Galaxy |

Changeset 0:f7f366ede872 (2015-07-24)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha commit ba69207568a546d7c3b71a144f78095811e3e99a-dirty

added:
piranha.xml
test-data/testPrianha_zntb_unbinned.bam
test-data/zntbr_unbinned_response.bed
test-data/ztnbBinningTestModelOutput.expected.xml
test-data/ztnbSimpleTest_output.expected.bed
test-data/ztnbSimpleTest_response.bed
test-data/ztnbrBinningTestModelOutput.expected.xml
test-data/ztnbr_binning_cov1.bed
test-data/ztnbr_binning_cov2.bed

diff -r 000000000000 -r f7f366ede872 piranha.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/piranha.xml Fri Jul 24 06:05:39 2015 -0400

[

b'@@ -0,0 +1,162 @@\n+<tool id="piranha" name="Piranha" version="0.1.0">\n+ <description>peak-caller for CLIP- and RIP-Seq data</description>\n+ <requirements>\n+ <requirement type="package" version="1.2.1">piranha</requirement>\n+ </requirements>\n+ <stdio>\n+ <exit_code range="1:" />\n+ </stdio>\n+ <command><![CDATA[\n+ ln -s $input ./foo.$input.ext &&\n+\n+ Piranha\n+ $sort\n+ #if $p_threshold:\n+ -p $p_threshold\n+ #end if\n+ $no_pval_correct\n+ #if $background_thresh:\n+ -a $background_thresh\n+ #end if\n+ #if $bin_size_reponse:\n+ -b $bin_size_reponse\n+ #end if\n+ #if $bin_size_covars:\n+ -i $bin_size_covars\n+ #end if\n+ #if $bin_size_both:\n+ -z $bin_size_both\n+ #end if\n+ #if $merge_bins.merge=="yes":\n+ -u $merge_bins.cluster_dist\n+ #else:\n+ -u $merge_bins.merge\n+ #end if\n+ $print_covars\n+ $fit\n+ #if $dist:\n+ -d $dist\n+ #end if\n+ $fitMethod\n+ #if $model:\n+ -m $model\n+ #end if\n+ $stranded\n+ $no_normalisation\n+ $log_covars\n+ ./foo.$input.ext\n+ #for $covariate in $covariates:\n+ $covariate.covariate_file\n+ #end for\n+\n+ -o ./piranha.out\n+ ]]></command>\n+ <inputs>\n+ <param name="input" type="data" format="bed,bam" label="Choose input BED or BAM file"/>\n+ <repeat name="covariates" title="Choose covariate">\n+ <param name="covariate_file" type="data" format="bed" label="Choose covariate BED file"/>\n+ </repeat>\n+ <param name="sort" type="boolean" label="Is your input file already sorted?" checked="False" falsevalue="-s" truevalue=""/>\n+ <param name="p_threshold" type="float" min="0" max="1" value="1" label="Significance threshold for sites"/>\n+ <param name="no_pval_correct" type="boolean" checked="False" falsevalue="" truevalue="-c"\n+ label="Disable p-values correction for multiple hypothesis testing?" help="We correct by default using B & H."/>\n+ <param name="background_thresh" type="float" optional="true"\n+ label="Indicates that this proportion of the lowest scores should be considered the background"/>\n+ <param name="bin_size_reponse" type="integer" optional="true"\n+ label="Indicates that input is raw reads and should be binned into bins of this size"/>\n+ <param name="bin_size_covars" type="integer" optional="true"\n+ label="Indicates that the covariates are raw reads and should be binned into bins of this size"/>\n+ <param name="bin_size_both" type="integer" optional="true" label="Synonymous with -b x -i x for any x"/>\n+ <conditional name="merge_bins">\n+ <param name="merge" type="select" label="Merge significant bins within certain distance?">\n+ <option value="yes">Yes</option>\n+ <option value="0" selected="true">No</option>\n+ </param>\n+ <when value="yes">\n+ <param name="cluster_dist" type="integer" value="1" label="Merge significant bins within this distance"\n+ help="Default is 1 (merge adjacent)"/>\n+ </when>\n+ </conditional>\n+ <param name="print_covars" type="boolean" checked="True" truevalue="" falsevalue="-r" label="Print covariate values in output" help="(-r)" />\n+ <param name="fit" type="boolean" checked="False" truevalue="-f" falsevalue="" label="Fit only" />\n+ <param name="dist" type="select" label="Select distribution type">\n+ <option value="">None</option>\n+ <option value="Poisson">Poisson</option>\n+ <option value="NegativeBinomial">NegativeBinomial</option>\n+ <option value="ZeroTruncatedPoisson">ZeroTruncatedPoisson</option>\n+ <option value="ZeroTruncatedNegativeBinom'..b'ialRegression">NegativeBinomialRegression</option>\n+ <option value="ZeroTruncatedPoissonRegression">ZeroTruncatedPoissonRegression</option>\n+ <option value="ZeroTruncatedNegativeBinomialRegression">ZeroTruncatedNegativeBinomialRegression</option>\n+ </param>\n+ <param name="fitMethod" type="boolean" checked="False" truevalue="-t"\n+ falsevalue="" label="Use component fitting method" help="(-t)"/>\n+ <param name="model" type="data" optional="True" format="xml" label="Select the model file"/>\n+\n+ <param name="stranded" type="boolean" checked="True" truevalue=""\n+ falsevalue="-x" label="Preserve strand information"\n+ help="If not set all the peaks will be associated to the positive strand. (-x)"/>\n+ <param name="no_normalisation" type="boolean" checked="yes" falsevalue="-n" \n+ truevalue="" label="Normalise covariates?" help="(-n)"/>\n+ <param name="log_covars" type="boolean" checked="False" truevalue="-l" \n+ falsevalue="" label="Convert covariates to log scale?" help="(-l)"/>\n+ </inputs>\n+ <outputs>\n+ <data format="tabular" name="output_bed" from_work_dir="piranha.out"\n+ label="${tool.name} on ${on_string}: BED with p-values">\n+ <filter>fit is False</filter>\n+ </data>\n+ <data format="xml" name="output_xml" from_work_dir="piranha.out"\n+ label="${tool.name} on ${on_string}: Model file">\n+ <filter>fit is True</filter>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="input" value="zntbr_unbinned_response.bed" ftype="bed"/>\n+ <repeat name="covariates">\n+ <param name="covariate_file" value="ztnbr_binning_cov1.bed" ftype="bed"/>\n+ </repeat>\n+ <repeat name="covariates">\n+ <param name="covariate_file" value="ztnbr_binning_cov2.bed" ftype="bed"/>\n+ </repeat>\n+ <param name="fit" value="True"/>\n+ <param name="bin_size_reponse" value="1"/>\n+ <param name="background_thresh" value="1"/>\n+ <output name="output_xml" file="ztnbrBinningTestModelOutput.expected.xml" ftype="xml"/>\n+ </test>\n+ <test>\n+ <param name="input" value="testPrianha_zntb_unbinned.bam" ftype="bam"/>\n+ <param name="fit" value="True"/>\n+ <param name="bin_size_reponse" value="1"/>\n+ <param name="background_thresh" value="1"/>\n+ <output name="output_xml" file="ztnbBinningTestModelOutput.expected.xml" ftype="xml"/>\n+ </test>\n+ <test>\n+ <param name="input" value="ztnbSimpleTest_response.bed" ftype="bed"/>\n+ <param name="no_pval_correct" value="True"/>\n+ <param name="p_threshold" value="1"/>\n+ <param name="background_thresh" value="1"/>\n+ <param name="-" value="ZeroTruncatedNegativeBinomial"/>\n+ <output name="output_xml" file="ztnbSimpleTest_output.expected.bed" ftype="tabular"/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+**What it does**\n+\n+`Piranha <http://smithlabresearch.org/software/piranha/>`_ is a peak-caller for CLIP- and RIP-Seq data. It takes input in BED or BAM format and identifies regions of statistically significant read enrichment. Additional covariates may optionally be provided to further inform the peak-calling process. \n+\n+\n+ ]]></help>\n+ <citations>\n+ <citation type="bibtex">\n+ @ARTICLE{bgruening_galaxytools,\n+ Author = {Bj\xc3\xb6rn Gr\xc3\xbcning, Cameron Smith, Torsten Houwaart, Nicola Soranzo, Eric Rasche},\n+ keywords = {bioinformatics, ngs, galaxy, cheminformatics, rna},\n+ title = {{Galaxy Tools - A collection of bioinformatics and cheminformatics tools for the Galaxy environment}},\n+ url = {https://github.com/bgruening/galaxytools}\n+ }\n+ </citation>\n+ </citations>\n+</tool>\n'

diff -r 000000000000 -r f7f366ede872 test-data/testPrianha_zntb_unbinned.bam

Binary file test-data/testPrianha_zntb_unbinned.bam has changed

diff -r 000000000000 -r f7f366ede872 test-data/zntbr_unbinned_response.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/zntbr_unbinned_response.bed Fri Jul 24 06:05:39 2015 -0400

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diff -r 000000000000 -r f7f366ede872 test-data/ztnbBinningTestModelOutput.expected.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ztnbBinningTestModelOutput.expected.xml Fri Jul 24 06:05:39 2015 -0400

@@ -0,0 +1,5 @@
+<ZTNB>
+ <mean> 156.449 </mean>
+
+ <alpha> 1.31103 </alpha>
+</ZTNB>

diff -r 000000000000 -r f7f366ede872 test-data/ztnbSimpleTest_output.expected.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ztnbSimpleTest_output.expected.bed Fri Jul 24 06:05:39 2015 -0400

b'@@ -0,0 +1,1000 @@\n+chr1\t996627\t1028823\tX\t2050\t+\t0.029567\n+chr1\t1311660\t1375442\tX\t89\t+\t0.411186\n+chr1\t2308261\t2397744\tX\t80\t+\t0.426373\n+chr1\t2859581\t2868421\tX\t9\t+\t0.718909\n+chr1\t3751661\t3813769\tX\t577\t+\t0.149731\n+chr1\t4420482\t4423777\tX\t3\t+\t0.855385\n+chr1\t5377574\t5424483\tX\t1\t+\t1\n+chr1\t5550947\t5598386\tX\t1882\t+\t0.0346443\n+chr1\t5817866\t5897733\tX\t294\t+\t0.24005\n+chr1\t6156669\t6249618\tX\t959\t+\t0.0911567\n+chr1\t6310781\t6406983\tX\t271\t+\t0.251515\n+chr1\t7124613\t7144897\tX\t306\t+\t0.234449\n+chr1\t7319760\t7411588\tX\t327\t+\t0.225204\n+chr1\t8035466\t8086940\tX\t49\t+\t0.495279\n+chr1\t8428461\t8523025\tX\t119\t+\t0.369547\n+chr1\t8919018\t8963759\tX\t56\t+\t0.476677\n+chr1\t9589823\t9616491\tX\t263\t+\t0.255751\n+chr1\t9835807\t9840347\tX\t331\t+\t0.223518\n+chr1\t9894641\t9945719\tX\t51\t+\t0.489721\n+chr1\t10642372\t10706822\tX\t19\t+\t0.623095\n+chr1\t10896457\t10915369\tX\t7\t+\t0.750363\n+chr1\t11556026\t11607875\tX\t405\t+\t0.195906\n+chr1\t11879118\t11957607\tX\t94\t+\t0.403378\n+chr1\t12735933\t12768200\tX\t230\t+\t0.274806\n+chr1\t12903142\t12999639\tX\t5\t+\t0.792109\n+chr1\t13275890\t13369916\tX\t2522\t+\t0.0192696\n+chr1\t13413513\t13485508\tX\t2\t+\t0.906522\n+chr1\t13841696\t13886684\tX\t1\t+\t1\n+chr1\t14063765\t14083305\tX\t203\t+\t0.29267\n+chr1\t14296714\t14372118\tX\t334\t+\t0.222268\n+chr1\t14630393\t14712564\tX\t1\t+\t1\n+chr1\t15216384\t15287099\tX\t34\t+\t0.545469\n+chr1\t15421443\t15513085\tX\t1\t+\t1\n+chr1\t15950854\t16008505\tX\t79\t+\t0.428161\n+chr1\t16553620\t16628595\tX\t48\t+\t0.49814\n+chr1\t16840844\t16867604\tX\t64\t+\t0.457944\n+chr1\t17553297\t17597684\tX\t130\t+\t0.356821\n+chr1\t17822436\t17862204\tX\t10\t+\t0.705625\n+chr1\t18780224\t18796325\tX\t160\t+\t0.326902\n+chr1\t18991988\t19041610\tX\t219\t+\t0.281806\n+chr1\t19087925\t19128238\tX\t110\t+\t0.38085\n+chr1\t19602992\t19621630\tX\t242\t+\t0.26756\n+chr1\t20145359\t20176622\tX\t2335\t+\t0.0227708\n+chr1\t20553199\t20566262\tX\t728\t+\t0.121574\n+chr1\t21201533\t21201880\tX\t9\t+\t0.718909\n+chr1\t21653510\t21708273\tX\t35\t+\t0.541529\n+chr1\t21837353\t21881630\tX\t130\t+\t0.356821\n+chr1\t22632604\t22695709\tX\t1175\t+\t0.0712204\n+chr1\t22764138\t22772254\tX\t73\t+\t0.439366\n+chr1\t22944065\t23006862\tX\t53\t+\t0.484364\n+chr1\t23447699\t23462259\tX\t1193\t+\t0.0698225\n+chr1\t23697967\t23751574\tX\t43\t+\t0.513342\n+chr1\t24645985\t24683878\tX\t273\t+\t0.250477\n+chr1\t25416328\t25445190\tX\t30\t+\t0.562405\n+chr1\t26403635\t26462936\tX\t2\t+\t0.906522\n+chr1\t27337472\t27371561\tX\t51\t+\t0.489721\n+chr1\t27877569\t27925838\tX\t1\t+\t1\n+chr1\t28655946\t28748130\tX\t25\t+\t0.586839\n+chr1\t29132997\t29179584\tX\t6\t+\t0.769526\n+chr1\t30176193\t30177606\tX\t124\t+\t0.363625\n+chr1\t30816159\t30833088\tX\t54\t+\t0.481757\n+chr1\t31138919\t31148304\tX\t12\t+\t0.682478\n+chr1\t31507424\t31580380\tX\t37\t+\t0.533954\n+chr1\t32356576\t32410061\tX\t27\t+\t0.576559\n+chr1\t32675792\t32688716\tX\t80\t+\t0.426373\n+chr1\t32957767\t33051777\tX\t934\t+\t0.0939131\n+chr1\t33387990\t33460126\tX\t22\t+\t0.603804\n+chr1\t33511602\t33526711\tX\t152\t+\t0.334293\n+chr1\t34000587\t34043099\tX\t840\t+\t0.105334\n+chr1\t34065376\t34105743\tX\t1\t+\t1\n+chr1\t34679050\t34736402\tX\t1\t+\t1\n+chr1\t34983054\t35031268\tX\t1\t+\t1\n+chr1\t35492466\t35527632\tX\t2373\t+\t0.0220055\n+chr1\t35928528\t36014421\tX\t3\t+\t0.855385\n+chr1\t36181953\t36252803\tX\t2739\t+\t0.0159349\n+chr1\t37105570\t37152124\tX\t127\t+\t0.360183\n+chr1\t37497187\t37544458\tX\t2\t+\t0.906522\n+chr1\t38490169\t38547231\tX\t127\t+\t0.360183\n+chr1\t39106650\t39122855\tX\t17\t+\t0.637615\n+chr1\t39811892\t39877459\tX\t7\t+\t0.750363\n+chr1\t40850258\t40934218\tX\t3\t+\t0.855385\n+chr1\t41213760\t41239391\tX\t112\t+\t0.378262\n+chr1\t42136568\t42223161\tX\t5\t+\t0.792109\n+chr1\t43057321\t43130976\tX\t13\t+\t0.672246\n+chr1\t43473819\t43490585\tX\t985\t+\t0.0884023\n+chr1\t44388400\t44445993\tX\t271\t+\t0.251515\n+chr1\t45166338\t45250309\tX\t15\t+\t0.65384\n+chr1\t45366183\t45415552\tX\t45\t+\t0.507071\n+chr1\t46011898\t46089997\tX\t139\t+\t0.347178\n+chr1\t46232141\t46232769\tX\t7\t+\t0.750363\n+chr1\t46842093\t46933256\tX\t1514\t+\t0.0497623\n+chr1\t47863958\t47894846\tX\t8\t+\t0.733688\n+chr1\t48241641\t48299717\tX\t329\t+\t0.224358\n+chr1\t49138610\t49167238\tX\t59\t+\t0.469371\n+chr1\t49680861\t49726476\tX\t105\t+\t0.387527\n+chr1\t50333203\t50359453\tX\t9\t+\t0.718909\n+chr1\t51316576\t51353895\tX\t25\t+\t0.586839\n+chr1\t51688728\t51742475\tX\t4\t+\t0.8197\n+chr1\t52034890\t52096616\tX\t1\t+\t1\n+chr1\t52457697\t52527005\tX\t48\t+\t0.49814\n+chr1\t53130806\t53138601\tX\t1913\t+\t0.0336364\n+chr1\t533384'..b'\t0.241972\n+chr5\t54090484\t54103259\tX\t283\t+\t0.245407\n+chr5\t54252271\t54296495\tX\t27\t+\t0.576559\n+chr5\t55165033\t55217871\tX\t9\t+\t0.718909\n+chr5\t55848744\t55856383\tX\t99\t+\t0.395961\n+chr5\t56778067\t56852659\tX\t495\t+\t0.169308\n+chr5\t57617903\t57663946\tX\t6\t+\t0.769526\n+chr5\t58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diff -r 000000000000 -r f7f366ede872 test-data/ztnbSimpleTest_response.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ztnbSimpleTest_response.bed Fri Jul 24 06:05:39 2015 -0400

b'@@ -0,0 +1,1000 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diff -r 000000000000 -r f7f366ede872 test-data/ztnbrBinningTestModelOutput.expected.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ztnbrBinningTestModelOutput.expected.xml Fri Jul 24 06:05:39 2015 -0400

@@ -0,0 +1,5 @@
+<ZeroTruncatedNegativeBinomialRegression>
+<coefficient> 0.2419 </coefficient>
+<coefficient> 2.67587 </coefficient>
+<alpha>3.82529</alpha>
+</ZeroTruncatedNegativeBinomialRegression>

diff -r 000000000000 -r f7f366ede872 test-data/ztnbr_binning_cov1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ztnbr_binning_cov1.bed Fri Jul 24 06:05:39 2015 -0400

b'@@ -0,0 +1,6000 @@\n+chr1\t15\t16\tX\t0.937841\t+\n+chr1\t80\t81\tX\t0.856059\t+\n+chr1\t1190\t1191\tX\t1.89456\t+\n+chr1\t1414\t1415\tX\t1.24448\t+\n+chr1\t1757\t1758\tX\t0.455693\t+\n+chr1\t3314\t3315\tX\t0.370419\t+\n+chr1\t3707\t3708\tX\t0.250848\t+\n+chr1\t4549\t4550\tX\t0.284407\t+\n+chr1\t5999\t6000\tX\t1.63228\t+\n+chr1\t6457\t6458\tX\t1.5821\t+\n+chr1\t8507\t8508\tX\t0.139908\t+\n+chr1\t9045\t9046\tX\t1.34526\t+\n+chr1\t9631\t9632\tX\t0.18576\t+\n+chr1\t10117\t10118\tX\t0.0349718\t+\n+chr1\t11176\t11177\tX\t0.251664\t+\n+chr1\t11911\t11912\tX\t1.69444\t+\n+chr1\t11939\t11940\tX\t0.442794\t+\n+chr1\t12158\t12159\tX\t0.371085\t+\n+chr1\t12683\t12684\tX\t0.965383\t+\n+chr1\t13639\t13640\tX\t1.34655\t+\n+chr1\t14015\t14016\tX\t1.00787\t+\n+chr1\t15396\t15397\tX\t1.05015\t+\n+chr1\t18695\t18696\tX\t0.80826\t+\n+chr1\t19215\t19216\tX\t1.75573\t+\n+chr1\t19316\t19317\tX\t0.156797\t+\n+chr1\t22632\t22633\tX\t1.13912\t+\n+chr1\t23061\t23062\tX\t1.75873\t+\n+chr1\t26296\t26297\tX\t0.480598\t+\n+chr1\t26547\t26548\tX\t1.74772\t+\n+chr1\t27872\t27873\tX\t0.247971\t+\n+chr1\t28869\t28870\tX\t0.948629\t+\n+chr1\t29180\t29181\tX\t0.413779\t+\n+chr1\t29318\t29319\tX\t0.674768\t+\n+chr1\t29901\t29902\tX\t1.33647\t+\n+chr1\t31735\t31736\tX\t1.50669\t+\n+chr1\t32583\t32584\tX\t0.0128481\t+\n+chr1\t33062\t33063\tX\t1.89563\t+\n+chr1\t33816\t33817\tX\t0.256621\t+\n+chr1\t34290\t34291\tX\t1.50553\t+\n+chr1\t35414\t35415\tX\t1.66374\t+\n+chr1\t35570\t35571\tX\t1.37338\t+\n+chr1\t35889\t35890\tX\t1.18951\t+\n+chr1\t36167\t36168\tX\t0.563957\t+\n+chr1\t36502\t36503\tX\t1.72694\t+\n+chr1\t36956\t36957\tX\t1.87207\t+\n+chr1\t37546\t37547\tX\t0.736448\t+\n+chr1\t37832\t37833\tX\t0.416827\t+\n+chr1\t38184\t38185\tX\t0.335001\t+\n+chr1\t38349\t38350\tX\t1.15713\t+\n+chr1\t38606\t38607\tX\t1.40798\t+\n+chr1\t38673\t38674\tX\t0.479435\t+\n+chr1\t38832\t38833\tX\t0.540252\t+\n+chr1\t39976\t39977\tX\t0.897101\t+\n+chr1\t41920\t41921\tX\t0.394162\t+\n+chr1\t44126\t44127\tX\t1.23074\t+\n+chr1\t44167\t44168\tX\t0.987501\t+\n+chr1\t44429\t44430\tX\t0.189879\t+\n+chr1\t44810\t44811\tX\t1.87326\t+\n+chr1\t45112\t45113\tX\t1.68081\t+\n+chr1\t45599\t45600\tX\t0.16825\t+\n+chr1\t45615\t45616\tX\t0.0463213\t+\n+chr1\t46144\t46145\tX\t0.609863\t+\n+chr1\t47543\t47544\tX\t0.066092\t+\n+chr1\t49974\t49975\tX\t0.474801\t+\n+chr1\t51340\t51341\tX\t0.431986\t+\n+chr1\t52246\t52247\tX\t1.93053\t+\n+chr1\t52363\t52364\tX\t0.903501\t+\n+chr1\t52675\t52676\tX\t0.286809\t+\n+chr1\t52679\t52680\tX\t0.763679\t+\n+chr1\t52908\t52909\tX\t1.63843\t+\n+chr1\t53752\t53753\tX\t0.386539\t+\n+chr1\t53857\t53858\tX\t0.700525\t+\n+chr1\t54825\t54826\tX\t1.42488\t+\n+chr1\t54878\t54879\tX\t0.138667\t+\n+chr1\t56750\t56751\tX\t1.10789\t+\n+chr1\t57096\t57097\tX\t1.34182\t+\n+chr1\t58710\t58711\tX\t1.8859\t+\n+chr1\t59270\t59271\tX\t0.991122\t+\n+chr1\t59400\t59401\tX\t1.91092\t+\n+chr1\t59494\t59495\tX\t1.06421\t+\n+chr1\t60979\t60980\tX\t0.34133\t+\n+chr1\t62807\t62808\tX\t0.0406479\t+\n+chr1\t62854\t62855\tX\t1.81581\t+\n+chr1\t63277\t63278\tX\t0.890084\t+\n+chr1\t63313\t63314\tX\t1.01181\t+\n+chr1\t64538\t64539\tX\t0.47069\t+\n+chr1\t65534\t65535\tX\t0.0452146\t+\n+chr1\t66007\t66008\tX\t1.85495\t+\n+chr1\t66107\t66108\tX\t0.207247\t+\n+chr1\t66154\t66155\tX\t1.35955\t+\n+chr1\t67064\t67065\tX\t1.72438\t+\n+chr1\t68397\t68398\tX\t0.761503\t+\n+chr1\t68486\t68487\tX\t0.584847\t+\n+chr1\t68899\t68900\tX\t1.99113\t+\n+chr1\t69144\t69145\tX\t0.660775\t+\n+chr1\t69752\t69753\tX\t1.18991\t+\n+chr1\t70119\t70120\tX\t0.9701\t+\n+chr1\t71175\t71176\tX\t0.886059\t+\n+chr1\t71912\t71913\tX\t0.538262\t+\n+chr1\t72533\t72534\tX\t0.920545\t+\n+chr1\t72735\t72736\tX\t1.52398\t+\n+chr1\t73056\t73057\tX\t0.229808\t+\n+chr1\t74607\t74608\tX\t1.03662\t+\n+chr1\t74851\t74852\tX\t1.03717\t+\n+chr1\t77322\t77323\tX\t0.404528\t+\n+chr1\t79009\t79010\tX\t1.62122\t+\n+chr1\t82149\t82150\tX\t1.88517\t+\n+chr1\t82840\t82841\tX\t1.1593\t+\n+chr1\t83069\t83070\tX\t0.428971\t+\n+chr1\t83420\t83421\tX\t0.752991\t+\n+chr1\t84786\t84787\tX\t0.115763\t+\n+chr1\t87896\t87897\tX\t1.88183\t+\n+chr1\t88045\t88046\tX\t0.449229\t+\n+chr1\t90681\t90682\tX\t0.719652\t+\n+chr1\t91040\t91041\tX\t0.880861\t+\n+chr1\t92273\t92274\tX\t1.91486\t+\n+chr1\t93949\t93950\tX\t1.15468\t+\n+chr1\t94089\t94090\tX\t0.0980611\t+\n+chr1\t94929\t94930\tX\t1.97486\t+\n+chr1\t95277\t95278\tX\t0.736446\t+\n+chr1\t97394\t97395\tX\t1.79339\t+\n+chr1\t97472\t97473\tX\t0.140369\t+\n+chr1\t100086\t100087\tX\t1.87577\t+\n+chr1\t100167\t100168\tX\t0.867716\t+\n+chr1\t100786\t100787\tX\t1.92829\t+\n+chr1\t100963\t100964\tX\t1.21461\t+\n+chr1\t101205\t101206\tX\t1.43321\t+\n+chr1\t103233\t103234\tX\t1.58358\t+\n+chr1\t103658\t103659\tX\t0.176259\t+\n+chr1\t105724\t105725\tX\t1.34591\t+\n+chr1\t106923\t106924\tX\t1.74876\t+'..b'\t901588\t901589\tX\t0.124649\t+\n+chr5\t901774\t901775\tX\t1.63511\t+\n+chr5\t902860\t902861\tX\t1.96621\t+\n+chr5\t902906\t902907\tX\t0.68492\t+\n+chr5\t903179\t903180\tX\t0.0100725\t+\n+chr5\t903238\t903239\tX\t0.963268\t+\n+chr5\t904588\t904589\tX\t0.385787\t+\n+chr5\t904988\t904989\tX\t0.706646\t+\n+chr5\t905763\t905764\tX\t0.152904\t+\n+chr5\t906395\t906396\tX\t0.326339\t+\n+chr5\t907243\t907244\tX\t0.321312\t+\n+chr5\t907561\t907562\tX\t0.461994\t+\n+chr5\t909164\t909165\tX\t1.83356\t+\n+chr5\t909826\t909827\tX\t0.602208\t+\n+chr5\t910969\t910970\tX\t1.57445\t+\n+chr5\t911922\t911923\tX\t1.06162\t+\n+chr5\t912126\t912127\tX\t1.69508\t+\n+chr5\t913193\t913194\tX\t0.370461\t+\n+chr5\t913334\t913335\tX\t1.81563\t+\n+chr5\t914201\t914202\tX\t0.90553\t+\n+chr5\t915000\t915001\tX\t0.258766\t+\n+chr5\t915015\t915016\tX\t1.23921\t+\n+chr5\t917339\t917340\tX\t0.442287\t+\n+chr5\t917560\t917561\tX\t1.83691\t+\n+chr5\t917619\t917620\tX\t0.880481\t+\n+chr5\t918484\t918485\tX\t1.73239\t+\n+chr5\t919311\t919312\tX\t1.81817\t+\n+chr5\t920471\t920472\tX\t1.29491\t+\n+chr5\t922841\t922842\tX\t0.787163\t+\n+chr5\t922996\t922997\tX\t0.770596\t+\n+chr5\t923018\t923019\tX\t0.0925997\t+\n+chr5\t926572\t926573\tX\t1.59726\t+\n+chr5\t926677\t926678\tX\t1.31151\t+\n+chr5\t926947\t926948\tX\t1.2063\t+\n+chr5\t928787\t928788\tX\t0.439252\t+\n+chr5\t930071\t930072\tX\t1.05369\t+\n+chr5\t930698\t930699\tX\t0.870024\t+\n+chr5\t931636\t931637\tX\t1.91354\t+\n+chr5\t932071\t932072\tX\t1.49651\t+\n+chr5\t932346\t932347\tX\t0.811263\t+\n+chr5\t934744\t934745\tX\t1.90298\t+\n+chr5\t934954\t934955\tX\t1.14743\t+\n+chr5\t935139\t935140\tX\t0.865671\t+\n+chr5\t935760\t935761\tX\t0.0204511\t+\n+chr5\t936333\t936334\tX\t0.0347518\t+\n+chr5\t936765\t936766\tX\t1.80367\t+\n+chr5\t936962\t936963\tX\t0.514709\t+\n+chr5\t937504\t937505\tX\t1.48227\t+\n+chr5\t938899\t938900\tX\t1.08512\t+\n+chr5\t940442\t940443\tX\t1.00468\t+\n+chr5\t942165\t942166\tX\t1.57674\t+\n+chr5\t943367\t943368\tX\t0.515381\t+\n+chr5\t943730\t943731\tX\t0.421601\t+\n+chr5\t944885\t944886\tX\t1.60003\t+\n+chr5\t946337\t946338\tX\t0.402714\t+\n+chr5\t948104\t948105\tX\t0.532752\t+\n+chr5\t948314\t948315\tX\t0.225837\t+\n+chr5\t948701\t948702\tX\t0.557612\t+\n+chr5\t949463\t949464\tX\t1.46497\t+\n+chr5\t949637\t949638\tX\t0.0204203\t+\n+chr5\t950561\t950562\tX\t1.96697\t+\n+chr5\t950950\t950951\tX\t1.10505\t+\n+chr5\t951098\t951099\tX\t1.61955\t+\n+chr5\t951958\t951959\tX\t0.874007\t+\n+chr5\t954289\t954290\tX\t1.58268\t+\n+chr5\t954373\t954374\tX\t0.0776612\t+\n+chr5\t955379\t955380\tX\t1.46136\t+\n+chr5\t955387\t955388\tX\t1.5604\t+\n+chr5\t955653\t955654\tX\t1.37134\t+\n+chr5\t956109\t956110\tX\t1.59023\t+\n+chr5\t956823\t956824\tX\t0.870337\t+\n+chr5\t957195\t957196\tX\t0.489102\t+\n+chr5\t957261\t957262\tX\t0.53349\t+\n+chr5\t957714\t957715\tX\t1.51231\t+\n+chr5\t960901\t960902\tX\t0.535719\t+\n+chr5\t961311\t961312\tX\t0.912848\t+\n+chr5\t962998\t962999\tX\t1.32854\t+\n+chr5\t963049\t963050\tX\t0.288613\t+\n+chr5\t966196\t966197\tX\t1.21976\t+\n+chr5\t966761\t966762\tX\t0.489067\t+\n+chr5\t968861\t968862\tX\t1.46246\t+\n+chr5\t968886\t968887\tX\t1.66972\t+\n+chr5\t970159\t970160\tX\t1.03466\t+\n+chr5\t971246\t971247\tX\t1.41681\t+\n+chr5\t973013\t973014\tX\t1.23073\t+\n+chr5\t974071\t974072\tX\t1.09954\t+\n+chr5\t974282\t974283\tX\t0.380615\t+\n+chr5\t974507\t974508\tX\t0.0339671\t+\n+chr5\t974529\t974530\tX\t0.113886\t+\n+chr5\t976758\t976759\tX\t0.635588\t+\n+chr5\t977058\t977059\tX\t0.454781\t+\n+chr5\t977612\t977613\tX\t0.540581\t+\n+chr5\t978608\t978609\tX\t0.626268\t+\n+chr5\t978961\t978962\tX\t0.485206\t+\n+chr5\t979460\t979461\tX\t0.488413\t+\n+chr5\t979751\t979752\tX\t0.705387\t+\n+chr5\t980716\t980717\tX\t0.370287\t+\n+chr5\t981025\t981026\tX\t1.7251\t+\n+chr5\t982067\t982068\tX\t1.18116\t+\n+chr5\t982104\t982105\tX\t0.870954\t+\n+chr5\t983267\t983268\tX\t1.3199\t+\n+chr5\t983289\t983290\tX\t0.304294\t+\n+chr5\t983545\t983546\tX\t1.19256\t+\n+chr5\t983603\t983604\tX\t1.44016\t+\n+chr5\t983840\t983841\tX\t0.387686\t+\n+chr5\t985162\t985163\tX\t0.798185\t+\n+chr5\t985794\t985795\tX\t1.71795\t+\n+chr5\t986466\t986467\tX\t1.16394\t+\n+chr5\t988990\t988991\tX\t0.893724\t+\n+chr5\t988995\t988996\tX\t0.100857\t+\n+chr5\t989039\t989040\tX\t0.984503\t+\n+chr5\t989298\t989299\tX\t0.607637\t+\n+chr5\t989734\t989735\tX\t1.12427\t+\n+chr5\t990227\t990228\tX\t0.0125343\t+\n+chr5\t994522\t994523\tX\t0.684804\t+\n+chr5\t995636\t995637\tX\t1.27112\t+\n+chr5\t996389\t996390\tX\t0.41321\t+\n+chr5\t996409\t996410\tX\t1.59288\t+\n+chr5\t996641\t996642\tX\t0.785893\t+\n+chr5\t996686\t996687\tX\t0.807039\t+\n+chr5\t997183\t997184\tX\t0.971826\t+\n+chr5\t998263\t998264\tX\t1.24186\t+\n+chr5\t999924\t999925\tX\t0.187548\t+\n'

diff -r 000000000000 -r f7f366ede872 test-data/ztnbr_binning_cov2.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ztnbr_binning_cov2.bed Fri Jul 24 06:05:39 2015 -0400

b'@@ -0,0 +1,6000 @@\n+chr1\t15\t16\tX\t0.285884\t+\n+chr1\t80\t81\tX\t1.78437\t+\n+chr1\t1190\t1191\tX\t1.85859\t+\n+chr1\t1414\t1415\tX\t1.98967\t+\n+chr1\t1757\t1758\tX\t0.83515\t+\n+chr1\t3314\t3315\tX\t1.62779\t+\n+chr1\t3707\t3708\tX\t0.000849908\t+\n+chr1\t4549\t4550\tX\t0.0355585\t+\n+chr1\t5999\t6000\tX\t1.70938\t+\n+chr1\t6457\t6458\tX\t0.424355\t+\n+chr1\t8507\t8508\tX\t1.4421\t+\n+chr1\t9045\t9046\tX\t1.82473\t+\n+chr1\t9631\t9632\tX\t0.063309\t+\n+chr1\t10117\t10118\tX\t1.77154\t+\n+chr1\t11176\t11177\tX\t1.72367\t+\n+chr1\t11911\t11912\tX\t0.452338\t+\n+chr1\t11939\t11940\tX\t0.0455983\t+\n+chr1\t12158\t12159\tX\t0.830783\t+\n+chr1\t12683\t12684\tX\t1.19446\t+\n+chr1\t13639\t13640\tX\t1.43541\t+\n+chr1\t14015\t14016\tX\t1.34891\t+\n+chr1\t15396\t15397\tX\t1.83012\t+\n+chr1\t18695\t18696\tX\t0.422904\t+\n+chr1\t19215\t19216\tX\t0.521697\t+\n+chr1\t19316\t19317\tX\t1.2931\t+\n+chr1\t22632\t22633\tX\t1.18818\t+\n+chr1\t23061\t23062\tX\t0.989616\t+\n+chr1\t26296\t26297\tX\t1.41059\t+\n+chr1\t26547\t26548\tX\t1.9492\t+\n+chr1\t27872\t27873\tX\t1.65687\t+\n+chr1\t28869\t28870\tX\t1.60162\t+\n+chr1\t29180\t29181\tX\t0.386784\t+\n+chr1\t29318\t29319\tX\t0.819143\t+\n+chr1\t29901\t29902\tX\t0.0682755\t+\n+chr1\t31735\t31736\tX\t0.947939\t+\n+chr1\t32583\t32584\tX\t1.93859\t+\n+chr1\t33062\t33063\tX\t1.83032\t+\n+chr1\t33816\t33817\tX\t1.02466\t+\n+chr1\t34290\t34291\tX\t1.43902\t+\n+chr1\t35414\t35415\tX\t0.46227\t+\n+chr1\t35570\t35571\tX\t0.413351\t+\n+chr1\t35889\t35890\tX\t0.157111\t+\n+chr1\t36167\t36168\tX\t0.419452\t+\n+chr1\t36502\t36503\tX\t0.697678\t+\n+chr1\t36956\t36957\tX\t1.79965\t+\n+chr1\t37546\t37547\tX\t1.48405\t+\n+chr1\t37832\t37833\tX\t1.61137\t+\n+chr1\t38184\t38185\tX\t0.370391\t+\n+chr1\t38349\t38350\tX\t1.83134\t+\n+chr1\t38606\t38607\tX\t1.98277\t+\n+chr1\t38673\t38674\tX\t1.86473\t+\n+chr1\t38832\t38833\tX\t0.0157611\t+\n+chr1\t39976\t39977\tX\t1.57853\t+\n+chr1\t41920\t41921\tX\t0.683479\t+\n+chr1\t44126\t44127\tX\t1.08818\t+\n+chr1\t44167\t44168\tX\t0.924745\t+\n+chr1\t44429\t44430\tX\t1.29814\t+\n+chr1\t44810\t44811\tX\t1.93596\t+\n+chr1\t45112\t45113\tX\t1.30542\t+\n+chr1\t45599\t45600\tX\t1.78117\t+\n+chr1\t45615\t45616\tX\t0.522557\t+\n+chr1\t46144\t46145\tX\t1.96799\t+\n+chr1\t47543\t47544\tX\t0.807906\t+\n+chr1\t49974\t49975\tX\t1.98444\t+\n+chr1\t51340\t51341\tX\t0.387334\t+\n+chr1\t52246\t52247\tX\t0.405837\t+\n+chr1\t52363\t52364\tX\t1.14299\t+\n+chr1\t52675\t52676\tX\t0.40214\t+\n+chr1\t52679\t52680\tX\t1.14962\t+\n+chr1\t52908\t52909\tX\t1.16739\t+\n+chr1\t53752\t53753\tX\t0.564092\t+\n+chr1\t53857\t53858\tX\t1.73067\t+\n+chr1\t54825\t54826\tX\t0.0395156\t+\n+chr1\t54878\t54879\tX\t0.580895\t+\n+chr1\t56750\t56751\tX\t0.327205\t+\n+chr1\t57096\t57097\tX\t1.92645\t+\n+chr1\t58710\t58711\tX\t0.25293\t+\n+chr1\t59270\t59271\tX\t1.79532\t+\n+chr1\t59400\t59401\tX\t0.897785\t+\n+chr1\t59494\t59495\tX\t0.253605\t+\n+chr1\t60979\t60980\tX\t0.735648\t+\n+chr1\t62807\t62808\tX\t1.16891\t+\n+chr1\t62854\t62855\tX\t0.251496\t+\n+chr1\t63277\t63278\tX\t1.64902\t+\n+chr1\t63313\t63314\tX\t1.41063\t+\n+chr1\t64538\t64539\tX\t0.88392\t+\n+chr1\t65534\t65535\tX\t1.92145\t+\n+chr1\t66007\t66008\tX\t0.175415\t+\n+chr1\t66107\t66108\tX\t1.19387\t+\n+chr1\t66154\t66155\tX\t0.0100984\t+\n+chr1\t67064\t67065\tX\t1.67506\t+\n+chr1\t68397\t68398\tX\t0.581221\t+\n+chr1\t68486\t68487\tX\t1.52365\t+\n+chr1\t68899\t68900\tX\t0.957973\t+\n+chr1\t69144\t69145\tX\t1.6432\t+\n+chr1\t69752\t69753\tX\t0.7551\t+\n+chr1\t70119\t70120\tX\t0.463907\t+\n+chr1\t71175\t71176\tX\t1.98611\t+\n+chr1\t71912\t71913\tX\t0.575172\t+\n+chr1\t72533\t72534\tX\t1.6018\t+\n+chr1\t72735\t72736\tX\t1.50379\t+\n+chr1\t73056\t73057\tX\t0.381569\t+\n+chr1\t74607\t74608\tX\t0.448922\t+\n+chr1\t74851\t74852\tX\t1.78642\t+\n+chr1\t77322\t77323\tX\t0.895438\t+\n+chr1\t79009\t79010\tX\t1.89658\t+\n+chr1\t82149\t82150\tX\t1.98139\t+\n+chr1\t82840\t82841\tX\t0.295855\t+\n+chr1\t83069\t83070\tX\t1.72147\t+\n+chr1\t83420\t83421\tX\t1.51854\t+\n+chr1\t84786\t84787\tX\t1.633\t+\n+chr1\t87896\t87897\tX\t1.88246\t+\n+chr1\t88045\t88046\tX\t0.193891\t+\n+chr1\t90681\t90682\tX\t1.19527\t+\n+chr1\t91040\t91041\tX\t0.626282\t+\n+chr1\t92273\t92274\tX\t1.11234\t+\n+chr1\t93949\t93950\tX\t0.768138\t+\n+chr1\t94089\t94090\tX\t0.112809\t+\n+chr1\t94929\t94930\tX\t1.50989\t+\n+chr1\t95277\t95278\tX\t1.45248\t+\n+chr1\t97394\t97395\tX\t1.4995\t+\n+chr1\t97472\t97473\tX\t1.18736\t+\n+chr1\t100086\t100087\tX\t0.0533627\t+\n+chr1\t100167\t100168\tX\t1.70107\t+\n+chr1\t100786\t100787\tX\t0.817351\t+\n+chr1\t100963\t100964\tX\t1.90155\t+\n+chr1\t101205\t101206\tX\t1.9143\t+\n+chr1\t103233\t103234\tX\t1.26686\t+\n+chr1\t103658\t103659\tX\t0.389442\t+\n+chr1\t105724\t105725\tX\t0.786324\t+\n+chr1\t106923\t106924\tX\t1.36636\t+\n+chr1\t107388\t'..b'01288\tX\t1.74726\t+\n+chr5\t901588\t901589\tX\t0.976595\t+\n+chr5\t901774\t901775\tX\t1.22354\t+\n+chr5\t902860\t902861\tX\t0.0259823\t+\n+chr5\t902906\t902907\tX\t1.45451\t+\n+chr5\t903179\t903180\tX\t1.28928\t+\n+chr5\t903238\t903239\tX\t1.63922\t+\n+chr5\t904588\t904589\tX\t1.92305\t+\n+chr5\t904988\t904989\tX\t0.592738\t+\n+chr5\t905763\t905764\tX\t1.85639\t+\n+chr5\t906395\t906396\tX\t0.77541\t+\n+chr5\t907243\t907244\tX\t0.282648\t+\n+chr5\t907561\t907562\tX\t0.73992\t+\n+chr5\t909164\t909165\tX\t0.659404\t+\n+chr5\t909826\t909827\tX\t1.31086\t+\n+chr5\t910969\t910970\tX\t1.80871\t+\n+chr5\t911922\t911923\tX\t0.662325\t+\n+chr5\t912126\t912127\tX\t1.23451\t+\n+chr5\t913193\t913194\tX\t0.341037\t+\n+chr5\t913334\t913335\tX\t1.33628\t+\n+chr5\t914201\t914202\tX\t1.24497\t+\n+chr5\t915000\t915001\tX\t1.07344\t+\n+chr5\t915015\t915016\tX\t1.423\t+\n+chr5\t917339\t917340\tX\t1.52043\t+\n+chr5\t917560\t917561\tX\t1.02058\t+\n+chr5\t917619\t917620\tX\t0.235957\t+\n+chr5\t918484\t918485\tX\t0.299507\t+\n+chr5\t919311\t919312\tX\t1.92558\t+\n+chr5\t920471\t920472\tX\t1.61913\t+\n+chr5\t922841\t922842\tX\t1.84297\t+\n+chr5\t922996\t922997\tX\t1.40418\t+\n+chr5\t923018\t923019\tX\t0.322818\t+\n+chr5\t926572\t926573\tX\t1.1208\t+\n+chr5\t926677\t926678\tX\t0.527471\t+\n+chr5\t926947\t926948\tX\t0.221243\t+\n+chr5\t928787\t928788\tX\t0.509374\t+\n+chr5\t930071\t930072\tX\t1.40494\t+\n+chr5\t930698\t930699\tX\t0.494194\t+\n+chr5\t931636\t931637\tX\t0.829981\t+\n+chr5\t932071\t932072\tX\t1.92258\t+\n+chr5\t932346\t932347\tX\t0.904379\t+\n+chr5\t934744\t934745\tX\t1.3476\t+\n+chr5\t934954\t934955\tX\t0.806977\t+\n+chr5\t935139\t935140\tX\t1.33671\t+\n+chr5\t935760\t935761\tX\t1.72202\t+\n+chr5\t936333\t936334\tX\t0.0737671\t+\n+chr5\t936765\t936766\tX\t0.343459\t+\n+chr5\t936962\t936963\tX\t0.719074\t+\n+chr5\t937504\t937505\tX\t0.593508\t+\n+chr5\t938899\t938900\tX\t1.58214\t+\n+chr5\t940442\t940443\tX\t1.6669\t+\n+chr5\t942165\t942166\tX\t0.252544\t+\n+chr5\t943367\t943368\tX\t0.00942593\t+\n+chr5\t943730\t943731\tX\t1.85373\t+\n+chr5\t944885\t944886\tX\t1.7299\t+\n+chr5\t946337\t946338\tX\t0.418429\t+\n+chr5\t948104\t948105\tX\t1.96479\t+\n+chr5\t948314\t948315\tX\t1.64042\t+\n+chr5\t948701\t948702\tX\t1.78589\t+\n+chr5\t949463\t949464\tX\t1.69846\t+\n+chr5\t949637\t949638\tX\t1.2045\t+\n+chr5\t950561\t950562\tX\t0.916232\t+\n+chr5\t950950\t950951\tX\t0.577118\t+\n+chr5\t951098\t951099\tX\t1.84678\t+\n+chr5\t951958\t951959\tX\t1.43938\t+\n+chr5\t954289\t954290\tX\t0.123763\t+\n+chr5\t954373\t954374\tX\t1.25242\t+\n+chr5\t955379\t955380\tX\t1.04847\t+\n+chr5\t955387\t955388\tX\t1.58525\t+\n+chr5\t955653\t955654\tX\t0.110406\t+\n+chr5\t956109\t956110\tX\t1.05235\t+\n+chr5\t956823\t956824\tX\t1.74894\t+\n+chr5\t957195\t957196\tX\t0.332988\t+\n+chr5\t957261\t957262\tX\t0.370055\t+\n+chr5\t957714\t957715\tX\t1.41242\t+\n+chr5\t960901\t960902\tX\t1.82322\t+\n+chr5\t961311\t961312\tX\t0.237837\t+\n+chr5\t962998\t962999\tX\t0.765532\t+\n+chr5\t963049\t963050\tX\t0.719178\t+\n+chr5\t966196\t966197\tX\t0.508627\t+\n+chr5\t966761\t966762\tX\t1.74603\t+\n+chr5\t968861\t968862\tX\t1.4821\t+\n+chr5\t968886\t968887\tX\t0.935148\t+\n+chr5\t970159\t970160\tX\t1.5711\t+\n+chr5\t971246\t971247\tX\t0.365992\t+\n+chr5\t973013\t973014\tX\t0.876724\t+\n+chr5\t974071\t974072\tX\t1.98015\t+\n+chr5\t974282\t974283\tX\t0.992922\t+\n+chr5\t974507\t974508\tX\t0.884519\t+\n+chr5\t974529\t974530\tX\t0.0751256\t+\n+chr5\t976758\t976759\tX\t0.322036\t+\n+chr5\t977058\t977059\tX\t1.50084\t+\n+chr5\t977612\t977613\tX\t1.54154\t+\n+chr5\t978608\t978609\tX\t1.69385\t+\n+chr5\t978961\t978962\tX\t0.860385\t+\n+chr5\t979460\t979461\tX\t0.751277\t+\n+chr5\t979751\t979752\tX\t1.4349\t+\n+chr5\t980716\t980717\tX\t1.40595\t+\n+chr5\t981025\t981026\tX\t1.69472\t+\n+chr5\t982067\t982068\tX\t1.679\t+\n+chr5\t982104\t982105\tX\t0.119196\t+\n+chr5\t983267\t983268\tX\t1.60911\t+\n+chr5\t983289\t983290\tX\t0.270315\t+\n+chr5\t983545\t983546\tX\t1.41069\t+\n+chr5\t983603\t983604\tX\t0.732813\t+\n+chr5\t983840\t983841\tX\t1.83059\t+\n+chr5\t985162\t985163\tX\t1.08774\t+\n+chr5\t985794\t985795\tX\t1.52408\t+\n+chr5\t986466\t986467\tX\t0.288504\t+\n+chr5\t988990\t988991\tX\t0.819902\t+\n+chr5\t988995\t988996\tX\t1.0977\t+\n+chr5\t989039\t989040\tX\t0.545999\t+\n+chr5\t989298\t989299\tX\t0.547696\t+\n+chr5\t989734\t989735\tX\t1.52484\t+\n+chr5\t990227\t990228\tX\t0.664526\t+\n+chr5\t994522\t994523\tX\t1.49338\t+\n+chr5\t995636\t995637\tX\t1.70765\t+\n+chr5\t996389\t996390\tX\t0.82487\t+\n+chr5\t996409\t996410\tX\t1.48312\t+\n+chr5\t996641\t996642\tX\t0.499364\t+\n+chr5\t996686\t996687\tX\t1.90581\t+\n+chr5\t997183\t997184\tX\t1.47898\t+\n+chr5\t998263\t998264\tX\t1.86614\t+\n+chr5\t999924\t999925\tX\t0.127258\t+\n'