\t10.06\t+\n+chr1\t9241504\t9241522\t.\t10.86\t+\n+chr1\t9294646\t9294664\t.\t9.01\t+\n+chr1\t9333561\t9333579\t.\t10.61\t-\n+chr1\t9349239\t9349257\t.\t13.61\t+\n+chr1\t9493871\t9493889\t.\t8.14\t-\n+chr1\t9551297\t9551315\t.\t11.15\t-\n+chr1\t9555464\t9555482\t.\t11.25\t+\n+chr1\t9633140\t9633158\t.\t10.18\t-\n+chr1\t9637151\t9637169\t.\t11.04\t+\n+chr1\t9661302\t9661320\t.\t9.05\t-\n+chr1\t9687242\t9687260\t.\t13.42\t+\n+chr1\t9782023\t9782041\t.\t8.76\t+\n+chr1\t9785220\t9785238\t.\t8.88\t-\n+chr1\t9785272\t9785290\t.\t11.83\t+\n+chr1\t9844779\t9844797\t.\t11.56\t+\n+chr1\t9846805\t9846823\t.\t8.15\t-\n+chr1\t9921005\t9921023\t.\t8.80\t+\n+chr1\t9927707\t9927725\t.\t13.11\t-\n+chr1\t9935097\t9935115\t.\t14.99\t+\n'
b
diff -r 000000000000 -r 4bff424dfa47 test-data/input_SeqBias_ATAC.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_SeqBias_ATAC.txt Tue May 02 15:05:59 2017 -0400
b
b'@@ -0,0 +1,4096 @@\n+AAAAAA\t0.153871\n+AAAAAC\t0.368301\n+AAAAAG\t0.308933\n+AAAAAT\t0.331687\n+AAAACA\t0.840427\n+AAAACC\t1.27986\n+AAAACG\t0.652305\n+AAAACT\t0.952561\n+AAAAGA\t0.5023\n+AAAAGC\t0.75897\n+AAAAGG\t0.535813\n+AAAAGT\t0.68961\n+AAAATA\t1.15808\n+AAAATC\t1.03609\n+AAAATG\t0.865791\n+AAAATT\t0.618362\n+AAACAA\t1.21722\n+AAACAC\t1.73801\n+AAACAG\t1.16132\n+AAACAT\t2.59454\n+AAACCA\t1.79943\n+AAACCC\t2.30419\n+AAACCG\t1.14883\n+AAACCT\t3.122\n+AAACGA\t0.826049\n+AAACGC\t1.38568\n+AAACGG\t0.841398\n+AAACGT\t1.85954\n+AAACTA\t2.7081\n+AAACTC\t2.62284\n+AAACTG\t1.41811\n+AAACTT\t1.96681\n+AAAGAA\t1.79194\n+AAAGAC\t1.98906\n+AAAGAG\t1.91639\n+AAAGAT\t2.68382\n+AAAGCA\t2.07637\n+AAAGCC\t2.96454\n+AAAGCG\t1.77491\n+AAAGCT\t2.87299\n+AAAGGA\t2.22903\n+AAAGGC\t2.63817\n+AAAGGG\t2.2479\n+AAAGGT\t3.61029\n+AAAGTA\t4.55623\n+AAAGTC\t3.77663\n+AAAGTG\t3.7259\n+AAAGTT\t2.84517\n+AAATAA\t0.430302\n+AAATAC\t0.501123\n+AAATAG\t0.482748\n+AAATAT\t0.834716\n+AAATCA\t0.472434\n+AAATCC\t0.846793\n+AAATCG\t0.302385\n+AAATCT\t0.750168\n+AAATGA\t0.383766\n+AAATGC\t0.627809\n+AAATGG\t0.3627\n+AAATGT\t0.77905\n+AAATTA\t0.447959\n+AAATTC\t0.573359\n+AAATTG\t0.371636\n+AAATTT\t0.305727\n+AACAAA\t0.168769\n+AACAAC\t0.167234\n+AACAAG\t0.169468\n+AACAAT\t0.191942\n+AACACA\t0.352504\n+AACACC\t0.617191\n+AACACG\t0.221886\n+AACACT\t0.521445\n+AACAGA\t0.172395\n+AACAGC\t0.228142\n+AACAGG\t0.157018\n+AACAGT\t0.252264\n+AACATA\t0.80307\n+AACATC\t0.800986\n+AACATG\t0.472928\n+AACATT\t0.608034\n+AACCAA\t0.363509\n+AACCAC\t0.372171\n+AACCAG\t0.272435\n+AACCAT\t0.542391\n+AACCCA\t0.34006\n+AACCCC\t0.546447\n+AACCCG\t0.119428\n+AACCCT\t0.713034\n+AACCGA\t0.143926\n+AACCGC\t0.215877\n+AACCGG\t0.140766\n+AACCGT\t0.324729\n+AACCTA\t0.763079\n+AACCTC\t0.765182\n+AACCTG\t0.383618\n+AACCTT\t0.655634\n+AACGAA\t0.634171\n+AACGAC\t0.500751\n+AACGAG\t0.520789\n+AACGAT\t0.710008\n+AACGCA\t0.614443\n+AACGCC\t0.80997\n+AACGCG\t0.395809\n+AACGCT\t1.00107\n+AACGGA\t0.534063\n+AACGGC\t0.553055\n+AACGGG\t0.579845\n+AACGGT\t0.915745\n+AACGTA\t1.97055\n+AACGTC\t1.75047\n+AACGTG\t1.23476\n+AACGTT\t1.52329\n+AACTAA\t0.102511\n+AACTAC\t0.0715876\n+AACTAG\t0.0748125\n+AACTAT\t0.091305\n+AACTCA\t0.111577\n+AACTCC\t0.12993\n+AACTCG\t0.0526311\n+AACTCT\t0.218459\n+AACTGA\t0.0415657\n+AACTGC\t0.0598108\n+AACTGG\t0.0344466\n+AACTGT\t0.0731387\n+AACTTA\t0.156884\n+AACTTC\t0.201986\n+AACTTG\t0.108349\n+AACTTT\t0.103407\n+AAGAAA\t0.34123\n+AAGAAC\t0.399472\n+AAGAAG\t0.378589\n+AAGAAT\t0.409776\n+AAGACA\t0.768645\n+AAGACC\t1.13809\n+AAGACG\t0.529588\n+AAGACT\t0.96179\n+AAGAGA\t0.52593\n+AAGAGC\t0.644551\n+AAGAGG\t0.484844\n+AAGAGT\t0.724822\n+AAGATA\t1.47466\n+AAGATC\t1.13478\n+AAGATG\t0.874436\n+AAGATT\t0.871327\n+AAGCAA\t0.612985\n+AAGCAC\t0.683868\n+AAGCAG\t0.548577\n+AAGCAT\t1.05336\n+AAGCCA\t0.720704\n+AAGCCC\t1.22022\n+AAGCCG\t0.342183\n+AAGCCT\t1.2725\n+AAGCGA\t0.379913\n+AAGCGC\t0.526077\n+AAGCGG\t0.307676\n+AAGCGT\t0.789501\n+AAGCTA\t1.23829\n+AAGCTC\t1.13391\n+AAGCTG\t0.65095\n+AAGCTT\t1.07663\n+AAGGAA\t1.77232\n+AAGGAC\t1.62171\n+AAGGAG\t1.59042\n+AAGGAT\t2.1927\n+AAGGCA\t1.10713\n+AAGGCC\t1.98211\n+AAGGCG\t0.643766\n+AAGGCT\t1.87306\n+AAGGGA\t1.69139\n+AAGGGC\t2.02792\n+AAGGGG\t1.63759\n+AAGGGT\t2.87224\n+AAGGTA\t3.76282\n+AAGGTC\t3.51276\n+AAGGTG\t2.43394\n+AAGGTT\t2.93026\n+AAGTAA\t0.211311\n+AAGTAC\t0.180183\n+AAGTAG\t0.201428\n+AAGTAT\t0.245702\n+AAGTCA\t0.208853\n+AAGTCC\t0.354399\n+AAGTCG\t0.185505\n+AAGTCT\t0.317537\n+AAGTGA\t0.176256\n+AAGTGC\t0.143823\n+AAGTGG\t0.167827\n+AAGTGT\t0.236418\n+AAGTTA\t0.284882\n+AAGTTC\t0.263376\n+AAGTTG\t0.206463\n+AAGTTT\t0.154464\n+AATAAA\t0.395943\n+AATAAC\t0.490818\n+AATAAG\t0.405935\n+AATAAT\t0.551631\n+AATACA\t0.72643\n+AATACC\t1.53202\n+AATACG\t0.699368\n+AATACT\t1.22329\n+AATAGA\t0.499855\n+AATAGC\t0.774619\n+AATAGG\t0.514372\n+AATAGT\t0.885523\n+AATATA\t1.76714\n+AATATC\t1.69309\n+AATATG\t1.26117\n+AATATT\t1.37124\n+AATCAA\t0.61339\n+AATCAC\t0.73178\n+AATCAG\t0.499782\n+AATCAT\t1.05513\n+AATCCA\t0.655735\n+AATCCC\t0.795584\n+AATCCG\t0.518338\n+AATCCT\t1.50452\n+AATCGA\t0.297304\n+AATCGC\t0.497983\n+AATCGG\t0.237361\n+AATCGT\t0.636953\n+AATCTA\t1.39863\n+AATCTC\t1.32898\n+AATCTG\t0.847962\n+AATCTT\t1.25143\n+AATGAA\t1.22133\n+AATGAC\t1.06046\n+AATGAG\t1.15216\n+AATGAT\t1.56683\n+AATGCA\t1.1273\n+AATGCC\t1.71667\n+AATGCG\t1.08871\n+AATGCT\t1.86029\n+AATGGA\t1.25712\n+AATGGC\t1.35497\n+AATGGG\t1.15779\n+AATGGT\t1.98378\n+AATGTA\t3.34451\n+AATGTC\t3.06291\n+AATGTG\t2.35558\n+AATGTT\t2.69828\n+AATTAA\t'..b'TTACAC\t0.984861\n+TTACAG\t0.543294\n+TTACAT\t1.5325\n+TTACCA\t1.27127\n+TTACCC\t1.89003\n+TTACCG\t0.884597\n+TTACCT\t2.1041\n+TTACGA\t0.453445\n+TTACGC\t0.727426\n+TTACGG\t0.452655\n+TTACGT\t1.01335\n+TTACTA\t2.22215\n+TTACTC\t1.87707\n+TTACTG\t1.18943\n+TTACTT\t1.64377\n+TTAGAA\t1.33671\n+TTAGAC\t1.24798\n+TTAGAG\t1.33249\n+TTAGAT\t1.7924\n+TTAGCA\t1.70012\n+TTAGCC\t1.35228\n+TTAGCG\t1.37528\n+TTAGCT\t1.73238\n+TTAGGA\t1.4728\n+TTAGGC\t1.80818\n+TTAGGG\t1.50527\n+TTAGGT\t2.3495\n+TTAGTA\t2.92722\n+TTAGTC\t3.04203\n+TTAGTG\t2.58568\n+TTAGTT\t2.45679\n+TTATAA\t0.283038\n+TTATAC\t0.369991\n+TTATAG\t0.323842\n+TTATAT\t0.436896\n+TTATCA\t0.47848\n+TTATCC\t0.828039\n+TTATCG\t0.334063\n+TTATCT\t0.697427\n+TTATGA\t0.241664\n+TTATGC\t0.444936\n+TTATGG\t0.263865\n+TTATGT\t0.44444\n+TTATTA\t0.552797\n+TTATTC\t0.594055\n+TTATTG\t0.379603\n+TTATTT\t0.353785\n+TTCAAA\t0.166361\n+TTCAAC\t0.198514\n+TTCAAG\t0.172805\n+TTCAAT\t0.18606\n+TTCACA\t0.322338\n+TTCACC\t0.47101\n+TTCACG\t0.241084\n+TTCACT\t0.543429\n+TTCAGA\t0.136455\n+TTCAGC\t0.203354\n+TTCAGG\t0.118706\n+TTCAGT\t0.20925\n+TTCATA\t0.637921\n+TTCATC\t0.701688\n+TTCATG\t0.422474\n+TTCATT\t0.560722\n+TTCCAA\t0.26479\n+TTCCAC\t0.325134\n+TTCCAG\t0.211611\n+TTCCAT\t0.428375\n+TTCCCA\t0.393442\n+TTCCCC\t0.812246\n+TTCCCG\t0.221234\n+TTCCCT\t0.829969\n+TTCCGA\t0.117276\n+TTCCGC\t0.204436\n+TTCCGG\t0.0990103\n+TTCCGT\t0.225113\n+TTCCTA\t0.761636\n+TTCCTC\t0.840975\n+TTCCTG\t0.376673\n+TTCCTT\t0.716179\n+TTCGAA\t0.388806\n+TTCGAC\t0.365877\n+TTCGAG\t0.193203\n+TTCGAT\t0.470606\n+TTCGCA\t0.442066\n+TTCGCC\t0.487296\n+TTCGCG\t0.227382\n+TTCGCT\t0.67754\n+TTCGGA\t0.280611\n+TTCGGC\t0.363919\n+TTCGGG\t0.300583\n+TTCGGT\t0.554833\n+TTCGTA\t1.30355\n+TTCGTC\t1.21392\n+TTCGTG\t0.858303\n+TTCGTT\t1.04132\n+TTCTAA\t0.0807059\n+TTCTAC\t0.0882522\n+TTCTAG\t0.068444\n+TTCTAT\t0.0755558\n+TTCTCA\t0.142714\n+TTCTCC\t0.301882\n+TTCTCG\t0.0963247\n+TTCTCT\t0.267836\n+TTCTGA\t0.0319241\n+TTCTGC\t0.0492803\n+TTCTGG\t0.0225439\n+TTCTGT\t0.0488196\n+TTCTTA\t0.19579\n+TTCTTC\t0.252606\n+TTCTTG\t0.134837\n+TTCTTT\t0.142101\n+TTGAAA\t0.319821\n+TTGAAC\t0.358994\n+TTGAAG\t0.336209\n+TTGAAT\t0.388022\n+TTGACA\t0.696581\n+TTGACC\t1.02721\n+TTGACG\t0.546828\n+TTGACT\t0.795844\n+TTGAGA\t0.435192\n+TTGAGC\t0.515186\n+TTGAGG\t0.462014\n+TTGAGT\t0.549597\n+TTGATA\t1.16973\n+TTGATC\t1.07763\n+TTGATG\t0.741343\n+TTGATT\t0.812368\n+TTGCAA\t0.380301\n+TTGCAC\t0.439677\n+TTGCAG\t0.324349\n+TTGCAT\t0.600908\n+TTGCCA\t0.434754\n+TTGCCC\t0.621888\n+TTGCCG\t0.30894\n+TTGCCT\t0.794587\n+TTGCGA\t0.21469\n+TTGCGC\t0.441588\n+TTGCGG\t0.176994\n+TTGCGT\t0.404176\n+TTGCTA\t0.925662\n+TTGCTC\t0.754274\n+TTGCTG\t0.46687\n+TTGCTT\t0.721938\n+TTGGAA\t0.978285\n+TTGGAC\t0.886098\n+TTGGAG\t0.912242\n+TTGGAT\t1.31232\n+TTGGCA\t0.791668\n+TTGGCC\t0.861884\n+TTGGCG\t0.517906\n+TTGGCT\t1.04393\n+TTGGGA\t0.643488\n+TTGGGC\t1.03162\n+TTGGGG\t0.883592\n+TTGGGT\t1.53643\n+TTGGTA\t2.44881\n+TTGGTC\t2.09818\n+TTGGTG\t1.71135\n+TTGGTT\t1.73004\n+TTGTAA\t0.135408\n+TTGTAC\t0.126518\n+TTGTAG\t0.145055\n+TTGTAT\t0.115491\n+TTGTCA\t0.176753\n+TTGTCC\t0.33368\n+TTGTCG\t0.124535\n+TTGTCT\t0.266007\n+TTGTGA\t0.099688\n+TTGTGC\t0.14813\n+TTGTGG\t0.105706\n+TTGTGT\t0.139805\n+TTGTTA\t0.278497\n+TTGTTC\t0.230741\n+TTGTTG\t0.210486\n+TTGTTT\t0.129418\n+TTTAAA\t0.220004\n+TTTAAC\t0.349021\n+TTTAAG\t0.267866\n+TTTAAT\t0.381953\n+TTTACA\t0.597156\n+TTTACC\t0.989744\n+TTTACG\t0.475471\n+TTTACT\t0.90861\n+TTTAGA\t0.296099\n+TTTAGC\t0.48966\n+TTTAGG\t0.303442\n+TTTAGT\t0.511221\n+TTTATA\t0.979601\n+TTTATC\t1.07544\n+TTTATG\t0.714164\n+TTTATT\t0.848905\n+TTTCAA\t0.336621\n+TTTCAC\t0.363614\n+TTTCAG\t0.312807\n+TTTCAT\t0.614589\n+TTTCCA\t0.5014\n+TTTCCC\t1.03751\n+TTTCCG\t0.385297\n+TTTCCT\t1.0819\n+TTTCGA\t0.146292\n+TTTCGC\t0.170515\n+TTTCGG\t0.145161\n+TTTCGT\t0.32553\n+TTTCTA\t0.881692\n+TTTCTC\t1.02982\n+TTTCTG\t0.490572\n+TTTCTT\t0.838035\n+TTTGAA\t0.649174\n+TTTGAC\t0.678647\n+TTTGAG\t0.526665\n+TTTGAT\t0.951306\n+TTTGCA\t0.796307\n+TTTGCC\t1.17743\n+TTTGCG\t0.667722\n+TTTGCT\t1.31187\n+TTTGGA\t0.615429\n+TTTGGC\t0.865593\n+TTTGGG\t0.529575\n+TTTGGT\t1.15838\n+TTTGTA\t1.67544\n+TTTGTC\t2.05786\n+TTTGTG\t1.51392\n+TTTGTT\t1.54629\n+TTTTAA\t0.0876288\n+TTTTAC\t0.143857\n+TTTTAG\t0.10428\n+TTTTAT\t0.143075\n+TTTTCA\t0.174232\n+TTTTCC\t0.391372\n+TTTTCG\t0.133896\n+TTTTCT\t0.308827\n+TTTTGA\t0.0606033\n+TTTTGC\t0.120444\n+TTTTGG\t0.0643011\n+TTTTGT\t0.105175\n+TTTTTA\t0.14435\n+TTTTTC\t0.237986\n+TTTTTG\t0.111547\n+TTTTTT\t0.0675423\n'
b
diff -r 000000000000 -r 4bff424dfa47 test-data/input_hg19.chr1.chrom.size
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_hg19.chr1.chrom.size Tue May 02 15:05:59 2017 -0400
b
@@ -0,0 +1,1 @@
+chr1 10000000
b
diff -r 000000000000 -r 4bff424dfa47 test-data/input_hg19_chr1.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_hg19_chr1.fa Tue May 02 15:05:59 2017 -0400
b
b'@@ -0,0 +1,200001 @@\n+>chr1\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNN'..b'ccagcctgggcaatacagcaagactctgtctcaaaaaaaaaaaaaa\n+aaGCTGCAATGAACTGTTGTGGTCCTTTGTGCAGGTAAGGCTGAAACTAC\n+ATGCCAGAAGTTCAAGTAGTACCTTCTTAGCCTGACAGCAGGTAGGACTG\n+ATTTAAATACTAAAGACAAAGTAGGTGTTATTTCTACTtcaaggaaggta\n+agtattttgctcaagttcacatgcacttagtagttaactgaatgactttc\n+atttcccagcctttatgactccaaagcctgCAATAAGTTTACTTCTCTAA\n+TAGACAAAGCACTGCAAAGAACACTACAGGGGAATGCAGAATCATCACAC\n+ATGGGCCTGCATCCACGGAGCTAGCTGCAGAAAAAACGCCAGTTTCCAGC\n+ATAACAACATACAATTAAACTCTTACCTGCATTCCTCCAGATCTTGTAAT\n+TGTTGCATGAGTCTATCCAACTGTTCTTCTAAATTCTGCTTTAATTTGCT\n+TGTCTCTGTCTTTCCTCTGGAAGCCATTTTAATCTCTATGTGAAACAATA\n+AACCCACATACCATATGAAATTAACATACCAGTGCAATTTTTTtaagttt\n+tattttttgtagagacagagtctcactatgttgcccaggctggtctcgga\n+acatctggcctaaagtgaccctcccatcttggactaccaaagaggtggga\n+ttataggcataagccaccacacccagtcCCTAGTGCAATTAAAAATATGC\n+AGCTGCggccaggcgccggtggctcaggcctgtaatcccagcactttggg\n+aggccgaggcgggtggatcacaaggtcaggagatcaagaccatcctggct\n+aacatggtgaaaccccatctctactaaaaatacaaaaaaggccggatgtg\n+gtggctcacgcctgtaaccccagcacttttggaagccgaggtgggtggat\n+cacctgaggtcaggagttcaagaccagcctgagcaacatgggggaaaccc\n+catctctaaagagaaaaaaaggccaggcacggtgctcacgcctgtaatcc\n+cagcactttgggaggctgaggtgggcggatcatgaagtcaggagattgag\n+accatcccggctaacacggtgaaaccccgtctctcctaaaaatataaaaa\n+attaggcaggcgtggtggcaggcgcctgtagtcccagctacttgggaggc\n+tgaggcaggagaatggtgtgaacgcgggaggcagagcttgcagtgagccg\n+agatcacgccactgcactcctgcctgggcgacagagcaagactcaggctc\n+aaaaaaaaaaaaagaaaaaaaaaTTAcctgtagtcccagctatttgggag\n+gctgaggcagcaggcttgcttgaacctgggaggcagaggttgcagtgagc\n+tgagatcacgccactgcactccagcttgggcaacagagtgagactacatt\n+tcagaaaaaaaaaaaGGCAgctgggtgcagtggctcacgcatgtctgtaa\n+tctcaacactttgggagcctgaggtgggaggattgcttgagcccaggagt\n+tcgagaccagcctggccaatatagtgagacttcatctctacaaagaatag\n+acaatcttagctaggcatggtggcggatgcctctagtcccacctactcag\n+gaggcttaggtgagaggactgcttgagcccaggaatttgaggttgcagtg\n+agccatgatcttgccactccactctggcctggttgacagagcgagaccct\n+gactcaaaaaaaaaaaaaaaaaaaaaaaaGCTACAGGTATATGAAAGATA\n+GTTAAACAAAGAAAATCTTAATTTAGATATAAAAGTTTAAACTCATATAG\n+TAATAACACCCCACAAAAATACCTGAAAGTCCTCTTTATGTGACTTGACA\n+TATTAATTAGAAGTCTTCATTATTGGTCTATCTTACTCTAAACAAATTTG\n+GTAAATGGAAATATATATATATATGTAGATCAAATGTGACTTTGCTTTAT\n+AAAATGAATCATTATAGCCCCAAACACTCCagatattatcttattggtct\n+tatgtatattgacctaattacttgtgagcatgaacttttttttgagatag\n+ggtctcactctgttgcctaggctgaagcacagtggcacaatcatagctca\n+ctatagcctcaacctctcgagctcaagccatcttcccacctctgcctcct\n+gagtagctgcaaacacaggcacacaccaccacacctggctaatttatttt\n+tttgtagagatggggtctcccatgttgcccaagctggtcttgaactgggc\n+tcaagagatcctcccacctcagcctcccaaaatgctgggattataggtgt\n+aagcccacaagcccagctgatgaacatcttttaatatgaatttcttcttt\n+ggaaatgtgaccatctttctgctgggttatctttctcttactgatttata\n+ACATGGATACAAAGCCTTTGGCttttttgagacagggtcttgctctgtca\n+cccaggctggagtgcagtggcatgatcatggctcatgcagctttgacctc\n+ctaagatcaagcaatGAAGCCTTTGTAATTGCAAATATTATTTCGTCTCC\n+TGACTAAATTTTATGTTTTTTTGTCATGGCAAATTATTATTTTTTAATAG\n+ACAAATCTATCTTCTCCTTTAAATCTTCTTCGTTTTGTGACCCATGAAGG\n+CAGGCCCTAACCATCTCAAGATTTATACATCTTTATATTCAAGACTTTTA\n+CAAATTTTTGTTTTCTAGCTGCAGACAAAAGCCACCTGCAACATTTTTTG\n+TTATGCTTTGAAGTAGGGGTCTAACTTTCCTTTCAAAAACACCCTTTACT\n+AATCAGTCTTTTATTTATTGATCCAGGAGAATTTGGTCTACAATAAAGGT\n+GGCATATTGATTAATAAATAAAAGACTGACTAGTAAAGGGTATTAGGGCA\n+ATTGGCTAGTCATTGATAATTTTCTGTTCCTAAGGAATCACttctttttt\n+ttttagactgagtcttgctctgtcgccccgactggagtgcggtggcacga\n+tttcggctcactgcaacctccacctcctgggtttcagcaattctcctgcc\n+tcagcctcttgagtgcgtgccaccacgtccggctaatttttgtattttta\n+gtagaaatgtggttttgccatattggccaggtcggtcttgaactcctgac\n+ctcaaatgatccactcaccccagcctcccaaagtgctaggattacaggca\n+tgaggcaccccacttggcttttttttttttcttttttttttgacacagag\n+tatcgctctgtcacccaggctggagtgcagtaggctggagtgcagtgatg\n+tgatctcagctcactgcaacctccacatcctgggctcaagtgattctcct\n+gcctcagcctcctgagtagctaggattacaggtgtgccaccacatctgcc\n+tttttttttttttttttttttggtatttttagtagagacagtgtttcgcc\n+atgttggccttggcctcctaaaatgctgggattacaggcatgagccactg\n+tgtccagccCTCAGGCAACATTTCTTGCTATTTACattattatggcttta\n+tcactgatatatctcgataactgataatgacttgcctttattgttttctc\n+ctccccaaaattcttggctcttcttgtgcactttctcttccagatgaatt\n+taacaatcagtatgtcaagtttcattaaatatcctattgACTGGggccag\n+gcatggtgtctcacacctgtaatcccagcactttaggaggctaaggcagg\n+cagatcacttgagaccaggagttacagaccagcctggccgacacggcgaa\n'
b
diff -r 000000000000 -r 4bff424dfa47 test-data/output.PARAM
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.PARAM Tue May 02 15:05:59 2017 -0400
b
@@ -0,0 +1,2 @@
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b
diff -r 000000000000 -r 4bff424dfa47 test-data/output.RESULTS
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.RESULTS Tue May 02 15:05:59 2017 -0400
b
b'@@ -0,0 +1,265 @@\n+chr\tstart\tend\tname\tscore\tstrand\tllr\tz1\tz2\tz3\n+chr1\t24782\t24800\tregion_0\t0\t-\t0\t0.5\t0.5\t.\n+chr1\t91420\t91438\tregion_1\t0\t+\t0\t0.5\t0.5\t.\n+chr1\t135612\t135630\tregion_2\t0\t+\t0\t0.5\t0.5\t.\n+chr1\t138971\t138989\tregion_3\t0\t+\t0\t0.5\t0.5\t.\n+chr1\t325146\t325164\tregion_4\t0\t-\t0\t0.5\t0.5\t.\n+chr1\t327724\t327742\tregion_5\t0\t-\t0\t0.5\t0.5\t.\n+chr1\t369529\t369547\tregion_6\t0\t-\t0\t0.5\t0.5\t.\n+chr1\t383613\t383631\tregion_7\t0\t+\t0\t0.5\t0.5\t.\n+chr1\t423194\t423212\tregion_8\t0\t-\t0\t0.5\t0.5\t.\n+chr1\t437646\t437664\tregion_9\t0\t-\t0\t0.5\t0.5\t.\n+chr1\t438122\t438140\tregion_10\t0\t-\t0\t0.5\t0.5\t.\n+chr1\t441994\t442012\tregion_11\t0\t-\t0\t0.5\t0.5\t.\n+chr1\t461938\t461956\tregion_12\t0\t-\t0\t0.5\t0.5\t.\n+chr1\t521533\t521551\tregion_13\t0\t+\t0\t0.5\t0.5\t.\n+chr1\t544763\t544781\tregion_14\t0\t+\t0\t0.5\t0.5\t.\n+chr1\t561393\t561411\tregion_15\t0\t+\t0\t0.5\t0.5\t.\n+chr1\t606065\t606083\tregion_16\t0\t-\t0\t0.5\t0.5\t.\n+chr1\t620146\t620164\tregion_17\t0\t+\t0\t0.5\t0.5\t.\n+chr1\t621450\t621468\tregion_18\t0\t+\t0\t0.5\t0.5\t.\n+chr1\t661978\t661996\tregion_19\t0\t+\t0\t0.5\t0.5\t.\n+chr1\t664459\t664477\tregion_20\t0\t+\t0\t0.5\t0.5\t.\n+chr1\t730231\t730249\tregion_21\t0\t+\t0\t0.5\t0.5\t.\n+chr1\t739162\t739180\tregion_22\t0\t+\t0\t0.5\t0.5\t.\n+chr1\t793459\t793477\tregion_23\t0\t-\t0.580654728334897\t0.641218045397551\t0.358781954602449\t.\n+chr1\t793464\t793482\tregion_24\t0\t+\t0.514248286397137\t0.625801842716764\t0.374198157283236\t.\n+chr1\t805298\t805316\tregion_25\t0\t+\t-0.532717301480656\t0.369883343901835\t0.630116656098165\t.\n+chr1\t919697\t919715\tregion_26\t0\t+\t-0.176978657267171\t0.455870459015867\t0.544129540984133\t.\n+chr1\t967961\t967979\tregion_27\t0\t+\t-1.72643757172105\t0.151043820795562\t0.848956179204438\t.\n+chr1\t999344\t999362\tregion_28\t0\t-\t6.97742411699102\t0.999068166479157\t0.000931833520843445\t.\n+chr1\t1153543\t1153561\tregion_29\t0\t-\t-10.7129201810791\t2.22550315829411e-05\t0.999977744968417\t.\n+chr1\t1237496\t1237514\tregion_30\t0\t+\t-12.0181372193609\t6.03374153375604e-06\t0.999993966258466\t.\n+chr1\t1248359\t1248377\tregion_31\t0\t+\t-5.60065377017305\t0.00368184090581199\t0.996318159094188\t.\n+chr1\t1285330\t1285348\tregion_32\t0\t+\t6.62355308406424\t0.998673061544899\t0.0013269384551013\t.\n+chr1\t1337539\t1337557\tregion_33\t0\t-\t4.21916484336947\t0.985502348564532\t0.0144976514354677\t.\n+chr1\t1365952\t1365970\tregion_34\t0\t+\t-9.41360916193653\t8.15992273741317e-05\t0.999918400772626\t.\n+chr1\t1376447\t1376465\tregion_35\t0\t-\t5.18555731798199\t0.994434333475007\t0.00556566652499259\t.\n+chr1\t1483562\t1483580\tregion_36\t0\t+\t-1.38831028865582\t0.199677646655716\t0.800322353344284\t.\n+chr1\t1542346\t1542364\tregion_37\t0\t-\t-1.51953048697943\t0.179530667991269\t0.820469332008731\t.\n+chr1\t1565745\t1565763\tregion_38\t0\t+\t-5.48508814993825\t0.00413103317686551\t0.995868966823134\t.\n+chr1\t1580425\t1580443\tregion_39\t0\t+\t0\t0.5\t0.5\t.\n+chr1\t1597305\t1597323\tregion_40\t0\t-\t7.27541008268338\t0.999308122886148\t0.00069187711385205\t.\n+chr1\t1624393\t1624411\tregion_41\t0\t-\t0\t0.5\t0.5\t.\n+chr1\t1643641\t1643659\tregion_42\t0\t+\t0\t0.5\t0.5\t.\n+chr1\t1720652\t1720670\tregion_43\t0\t+\t-4.32786634827356\t0.0130238144547537\t0.986976185545246\t.\n+chr1\t1840568\t1840586\tregion_44\t0\t-\t-18.0925755678979\t1.38833496493192e-08\t0.99999998611665\t.\n+chr1\t1905883\t1905901\tregion_45\t0\t-\t0.565994692367397\t0.637838458604184\t0.362161541395816\t.\n+chr1\t1961688\t1961706\tregion_46\t0\t-\t3.02374992213174\t0.953635609624457\t0.0463643903755429\t.\n+chr1\t1978075\t1978093\tregion_47\t0\t-\t21.8100326587302\t0.999999999662695\t3.37305300641468e-10\t.\n+chr1\t1986280\t1986298\tregion_48\t0\t+\t-0.882694404341578\t0.292619743438358\t0.707380256561642\t.\n+chr1\t2024648\t2024666\tregion_49\t0\t-\t-2.60926454348926\t0.0685445449233132\t0.931455455076687\t.\n+chr1\t2040690\t2040708\tregion_50\t0\t-\t-2.88352578195537\t0.0529739768640288\t0.947026023135971\t.\n+chr1\t2046245\t2046263\tregion_51\t0\t+\t0.176137285406812\t0.543920828783355\t0.456079171216645\t.\n+chr1\t2057549\t2057567\tregion_52\t0\t-\t-2.43284364144376\t0.0807022474761077\t0.919297752523892\t.\n+chr1\t2105895\t2105913\tregion_53\t0\t-\t26.6911701496904\t0.99999999999744\t2.55959992309013e-12\t.\n+chr1\t2126788\t2126806\tregion_54\t0\t+\t27.3083417284077\t0.999999999998619\t1.38082257097938e-12\t.\n+chr1\t2262537\t2262555\tregion_55\t0\t-\t-3.70329714786445\t0.0240'..b'99473\t8399491\tregion_221\t0\t+\t-2.99880548706746\t0.04747986646452\t0.95252013353548\t.\n+chr1\t8409222\t8409240\tregion_222\t0\t-\t22.9171033169806\t0.999999999888512\t1.11488093320681e-10\t.\n+chr1\t8508197\t8508215\tregion_223\t0\t-\t-6.23022213246063\t0.00196514506696467\t0.998034854933035\t.\n+chr1\t8520421\t8520439\tregion_224\t0\t+\t-2.6587018954889\t0.0654546941907814\t0.934545305809218\t.\n+chr1\t8566289\t85663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b
diff -r 000000000000 -r 4bff424dfa47 test-data/output_plot1.png
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Binary file test-data/output_plot1.png has changed
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diff -r 000000000000 -r 4bff424dfa47 test-data/output_plot2.png
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Binary file test-data/output_plot2.png has changed
b
diff -r 000000000000 -r 4bff424dfa47 tool-data/sam_fa_indices.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/sam_fa_indices.loc.sample Tue May 02 15:05:59 2017 -0400
b
@@ -0,0 +1,28 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Samtools indexed sequences data files.  You will need
+#to create these data files and then create a sam_fa_indices.loc file 
+#similar to this one (store it in this directory) that points to 
+#the directories in which those files are stored. The sam_fa_indices.loc 
+#file has this format (white space characters are TAB characters):
+#
+#index <seq> <location>
+#
+#So, for example, if you had hg18 indexed stored in 
+#/depot/data2/galaxy/sam/, 
+#then the sam_fa_indices.loc entry would look like this:
+#
+#index hg18 /depot/data2/galaxy/sam/hg18.fa
+#
+#and your /depot/data2/galaxy/sam/ directory
+#would contain hg18.fa and hg18.fa.fai files:
+#
+#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 hg18.fa
+#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg18.fa.fai
+#
+#Your sam_fa_indices.loc file should include an entry per line for 
+#each index set you have stored.  The file in the path does actually
+#exist, but it should never be directly used. Instead, the name serves
+#as a prefix for the index file.  For example:
+#
+#index hg18 /depot/data2/galaxy/sam/hg18.fa
+#index hg19 /depot/data2/galaxy/sam/hg19.fa
b
diff -r 000000000000 -r 4bff424dfa47 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Tue May 02 15:05:59 2017 -0400
b
@@ -0,0 +1,6 @@
+<tables>
+    <table name="sam_fa_indices" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/sam_fa_indices.loc" />
+    </table>
+</tables>