| Next changeset 1:859c982b1f7f (2015-02-12) |
|
Commit message:
Uploaded |
|
added:
dir2html.py macs2_bdgbroadcall.xml macs2_bdgcmp.xml macs2_bdgdiff.xml macs2_bdgpeakcall.xml macs2_callpeak.xml macs2_filterdup.xml macs2_macros.xml macs2_predictd.xml macs2_randsample.xml macs2_refinepeak.xml readme.rst test-data/ChIP_200K.bed test-data/ChIP_200K_w_dups.bed test-data/Control_200K.bed test-data/bdgbroadcall_on_callpeak_treatment.tabular test-data/bdgcmp_on_Control_and_ChIP_slogLR.bdg test-data/bdgpeakcall_on_callpeak_treatment.tabular test-data/callpeak_control_part.bdg test-data/callpeak_part.bed test-data/callpeak_summits_part.bed test-data/callpeak_treatment_part.bdg test-data/filterdup_on_ChIP_200K_w_dups.bed test-data/predictd_on_ChIP_200K_and_Control_200K.pdf test-data/predictd_on_ChIP_200K_and_Control_200K.txt test-data/refinepeak_ChIP_and_summits.bed tool_dependencies.xml |
| b |
| diff -r 000000000000 -r fe62ba547975 dir2html.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dir2html.py Wed Feb 11 10:18:02 2015 -0500 |
| [ |
| @@ -0,0 +1,38 @@ +#!/usr/bin/env python +import os +import sys +from xml.sax.saxutils import escape + +def make_table( directory ): + ret = ['<table class="fileList">\n'] + for file in os.listdir( directory ): + ret.append('<tr><td class="file"><a href="%s">%s</a></td></tr>\n' % ( file, escape(file).replace( 'MACS2_', '' ) )) + ret.append('</table>') + return ''.join(ret) + +def make_html( directory, stderr ): + return '\n'.join(['<html>' + '<head>', + ' <title>Additional output created by MACS2</title>', + ' <style type="text/css">', + ' table.fileList { text-align: left; }', + ' td.directory { font-weight: bold; }', + ' td.file { padding-left: 4em; }', + ' </style>', + '</head>', + '<body>', + '<h1>Additional Files:</h1>', + make_table( directory ), + '<h3>Messages from MACS2:</h3>', + stderr.read().replace('\n', '<br>'), + '</body>', + '</html>']) + +if __name__ == '__main__': + if len(sys.argv) == 3: + directory_path = sys.argv[1] + stderr = open( sys.argv[2] ) + print make_html( directory_path, stderr ) + else: + sys.exit( 'Two parameter expected: directory path and stderr path' ) + |
| b |
| diff -r 000000000000 -r fe62ba547975 macs2_bdgbroadcall.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macs2_bdgbroadcall.xml Wed Feb 11 10:18:02 2015 -0500 |
| b |
| @@ -0,0 +1,59 @@ +<tool id="macs2_bdgbroadcall" name="MACS2 bdgbroadcall" version="@VERSION_STRING@.0"> + <description>Call broad peaks from bedGraph output</description> + <expand macro="requirements"> + <requirement type="package" version="4.1.0">gnu_awk</requirement> + </expand> + <expand macro="version_command" /> + <macros> + <import>macs2_macros.xml</import> + </macros> + <command> + macs2 bdgbroadcall + --ifile "${ infile }" + --cutoff-peak "${ cutoffpeak }" + --cutoff-link "${ cutofflink }" + --min-length "${ minlen }" + --lvl1-max-gap "${ LVL1MAXGAP }" + --lvl2-max-gap "${ LVL2MAXGAP }" + --ofile "macs2_bdgbroadcall.bdg" + && + awk '!/^track name/' "macs2_bdgbroadcall.bdg" > "${ outfile }" + </command> + <expand macro="stdio" /> + <inputs> + <param name="infile" type="data" format="bedgraph" label="MACS score in bedGraph" /> + <param name="cutoffpeak" type="float" label="Cutoff for peaks" value="2.0" + help="Cutoff for peaks depending on which method you used for score track. If the file contains qvalue scores from MACS2, score 2 means qvalue 0.01. default: 2.0 (--cutoff-peak)"/> + <param name="cutofflink" type="float" label="Cutoff for peaks" value="1.0" + help=" Cutoff for linking regions/low abundance regions depending on which method you used for score track. If the file contains qvalue scores from MACS2, score 1 means qvalue 0.1, and score 0.3 means qvalue 0.5. default: 1 (--cutoff-link)"/> + <param name="minlen" type="integer" label="Minimum length of peak" value="200" + help="It is recommended to set it as d value." /> + <param name="LVL1MAXGAP" type="integer" label="Maximum gap between significant peaks" value="30" + help="It is recommended to set it to tag size" /> + <param name="LVL2MAXGAP" type="integer" label="Maximum linking between significant peaks" value="800" + help="It is recommended to set it to 4 times of d value" /> + </inputs> + <outputs> + <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" /> + </outputs> + <tests> + <test> + <param name="infile" value="callpeak_treatment_part.bdg" ftype="bedgraph" /> + <param name="cutoffpeak" value="2.0"/> + <param name="cutofflink" value="1.0"/> + <param name="minlen" value="200"/> + <param name="LVL1MAXGAP" value="30"/> + <param name="LVL2MAXGAP" value="800"/> + <output name="outfile" file="bdgbroadcall_on_callpeak_treatment.tabular"/> + </test> + </tests> + <help> +**What it does** + +Call broad peaks from bedGraph output. +bdgbroadcall from macs2 + +@citation@ + </help> + <expand macro="citations" /> +</tool> |
| b |
| diff -r 000000000000 -r fe62ba547975 macs2_bdgcmp.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macs2_bdgcmp.xml Wed Feb 11 10:18:02 2015 -0500 |
| [ |
| @@ -0,0 +1,81 @@ +<tool id="macs2_bdgcmp" name="MACS2 bdgcmp" version="@VERSION_STRING@.0"> + <description>Deduct noise by comparing two signal tracks in bedGraph</description> + <expand macro="requirements" /> + <expand macro="version_command" /> + <macros> + <import>macs2_macros.xml</import> + </macros> + <command> + macs2 bdgcmp + -t "${ infile_treatment }" + -c "${ infile_control }" + + -m "${ bdgcmp_options.bdgcmp_options_selector }" + #if str($bdgcmp_options.bdgcmp_options_selector) in ['FE', 'logFE', 'logLR']: + -p "${ bdgcmp_options.pseudocount }" + #end if + -o "${ outfile }" + + </command> + <expand macro="stdio" /> + <inputs> + <param name="infile_treatment" type="data" format="bedgraph" label="Treatment bedGraph file" /> + <param name="infile_control" type="data" format="bedgraph" label="Control bedGraph file" /> + + <conditional name="bdgcmp_options"> + <param name="bdgcmp_options_selector" type="select" label="Method to use while calculating a score in any bin by comparing treatment value and control value"> + <option value="ppois" selected="true">Poisson pvalue (-log10) using control as lambda and treatment as observation (ppois)</option> + <option value="qpois">q-value through a BH process for poisson pvalues (qpois)</option> + <option value="subtract">subtraction from treatment (subtract)</option> + <option value="logFE">log10 fold enrichment (logFE)</option> + <option value="FE">linear scale fold enrichment (FE)</option> + <option value="logLR">log10 likelihood between ChIP-enriched model and open chromatin model (logLR)</option> + <option value="slogLR">symmetric log10 likelihood between two ChIP-enrichment models (slogLR)</option> + </param> + <when value="FE"> + <param name="pseudocount" type="float" label="Set pseudocount" value="0.0" help="The count will be applied after normalization of sequencing depth. default: 0.0, no pseudocount is applied."/> + </when> + <when value="logLR"> + <param name="pseudocount" type="float" label="Set pseudocount" value="0.0" help="The count will be applied after normalization of sequencing depth. default: 0.0, no pseudocount is applied."/> + </when> + <when value="logFE"> + <param name="pseudocount" type="float" label="Set pseudocount" value="0.0" help="The count will be applied after normalization of sequencing depth. default: 0.0, no pseudocount is applied."/> + </when> + <when value="ppois"/> + <when value="qpois"/> + <when value="subtract"/> + <when value="slogLR"/> + </conditional> + </inputs> + <outputs> + <data name="outfile" format="bedgraph" label="${tool.name} on ${on_string}" /> + </outputs> + <tests> + <test> + <param name="infile_control" value="callpeak_control_part.bdg" ftype="bedgraph"/> + <param name="infile_treatment" value="callpeak_treatment_part.bdg" ftype="bedgraph"/> + <param name="bdgcmp_options_selector" value="slogLR"/> + <output name="outfile" file="bdgcmp_on_Control_and_ChIP_slogLR.bdg"/> + </test> + </tests> + <help> +**What it does** + +With the improvement of sequencing techniques, chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq) +is getting popular to study genome-wide protein-DNA interactions. To address the lack of powerful ChIP-Seq analysis method, we present a novel algorithm, named Model-based Analysis of ChIP-Seq (MACS), for +identifying transcript factor binding sites. MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions, and MACS improves the spatial resolution of +binding sites through combining the information of both sequencing tag position and orientation. MACS can be easily used for ChIP-Seq data alone, or with control sample with the increase of specificity. + +View the original MACS2 documentation: https://github.com/taoliu/MACS/blob/master/README + +------ + +**Usage** + +**Compare .bdg files**: Deduct noise by comparing two signal tracks in bedGraph. + + +@citation@ + </help> + <expand macro="citations" /> +</tool> |
| b |
| diff -r 000000000000 -r fe62ba547975 macs2_bdgdiff.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macs2_bdgdiff.xml Wed Feb 11 10:18:02 2015 -0500 |
| b |
| @@ -0,0 +1,84 @@ +<tool id="macs2_bdgdiff" name="MACS2 bdgdiff" version="@VERSION_STRING@.0"> + <description>Differential peak detection based on paired four bedgraph files</description> + <expand macro="requirements" /> + <expand macro="version_command" /> + <macros> + <import>macs2_macros.xml</import> + </macros> + <command> + macs2 bdgdiff + --t1 "${ infile_pileup_cond1 }" + --t2 "${ infile_pileup_cond2 }" + --c1 "${ infile_control_cond1 }" + --c2 "${ infile_control_cond2 }" + --cutoff "${ cutoff }" + --min-len "${ minlen }" + --depth1 "${ depth1 }" + --depth2 "${ depth2 }" + --max-gap "${ maxgap }" + --o-prefix MACS2 + + </command> + <expand macro="stdio" /> + <inputs> + <param name="infile_pileup_cond1" type="data" format="bedgraph" label="MACS pileup bedGraph for condition 1" /> + <param name="infile_pileup_cond2" type="data" format="bedgraph" label="MACS pileup bedGraph for condition 2" /> + + <param name="infile_control_cond1" type="data" format="bedgraph" label="MACS control lambda bedGraph for condition 1" /> + <param name="infile_control_cond2" type="data" format="bedgraph" label="MACS control lambda bedGraph for condition 2" /> + + <param name="cutoff" type="float" label="Cutoff of log10 likelihood ratio cutoff" value="1.0" help="Default: 1.0 (likelihood ratio=10) (--cutoff)"/> + <param name="minlen" type="integer" label="Minimum length of differential region" value="200"/> + <param name="depth1" type="integer" value="1" label="Sequence depth of condition 1 in million reads" help="default: 1 (--depth1)" /> + <param name="depth2" type="integer" value="1" label="Sequence depth of condition 2 in million reads" help="default: 1 (--depth2)" /> + <param name="maxgap" type="integer" value="100" label="Maximum gap to merge nearby differential regions" help="Consider a wider gap for broad marks. Maximum gap should be smaller than minimum length. Default: 100 (-g)." /> + + <param name="outputs" type="select" display="checkboxes" multiple="True" label="Outputs"> + <option value="--ofile-cond1">Unique regions in condition 1</option> + <option value="--ofile-cond2">Unique regions in condition 2</option> + <option value="--ofile-both-conditions" selected="true">Common regions in both conditions</option> + <validator type="no_options" message="Please select at least one output file." /> + </param> + </inputs> + <outputs> + <data name="output_cond1" format="bed" from_work_dir="MACS2_cond1.bed" label="${tool.name} on ${on_string} (cond 1)"> + <filter>'--ofile-cond1' in outputs</filter> + </data> + <data name="output_cond2" format="bed" from_work_dir="MACS2_cond1.bed" label="${tool.name} on ${on_string} (cond 2)"> + <filter>'--ofile-cond2' in outputs</filter> + </data> + <data name="output_both" format="bed" from_work_dir="MACS2_common.bed" label="${tool.name} on ${on_string} (both)"> + <filter>'--ofile-both-conditions' in outputs</filter> + </data> + </outputs> + <tests> + <!-- we need a second condition here --> + <!-- + <test> + + <param name="infile_control_cond1" value="Control_200K.bed" ftype="bed"/> + <param name="infile_control_cond2" value="Control_200K.bed" ftype="bed"/> + <param name="infile_pileup_cond1" value="ChIP_200K.bed" ftype="bed"/> + <param name="infile_pileup_cond2" value="ChIP_200K.bed" ftype="bed"/> + <param name="cutoff" value="1.0"/> + <param name="minlen" value="200"/> + <param name="depth1" value="1"/> + <param name="depth2" value="1"/> + <param name="maxgap" value="100"/> + <param name="outputs" value="-ofile-cond1,-ofile-cond2,-ofile-both-conditions"/> + <output name="output_cond1" file=""/> + <output name="output_cond2" file=""/> + <output name="output_both" file=""/> + </test> + --> + </tests> + <help> +**What it does** + +bdgdiff from macs2 + + +@citation@ + </help> + <expand macro="citations" /> +</tool> |
| b |
| diff -r 000000000000 -r fe62ba547975 macs2_bdgpeakcall.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macs2_bdgpeakcall.xml Wed Feb 11 10:18:02 2015 -0500 |
| b |
| @@ -0,0 +1,60 @@ +<tool id="macs2_bdgpeakcall" name="MACS2 bdgpeakcall" version="@VERSION_STRING@.0"> + <description>Call peaks from bedGraph output</description> + <expand macro="requirements"> + <requirement type="package" version="4.1.0">gnu_awk</requirement> + </expand> + <expand macro="version_command" /> + <macros> + <import>macs2_macros.xml</import> + </macros> + <command> + macs2 bdgpeakcall + --ifile "${ infile }" + --cutoff "${ cutoff }" + --min-length "${ minlen }" + --max-gap "${ maxgap }" + ${ callsummits } + ${ notrackline } + --ofile "macs2_bdgpeakcall.bdg" + && + awk '!/^track name/' "macs2_bdgpeakcall.bdg" > "${ outfile }" + </command> + <expand macro="stdio" /> + <inputs> + <param name="infile" type="data" format="bedgraph" label="MACS score in bedGraph" /> + + <param name="cutoff" type="float" label="Cutoff for peaks" value="5.0" + help="Cutoff depends on which method you used for score track. If the file contains pvalue scores from MACS2, score 5 means pvalue 1e-5. DEFAULT: 5.0 (--cutoff)"/> + <param name="minlen" type="integer" value="200" label="Minimum length of peak" help="better to set it as d value (--min-length)"/> + <param name="maxgap" type="integer" value="30" label="Maximum gap between significant points in a peak" help="better to set it as tag size DEFAULT: 30 (--max-gap)"/> + + <param name="callsummits" type="boolean" truevalue="--call-summits" falsevalue="" checked="False" + label="If set, MACS will use a more sophisticated approach to find all summits in each enriched peak region." + help="(-call-summits)"/> + <param name="notrackline" type="boolean" truevalue="" falsevalue="--no-trackline" checked="False" + label="Include trackline into bedGraph output" + help="required by USCS (--no-trackline)"/> + </inputs> + <outputs> + <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" /> + </outputs> + <tests> + <test> + <param name="infile" value="callpeak_treatment_part.bdg" ftype="bedgraph" /> + <param name="cutoff" value="5.0"/> + <param name="minlen" value="200"/> + <param name="maxgap" value="30"/> + <output name="outfile" file="bdgpeakcall_on_callpeak_treatment.tabular"/> + </test> + </tests> + <help> +**What it does** + +Call peaks from bedGraph output. +bdgpeakcall from macs2 + + +@citation@ + </help> + <expand macro="citations" /> +</tool> |
| b |
| diff -r 000000000000 -r fe62ba547975 macs2_callpeak.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macs2_callpeak.xml Wed Feb 11 10:18:02 2015 -0500 |
| [ |
| b'@@ -0,0 +1,291 @@\n+<tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.0">\n+ <description>Call peaks from alignment results</description>\n+ <expand macro="requirements">\n+ <requirement type="package" version="3.0.1">R_3_0_1</requirement>\n+ <requirement type="package" version="4.1.0">gnu_awk</requirement>\n+ <requirement type="set_environment">MACS2_SCRIPT_PATH</requirement>\n+ </expand>\n+ <expand macro="version_command" />\n+ <macros>\n+ <import>macs2_macros.xml</import>\n+ </macros>\n+ <command>\n+ #set $temp_stderr = \'macs2_stderr\'\n+ (macs2 callpeak\n+\n+ --name "MACS2"\n+ -t ${ \' \'.join( map( lambda x:\'"%s"\' % ( x ), $input_treatment_file ) ) }\n+\n+ #if str( $input_control_file ) != \'None\':\n+ -c ${ \' \'.join( map( lambda x:\'"%s"\' % ( x ), $input_control_file ) ) }\n+ #end if\n+\n+ #for $ifile in $input_treatment_file:\n+ #if $ifile.ext.upper() == \'BAM\' and $bampe:\n+ --format BAMPE\n+ #else\n+ --format=\'$ifile.ext.upper()\'\n+ #end if\n+ #end for\n+\n+ @effective_genome_size@\n+\n+ --bw=\'$band_width\'\n+\n+ ## advanced options\n+ #if $advanced_options.advanced_options_selector == \'on\':\n+ $advanced_options.nolambda\n+ $advanced_options.to_large\n+ --ratio $advanced_options.ratio\n+ --slocal $advanced_options.slocal\n+ --llocal $advanced_options.llocal\n+ #if $advanced_options.broad_options.broad_options_selector == \'broad\':\n+ --broad\n+ --broad-cutoff=\'${ advanced_options.broad_options.broad_cutoff }\'\n+ #else:\n+ $advanced_options.broad_options.call_summits\n+ #end if\n+\n+ #if str( $advanced_options.keep_dup_options.keep_dup_options_selector ) == "user":\n+ --keep-dup "${ advanced_options.keep_dup_options.user_keepdup }"\n+ #else\n+ --keep-dup "${ advanced_options.keep_dup_options.keep_dup_options_selector }"\n+ #end if\n+\n+ #end if\n+\n+ ## With --bdg two additional output files will be generated.\n+ #if \'bdg\' in str($outputs).split(\',\'):\n+ --bdg\n+ #end if\n+\n+ ## cutoff selection\n+ #if str( $cutoff_options.cutoff_options_selector ) == \'qvalue\':\n+ --qvalue "${ cutoff_options.qvalue }"\n+ #elif str( $cutoff_options.cutoff_options_selector ) == \'pvalue\':\n+ #if str($cutoff_options.pvalue).strip() != \'\':\n+ --pvalue "${ cutoff_options.pvalue }"\n+ #end if\n+ #else:\n+ --foldenrichment "${ cutoff_options.foldenrichment }"\n+ #end if\n+\n+ ## model options\n+ #if $nomodel_type.nomodel_type_selector == \'nomodel\':\n+ --nomodel\n+ ##--shiftsize \'$nomodel_type.shiftsize\'\n+ --extsize \'${ nomodel_type.extsize }\'\n+ #end if\n+\n+ 2> $temp_stderr)\n+ #if \'peaks_bed\' in str($outputs).split(\',\'):\n+ &&\n+ awk \'$2-=1\' MACS2_peaks.xls | awk \'!/^#/\' | awk -v OFS=\'\\t\' \'$1=$1\' | tail -n+3 > "${ output_bed }"\n+ #end if\n+\n+ ## run R to create pdf from model script\n+ #if \'pdf\' in str($outputs).split(\',\'):\n+ &&\n+ Rscript MACS2_model.r > MACS2_model.r.log\n+ #end if\n+\n+ #if \'html\' in str($outputs).split(\',\'):\n+ ## if output files exists, move them to the files_path and create a html result page linking to them\n+ &&\n+ (\n+ count=`ls -1 MACS2* 2>/dev/null | wc -l`;\n+ if [ \\$count != 0 ];\n+ then \n+ mkdir "${ output_extra_files.files_path }";\n+ cp MACS2* "${ output_extra_files.files_path }";\n+ python "\\$MACS2_SCRIPT_PATH/dir2html.py" "${ output_extra_files.files_path }" $te'..b's_selector\'] == "broad"\n+ ))\n+ </filter>\n+ </data>\n+ <data name="output_narrowpeaks" format="tabular" from_work_dir="MACS2_peaks.narrowPeak" label="${tool.name} on ${on_string} (narrow Peaks)">\n+ <filter>\n+ (\n+ advanced_options[\'advanced_options_selector\'] == "off" or\n+ (\n+ advanced_options[\'advanced_options_selector\'] == "on" and\n+ advanced_options[\'broad_options\'][\'broad_options_selector\'] == "nobroad"\n+ ))\n+ </filter>\n+ </data>\n+ <data name="output_summits" format="bed" from_work_dir="MACS2_summits.bed" label="${tool.name} on ${on_string} (summits in BED)">\n+ <filter>\'summits\' in outputs</filter>\n+ </data>\n+ <data name="output_plot" format="pdf" from_work_dir="MACS2_model.pdf" label="${tool.name} on ${on_string} (plot)">\n+ <filter>\'pdf\' in outputs</filter>\n+ </data>\n+ <data name="output_treat_pileup" format="bedgraph" from_work_dir="MACS2_treat_pileup.bdg" label="${tool.name} on ${on_string} (Bedgraph Treatment)">\n+ <filter>\'bdg\' in outputs</filter>\n+ </data>\n+ <data name="output_control_lambda" format="bedgraph" from_work_dir="MACS2_control_lambda.bdg" label="${tool.name} on ${on_string} (Bedgraph Control)">\n+ <filter>\'bdg\' in outputs</filter>\n+ </data>\n+ <data name="output_extra_files" format="html" label="${tool.name} on ${on_string} (html report)">\n+ <filter>\'html\' in outputs</filter>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="input_control_file" value="Control_200K.bed" ftype="bed"/>\n+ <param name="input_treatment_file" value="ChIP_200K.bed" ftype="bed"/>\n+ <param name="cutoff_options_selector" value="qvalue"/>\n+ <param name="qvalue" value="0.05"/>\n+ <param name="band_width" value="300"/>\n+ <param name="outputs" value="peaks_bed,bdg"/>\n+ <param name="effective_genome_size_options_selector" value="user_defined" />\n+ <param name="gsize" value="3300000000" />\n+ <output name="output_control_lambda" compare="contains" file="callpeak_control_part.bdg"/>\n+ <output name="output_treat_pileup" compare="contains" file="callpeak_treatment_part.bdg"/>\n+ <output name="output_bed" compare="contains" file="callpeak_part.bed"/>\n+ <output name="output_summits" compare="contains" file="callpeak_summits_part.bed"/>\n+ </test>\n+ </tests>\n+ <help>\n+**What it does**\n+\n+With the improvement of sequencing techniques, chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq)\n+is getting popular to study genome-wide protein-DNA interactions. To address the lack of powerful ChIP-Seq analysis method, we present a novel algorithm, named Model-based Analysis of ChIP-Seq (MACS), for\n+identifying transcript factor binding sites. MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions, and MACS improves the spatial resolution of\n+binding sites through combining the information of both sequencing tag position and orientation. MACS can be easily used for ChIP-Seq data alone, or with control sample with the increase of specificity.\n+\n+View the original MACS2 documentation: https://github.com/taoliu/MACS/blob/master/README\n+\n+------\n+\n+**Usage**\n+\n+**Peak Calling**: Main MACS2 Function to Call peaks from alignment results.\n+\n+If you choose "Scores in bedGraph files" MACS will output the fragment pileup, control lambda, -log10-pvalue and -log10-qvalue scores in bedGraph files.\n+The peaks in BED format contain the following colomns: chr end length abs_summit pileup -log10(pvalue) fold_enrichment -log10(qvalue) name\n+\n+**Compare .bdg files**: Deduct noise by comparing two signal tracks in bedGraph.\n+\n+\n+@citation@\n+ </help>\n+ <expand macro="citations" />\n+</tool>\n' |
| b |
| diff -r 000000000000 -r fe62ba547975 macs2_filterdup.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macs2_filterdup.xml Wed Feb 11 10:18:02 2015 -0500 |
| b |
| @@ -0,0 +1,57 @@ +<tool id="macs2_filterdup" name="MACS2 filterdup" version="@VERSION_STRING@.0"> + <description>Remove duplicate reads at the same position</description> + <expand macro="requirements" /> + <expand macro="version_command" /> + <macros> + <import>macs2_macros.xml</import> + </macros> + <command> + macs2 filterdup + -i "${ infile }" + -o temp_outfile + + --format '${ infile.extension.upper() }' + @effective_genome_size@ + @tag_size@ + --pvalue "${ pvalue }" + #if str( $keep_dup_options.keep_dup_options_selector ) == "user": + --keep-dup "${ keep_dup_options.user_keepdup }" + #else + --keep-dup "${ keep_dup_options.keep_dup_options_selector }" + #end if + ; + mv temp_outfile "${ outfile }" + </command> + <expand macro="stdio" /> + <inputs> + <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" /> + <expand macro="conditional_effective_genome_size" /> + <expand macro="tag_size" /> + <param name="pvalue" type="text" value="1e-5" label="Pvalue cutoff for binomial distribution test" help="default: 1e-5 (--pvalue)" /> + + <expand macro="keep_duplicates" /> + + </inputs> + <outputs> + <data name="outfile" format="bed" label="${tool.name} on ${on_string}" /> + </outputs> + <tests> + <test> + <param name="infile" value="ChIP_200K_w_dups.bed" ftype="bed"/> + <param name="pvalue" value="1e-5"/> + <param name="keep_dup_options_selector" value="auto"/> + <param name="effective_genome_size_options_selector" value="user_defined" /> + <param name="gsize" value="3300000000" /> + <output name="outfile" file="filterdup_on_ChIP_200K_w_dups.bed"/> + </test> + </tests> + <help> +**What it does** + +Remove duplicate reads at the same position, then convert acceptable format to BED format. +filterdup tool from macs2 + +@citation@ + </help> + <expand macro="citations" /> +</tool> |
| b |
| diff -r 000000000000 -r fe62ba547975 macs2_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macs2_macros.xml Wed Feb 11 10:18:02 2015 -0500 |
| b |
| @@ -0,0 +1,99 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="2.1.0">macs2</requirement> + <requirement type="package" version="1.7.1">numpy</requirement> + <requirement type="package" version="0.12.0">scipy</requirement> + <yield /> + </requirements> + </xml> + + <token name="@VERSION_STRING@">2.1.0.20140616</token> + + <xml name="conditional_effective_genome_size"> + <conditional name="effective_genome_size_options"> + <param name="effective_genome_size_options_selector" type="select" label="Effective genome size" + help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded. + Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly. + See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes. (--gsize)"> + <option value="2451960000">Human (2,451,960,000)</option> + <option value="2150570000">Mouse (2,150,570,000)</option> + <option value="121400000">Fly (121,400,000)</option> + <option value="93260000">Worm (93,260,000)</option> + <option value="user_defined">User defined</option> + </param> + <when value="user_defined"> + <param name="gsize" type="integer" size="12" label="Effective genome size" value=""/> + </when> + </conditional> + </xml> + + <xml name="keep_duplicates"> + <conditional name="keep_dup_options"> + <param name="keep_dup_options_selector" type="select" label="How many duplicate tags at the exact same location are allowed?" + help="The default 'auto' option calculates the maximum tags at the exact same location based on binomial distribution using 1e-5 as pvalue cutoff. The 'all' option keeps every tags. If an integer is given, at most this number of tags will be kept at the same location. The default is to keep one tag at the same location. (--keep-dup 1)"> + <option value="1" selected="true">1</option> + <option value="all">all</option> + <option value="auto">auto</option> + <option value="user">user defined</option> + </param> + <when value="user"> + <param name="user_keepdup" type="integer" value="1" label="Keep at most this number of tags at the exact same location" + help=""/> + </when> + <when value="1" /> + <when value="all" /> + <when value="auto" /> + </conditional> + </xml> + + <token name="@effective_genome_size@"> + #if $effective_genome_size_options.effective_genome_size_options_selector == 'user_defined': + --gsize "${ effective_genome_size_options.gsize }" + #else: + --gsize "${ effective_genome_size_options.effective_genome_size_options_selector }" + #end if + </token> + + <xml name="version_command"> + <version_command>macs2 --version</version_command> + </xml> + + <xml name="tag_size"> + <param name="tsize" type="float" label="Tag size" value="-1.0" help="This will override the auto detected tag size. Per default that option is deactivated: -1.0 (--tsize)" /> + </xml> + <xml name="band_width"> + <param name="band_width" type="integer" value="300" label="Band width for picking regions to compute fragment size" + help="This value is only used while building the shifting model. (--bw)" /> + </xml> + + <token name="@tag_size@"> + #if $tsize == -1.0: + --tsize "${ tsize }" + #end if + </token> + + <xml name="stdio"> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + <regex match="Error:" /> + <regex match="Exception:" /> + </stdio> + </xml> + + <token name="@citation@"> +------ + +**Citation** + +For the underlying tool, please cite Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137. + +Integration of MACS2 with Galaxy performed by Ziru Zhou and Bjoern Gruening. + </token> + <xml name="citations"> + <citations> + <citation type="doi">10.1186/gb-2008-9-9-r137</citation> + </citations> + </xml> +</macros> |
| b |
| diff -r 000000000000 -r fe62ba547975 macs2_predictd.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macs2_predictd.xml Wed Feb 11 10:18:02 2015 -0500 |
| b |
| @@ -0,0 +1,71 @@ +<tool id="macs2_predictd" name="MACS2 predictd" version="@VERSION_STRING@.0"> + <description>Predict 'd' or fragment size from alignment results</description> + <expand macro="requirements"> + <requirement type="package" version="3.0.1">R_3_0_1</requirement> + <requirement type="package" version="4.1.0">gnu_awk</requirement> + </expand> + <expand macro="version_command" /> + <macros> + <import>macs2_macros.xml</import> + </macros> + <command> + macs2 predictd + -i ${ ' '.join( map( lambda x:'"%s"' % ( x ), $infiles ) ) } + @tag_size@ + @effective_genome_size@ + --bw "${ band_width }" + --mfold "${ mfoldlo }" "${ mfoldhi }" + + ## remove the timepoint and strip the output + 2>&1 | awk -F: '{print $4}' | awk '{$1=$1}1' + + > "${ outfile }" + + && + + Rscript predictd + </command> + <expand macro="stdio" /> + <inputs> + <param name="infiles" type="data" format="bam,sam,bed" multiple="True" label="ChIP-seq alignment file" help="If multiple files are given, then they will all be read and combined. Note that pair-end data is not supposed to work with this command. (-i)" /> + <expand macro="conditional_effective_genome_size" /> + <expand macro="tag_size" /> + <expand macro="band_width" /> + + <param name="mfoldlo" type="integer" label="Fold-enrichment lower limit" value="5" + help="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (--mfold)"/> + <param name="mfoldhi" type="integer" label="Fold-enrichment upper-limit" value="50" + help="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (--mfold)"/> + + </inputs> + + <outputs> + <data name="outfile" format="txt" label="${tool.name} on ${on_string} - d value" /> + <data name="outfile_image" from_work_dir="predictd_model.pdf" format="pdf" label="${tool.name} on ${on_string} - X-correlation image" /> + </outputs> + <tests> + <test> + <param name="infiles" value="Control_200K.bed,ChIP_200K.bed" ftype="bed" /> + <param name="effective_genome_size_options_selector" value="user_defined" /> + <param name="gsize" value="3300000000" /> + <param name="tsize" value="-1.0"/> + <param name="band_width" value="300"/> + <param name="mfoldlo" value="5"/> + <param name="mfoldhi" value="50"/> + <output name="outfile" file="predictd_on_ChIP_200K_and_Control_200K.txt"/> + <output name="outfile_image" file="predictd_on_ChIP_200K_and_Control_200K.pdf" compare="sim_size"/> + </test> + </tests> + <help> +**What it does** + +predictd from macs2 + + +Note that pair-end data is not supposed to work with this command. + + +@citation@ + </help> + <expand macro="citations" /> +</tool> |
| b |
| diff -r 000000000000 -r fe62ba547975 macs2_randsample.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macs2_randsample.xml Wed Feb 11 10:18:02 2015 -0500 |
| b |
| @@ -0,0 +1,54 @@ +<tool id="macs2_randsample" name="MACS2 randsample" version="@VERSION_STRING@.0"> + <description>Randomly sample number or percentage of total reads</description> + <expand macro="requirements" /> + <expand macro="version_command" /> + <macros> + <import>macs2_macros.xml</import> + </macros> + <command> + macs2 randsample + -t "${ infile }" + -o "${ outfile }" + + --format '${ infile.extension.upper() }' + + @tag_size@ + #if $method_options.method_options_selector == 'percentage': + --percentage "${ method_options.percentage }" + #else: + --number "${ method_options.number }" + #end if + </command> + <expand macro="stdio" /> + <inputs> + <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" /> + <expand macro="tag_size" /> + + <conditional name="method_options"> + <param name="method_options_selector" type="select" label="Select action to be performed"> + <option value="percentage" selected="true">Percentage</option> + <option value="number">Number</option> + </param> + <when value="percentage"> + <param name="percentage" type="float" value="80.0" label="Pvalue cutoff for binomial distribution test" help="(--percentage)" /> + </when> + <when value="number"> + <param name="number" type="integer" value="800000" label="Number of tags you want to keep" help="Note that the number of tags in output is approximate as the number specified here (--number)" /> + </when> + </conditional> + </inputs> + <outputs> + <data name="outfile" format="bed" label="${tool.name} on ${on_string}" /> + </outputs> + <tests> + <!-- No test, due to the randomness --> + </tests> + <help> +**What it does** + +randsample tool from macs2 + +@citation@ + </help> + <expand macro="citations" /> +</tool> |
| b |
| diff -r 000000000000 -r fe62ba547975 macs2_refinepeak.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macs2_refinepeak.xml Wed Feb 11 10:18:02 2015 -0500 |
| b |
| @@ -0,0 +1,45 @@ +<tool id="macs2_refinepeak" name="MACS2 refinepeak" version="@VERSION_STRING@.0"> + <description>Refine peak summits and give scores measuring balance of forward- backward tags (Experimental)</description> + <expand macro="requirements" /> + <expand macro="version_command" /> + <macros> + <import>macs2_macros.xml</import> + </macros> + <command> + macs2 refinepeak + -b "${ bed_infile }" + -i "${ infile }" + --format '${ infile.extension.upper() }' + --cutoff "${ cutoff }" + --window-size "${ winsize }" + --ofile "${ outfile }" + </command> + <expand macro="stdio" /> + <inputs> + <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" /> + <param name="bed_infile" type="data" format="bed" label="Candidate peak file in BED format" /> + <param name="cutoff" type="float" label="Cutoff" value="5.0" help="default: 5.0 (--cutoff)"/> + <param name="winsize" type="integer" value="200" label="Scan window size on both side of the summit" help="default: 200bp (--window-size)" /> + </inputs> + + <outputs> + <data name="outfile" format="bed" label="${tool.name} on ${on_string}" /> + </outputs> + <tests> + <test> + <param name="infile" value="ChIP_200K.bed" ftype="bed"/> + <param name="bed_infile" value="callpeak_summits_part.bed" ftype="bed"/> + <param name="cutoff" value="5.0"/> + <param name="winsize" value="200"/> + <output name="outfile" file="refinepeak_ChIP_and_summits.bed"/> + </test> + </tests> + <help> +**What it does** + +(Experimental) Take raw reads alignment, refine peak summits and give scores measuring balance of forward- backward tags. Inspired by SPP. + +@citation@ + </help> + <expand macro="citations" /> +</tool> |
| b |
| diff -r 000000000000 -r fe62ba547975 readme.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.rst Wed Feb 11 10:18:02 2015 -0500 |
| b |
| @@ -0,0 +1,60 @@ +======================== +Galaxy wrapper for MACS2 +======================== + +With the improvement of sequencing techniques, chromatin immunoprecipitation +followed by high throughput sequencing (ChIP-Seq) is getting popular to study +genome-wide protein-DNA interactions. To address the lack of powerful ChIP-Seq +analysis method, we present a novel algorithm, named Model-based Analysis of +ChIP-Seq (MACS), for identifying transcript factor binding sites. MACS captures +the influence of genome complexity to evaluate the significance of enriched ChIP +regions, and MACS improves the spatial resolution of binding sites through +combining the information of both sequencing tag position and orientation. +MACS can be easily used for ChIP-Seq data alone, or with control sample with the increase of specificity. + + +============ +Installation +============ + +It is recommended to install this wrapper via the `Galaxy Tool Shed`. + +.. _`Galaxy Tool Shed`: http://toolshed.g2.bx.psu.edu/view/modencode-dcc/macs2 + + +======= +History +======= +- v2.0.10.1: Initial public release +- v2.0.10.3: add "broad peaks" options + + +==================== +Detailed description +==================== + +View the original MACS2 documentation: https://github.com/taoliu/MACS/blob/master/README.rst + + +=============================== +Wrapper Licence (MIT/BSD style) +=============================== + +Permission to use, copy, modify, and distribute this software and its +documentation with or without modifications and for any purpose and +without fee is hereby granted, provided that any copyright notices +appear in all copies and that both those copyright notices and this +permission notice appear in supporting documentation, and that the +names of the contributors or copyright holders not be used in +advertising or publicity pertaining to distribution of the software +without specific prior permission. + +THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL +WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE +CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT +OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS +OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE +OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE +OR PERFORMANCE OF THIS SOFTWARE. + |
| b |
| diff -r 000000000000 -r fe62ba547975 test-data/ChIP_200K.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ChIP_200K.bed Wed Feb 11 10:18:02 2015 -0500 |
| b |
| b'@@ -0,0 +1,199977 @@\n+chr1\t564917\t565017\t.\t.\t+\n+chr1\t565533\t565633\t.\t.\t+\n+chr1\t565844\t565944\t.\t.\t+\n+chr1\t565858\t565958\t.\t.\t+\n+chr1\t566132\t566232\t.\t.\t+\n+chr1\t566212\t566312\t.\t.\t+\n+chr1\t566736\t566836\t.\t.\t+\n+chr1\t566976\t567076\t.\t.\t+\n+chr1\t567211\t567311\t.\t.\t+\n+chr1\t567320\t567420\t.\t.\t+\n+chr1\t567833\t567933\t.\t.\t+\n+chr1\t568094\t568194\t.\t.\t+\n+chr1\t568128\t568228\t.\t.\t+\n+chr1\t568449\t568549\t.\t.\t+\n+chr1\t569053\t569153\t.\t.\t+\n+chr1\t569100\t569200\t.\t.\t+\n+chr1\t569553\t569653\t.\t.\t+\n+chr1\t569554\t569654\t.\t.\t+\n+chr1\t569623\t569723\t.\t.\t+\n+chr1\t569694\t569794\t.\t.\t+\n+chr1\t569837\t569937\t.\t.\t+\n+chr1\t713744\t713844\t.\t.\t+\n+chr1\t714193\t714293\t.\t.\t+\n+chr1\t739124\t739224\t.\t.\t+\n+chr1\t811788\t811888\t.\t.\t+\n+chr1\t812107\t812207\t.\t.\t+\n+chr1\t840078\t840178\t.\t.\t+\n+chr1\t840146\t840246\t.\t.\t+\n+chr1\t840147\t840247\t.\t.\t+\n+chr1\t858768\t858868\t.\t.\t+\n+chr1\t894060\t894160\t.\t.\t+\n+chr1\t902085\t902185\t.\t.\t+\n+chr1\t919486\t919586\t.\t.\t+\n+chr1\t919675\t919775\t.\t.\t+\n+chr1\t937146\t937246\t.\t.\t+\n+chr1\t937349\t937449\t.\t.\t+\n+chr1\t953007\t953107\t.\t.\t+\n+chr1\t954262\t954362\t.\t.\t+\n+chr1\t954290\t954390\t.\t.\t+\n+chr1\t954763\t954863\t.\t.\t+\n+chr1\t994722\t994822\t.\t.\t+\n+chr1\t994762\t994862\t.\t.\t+\n+chr1\t999267\t999367\t.\t.\t+\n+chr1\t1051449\t1051549\t.\t.\t+\n+chr1\t1057394\t1057494\t.\t.\t+\n+chr1\t1185598\t1185698\t.\t.\t+\n+chr1\t1185643\t1185743\t.\t.\t+\n+chr1\t1185654\t1185754\t.\t.\t+\n+chr1\t1185698\t1185798\t.\t.\t+\n+chr1\t1204173\t1204273\t.\t.\t+\n+chr1\t1220903\t1221003\t.\t.\t+\n+chr1\t1227177\t1227277\t.\t.\t+\n+chr1\t1240750\t1240850\t.\t.\t+\n+chr1\t1240869\t1240969\t.\t.\t+\n+chr1\t1284324\t1284424\t.\t.\t+\n+chr1\t1284634\t1284734\t.\t.\t+\n+chr1\t1307407\t1307507\t.\t.\t+\n+chr1\t1307481\t1307581\t.\t.\t+\n+chr1\t1310553\t1310653\t.\t.\t+\n+chr1\t1316443\t1316543\t.\t.\t+\n+chr1\t1318226\t1318326\t.\t.\t+\n+chr1\t1334773\t1334873\t.\t.\t+\n+chr1\t1365742\t1365842\t.\t.\t+\n+chr1\t1370983\t1371083\t.\t.\t+\n+chr1\t1397321\t1397421\t.\t.\t+\n+chr1\t1406355\t1406455\t.\t.\t+\n+chr1\t1440208\t1440308\t.\t.\t+\n+chr1\t1440379\t1440479\t.\t.\t+\n+chr1\t1440461\t1440561\t.\t.\t+\n+chr1\t1506071\t1506171\t.\t.\t+\n+chr1\t1543963\t1544063\t.\t.\t+\n+chr1\t1555471\t1555571\t.\t.\t+\n+chr1\t1555484\t1555584\t.\t.\t+\n+chr1\t1556891\t1556991\t.\t.\t+\n+chr1\t1590594\t1590694\t.\t.\t+\n+chr1\t1590667\t1590767\t.\t.\t+\n+chr1\t1590692\t1590792\t.\t.\t+\n+chr1\t1619960\t1620060\t.\t.\t+\n+chr1\t1655694\t1655794\t.\t.\t+\n+chr1\t1680362\t1680462\t.\t.\t+\n+chr1\t1707735\t1707835\t.\t.\t+\n+chr1\t1709800\t1709900\t.\t.\t+\n+chr1\t1710100\t1710200\t.\t.\t+\n+chr1\t1710577\t1710677\t.\t.\t+\n+chr1\t1720443\t1720543\t.\t.\t+\n+chr1\t1743660\t1743760\t.\t.\t+\n+chr1\t1756325\t1756425\t.\t.\t+\n+chr1\t1759509\t1759609\t.\t.\t+\n+chr1\t1760855\t1760955\t.\t.\t+\n+chr1\t1766487\t1766587\t.\t.\t+\n+chr1\t1791335\t1791435\t.\t.\t+\n+chr1\t1837745\t1837845\t.\t.\t+\n+chr1\t1837879\t1837979\t.\t.\t+\n+chr1\t1839918\t1840018\t.\t.\t+\n+chr1\t1840297\t1840397\t.\t.\t+\n+chr1\t1840365\t1840465\t.\t.\t+\n+chr1\t1840541\t1840641\t.\t.\t+\n+chr1\t1840574\t1840674\t.\t.\t+\n+chr1\t1840753\t1840853\t.\t.\t+\n+chr1\t1875363\t1875463\t.\t.\t+\n+chr1\t1875625\t1875725\t.\t.\t+\n+chr1\t1875837\t1875937\t.\t.\t+\n+chr1\t1974822\t1974922\t.\t.\t+\n+chr1\t1976255\t1976355\t.\t.\t+\n+chr1\t1976427\t1976527\t.\t.\t+\n+chr1\t2023183\t2023283\t.\t.\t+\n+chr1\t2063735\t2063835\t.\t.\t+\n+chr1\t2071198\t2071298\t.\t.\t+\n+chr1\t2090975\t2091075\t.\t.\t+\n+chr1\t2105693\t2105793\t.\t.\t+\n+chr1\t2105716\t2105816\t.\t.\t+\n+chr1\t2105889\t2105989\t.\t.\t+\n+chr1\t2126521\t2126621\t.\t.\t+\n+chr1\t2126579\t2126679\t.\t.\t+\n+chr1\t2126607\t2126707\t.\t.\t+\n+chr1\t2136679\t2136779\t.\t.\t+\n+chr1\t2246468\t2246568\t.\t.\t+\n+chr1\t2246520\t2246620\t.\t.\t+\n+chr1\t2246695\t2246795\t.\t.\t+\n+chr1\t2246763\t2246863\t.\t.\t+\n+chr1\t2313306\t2313406\t.\t.\t+\n+chr1\t2314030\t2314130\t.\t.\t+\n+chr1\t2339303\t2339403\t.\t.\t+\n+chr1\t2345827\t2345927\t.\t.\t+\n+chr1\t2345913\t2346013\t.\t.\t+\n+chr1\t2346009\t2346109\t.\t.\t+\n+chr1\t2357572\t2357672\t.\t.\t+\n+chr1\t2361575\t2361675\t.\t.\t+\n+chr1\t2366865\t2366965\t.\t.\t+\n+chr1\t2416008\t2416108\t.\t.\t+\n+chr1\t2432624\t2432724\t.\t.\t+\n+chr1\t2450468\t2450568\t.\t.\t+\n+chr1\t2455125\t2455225\t.\t.\t+\n+chr1\t2465845\t2465945\t.\t.\t+\n+chr1\t2476008\t2476108\t.\t.\t+\n+chr1\t2479407\t2479507\t.\t.\t+\n+chr1\t2479551\t2479651\t.\t.\t+\n+chr1\t2479552\t2479652\t.\t.\t+\n+chr1\t2479613\t2479713\t.\t.\t+\n+chr1\t2480134\t2480234\t.\t.\t+\n+chr1\t2486437\t2486537\t.\t.\t+\n+chr1\t2486452\t2486552\t.\t.\t+\n+chr1\t2499013\t2499113\t.\t.\t+\n+chr1\t2506345\t2506445\t.\t.\t+\n+chr1\t2510054\t2510154\t.\t.\t+\n+chr'..b'chrX\t151240666\t151240766\t.\t.\t-\n+chrX\t151240806\t151240906\t.\t.\t-\n+chrX\t151582838\t151582938\t.\t.\t-\n+chrX\t151771014\t151771114\t.\t.\t-\n+chrX\t151802193\t151802293\t.\t.\t-\n+chrX\t151804534\t151804634\t.\t.\t-\n+chrX\t151842724\t151842824\t.\t.\t-\n+chrX\t151985773\t151985873\t.\t.\t-\n+chrX\t151985839\t151985939\t.\t.\t-\n+chrX\t151988472\t151988572\t.\t.\t-\n+chrX\t152073172\t152073272\t.\t.\t-\n+chrX\t152084321\t152084421\t.\t.\t-\n+chrX\t152084424\t152084524\t.\t.\t-\n+chrX\t152084544\t152084644\t.\t.\t-\n+chrX\t152094872\t152094972\t.\t.\t-\n+chrX\t152110256\t152110356\t.\t.\t-\n+chrX\t152110382\t152110482\t.\t.\t-\n+chrX\t152110437\t152110537\t.\t.\t-\n+chrX\t152127574\t152127674\t.\t.\t-\n+chrX\t152127800\t152127900\t.\t.\t-\n+chrX\t152146319\t152146419\t.\t.\t-\n+chrX\t152201244\t152201344\t.\t.\t-\n+chrX\t152629058\t152629158\t.\t.\t-\n+chrX\t152638220\t152638320\t.\t.\t-\n+chrX\t152665869\t152665969\t.\t.\t-\n+chrX\t152726458\t152726558\t.\t.\t-\n+chrX\t152726593\t152726693\t.\t.\t-\n+chrX\t152726690\t152726790\t.\t.\t-\n+chrX\t152731116\t152731216\t.\t.\t-\n+chrX\t152735875\t152735975\t.\t.\t-\n+chrX\t152736423\t152736523\t.\t.\t-\n+chrX\t152736564\t152736664\t.\t.\t-\n+chrX\t152770035\t152770135\t.\t.\t-\n+chrX\t152772703\t152772803\t.\t.\t-\n+chrX\t152773145\t152773245\t.\t.\t-\n+chrX\t152773255\t152773355\t.\t.\t-\n+chrX\t152820417\t152820517\t.\t.\t-\n+chrX\t152820502\t152820602\t.\t.\t-\n+chrX\t152915226\t152915326\t.\t.\t-\n+chrX\t152927792\t152927892\t.\t.\t-\n+chrX\t152927842\t152927942\t.\t.\t-\n+chrX\t152928044\t152928144\t.\t.\t-\n+chrX\t152952814\t152952914\t.\t.\t-\n+chrX\t152973923\t152974023\t.\t.\t-\n+chrX\t152989305\t152989405\t.\t.\t-\n+chrX\t152990853\t152990953\t.\t.\t-\n+chrX\t153010206\t153010306\t.\t.\t-\n+chrX\t153020745\t153020845\t.\t.\t-\n+chrX\t153029607\t153029707\t.\t.\t-\n+chrX\t153044429\t153044529\t.\t.\t-\n+chrX\t153165992\t153166092\t.\t.\t-\n+chrX\t153190621\t153190721\t.\t.\t-\n+chrX\t153191871\t153191971\t.\t.\t-\n+chrX\t153200865\t153200965\t.\t.\t-\n+chrX\t153203759\t153203859\t.\t.\t-\n+chrX\t153203877\t153203977\t.\t.\t-\n+chrX\t153212993\t153213093\t.\t.\t-\n+chrX\t153212999\t153213099\t.\t.\t-\n+chrX\t153277188\t153277288\t.\t.\t-\n+chrX\t153279338\t153279438\t.\t.\t-\n+chrX\t153279350\t153279450\t.\t.\t-\n+chrX\t153318552\t153318652\t.\t.\t-\n+chrX\t153320296\t153320396\t.\t.\t-\n+chrX\t153396988\t153397088\t.\t.\t-\n+chrX\t153402255\t153402355\t.\t.\t-\n+chrX\t153402319\t153402419\t.\t.\t-\n+chrX\t153544588\t153544688\t.\t.\t-\n+chrX\t153562113\t153562213\t.\t.\t-\n+chrX\t153599790\t153599890\t.\t.\t-\n+chrX\t153599904\t153600004\t.\t.\t-\n+chrX\t153599989\t153600089\t.\t.\t-\n+chrX\t153601949\t153602049\t.\t.\t-\n+chrX\t153602000\t153602100\t.\t.\t-\n+chrX\t153602086\t153602186\t.\t.\t-\n+chrX\t153606444\t153606544\t.\t.\t-\n+chrX\t153626366\t153626466\t.\t.\t-\n+chrX\t153627379\t153627479\t.\t.\t-\n+chrX\t153672651\t153672751\t.\t.\t-\n+chrX\t153679069\t153679169\t.\t.\t-\n+chrX\t153713887\t153713987\t.\t.\t-\n+chrX\t153733660\t153733760\t.\t.\t-\n+chrX\t153755437\t153755537\t.\t.\t-\n+chrX\t153763090\t153763190\t.\t.\t-\n+chrX\t153763187\t153763287\t.\t.\t-\n+chrX\t153763211\t153763311\t.\t.\t-\n+chrX\t153763216\t153763316\t.\t.\t-\n+chrX\t153763220\t153763320\t.\t.\t-\n+chrX\t153763239\t153763339\t.\t.\t-\n+chrX\t153763315\t153763415\t.\t.\t-\n+chrX\t153763341\t153763441\t.\t.\t-\n+chrX\t153938851\t153938951\t.\t.\t-\n+chrX\t153943509\t153943609\t.\t.\t-\n+chrX\t153943515\t153943615\t.\t.\t-\n+chrX\t153977100\t153977200\t.\t.\t-\n+chrX\t153977134\t153977234\t.\t.\t-\n+chrX\t153977152\t153977252\t.\t.\t-\n+chrX\t154011212\t154011312\t.\t.\t-\n+chrX\t154039587\t154039687\t.\t.\t-\n+chrX\t154069298\t154069398\t.\t.\t-\n+chrX\t154069353\t154069453\t.\t.\t-\n+chrX\t154070074\t154070174\t.\t.\t-\n+chrX\t154146471\t154146571\t.\t.\t-\n+chrX\t154209343\t154209443\t.\t.\t-\n+chrX\t154209507\t154209607\t.\t.\t-\n+chrX\t154220892\t154220992\t.\t.\t-\n+chrX\t154285839\t154285939\t.\t.\t-\n+chrX\t154286034\t154286134\t.\t.\t-\n+chrX\t154314834\t154314934\t.\t.\t-\n+chrX\t154331242\t154331342\t.\t.\t-\n+chrX\t154365903\t154366003\t.\t.\t-\n+chrX\t154365921\t154366021\t.\t.\t-\n+chrX\t154384620\t154384720\t.\t.\t-\n+chrX\t154444870\t154444970\t.\t.\t-\n+chrX\t154445352\t154445452\t.\t.\t-\n+chrX\t154528235\t154528335\t.\t.\t-\n+chrX\t154739628\t154739728\t.\t.\t-\n+chrX\t154807657\t154807757\t.\t.\t-\n+chrX\t154850049\t154850149\t.\t.\t-\n+chrX\t154882562\t154882662\t.\t.\t-\n+chrX\t155049861\t155049961\t.\t.\t-\n+chrX\t155087389\t155087489\t.\t.\t-\n+chrX\t155087414\t155087514\t.\t.\t-\n+chrX\t155168161\t155168261\t.\t.\t-\n+chrX\t155196647\t155196747\t.\t.\t-\n+chrX\t155196839\t155196939\t.\t.\t-\n' |
| b |
| diff -r 000000000000 -r fe62ba547975 test-data/ChIP_200K_w_dups.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ChIP_200K_w_dups.bed Wed Feb 11 10:18:02 2015 -0500 |
| b |
| @@ -0,0 +1,13 @@ +chr1 564917 565017 . . + +chr1 565533 565633 . . + +chr1 565533 565633 . . + +chr1 565844 565944 . . + +chr1 565858 565958 . . + +chr1 566132 566232 . . + +chr1 566212 566312 . . + +chr1 566736 566836 . . + +chr1 566736 566836 . . + +chr1 566976 567076 . . + +chr1 567211 567311 . . + +chr1 567320 567420 . . + +chr1 567320 567420 . . + |
| b |
| diff -r 000000000000 -r fe62ba547975 test-data/Control_200K.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Control_200K.bed Wed Feb 11 10:18:02 2015 -0500 |
| b |
| b'@@ -0,0 +1,199978 @@\n+chr1\t564459\t564545\t.\t.\t+\n+chr1\t564461\t564547\t.\t.\t+\n+chr1\t564482\t564568\t.\t.\t+\n+chr1\t564484\t564570\t.\t.\t+\n+chr1\t564489\t564575\t.\t.\t+\n+chr1\t564494\t564580\t.\t.\t+\n+chr1\t564505\t564591\t.\t.\t+\n+chr1\t564517\t564603\t.\t.\t+\n+chr1\t564521\t564607\t.\t.\t+\n+chr1\t564526\t564612\t.\t.\t+\n+chr1\t564530\t564616\t.\t.\t+\n+chr1\t564542\t564628\t.\t.\t+\n+chr1\t564548\t564634\t.\t.\t+\n+chr1\t564555\t564641\t.\t.\t+\n+chr1\t564558\t564644\t.\t.\t+\n+chr1\t564590\t564676\t.\t.\t+\n+chr1\t564591\t564677\t.\t.\t+\n+chr1\t564597\t564683\t.\t.\t+\n+chr1\t564600\t564686\t.\t.\t+\n+chr1\t564623\t564709\t.\t.\t+\n+chr1\t564629\t564715\t.\t.\t+\n+chr1\t564643\t564729\t.\t.\t+\n+chr1\t564645\t564731\t.\t.\t+\n+chr1\t564665\t564751\t.\t.\t+\n+chr1\t564671\t564757\t.\t.\t+\n+chr1\t564676\t564762\t.\t.\t+\n+chr1\t564716\t564802\t.\t.\t+\n+chr1\t564718\t564804\t.\t.\t+\n+chr1\t564724\t564810\t.\t.\t+\n+chr1\t564736\t564822\t.\t.\t+\n+chr1\t564741\t564827\t.\t.\t+\n+chr1\t564748\t564834\t.\t.\t+\n+chr1\t564756\t564842\t.\t.\t+\n+chr1\t564758\t564844\t.\t.\t+\n+chr1\t564759\t564845\t.\t.\t+\n+chr1\t564764\t564850\t.\t.\t+\n+chr1\t564769\t564855\t.\t.\t+\n+chr1\t564782\t564868\t.\t.\t+\n+chr1\t564784\t564870\t.\t.\t+\n+chr1\t564796\t564882\t.\t.\t+\n+chr1\t564799\t564885\t.\t.\t+\n+chr1\t564814\t564900\t.\t.\t+\n+chr1\t564822\t564908\t.\t.\t+\n+chr1\t564827\t564913\t.\t.\t+\n+chr1\t564828\t564914\t.\t.\t+\n+chr1\t564829\t564915\t.\t.\t+\n+chr1\t564837\t564923\t.\t.\t+\n+chr1\t564848\t564934\t.\t.\t+\n+chr1\t564854\t564940\t.\t.\t+\n+chr1\t564870\t564956\t.\t.\t+\n+chr1\t564878\t564964\t.\t.\t+\n+chr1\t564884\t564970\t.\t.\t+\n+chr1\t564889\t564975\t.\t.\t+\n+chr1\t564901\t564987\t.\t.\t+\n+chr1\t564901\t564987\t.\t.\t+\n+chr1\t564907\t564993\t.\t.\t+\n+chr1\t564910\t564996\t.\t.\t+\n+chr1\t564917\t565003\t.\t.\t+\n+chr1\t564920\t565006\t.\t.\t+\n+chr1\t564950\t565036\t.\t.\t+\n+chr1\t564954\t565040\t.\t.\t+\n+chr1\t564958\t565044\t.\t.\t+\n+chr1\t564962\t565048\t.\t.\t+\n+chr1\t564965\t565051\t.\t.\t+\n+chr1\t564995\t565081\t.\t.\t+\n+chr1\t565000\t565086\t.\t.\t+\n+chr1\t565002\t565088\t.\t.\t+\n+chr1\t565007\t565093\t.\t.\t+\n+chr1\t565008\t565094\t.\t.\t+\n+chr1\t565044\t565130\t.\t.\t+\n+chr1\t565046\t565132\t.\t.\t+\n+chr1\t565047\t565133\t.\t.\t+\n+chr1\t565065\t565151\t.\t.\t+\n+chr1\t565079\t565165\t.\t.\t+\n+chr1\t565083\t565169\t.\t.\t+\n+chr1\t565085\t565171\t.\t.\t+\n+chr1\t565116\t565202\t.\t.\t+\n+chr1\t565120\t565206\t.\t.\t+\n+chr1\t565123\t565209\t.\t.\t+\n+chr1\t565129\t565215\t.\t.\t+\n+chr1\t565132\t565218\t.\t.\t+\n+chr1\t565151\t565237\t.\t.\t+\n+chr1\t565170\t565256\t.\t.\t+\n+chr1\t565173\t565259\t.\t.\t+\n+chr1\t565174\t565260\t.\t.\t+\n+chr1\t565185\t565271\t.\t.\t+\n+chr1\t565191\t565277\t.\t.\t+\n+chr1\t565193\t565279\t.\t.\t+\n+chr1\t565194\t565280\t.\t.\t+\n+chr1\t565202\t565288\t.\t.\t+\n+chr1\t565202\t565288\t.\t.\t+\n+chr1\t565231\t565317\t.\t.\t+\n+chr1\t565242\t565328\t.\t.\t+\n+chr1\t565245\t565331\t.\t.\t+\n+chr1\t565266\t565352\t.\t.\t+\n+chr1\t565273\t565359\t.\t.\t+\n+chr1\t565284\t565370\t.\t.\t+\n+chr1\t565290\t565376\t.\t.\t+\n+chr1\t565293\t565379\t.\t.\t+\n+chr1\t565299\t565385\t.\t.\t+\n+chr1\t565304\t565390\t.\t.\t+\n+chr1\t565306\t565392\t.\t.\t+\n+chr1\t565316\t565402\t.\t.\t+\n+chr1\t565336\t565422\t.\t.\t+\n+chr1\t565338\t565424\t.\t.\t+\n+chr1\t565342\t565428\t.\t.\t+\n+chr1\t565344\t565430\t.\t.\t+\n+chr1\t565380\t565466\t.\t.\t+\n+chr1\t565382\t565468\t.\t.\t+\n+chr1\t565388\t565474\t.\t.\t+\n+chr1\t565392\t565478\t.\t.\t+\n+chr1\t565415\t565501\t.\t.\t+\n+chr1\t565416\t565502\t.\t.\t+\n+chr1\t565449\t565535\t.\t.\t+\n+chr1\t565463\t565549\t.\t.\t+\n+chr1\t565467\t565553\t.\t.\t+\n+chr1\t565475\t565561\t.\t.\t+\n+chr1\t565476\t565562\t.\t.\t+\n+chr1\t565482\t565568\t.\t.\t+\n+chr1\t565496\t565582\t.\t.\t+\n+chr1\t565498\t565584\t.\t.\t+\n+chr1\t565508\t565594\t.\t.\t+\n+chr1\t565509\t565595\t.\t.\t+\n+chr1\t565513\t565599\t.\t.\t+\n+chr1\t565549\t565635\t.\t.\t+\n+chr1\t565551\t565637\t.\t.\t+\n+chr1\t565552\t565638\t.\t.\t+\n+chr1\t565557\t565643\t.\t.\t+\n+chr1\t565559\t565645\t.\t.\t+\n+chr1\t565568\t565654\t.\t.\t+\n+chr1\t565569\t565655\t.\t.\t+\n+chr1\t565589\t565675\t.\t.\t+\n+chr1\t565593\t565679\t.\t.\t+\n+chr1\t565594\t565680\t.\t.\t+\n+chr1\t565607\t565693\t.\t.\t+\n+chr1\t565611\t565697\t.\t.\t+\n+chr1\t565616\t565702\t.\t.\t+\n+chr1\t565622\t565708\t.\t.\t+\n+chr1\t565637\t565723\t.\t.\t+\n+chr1\t565638\t565724\t.\t.\t+\n+chr1\t565638\t565724\t.\t.\t+\n+chr1\t565640\t565726\t.\t.\t+\n+chr1\t565649\t565735\t.\t.\t+\n+chr1\t565660\t565746\t.\t.\t+\n+chr1\t565664\t565750\t.\t.\t+\n+chr1\t565671\t565757\t.\t.\t+\n+chr1\t565671\t565757\t.\t.\t+\n+chr1\t565678\t565764\t.\t.\t+\n+chr1\t565681\t565767\t.\t.\t+\n+chr1\t565695\t565781\t.\t.\t+\n+chr1\t565703\t565789\t.\t.\t+\n+chr1\t565722\t565808\t.\t.\t+\n+chr1\t565727\t565813\t.\t.\t+\n'..b'chrX\t149607674\t149607760\t.\t.\t-\n+chrX\t149614632\t149614718\t.\t.\t-\n+chrX\t149688873\t149688959\t.\t.\t-\n+chrX\t149721420\t149721506\t.\t.\t-\n+chrX\t149738923\t149739009\t.\t.\t-\n+chrX\t149817691\t149817777\t.\t.\t-\n+chrX\t149867596\t149867682\t.\t.\t-\n+chrX\t149934411\t149934497\t.\t.\t-\n+chrX\t149938968\t149939054\t.\t.\t-\n+chrX\t150063381\t150063467\t.\t.\t-\n+chrX\t150065863\t150065949\t.\t.\t-\n+chrX\t150094810\t150094896\t.\t.\t-\n+chrX\t150107603\t150107689\t.\t.\t-\n+chrX\t150173663\t150173749\t.\t.\t-\n+chrX\t150238925\t150239011\t.\t.\t-\n+chrX\t150239479\t150239565\t.\t.\t-\n+chrX\t150267378\t150267464\t.\t.\t-\n+chrX\t150390682\t150390768\t.\t.\t-\n+chrX\t150416472\t150416558\t.\t.\t-\n+chrX\t150454190\t150454276\t.\t.\t-\n+chrX\t150531072\t150531158\t.\t.\t-\n+chrX\t150539946\t150540032\t.\t.\t-\n+chrX\t150543744\t150543830\t.\t.\t-\n+chrX\t150591315\t150591401\t.\t.\t-\n+chrX\t150651552\t150651638\t.\t.\t-\n+chrX\t150666850\t150666936\t.\t.\t-\n+chrX\t150685255\t150685341\t.\t.\t-\n+chrX\t150727540\t150727626\t.\t.\t-\n+chrX\t150847584\t150847670\t.\t.\t-\n+chrX\t150856002\t150856088\t.\t.\t-\n+chrX\t150868245\t150868331\t.\t.\t-\n+chrX\t151005896\t151005982\t.\t.\t-\n+chrX\t151101154\t151101240\t.\t.\t-\n+chrX\t151157493\t151157579\t.\t.\t-\n+chrX\t151183804\t151183890\t.\t.\t-\n+chrX\t151243885\t151243971\t.\t.\t-\n+chrX\t151485937\t151486023\t.\t.\t-\n+chrX\t151572846\t151572932\t.\t.\t-\n+chrX\t151652002\t151652088\t.\t.\t-\n+chrX\t151698811\t151698897\t.\t.\t-\n+chrX\t151762449\t151762535\t.\t.\t-\n+chrX\t151769949\t151770035\t.\t.\t-\n+chrX\t151770570\t151770656\t.\t.\t-\n+chrX\t151801314\t151801400\t.\t.\t-\n+chrX\t151831962\t151832048\t.\t.\t-\n+chrX\t151901686\t151901772\t.\t.\t-\n+chrX\t152039501\t152039587\t.\t.\t-\n+chrX\t152049008\t152049094\t.\t.\t-\n+chrX\t152096132\t152096218\t.\t.\t-\n+chrX\t152110788\t152110874\t.\t.\t-\n+chrX\t152178748\t152178834\t.\t.\t-\n+chrX\t152210875\t152210961\t.\t.\t-\n+chrX\t152366620\t152366706\t.\t.\t-\n+chrX\t152416856\t152416942\t.\t.\t-\n+chrX\t152562105\t152562191\t.\t.\t-\n+chrX\t152645480\t152645566\t.\t.\t-\n+chrX\t152669244\t152669330\t.\t.\t-\n+chrX\t152905579\t152905665\t.\t.\t-\n+chrX\t152942850\t152942936\t.\t.\t-\n+chrX\t153059265\t153059351\t.\t.\t-\n+chrX\t153089983\t153090069\t.\t.\t-\n+chrX\t153131499\t153131585\t.\t.\t-\n+chrX\t153205840\t153205926\t.\t.\t-\n+chrX\t153295532\t153295618\t.\t.\t-\n+chrX\t153343434\t153343520\t.\t.\t-\n+chrX\t153359712\t153359798\t.\t.\t-\n+chrX\t153370784\t153370870\t.\t.\t-\n+chrX\t153378236\t153378322\t.\t.\t-\n+chrX\t153404169\t153404255\t.\t.\t-\n+chrX\t153588729\t153588815\t.\t.\t-\n+chrX\t153612476\t153612562\t.\t.\t-\n+chrX\t153629471\t153629557\t.\t.\t-\n+chrX\t153653493\t153653579\t.\t.\t-\n+chrX\t153666449\t153666535\t.\t.\t-\n+chrX\t153687468\t153687554\t.\t.\t-\n+chrX\t153707956\t153708042\t.\t.\t-\n+chrX\t153719238\t153719324\t.\t.\t-\n+chrX\t153744430\t153744516\t.\t.\t-\n+chrX\t153756545\t153756631\t.\t.\t-\n+chrX\t153887257\t153887343\t.\t.\t-\n+chrX\t153901703\t153901789\t.\t.\t-\n+chrX\t153925213\t153925299\t.\t.\t-\n+chrX\t153929323\t153929409\t.\t.\t-\n+chrX\t153945213\t153945299\t.\t.\t-\n+chrX\t153977267\t153977353\t.\t.\t-\n+chrX\t154048131\t154048217\t.\t.\t-\n+chrX\t154086999\t154087085\t.\t.\t-\n+chrX\t154205489\t154205575\t.\t.\t-\n+chrX\t154209314\t154209400\t.\t.\t-\n+chrX\t154212920\t154213006\t.\t.\t-\n+chrX\t154239426\t154239512\t.\t.\t-\n+chrX\t154270432\t154270518\t.\t.\t-\n+chrX\t154275908\t154275994\t.\t.\t-\n+chrX\t154287230\t154287316\t.\t.\t-\n+chrX\t154291252\t154291338\t.\t.\t-\n+chrX\t154323066\t154323152\t.\t.\t-\n+chrX\t154324591\t154324677\t.\t.\t-\n+chrX\t154335532\t154335618\t.\t.\t-\n+chrX\t154382931\t154383017\t.\t.\t-\n+chrX\t154386021\t154386107\t.\t.\t-\n+chrX\t154398522\t154398608\t.\t.\t-\n+chrX\t154458082\t154458168\t.\t.\t-\n+chrX\t154462457\t154462543\t.\t.\t-\n+chrX\t154467066\t154467152\t.\t.\t-\n+chrX\t154545008\t154545094\t.\t.\t-\n+chrX\t154547820\t154547906\t.\t.\t-\n+chrX\t154651871\t154651957\t.\t.\t-\n+chrX\t154669765\t154669851\t.\t.\t-\n+chrX\t154769691\t154769777\t.\t.\t-\n+chrX\t154825953\t154826039\t.\t.\t-\n+chrX\t154832269\t154832355\t.\t.\t-\n+chrX\t154862554\t154862640\t.\t.\t-\n+chrX\t154960010\t154960096\t.\t.\t-\n+chrX\t154977656\t154977742\t.\t.\t-\n+chrX\t155080338\t155080424\t.\t.\t-\n+chrX\t155102953\t155103039\t.\t.\t-\n+chrX\t155105219\t155105305\t.\t.\t-\n+chrX\t155173263\t155173349\t.\t.\t-\n+chrX\t155180786\t155180872\t.\t.\t-\n+chrX\t155195897\t155195983\t.\t.\t-\n+chrX\t155198406\t155198492\t.\t.\t-\n+chrX\t155216572\t155216658\t.\t.\t-\n+chrX\t155229539\t155229625\t.\t.\t-\n+chrX\t155235961\t155236047\t.\t.\t-\n+chrX\t155238549\t155238635\t.\t.\t-\n' |
| b |
| diff -r 000000000000 -r fe62ba547975 test-data/bdgbroadcall_on_callpeak_treatment.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bdgbroadcall_on_callpeak_treatment.tabular Wed Feb 11 10:18:02 2015 -0500 |
| b |
| b'@@ -0,0 +1,398 @@\n+chrX\t1257632\t1258067\tmacs2_bdgbroadcall.bdg_broadRegion10\t0\t.\t1257716\t1257970\t0\t1\t254\t84\t0.00000\t0.00000\t0.00000\n+chrX\t1363567\t1363859\tmacs2_bdgbroadcall.bdg_broadRegion14\t0\t.\t1363605\t1363821\t0\t1\t216\t38\t0.00000\t0.00000\t0.00000\n+chrX\t1365758\t1366063\tmacs2_bdgbroadcall.bdg_broadRegion15\t0\t.\t1365809\t1366012\t0\t1\t203\t51\t0.00000\t0.00000\t0.00000\n+chrX\t1572536\t1573641\tmacs2_bdgbroadcall.bdg_broadRegion29\t0\t.\t1573072\t1573569\t0\t1\t497\t536\t0.00000\t0.00000\t0.00000\n+chrX\t1656256\t1656801\tmacs2_bdgbroadcall.bdg_broadRegion39\t0\t.\t1656323\t1656633\t0\t1\t310\t67\t0.00000\t0.00000\t0.00000\n+chrX\t1767435\t1767722\tmacs2_bdgbroadcall.bdg_broadRegion47\t0\t.\t1767445\t1767721\t0\t1\t276\t10\t0.00000\t0.00000\t0.00000\n+chrX\t1771093\t1771517\tmacs2_bdgbroadcall.bdg_broadRegion48\t0\t.\t1771107\t1771395\t0\t1\t288\t14\t0.00000\t0.00000\t0.00000\n+chrX\t1791977\t1792556\tmacs2_bdgbroadcall.bdg_broadRegion51\t0\t.\t1792290\t1792544\t0\t1\t254\t313\t0.00000\t0.00000\t0.00000\n+chrX\t2151050\t2151602\tmacs2_bdgbroadcall.bdg_broadRegion57\t0\t.\t2151348\t2151549\t0\t1\t201\t298\t0.00000\t0.00000\t0.00000\n+chrX\t2428648\t2428917\tmacs2_bdgbroadcall.bdg_broadRegion64\t0\t.\t2428663\t2428902\t0\t1\t239\t15\t0.00000\t0.00000\t0.00000\n+chrX\t2511222\t2511663\tmacs2_bdgbroadcall.bdg_broadRegion69\t0\t.\t2511277\t2511577\t0\t1\t300\t55\t0.00000\t0.00000\t0.00000\n+chrX\t2729584\t2730791\tmacs2_bdgbroadcall.bdg_broadRegion84\t0\t.\t2729586\t2729838\t0\t1\t252\t2\t0.00000\t0.00000\t0.00000\n+chrX\t3035797\t3036145\tmacs2_bdgbroadcall.bdg_broadRegion92\t0\t.\t3035877\t3036131\t0\t1\t254\t80\t0.00000\t0.00000\t0.00000\n+chrX\t3556278\t3556728\tmacs2_bdgbroadcall.bdg_broadRegion106\t0\t.\t3556301\t3556585\t0\t1\t284\t23\t0.00000\t0.00000\t0.00000\n+chrX\t3569242\t3569881\tmacs2_bdgbroadcall.bdg_broadRegion107\t0\t.\t3569295\t3569726\t0\t1\t431\t53\t0.00000\t0.00000\t0.00000\n+chrX\t3729980\t3730560\tmacs2_bdgbroadcall.bdg_broadRegion111\t0\t.\t3730024\t3730438\t0\t1\t414\t44\t0.00000\t0.00000\t0.00000\n+chrX\t3858117\t3858418\tmacs2_bdgbroadcall.bdg_broadRegion114\t0\t.\t3858164\t3858371\t0\t1\t207\t47\t0.00000\t0.00000\t0.00000\n+chrX\t3879587\t3881122\tmacs2_bdgbroadcall.bdg_broadRegion115\t0\t.\t3880481\t3880947\t0\t1\t466\t894\t0.00000\t0.00000\t0.00000\n+chrX\t4465231\t4465528\tmacs2_bdgbroadcall.bdg_broadRegion122\t0\t.\t4465274\t4465485\t0\t1\t211\t43\t0.00000\t0.00000\t0.00000\n+chrX\t5795315\t5795585\tmacs2_bdgbroadcall.bdg_broadRegion142\t0\t.\t5795331\t5795569\t0\t1\t238\t16\t0.00000\t0.00000\t0.00000\n+chrX\t7006942\t7007428\tmacs2_bdgbroadcall.bdg_broadRegion169\t0\t.\t7007126\t7007380\t0\t1\t254\t184\t0.00000\t0.00000\t0.00000\n+chrX\t7893819\t7896297\tmacs2_bdgbroadcall.bdg_broadRegion197\t0\t.\t7893945\t7894332\t0\t1\t387\t126\t0.00000\t0.00000\t0.00000\n+chrX\t7964515\t7964926\tmacs2_bdgbroadcall.bdg_broadRegion200\t0\t.\t7964541\t7964890\t0\t1\t349\t26\t0.00000\t0.00000\t0.00000\n+chrX\t8706564\t8706906\tmacs2_bdgbroadcall.bdg_broadRegion213\t0\t.\t8706600\t8706874\t0\t1\t274\t36\t0.00000\t0.00000\t0.00000\n+chrX\t8711107\t8711614\tmacs2_bdgbroadcall.bdg_broadRegion215\t0\t.\t8711343\t8711597\t0\t1\t254\t236\t0.00000\t0.00000\t0.00000\n+chrX\t8782729\t8783946\tmacs2_bdgbroadcall.bdg_broadRegion220\t0\t.\t8783512\t8783835\t0\t1\t323\t783\t0.00000\t0.00000\t0.00000\n+chrX\t9281380\t9281650\tmacs2_bdgbroadcall.bdg_broadRegion228\t0\t.\t9281396\t9281634\t0\t1\t238\t16\t0.00000\t0.00000\t0.00000\n+chrX\t9842112\t9842397\tmacs2_bdgbroadcall.bdg_broadRegion246\t0\t.\t9842123\t9842377\t0\t1\t254\t11\t0.00000\t0.00000\t0.00000\n+chrX\t9853222\t9853548\tmacs2_bdgbroadcall.bdg_broadRegion247\t0\t.\t9853249\t9853503\t0\t1\t254\t27\t0.00000\t0.00000\t0.00000\n+chrX\t9963732\t9964174\tmacs2_bdgbroadcall.bdg_broadRegion250\t0\t.\t9963752\t9964135\t0\t1\t383\t20\t0.00000\t0.00000\t0.00000\n+chrX\t10087428\t10088068\tmacs2_bdgbroadcall.bdg_broadRegion257\t0\t.\t10087429\t10088021\t0\t1\t592\t1\t0.00000\t0.00000\t0.00000\n+chrX\t10157646\t10159594\tmacs2_bdgbroadcall.bdg_broadRegion260\t0\t.\t10157668\t10158711\t0\t2\t254,254\t22,811\t0.00000\t0.00000\t0.00000\n+chrX\t10565873\t10566400\tmacs2_bdgbroadcall.bdg_broadRegion269\t0\t.\t10565891\t10566127\t0\t1\t236\t18\t0.00000\t0.00000\t0.00000\n+chrX\t10737182\t10737611\tmacs2_bdgbroadcall.bdg_broadRegion274\t0\t.\t10737303\t10737557\t0\t1\t254\t121\t0.00000\t0.00000\t0.00000\n+chrX\t11155170\t11156021\tmacs2_bdgbroadcall.bdg_broadR'..b'000\t0.00000\t0.00000\n+chrX\t114565237\t114565631\tmacs2_bdgbroadcall.bdg_broadRegion3151\t0\t.\t114565251\t114565505\t0\t1\t254\t14\t0.00000\t0.00000\t0.00000\n+chrX\t114877184\t114877653\tmacs2_bdgbroadcall.bdg_broadRegion3162\t0\t.\t114877211\t114877644\t0\t1\t433\t27\t0.00000\t0.00000\t0.00000\n+chrX\t114924947\t114925376\tmacs2_bdgbroadcall.bdg_broadRegion3167\t0\t.\t114925013\t114925347\t0\t1\t334\t66\t0.00000\t0.00000\t0.00000\n+chrX\t115330184\t115330488\tmacs2_bdgbroadcall.bdg_broadRegion3184\t0\t.\t115330234\t115330438\t0\t1\t204\t50\t0.00000\t0.00000\t0.00000\n+chrX\t115336336\t115336631\tmacs2_bdgbroadcall.bdg_broadRegion3185\t0\t.\t115336371\t115336625\t0\t1\t254\t35\t0.00000\t0.00000\t0.00000\n+chrX\t115471037\t115471315\tmacs2_bdgbroadcall.bdg_broadRegion3189\t0\t.\t115471061\t115471291\t0\t1\t230\t24\t0.00000\t0.00000\t0.00000\n+chrX\t117359915\t117360792\tmacs2_bdgbroadcall.bdg_broadRegion3218\t0\t.\t117360044\t117360340\t0\t1\t296\t129\t0.00000\t0.00000\t0.00000\n+chrX\t117388621\t117389088\tmacs2_bdgbroadcall.bdg_broadRegion3220\t0\t.\t117388632\t117389043\t0\t1\t411\t11\t0.00000\t0.00000\t0.00000\n+chrX\t117670755\t117671047\tmacs2_bdgbroadcall.bdg_broadRegion3235\t0\t.\t117670793\t117671009\t0\t1\t216\t38\t0.00000\t0.00000\t0.00000\n+chrX\t117735424\t117736440\tmacs2_bdgbroadcall.bdg_broadRegion3238\t0\t.\t117735431\t117735685\t0\t1\t254\t7\t0.00000\t0.00000\t0.00000\n+chrX\t117737788\t117738276\tmacs2_bdgbroadcall.bdg_broadRegion3239\t0\t.\t117737881\t117738223\t0\t1\t342\t93\t0.00000\t0.00000\t0.00000\n+chrX\t117885740\t117886002\tmacs2_bdgbroadcall.bdg_broadRegion3245\t0\t.\t117885748\t117885994\t0\t1\t246\t8\t0.00000\t0.00000\t0.00000\n+chrX\t118138087\t118139303\tmacs2_bdgbroadcall.bdg_broadRegion3255\t0\t.\t118138103\t118139302\t0\t2\t238,254\t16,961\t0.00000\t0.00000\t0.00000\n+chrX\t118201023\t118201279\tmacs2_bdgbroadcall.bdg_broadRegion3258\t0\t.\t118201025\t118201277\t0\t1\t252\t2\t0.00000\t0.00000\t0.00000\n+chrX\t118400235\t118400779\tmacs2_bdgbroadcall.bdg_broadRegion3269\t0\t.\t118400368\t118400730\t0\t1\t362\t133\t0.00000\t0.00000\t0.00000\n+chrX\t118523737\t118524251\tmacs2_bdgbroadcall.bdg_broadRegion3273\t0\t.\t118523918\t118524172\t0\t1\t254\t181\t0.00000\t0.00000\t0.00000\n+chrX\t118551972\t118552247\tmacs2_bdgbroadcall.bdg_broadRegion3275\t0\t.\t118551993\t118552226\t0\t1\t233\t21\t0.00000\t0.00000\t0.00000\n+chrX\t118602989\t118603352\tmacs2_bdgbroadcall.bdg_broadRegion3279\t0\t.\t118603044\t118603298\t0\t1\t254\t55\t0.00000\t0.00000\t0.00000\n+chrX\t118622629\t118623183\tmacs2_bdgbroadcall.bdg_broadRegion3281\t0\t.\t118622664\t118622883\t0\t1\t219\t35\t0.00000\t0.00000\t0.00000\n+chrX\t118650089\t118650826\tmacs2_bdgbroadcall.bdg_broadRegion3284\t0\t.\t118650252\t118650668\t0\t1\t416\t163\t0.00000\t0.00000\t0.00000\n+chrX\t119081256\t119082675\tmacs2_bdgbroadcall.bdg_broadRegion3308\t0\t.\t119082245\t119082499\t0\t1\t254\t989\t0.00000\t0.00000\t0.00000\n+chrX\t119115630\t119115921\tmacs2_bdgbroadcall.bdg_broadRegion3309\t0\t.\t119115667\t119115884\t0\t1\t217\t37\t0.00000\t0.00000\t0.00000\n+chrX\t119347622\t119348131\tmacs2_bdgbroadcall.bdg_broadRegion3316\t0\t.\t119347667\t119347921\t0\t1\t254\t45\t0.00000\t0.00000\t0.00000\n+chrX\t119443366\t119443738\tmacs2_bdgbroadcall.bdg_broadRegion3323\t0\t.\t119443387\t119443652\t0\t1\t265\t21\t0.00000\t0.00000\t0.00000\n+chrX\t119499109\t119499576\tmacs2_bdgbroadcall.bdg_broadRegion3326\t0\t.\t119499118\t119499372\t0\t1\t254\t9\t0.00000\t0.00000\t0.00000\n+chrX\t119584005\t119584487\tmacs2_bdgbroadcall.bdg_broadRegion3327\t0\t.\t119584138\t119584392\t0\t1\t254\t133\t0.00000\t0.00000\t0.00000\n+chrX\t119608806\t119609935\tmacs2_bdgbroadcall.bdg_broadRegion3329\t0\t.\t119609354\t119609691\t0\t1\t337\t548\t0.00000\t0.00000\t0.00000\n+chrX\t119619999\t119620297\tmacs2_bdgbroadcall.bdg_broadRegion3330\t0\t.\t119620043\t119620253\t0\t1\t210\t44\t0.00000\t0.00000\t0.00000\n+chrX\t119631826\t119632280\tmacs2_bdgbroadcall.bdg_broadRegion3331\t0\t.\t119631922\t119632255\t0\t1\t333\t96\t0.00000\t0.00000\t0.00000\n+chrX\t119887334\t119887769\tmacs2_bdgbroadcall.bdg_broadRegion3343\t0\t.\t119887390\t119887644\t0\t1\t254\t56\t0.00000\t0.00000\t0.00000\n+chrX\t119903862\t119904514\tmacs2_bdgbroadcall.bdg_broadRegion3344\t0\t.\t119903877\t119904131\t0\t1\t254\t15\t0.00000\t0.00000\t0.00000\n+chrX\t119923853\t119924452\tmacs2_bdgbroadcall.bdg_broadRegion3345\t0\t.\t119923868\t119924325\t0\t1\t457\t15\t0.00000\t0.00000\t0.00000\n' |
| b |
| diff -r 000000000000 -r fe62ba547975 test-data/bdgcmp_on_Control_and_ChIP_slogLR.bdg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bdgcmp_on_Control_and_ChIP_slogLR.bdg Wed Feb 11 10:18:02 2015 -0500 |
| b |
| b'@@ -0,0 +1,3162 @@\n+chrX\t0\t69671\t-inf\n+chrX\t69671\t69925\t1.38599\n+chrX\t69925\t284628\t-inf\n+chrX\t284628\t284843\t1.38599\n+chrX\t284843\t284882\t3.36736\n+chrX\t284882\t285097\t1.38599\n+chrX\t285097\t285556\t-inf\n+chrX\t285556\t285810\t1.38599\n+chrX\t285810\t461156\t-inf\n+chrX\t461156\t461410\t1.38599\n+chrX\t461410\t586983\t-inf\n+chrX\t586983\t587124\t0.88247\n+chrX\t587124\t587237\t0.27164\n+chrX\t587237\t593044\t-inf\n+chrX\t593044\t593298\t1.17257\n+chrX\t593298\t656045\t-inf\n+chrX\t656045\t656299\t1.17257\n+chrX\t656299\t920309\t-inf\n+chrX\t920309\t920563\t1.17257\n+chrX\t920563\t947933\t-inf\n+chrX\t947933\t948187\t1.38599\n+chrX\t948187\t1006805\t-inf\n+chrX\t1006805\t1007059\t1.17257\n+chrX\t1007059\t1257632\t-inf\n+chrX\t1257632\t1257716\t1.17257\n+chrX\t1257716\t1257813\t2.93619\n+chrX\t1257813\t1257886\t4.92705\n+chrX\t1257886\t1257970\t2.93619\n+chrX\t1257970\t1258067\t1.17257\n+chrX\t1258067\t1324083\t-inf\n+chrX\t1324083\t1324337\t1.38599\n+chrX\t1324337\t1332580\t-inf\n+chrX\t1332580\t1332834\t1.38599\n+chrX\t1332834\t1353039\t-inf\n+chrX\t1353039\t1353293\t1.38599\n+chrX\t1353293\t1363567\t-inf\n+chrX\t1363567\t1363605\t1.38599\n+chrX\t1363605\t1363821\t3.36736\n+chrX\t1363821\t1363859\t1.38599\n+chrX\t1363859\t1365758\t-inf\n+chrX\t1365758\t1365809\t1.38599\n+chrX\t1365809\t1366012\t3.36736\n+chrX\t1366012\t1366063\t1.38599\n+chrX\t1366063\t1372998\t-inf\n+chrX\t1372998\t1373252\t1.38599\n+chrX\t1373252\t1384092\t-inf\n+chrX\t1384092\t1384346\t1.38599\n+chrX\t1384346\t1397762\t-inf\n+chrX\t1397762\t1398016\t0.27164\n+chrX\t1398016\t1430076\t-inf\n+chrX\t1430076\t1430330\t1.38599\n+chrX\t1430330\t1442229\t-inf\n+chrX\t1442229\t1442483\t0.71742\n+chrX\t1442483\t1442730\t-inf\n+chrX\t1442730\t1442984\t0.71742\n+chrX\t1442984\t1444736\t-inf\n+chrX\t1444736\t1444990\t0.88247\n+chrX\t1444990\t1446470\t-inf\n+chrX\t1446470\t1446501\t1.17257\n+chrX\t1446501\t1446724\t0.27164\n+chrX\t1446724\t1453397\t-inf\n+chrX\t1453397\t1453651\t1.38599\n+chrX\t1453651\t1455341\t-inf\n+chrX\t1455341\t1455453\t1.38599\n+chrX\t1455453\t1455595\t3.36736\n+chrX\t1455595\t1455707\t1.38599\n+chrX\t1455707\t1456342\t-inf\n+chrX\t1456342\t1456596\t1.38599\n+chrX\t1456596\t1506622\t-inf\n+chrX\t1506622\t1506876\t1.38599\n+chrX\t1506876\t1533627\t-inf\n+chrX\t1533627\t1533881\t1.38599\n+chrX\t1533881\t1539210\t-inf\n+chrX\t1539210\t1539464\t1.38599\n+chrX\t1539464\t1545156\t-inf\n+chrX\t1545156\t1545410\t1.38599\n+chrX\t1545410\t1572536\t-inf\n+chrX\t1572536\t1572790\t0.88247\n+chrX\t1572790\t1573012\t-inf\n+chrX\t1573012\t1573072\t0.88247\n+chrX\t1573072\t1573141\t2.34497\n+chrX\t1573141\t1573266\t4.03472\n+chrX\t1573266\t1573315\t2.34497\n+chrX\t1573315\t1573326\t4.03472\n+chrX\t1573326\t1573387\t2.34497\n+chrX\t1573387\t1573395\t4.03472\n+chrX\t1573395\t1573569\t2.34497\n+chrX\t1573569\t1573641\t0.88247\n+chrX\t1573641\t1587254\t-inf\n+chrX\t1587254\t1587508\t0.88247\n+chrX\t1587508\t1600719\t-inf\n+chrX\t1600719\t1600850\t1.38599\n+chrX\t1600850\t1600973\t3.36736\n+chrX\t1600973\t1601104\t1.38599\n+chrX\t1601104\t1602854\t-inf\n+chrX\t1602854\t1603108\t1.38599\n+chrX\t1603108\t1603548\t-inf\n+chrX\t1603548\t1603802\t0.88247\n+chrX\t1603802\t1612360\t-inf\n+chrX\t1612360\t1612614\t0.88247\n+chrX\t1612614\t1614986\t-inf\n+chrX\t1614986\t1615240\t1.38599\n+chrX\t1615240\t1627130\t-inf\n+chrX\t1627130\t1627275\t0.08077\n+chrX\t1627275\t1627384\t0.27164\n+chrX\t1627384\t1630646\t-inf\n+chrX\t1630646\t1630900\t0.88247\n+chrX\t1630900\t1636122\t-inf\n+chrX\t1636122\t1636376\t1.17257\n+chrX\t1636376\t1654688\t-inf\n+chrX\t1654688\t1654942\t1.38599\n+chrX\t1654942\t1656256\t-inf\n+chrX\t1656256\t1656323\t1.38599\n+chrX\t1656323\t1656379\t3.36736\n+chrX\t1656379\t1656510\t5.57598\n+chrX\t1656510\t1656547\t3.36736\n+chrX\t1656547\t1656577\t5.57598\n+chrX\t1656577\t1656633\t3.36736\n+chrX\t1656633\t1656801\t1.38599\n+chrX\t1656801\t1673614\t-inf\n+chrX\t1673614\t1673844\t0.00000\n+chrX\t1673844\t1673868\t0.27164\n+chrX\t1673868\t1678732\t-inf\n+chrX\t1678732\t1678986\t1.17257\n+chrX\t1678986\t1683727\t-inf\n+chrX\t1683727\t1683981\t1.17257\n+chrX\t1683981\t1700130\t-inf\n+chrX\t1700130\t1700384\t1.38599\n+chrX\t1700384\t1702172\t-inf\n+chrX\t1702172\t1702426\t1.38599\n+chrX\t1702426\t1710407\t-inf\n+chrX\t1710407\t1710661\t0.88247\n+chrX\t1710661\t1742824\t-inf\n+chrX\t1742824\t1743078\t1.38599\n+chrX\t1743078\t1767435\t-inf\n+chrX\t1767435\t1767445\t0.60347\n+chrX\t1767445\t1767467\t1.76494\n+chrX\t1767467\t1767468\t3.15366\n+chrX\t1767468\t1767689\t4.68995\n+chrX\t1767689\t1767'..b'6471\t29692786\t-inf\n+chrX\t29692786\t29693040\t0.71742\n+chrX\t29693040\t29705961\t-inf\n+chrX\t29705961\t29706215\t1.17257\n+chrX\t29706215\t29708278\t-inf\n+chrX\t29708278\t29708532\t1.17257\n+chrX\t29708532\t29757736\t-inf\n+chrX\t29757736\t29757990\t1.38599\n+chrX\t29757990\t29766831\t-inf\n+chrX\t29766831\t29767085\t1.38599\n+chrX\t29767085\t29777376\t-inf\n+chrX\t29777376\t29777630\t1.38599\n+chrX\t29777630\t29853191\t-inf\n+chrX\t29853191\t29853208\t0.27164\n+chrX\t29853208\t29853445\t0.00000\n+chrX\t29853445\t29877950\t-inf\n+chrX\t29877950\t29878204\t1.17257\n+chrX\t29878204\t29886038\t-inf\n+chrX\t29886038\t29886292\t1.38599\n+chrX\t29886292\t29921461\t-inf\n+chrX\t29921461\t29921504\t1.17257\n+chrX\t29921504\t29921623\t2.93619\n+chrX\t29921623\t29921715\t4.92705\n+chrX\t29921715\t29921758\t2.93619\n+chrX\t29921758\t29921877\t1.17257\n+chrX\t29921877\t29929770\t-inf\n+chrX\t29929770\t29929782\t1.17257\n+chrX\t29929782\t29929842\t2.93619\n+chrX\t29929842\t29929844\t4.92705\n+chrX\t29929844\t29929873\t7.06548\n+chrX\t29929873\t29929900\t9.31365\n+chrX\t29929900\t29930024\t11.64926\n+chrX\t29930024\t29930036\t9.31365\n+chrX\t29930036\t29930096\t7.06548\n+chrX\t29930096\t29930098\t4.92705\n+chrX\t29930098\t29930127\t2.93619\n+chrX\t29930127\t29930154\t1.17257\n+chrX\t29930154\t30035206\t-inf\n+chrX\t30035206\t30035460\t1.38599\n+chrX\t30035460\t30046818\t-inf\n+chrX\t30046818\t30047072\t1.17257\n+chrX\t30047072\t30143756\t-inf\n+chrX\t30143756\t30144010\t1.38599\n+chrX\t30144010\t30155728\t-inf\n+chrX\t30155728\t30155982\t1.17257\n+chrX\t30155982\t30160027\t-inf\n+chrX\t30160027\t30160083\t0.88247\n+chrX\t30160083\t30160155\t2.34497\n+chrX\t30160155\t30160273\t4.03472\n+chrX\t30160273\t30160281\t5.87203\n+chrX\t30160281\t30160337\t4.03472\n+chrX\t30160337\t30160409\t2.34497\n+chrX\t30160409\t30160527\t0.88247\n+chrX\t30160527\t30214684\t-inf\n+chrX\t30214684\t30214922\t1.38599\n+chrX\t30214922\t30214938\t3.36736\n+chrX\t30214938\t30215176\t1.38599\n+chrX\t30215176\t30302352\t-inf\n+chrX\t30302352\t30302606\t1.38599\n+chrX\t30302606\t30315731\t-inf\n+chrX\t30315731\t30315985\t1.17257\n+chrX\t30315985\t30360082\t-inf\n+chrX\t30360082\t30360336\t1.17257\n+chrX\t30360336\t30361343\t-inf\n+chrX\t30361343\t30361597\t1.17257\n+chrX\t30361597\t30373440\t-inf\n+chrX\t30373440\t30373694\t1.38599\n+chrX\t30373694\t30407919\t-inf\n+chrX\t30407919\t30408173\t1.38599\n+chrX\t30408173\t30425799\t-inf\n+chrX\t30425799\t30426053\t1.38599\n+chrX\t30426053\t30447586\t-inf\n+chrX\t30447586\t30447840\t1.38599\n+chrX\t30447840\t30506224\t-inf\n+chrX\t30506224\t30506478\t1.17257\n+chrX\t30506478\t30511209\t-inf\n+chrX\t30511209\t30511463\t1.17257\n+chrX\t30511463\t30522309\t-inf\n+chrX\t30522309\t30522406\t0.27164\n+chrX\t30522406\t30522433\t1.03519\n+chrX\t30522433\t30522563\t2.02598\n+chrX\t30522563\t30522571\t1.03519\n+chrX\t30522571\t30522586\t2.02598\n+chrX\t30522586\t30522634\t3.16435\n+chrX\t30522634\t30522660\t1.10721\n+chrX\t30522660\t30522687\t0.56401\n+chrX\t30522687\t30522825\t0.16838\n+chrX\t30522825\t30522840\t0.00000\n+chrX\t30522840\t30531532\t-inf\n+chrX\t30531532\t30531533\t1.38599\n+chrX\t30531533\t30531586\t3.36736\n+chrX\t30531586\t30531592\t2.93619\n+chrX\t30531592\t30531786\t4.92705\n+chrX\t30531786\t30531787\t2.93619\n+chrX\t30531787\t30531846\t1.17257\n+chrX\t30531846\t30541235\t-inf\n+chrX\t30541235\t30541489\t1.17257\n+chrX\t30541489\t30542226\t-inf\n+chrX\t30542226\t30542480\t1.17257\n+chrX\t30542480\t30550740\t-inf\n+chrX\t30550740\t30550994\t0.71742\n+chrX\t30550994\t30588582\t-inf\n+chrX\t30588582\t30588596\t0.88247\n+chrX\t30588596\t30588680\t2.34497\n+chrX\t30588680\t30588835\t4.03472\n+chrX\t30588835\t30588836\t5.87203\n+chrX\t30588836\t30588850\t4.03472\n+chrX\t30588850\t30588934\t2.34497\n+chrX\t30588934\t30589089\t0.88247\n+chrX\t30589089\t30592772\t-inf\n+chrX\t30592772\t30593026\t1.17257\n+chrX\t30593026\t30594964\t-inf\n+chrX\t30594964\t30595218\t1.17257\n+chrX\t30595218\t30611776\t-inf\n+chrX\t30611776\t30611862\t0.27164\n+chrX\t30611862\t30612030\t0.00000\n+chrX\t30612030\t30612037\t-inf\n+chrX\t30612037\t30612065\t0.00000\n+chrX\t30612065\t30612116\t0.16838\n+chrX\t30612116\t30612133\t0.54328\n+chrX\t30612133\t30612291\t1.23305\n+chrX\t30612291\t30612319\t0.54328\n+chrX\t30612319\t30612387\t0.08077\n+chrX\t30612387\t30612910\t-inf\n+chrX\t30612910\t30613097\t0.00000\n+chrX\t30613097\t30613164\t0.27164\n+chrX\t30613164\t30625345\t-inf\n+chrX\t30625345\t30625599\t0.27164\n+chrX\t30625599\t30625915\t-inf\n' |
| b |
| diff -r 000000000000 -r fe62ba547975 test-data/bdgpeakcall_on_callpeak_treatment.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bdgpeakcall_on_callpeak_treatment.tabular Wed Feb 11 10:18:02 2015 -0500 |
| b |
| @@ -0,0 +1,22 @@ +chrX 10087531 10087974 macs2_bdgpeakcall.bdg_narrowPeak1 180 . 0.00000 0.00000 0.00000 236 +chrX 11551222 11551665 macs2_bdgpeakcall.bdg_narrowPeak2 150 . 0.00000 0.00000 0.00000 226 +chrX 12832669 12832882 macs2_bdgpeakcall.bdg_narrowPeak3 70 . 0.00000 0.00000 0.00000 81 +chrX 12964926 12965219 macs2_bdgpeakcall.bdg_narrowPeak4 100 . 0.00000 0.00000 0.00000 159 +chrX 14050535 14050735 macs2_bdgpeakcall.bdg_narrowPeak5 60 . 0.00000 0.00000 0.00000 187 +chrX 15705218 15705451 macs2_bdgpeakcall.bdg_narrowPeak6 60 . 0.00000 0.00000 0.00000 59 +chrX 19562934 19563188 macs2_bdgpeakcall.bdg_narrowPeak7 90 . 0.00000 0.00000 0.00000 85 +chrX 22003481 22003808 macs2_bdgpeakcall.bdg_narrowPeak8 100 . 0.00000 0.00000 0.00000 117 +chrX 30753978 30754219 macs2_bdgpeakcall.bdg_narrowPeak9 80 . 0.00000 0.00000 0.00000 144 +chrX 40653308 40653534 macs2_bdgpeakcall.bdg_narrowPeak10 70 . 0.00000 0.00000 0.00000 139 +chrX 41112952 41113317 macs2_bdgpeakcall.bdg_narrowPeak11 80 . 0.00000 0.00000 0.00000 179 +chrX 45046188 45046393 macs2_bdgpeakcall.bdg_narrowPeak12 70 . 0.00000 0.00000 0.00000 143 +chrX 46268264 46268516 macs2_bdgpeakcall.bdg_narrowPeak13 60 . 0.00000 0.00000 0.00000 108 +chrX 46763269 46763548 macs2_bdgpeakcall.bdg_narrowPeak14 70 . 0.00000 0.00000 0.00000 98 +chrX 47052916 47053224 macs2_bdgpeakcall.bdg_narrowPeak15 120 . 0.00000 0.00000 0.00000 135 +chrX 47886074 47886328 macs2_bdgpeakcall.bdg_narrowPeak16 70 . 0.00000 0.00000 0.00000 132 +chrX 52004649 52004903 macs2_bdgpeakcall.bdg_narrowPeak17 90 . 0.00000 0.00000 0.00000 118 +chrX 64815338 64815624 macs2_bdgpeakcall.bdg_narrowPeak18 110 . 0.00000 0.00000 0.00000 103 +chrX 73075495 73075708 macs2_bdgpeakcall.bdg_narrowPeak19 70 . 0.00000 0.00000 0.00000 42 +chrX 104166874 104167171 macs2_bdgpeakcall.bdg_narrowPeak20 90 . 0.00000 0.00000 0.00000 133 +chrX 108729097 108729349 macs2_bdgpeakcall.bdg_narrowPeak21 80 . 0.00000 0.00000 0.00000 98 +chrX 118650360 118650614 macs2_bdgpeakcall.bdg_narrowPeak22 80 . 0.00000 0.00000 0.00000 100 |
| b |
| diff -r 000000000000 -r fe62ba547975 test-data/callpeak_control_part.bdg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/callpeak_control_part.bdg Wed Feb 11 10:18:02 2015 -0500 |
| b |
| b'@@ -0,0 +1,10000 @@\n+chrX\t0\t173099\t0.01536\n+chrX\t173099\t177599\t0.02536\n+chrX\t177599\t177972\t0.25364\n+chrX\t177972\t178226\t0.99858\n+chrX\t178226\t178599\t0.25364\n+chrX\t178599\t183099\t0.02536\n+chrX\t183099\t196237\t0.01536\n+chrX\t196237\t200737\t0.02536\n+chrX\t200737\t201110\t0.25364\n+chrX\t201110\t201364\t0.99858\n+chrX\t201364\t201737\t0.25364\n+chrX\t201737\t205373\t0.02536\n+chrX\t205373\t206237\t0.05073\n+chrX\t206237\t209873\t0.02536\n+chrX\t209873\t210246\t0.25364\n+chrX\t210246\t210500\t0.99858\n+chrX\t210500\t210873\t0.25364\n+chrX\t210873\t215373\t0.02536\n+chrX\t215373\t222667\t0.01536\n+chrX\t222667\t227167\t0.02536\n+chrX\t227167\t227540\t0.25364\n+chrX\t227540\t227794\t0.99858\n+chrX\t227794\t228167\t0.25364\n+chrX\t228167\t232667\t0.02536\n+chrX\t232667\t342891\t0.01536\n+chrX\t342891\t347391\t0.02536\n+chrX\t347391\t347764\t0.25364\n+chrX\t347764\t348018\t0.99858\n+chrX\t348018\t348391\t0.25364\n+chrX\t348391\t350176\t0.02536\n+chrX\t350176\t352891\t0.05073\n+chrX\t352891\t354676\t0.02536\n+chrX\t354676\t355049\t0.25364\n+chrX\t355049\t355303\t0.99858\n+chrX\t355303\t355676\t0.25364\n+chrX\t355676\t359696\t0.05073\n+chrX\t359696\t360069\t0.25364\n+chrX\t360069\t360323\t0.99858\n+chrX\t360323\t360696\t0.25364\n+chrX\t360696\t365196\t0.02536\n+chrX\t365196\t435810\t0.01536\n+chrX\t435810\t440310\t0.02536\n+chrX\t440310\t440683\t0.25364\n+chrX\t440683\t440937\t0.99858\n+chrX\t440937\t441310\t0.25364\n+chrX\t441310\t445810\t0.02536\n+chrX\t445810\t479224\t0.01536\n+chrX\t479224\t483724\t0.02536\n+chrX\t483724\t484097\t0.25364\n+chrX\t484097\t484351\t0.99858\n+chrX\t484351\t484724\t0.25364\n+chrX\t484724\t489224\t0.02536\n+chrX\t489224\t582624\t0.01536\n+chrX\t582624\t586422\t0.02536\n+chrX\t586422\t587124\t0.05073\n+chrX\t587124\t587497\t0.25364\n+chrX\t587497\t587751\t0.99858\n+chrX\t587751\t588124\t0.25364\n+chrX\t588124\t590922\t0.05073\n+chrX\t590922\t591295\t0.25364\n+chrX\t591295\t591549\t0.99858\n+chrX\t591549\t591922\t0.25364\n+chrX\t591922\t592624\t0.05073\n+chrX\t592624\t594385\t0.02536\n+chrX\t594385\t596422\t0.05073\n+chrX\t596422\t598885\t0.02536\n+chrX\t598885\t599258\t0.25364\n+chrX\t599258\t599512\t0.99858\n+chrX\t599512\t599885\t0.25364\n+chrX\t599885\t604385\t0.02536\n+chrX\t604385\t620365\t0.01536\n+chrX\t620365\t624865\t0.02536\n+chrX\t624865\t625238\t0.25364\n+chrX\t625238\t625492\t0.99858\n+chrX\t625492\t625865\t0.25364\n+chrX\t625865\t630365\t0.02536\n+chrX\t630365\t636674\t0.01536\n+chrX\t636674\t641174\t0.02536\n+chrX\t641174\t641547\t0.25364\n+chrX\t641547\t641801\t0.99858\n+chrX\t641801\t642174\t0.25364\n+chrX\t642174\t646674\t0.02536\n+chrX\t646674\t654813\t0.01536\n+chrX\t654813\t659313\t0.02536\n+chrX\t659313\t659686\t0.25364\n+chrX\t659686\t659940\t0.99858\n+chrX\t659940\t660313\t0.25364\n+chrX\t660313\t664813\t0.02536\n+chrX\t664813\t707545\t0.01536\n+chrX\t707545\t712045\t0.02536\n+chrX\t712045\t712418\t0.25364\n+chrX\t712418\t712672\t0.99858\n+chrX\t712672\t713045\t0.25364\n+chrX\t713045\t717545\t0.02536\n+chrX\t717545\t756774\t0.01536\n+chrX\t756774\t761274\t0.02536\n+chrX\t761274\t761647\t0.25364\n+chrX\t761647\t761901\t0.99858\n+chrX\t761901\t762274\t0.25364\n+chrX\t762274\t766774\t0.02536\n+chrX\t766774\t841368\t0.01536\n+chrX\t841368\t845868\t0.02536\n+chrX\t845868\t846241\t0.25364\n+chrX\t846241\t846495\t0.99858\n+chrX\t846495\t846868\t0.25364\n+chrX\t846868\t851368\t0.02536\n+chrX\t851368\t916240\t0.01536\n+chrX\t916240\t920740\t0.02536\n+chrX\t920740\t921113\t0.25364\n+chrX\t921113\t921367\t0.99858\n+chrX\t921367\t921740\t0.25364\n+chrX\t921740\t922105\t0.02536\n+chrX\t922105\t926240\t0.05073\n+chrX\t926240\t926605\t0.02536\n+chrX\t926605\t926978\t0.25364\n+chrX\t926978\t927232\t0.99858\n+chrX\t927232\t927605\t0.25364\n+chrX\t927605\t932105\t0.02536\n+chrX\t932105\t934362\t0.01536\n+chrX\t934362\t938862\t0.02536\n+chrX\t938862\t939235\t0.25364\n+chrX\t939235\t939489\t0.99858\n+chrX\t939489\t939862\t0.25364\n+chrX\t939862\t944362\t0.02536\n+chrX\t944362\t972755\t0.01536\n+chrX\t972755\t977255\t0.02536\n+chrX\t977255\t977628\t0.25364\n+chrX\t977628\t977882\t0.99858\n+chrX\t977882\t978255\t0.25364\n+chrX\t978255\t980654\t0.02536\n+chrX\t980654\t981286\t0.05073\n+chrX\t981286\t982755\t0.07609\n+chrX\t982755\t985154\t0.05073\n+chrX\t985154\t985527\t0.25364\n+chrX\t985527\t985781\t0.99858\n+chrX\t985781\t985786\t0.25364\n+chrX\t985786\t986154\t0.50728\n+chrX\t986154\t986159\t0.25364\n+chrX\t986159\t986413\t0.99858\n+chrX\t986413\t986786\t0.25364\n+chrX\t986786\t990654\t0.05073\n+chrX\t990654\t991286\t0.02536\n+chrX\t99'..b'chrX\t30388899\t30393399\t0.02536\n+chrX\t30393399\t30393772\t0.25364\n+chrX\t30393772\t30394026\t0.99858\n+chrX\t30394026\t30394399\t0.25364\n+chrX\t30394399\t30398899\t0.02536\n+chrX\t30398899\t30412225\t0.01536\n+chrX\t30412225\t30416725\t0.02536\n+chrX\t30416725\t30417098\t0.25364\n+chrX\t30417098\t30417352\t0.99858\n+chrX\t30417352\t30417725\t0.25364\n+chrX\t30417725\t30422225\t0.02536\n+chrX\t30422225\t30468626\t0.01536\n+chrX\t30468626\t30473126\t0.02536\n+chrX\t30473126\t30473499\t0.25364\n+chrX\t30473499\t30473753\t0.99858\n+chrX\t30473753\t30474126\t0.25364\n+chrX\t30474126\t30478626\t0.02536\n+chrX\t30478626\t30487482\t0.01536\n+chrX\t30487482\t30491982\t0.02536\n+chrX\t30491982\t30492355\t0.25364\n+chrX\t30492355\t30492609\t0.99858\n+chrX\t30492609\t30492982\t0.25364\n+chrX\t30492982\t30497482\t0.02536\n+chrX\t30497482\t30502013\t0.01536\n+chrX\t30502013\t30506513\t0.02536\n+chrX\t30506513\t30506886\t0.25364\n+chrX\t30506886\t30507140\t0.99858\n+chrX\t30507140\t30507513\t0.25364\n+chrX\t30507513\t30512013\t0.02536\n+chrX\t30512013\t30517761\t0.01536\n+chrX\t30517761\t30522261\t0.02536\n+chrX\t30522261\t30522634\t0.25364\n+chrX\t30522634\t30522888\t0.99858\n+chrX\t30522888\t30523261\t0.25364\n+chrX\t30523261\t30527761\t0.02536\n+chrX\t30527761\t30531586\t0.01536\n+chrX\t30531586\t30536086\t0.02536\n+chrX\t30536086\t30536459\t0.25364\n+chrX\t30536459\t30536713\t0.99858\n+chrX\t30536713\t30537086\t0.25364\n+chrX\t30537086\t30541586\t0.02536\n+chrX\t30541586\t30542211\t0.01536\n+chrX\t30542211\t30546711\t0.02536\n+chrX\t30546711\t30547084\t0.25364\n+chrX\t30547084\t30547338\t0.99858\n+chrX\t30547338\t30547711\t0.25364\n+chrX\t30547711\t30549026\t0.02536\n+chrX\t30549026\t30550594\t0.05073\n+chrX\t30550594\t30552211\t0.07609\n+chrX\t30552211\t30553526\t0.05073\n+chrX\t30553526\t30553899\t0.25364\n+chrX\t30553899\t30554153\t0.99858\n+chrX\t30554153\t30554526\t0.25364\n+chrX\t30554526\t30555094\t0.05073\n+chrX\t30555094\t30555467\t0.25364\n+chrX\t30555467\t30555721\t0.99858\n+chrX\t30555721\t30556094\t0.25364\n+chrX\t30556094\t30559026\t0.05073\n+chrX\t30559026\t30560594\t0.02536\n+chrX\t30560594\t30562227\t0.01536\n+chrX\t30562227\t30565116\t0.02536\n+chrX\t30565116\t30566727\t0.05073\n+chrX\t30566727\t30567100\t0.25364\n+chrX\t30567100\t30567354\t0.99858\n+chrX\t30567354\t30567727\t0.25364\n+chrX\t30567727\t30568768\t0.05073\n+chrX\t30568768\t30569532\t0.07609\n+chrX\t30569532\t30569616\t0.10146\n+chrX\t30569616\t30569989\t0.25364\n+chrX\t30569989\t30570243\t0.99858\n+chrX\t30570243\t30570616\t0.25364\n+chrX\t30570616\t30572227\t0.10146\n+chrX\t30572227\t30573268\t0.07609\n+chrX\t30573268\t30573641\t0.25364\n+chrX\t30573641\t30573895\t0.99858\n+chrX\t30573895\t30574032\t0.25364\n+chrX\t30574032\t30574268\t0.50728\n+chrX\t30574268\t30574405\t0.25364\n+chrX\t30574405\t30574659\t0.99858\n+chrX\t30574659\t30575032\t0.25364\n+chrX\t30575032\t30575116\t0.07609\n+chrX\t30575116\t30577792\t0.05073\n+chrX\t30577792\t30578768\t0.07609\n+chrX\t30578768\t30579532\t0.05073\n+chrX\t30579532\t30580314\t0.02536\n+chrX\t30580314\t30582292\t0.05073\n+chrX\t30582292\t30582665\t0.25364\n+chrX\t30582665\t30582919\t0.99858\n+chrX\t30582919\t30583292\t0.25364\n+chrX\t30583292\t30584814\t0.05073\n+chrX\t30584814\t30585187\t0.25364\n+chrX\t30585187\t30585441\t0.99858\n+chrX\t30585441\t30585814\t0.25364\n+chrX\t30585814\t30586195\t0.05073\n+chrX\t30586195\t30587792\t0.07609\n+chrX\t30587792\t30590314\t0.05073\n+chrX\t30590314\t30590695\t0.02536\n+chrX\t30590695\t30591068\t0.25364\n+chrX\t30591068\t30591322\t0.99858\n+chrX\t30591322\t30591695\t0.25364\n+chrX\t30591695\t30596195\t0.02536\n+chrX\t30596195\t30606989\t0.01536\n+chrX\t30606989\t30607540\t0.02536\n+chrX\t30607540\t30607970\t0.05073\n+chrX\t30607970\t30610718\t0.07609\n+chrX\t30610718\t30611489\t0.10146\n+chrX\t30611489\t30611862\t0.25364\n+chrX\t30611862\t30612116\t0.99858\n+chrX\t30612116\t30612413\t0.50728\n+chrX\t30612413\t30612667\t0.99858\n+chrX\t30612667\t30612843\t0.50728\n+chrX\t30612843\t30613097\t0.99858\n+chrX\t30613097\t30613470\t0.25364\n+chrX\t30613470\t30615218\t0.10146\n+chrX\t30615218\t30615591\t0.25364\n+chrX\t30615591\t30615845\t0.99858\n+chrX\t30615845\t30616218\t0.25364\n+chrX\t30616218\t30616989\t0.10146\n+chrX\t30616989\t30617540\t0.07609\n+chrX\t30617540\t30617970\t0.05073\n+chrX\t30617970\t30620718\t0.02536\n+chrX\t30620718\t30620788\t0.01536\n+chrX\t30620788\t30625288\t0.02536\n+chrX\t30625288\t30625661\t0.25364\n+chrX\t30625661\t30625915\t0.99858\n' |
| b |
| diff -r 000000000000 -r fe62ba547975 test-data/callpeak_part.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/callpeak_part.bed Wed Feb 11 10:18:02 2015 -0500 |
| b |
| b'@@ -0,0 +1,1000 @@\n+chr1\t840081\t840400\t319\t840240\t4.00\t11.15252\t4.92435\t7.51487\tMACS2_peak_1\n+chr1\t919419\t919785\t366\t919550\t5.00\t12.44147\t5.85158\t8.70937\tMACS2_peak_2\n+chr1\t937220\t937483\t263\t937375\t4.00\t10.06728\t4.87632\t6.61760\tMACS2_peak_3\n+chr1\t954742\t954996\t254\t954814\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_4\n+chr1\t994762\t995016\t254\t994906\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_5\n+chr1\t1057394\t1057648\t254\t1057509\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_6\n+chr1\t1240579\t1241004\t425\t1240777\t3.00\t7.77216\t3.90105\t4.60941\tMACS2_peak_7\n+chr1\t1307392\t1307735\t343\t1307601\t5.00\t12.44147\t5.85158\t8.70937\tMACS2_peak_8\n+chr1\t1440350\t1440633\t283\t1440462\t4.00\t11.15252\t4.92435\t7.51487\tMACS2_peak_9\n+chr1\t1555432\t1555725\t293\t1555571\t4.00\t11.15252\t4.92435\t7.51487\tMACS2_peak_10\n+chr1\t1590667\t1590946\t279\t1590840\t4.00\t10.06728\t4.87632\t6.61760\tMACS2_peak_11\n+chr1\t1837668\t1838104\t436\t1837886\t6.00\t14.88255\t6.82684\t10.84923\tMACS2_peak_12\n+chr1\t1840365\t1840828\t463\t1840547\t5.00\t13.74439\t5.90922\t9.80599\tMACS2_peak_13\n+chr1\t1976399\t1976653\t254\t1976469\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_14\n+chr1\t2071301\t2071627\t326\t2071423\t4.00\t11.15252\t4.92435\t7.51487\tMACS2_peak_15\n+chr1\t2105716\t2106140\t424\t2105919\t4.00\t7.70001\t4.64644\t4.60941\tMACS2_peak_16\n+chr1\t2126521\t2126861\t340\t2126648\t4.00\t10.06728\t4.87632\t6.61760\tMACS2_peak_17\n+chr1\t2246520\t2246954\t434\t2246712\t5.00\t9.59761\t5.57573\t6.23290\tMACS2_peak_18\n+chr1\t2313157\t2313560\t403\t2313353\t5.00\t13.74439\t5.90922\t9.80599\tMACS2_peak_19\n+chr1\t2345827\t2346242\t415\t2346028\t7.00\t17.38158\t7.80211\t13.02599\tMACS2_peak_20\n+chr1\t2510054\t2510308\t254\t2510213\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_21\n+chr1\t3341407\t3341661\t254\t3341461\t3.00\t7.77216\t3.90105\t4.60941\tMACS2_peak_22\n+chr1\t3369638\t3369892\t254\t3369863\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_23\n+chr1\t3400440\t3400769\t329\t3400610\t4.00\t11.15252\t4.92435\t7.51487\tMACS2_peak_24\n+chr1\t3407840\t3408094\t254\t3407975\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_25\n+chr1\t3481747\t3482245\t498\t3481863\t4.00\t11.15252\t4.92435\t7.51487\tMACS2_peak_26\n+chr1\t3535561\t3535821\t260\t3535663\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_27\n+chr1\t3537756\t3538010\t254\t3537960\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_28\n+chr1\t3593609\t3593863\t254\t3593838\t3.00\t7.77216\t3.90105\t4.60941\tMACS2_peak_29\n+chr1\t3640883\t3641366\t483\t3641134\t12.00\t30.54970\t12.67843\t24.90332\tMACS2_peak_30\n+chr1\t3702143\t3702397\t254\t3702260\t3.00\t7.77216\t3.90105\t4.60941\tMACS2_peak_31\n+chr1\t3773698\t3774058\t360\t3773876\t7.00\t19.11990\t7.87896\t14.58582\tMACS2_peak_32\n+chr1\t3827305\t3827722\t417\t3827525\t5.00\t13.74439\t5.90922\t9.80599\tMACS2_peak_33\n+chr1\t4712783\t4713037\t254\t4712904\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_34\n+chr1\t4886186\t4886440\t254\t4886326\t3.00\t7.77216\t3.90105\t4.60941\tMACS2_peak_35\n+chr1\t5569918\t5570198\t280\t5570056\t4.00\t11.15252\t4.92435\t7.51487\tMACS2_peak_36\n+chr1\t5574776\t5575080\t304\t5574838\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_37\n+chr1\t5805837\t5806091\t254\t5805965\t2.00\t6.22382\t2.95461\t3.18933\tMACS2_peak_38\n+chr1\t5976145\t5976399\t254\t5976235\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_39\n+chr1\t6094645\t6094899\t254\t6094678\t2.00\t6.22382\t2.95461\t3.18933\tMACS2_peak_40\n+chr1\t6112956\t6113210\t254\t6113135\t3.00\t6.57684\t3.80689\t3.50365\tMACS2_peak_41\n+chr1\t6265252\t6265640\t388\t6265437\t6.00\t11.56197\t6.50502\t7.91704\tMACS2_peak_42\n+chr1\t6305228\t6305482\t254\t6305299\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_43\n+chr1\t6306873\t6307127\t254\t6307013\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_44\n+chr1\t6403480\t6403843\t363\t6403679\t6.00\t16.40316\t6.89409\t12.16639\tMACS2_peak_45\n+chr1\t6464656\t6465096\t440\t6464869\t6.00\t11.56197\t6.50502\t7.91704\tMACS2_peak_46\n+chr1\t6483603\t6483857\t254\t6483739\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_47\n+chr1\t6498109\t6498494\t385\t6498258\t6.00\t14.88255\t6.82684\t10.84923\tMACS2_peak_48\n+chr1\t6535512\t6535838\t326\t6535591\t5.00\t13.74439\t5.90922\t9.80599\tMACS2_peak_49\n+chr1\t6614467\t6614882\t415\t6614708\t4.00\t10.06728\t4.87632\t6.61760\tMACS2_peak_50\n+chr1\t6706585\t6706931\t346\t6706743\t5.00\t13.74439\t5.90922\t9.80599\tMACS2_peak_51\n+chr1\t6761832\t6762203\t371\t6762039\t7.00\t14.9'..b'ACS2_peak_953\n+chr1\t167411347\t167411617\t270\t167411508\t9.00\t9.70719\t6.63448\t6.34225\tMACS2_peak_954\n+chr1\t167509676\t167509994\t318\t167509766\t5.00\t13.74439\t5.90922\t9.80599\tMACS2_peak_955\n+chr1\t167606642\t167606904\t262\t167606794\t4.00\t11.15252\t4.92435\t7.51487\tMACS2_peak_956\n+chr1\t167657153\t167657498\t345\t167657336\t7.00\t17.38158\t7.80211\t13.02599\tMACS2_peak_957\n+chr1\t167684255\t167684787\t532\t167684669\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_958\n+chr1\t168051429\t168051903\t474\t168051540\t4.00\t11.15252\t4.92435\t7.51487\tMACS2_peak_959\n+chr1\t168054014\t168054268\t254\t168054128\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_960\n+chr1\t168115054\t168115312\t258\t168115182\t4.00\t11.15252\t4.92435\t7.51487\tMACS2_peak_961\n+chr1\t168312029\t168312283\t254\t168312087\t2.00\t6.22382\t2.95461\t3.18933\tMACS2_peak_962\n+chr1\t168409107\t168409398\t291\t168409236\t5.00\t12.44147\t5.85158\t8.70937\tMACS2_peak_963\n+chr1\t169317675\t169317929\t254\t169317779\t7.00\t9.46957\t6.38142\t6.11150\tMACS2_peak_964\n+chr1\t169435646\t169435900\t254\t169435730\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_965\n+chr1\t169515618\t169516039\t421\t169515830\t6.00\t14.88255\t6.82684\t10.84923\tMACS2_peak_966\n+chr1\t169570238\t169570598\t360\t169570357\t4.00\t11.15252\t4.92435\t7.51487\tMACS2_peak_967\n+chr1\t169681091\t169681643\t552\t169681360\t6.00\t14.88255\t6.82684\t10.84923\tMACS2_peak_968\n+chr1\t169778761\t169779123\t362\t169778927\t6.00\t16.40316\t6.89409\t12.16639\tMACS2_peak_969\n+chr1\t169898084\t169898451\t367\t169898207\t7.00\t17.38158\t7.80211\t13.02599\tMACS2_peak_970\n+chr1\t169979564\t169979919\t355\t169979736\t5.00\t13.74439\t5.90922\t9.80599\tMACS2_peak_971\n+chr1\t170658710\t170659105\t395\t170658858\t4.00\t11.15252\t4.92435\t7.51487\tMACS2_peak_972\n+chr1\t170936227\t170936611\t384\t170936406\t4.00\t11.15252\t4.92435\t7.51487\tMACS2_peak_973\n+chr1\t171157806\t171158175\t369\t171157946\t6.00\t12.78498\t6.66205\t9.02328\tMACS2_peak_974\n+chr1\t171454166\t171454693\t527\t171454409\t5.00\t12.44147\t5.85158\t8.70937\tMACS2_peak_975\n+chr1\t171624733\t171624987\t254\t171624826\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_976\n+chr1\t171770672\t171770926\t254\t171770811\t3.00\t6.57684\t3.80689\t3.50365\tMACS2_peak_977\n+chr1\t171952729\t171952983\t254\t171952866\t3.00\t7.77216\t3.90105\t4.60941\tMACS2_peak_978\n+chr1\t171953940\t171954438\t498\t171954190\t4.00\t10.06728\t4.87632\t6.61760\tMACS2_peak_979\n+chr1\t171971859\t171972280\t421\t171972046\t6.00\t16.40316\t6.89409\t12.16639\tMACS2_peak_980\n+chr1\t172104225\t172104597\t372\t172104448\t4.00\t11.15252\t4.92435\t7.51487\tMACS2_peak_981\n+chr1\t172398514\t172398852\t338\t172398693\t4.00\t10.06728\t4.87632\t6.61760\tMACS2_peak_982\n+chr1\t172688764\t172689204\t440\t172688964\t7.00\t9.46957\t6.38142\t6.11150\tMACS2_peak_983\n+chr1\t172711842\t172712109\t267\t172712013\t4.00\t10.06728\t4.87632\t6.61760\tMACS2_peak_984\n+chr1\t172714120\t172714382\t262\t172714306\t5.00\t12.44147\t5.85158\t8.70937\tMACS2_peak_985\n+chr1\t173171628\t173171882\t254\t173171751\t3.00\t5.88126\t3.71716\t3.00791\tMACS2_peak_986\n+chr1\t173389467\t173389819\t352\t173389640\t8.00\t17.23237\t8.56549\t12.97385\tMACS2_peak_987\n+chr1\t173400334\t173400718\t384\t173400558\t5.00\t12.44147\t5.85158\t8.70937\tMACS2_peak_988\n+chr1\t173684280\t173684534\t254\t173684329\t2.00\t5.57376\t2.92579\t2.70691\tMACS2_peak_989\n+chr1\t173794183\t173794465\t282\t173794324\t4.00\t7.70001\t4.64644\t4.60941\tMACS2_peak_990\n+chr1\t173883385\t173883681\t296\t173883565\t5.00\t13.74439\t5.90922\t9.80599\tMACS2_peak_991\n+chr1\t174084042\t174084320\t278\t174084167\t4.00\t11.15252\t4.92435\t7.51487\tMACS2_peak_992\n+chr1\t174186861\t174187115\t254\t174187033\t9.00\t6.95863\t5.00355\t3.88437\tMACS2_peak_993\n+chr1\t174227188\t174227538\t350\t174227378\t5.00\t12.44147\t5.85158\t8.70937\tMACS2_peak_994\n+chr1\t174695684\t174695942\t258\t174695865\t4.00\t10.06728\t4.87632\t6.61760\tMACS2_peak_995\n+chr1\t174713257\t174713511\t254\t174713320\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_996\n+chr1\t174739198\t174739503\t305\t174739348\t4.00\t8.57130\t4.75861\t5.28945\tMACS2_peak_997\n+chr1\t174967683\t174968030\t347\t174967847\t10.00\t8.00416\t5.50391\t4.83430\tMACS2_peak_998\n+chr1\t174998798\t174999052\t254\t174998982\t3.00\t8.63977\t3.93948\t5.28945\tMACS2_peak_999\n+chr1\t175094595\t175094849\t254\t175094659\t3.00\t7.77216\t3.90105\t4.60941\tMACS2_peak_1000\n' |
| b |
| diff -r 000000000000 -r fe62ba547975 test-data/callpeak_summits_part.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/callpeak_summits_part.bed Wed Feb 11 10:18:02 2015 -0500 |
| b |
| b'@@ -0,0 +1,1000 @@\n+chr1\t840239\t840240\tMACS2_peak_1\t7.51487\n+chr1\t919549\t919550\tMACS2_peak_2\t8.70937\n+chr1\t937374\t937375\tMACS2_peak_3\t6.61760\n+chr1\t954813\t954814\tMACS2_peak_4\t5.28945\n+chr1\t994905\t994906\tMACS2_peak_5\t5.28945\n+chr1\t1057508\t1057509\tMACS2_peak_6\t5.28945\n+chr1\t1240776\t1240777\tMACS2_peak_7\t4.60941\n+chr1\t1307600\t1307601\tMACS2_peak_8\t8.70937\n+chr1\t1440461\t1440462\tMACS2_peak_9\t7.51487\n+chr1\t1555570\t1555571\tMACS2_peak_10\t7.51487\n+chr1\t1590839\t1590840\tMACS2_peak_11\t6.61760\n+chr1\t1837885\t1837886\tMACS2_peak_12\t10.84923\n+chr1\t1840546\t1840547\tMACS2_peak_13\t9.80599\n+chr1\t1976468\t1976469\tMACS2_peak_14\t5.28945\n+chr1\t2071422\t2071423\tMACS2_peak_15\t7.51487\n+chr1\t2105918\t2105919\tMACS2_peak_16\t4.60941\n+chr1\t2126647\t2126648\tMACS2_peak_17\t6.61760\n+chr1\t2246711\t2246712\tMACS2_peak_18\t6.23290\n+chr1\t2313352\t2313353\tMACS2_peak_19\t9.80599\n+chr1\t2346027\t2346028\tMACS2_peak_20\t13.02599\n+chr1\t2510212\t2510213\tMACS2_peak_21\t5.28945\n+chr1\t3341460\t3341461\tMACS2_peak_22\t4.60941\n+chr1\t3369862\t3369863\tMACS2_peak_23\t5.28945\n+chr1\t3400609\t3400610\tMACS2_peak_24\t7.51487\n+chr1\t3407974\t3407975\tMACS2_peak_25\t5.28945\n+chr1\t3481862\t3481863\tMACS2_peak_26\t7.51487\n+chr1\t3535662\t3535663\tMACS2_peak_27\t5.28945\n+chr1\t3537959\t3537960\tMACS2_peak_28\t5.28945\n+chr1\t3593837\t3593838\tMACS2_peak_29\t4.60941\n+chr1\t3641133\t3641134\tMACS2_peak_30\t24.90332\n+chr1\t3702259\t3702260\tMACS2_peak_31\t4.60941\n+chr1\t3773875\t3773876\tMACS2_peak_32\t14.58582\n+chr1\t3827524\t3827525\tMACS2_peak_33\t9.80599\n+chr1\t4712903\t4712904\tMACS2_peak_34\t5.28945\n+chr1\t4886325\t4886326\tMACS2_peak_35\t4.60941\n+chr1\t5570055\t5570056\tMACS2_peak_36\t7.51487\n+chr1\t5574837\t5574838\tMACS2_peak_37\t5.28945\n+chr1\t5805964\t5805965\tMACS2_peak_38\t3.18933\n+chr1\t5976234\t5976235\tMACS2_peak_39\t5.28945\n+chr1\t6094677\t6094678\tMACS2_peak_40\t3.18933\n+chr1\t6113134\t6113135\tMACS2_peak_41\t3.50365\n+chr1\t6265436\t6265437\tMACS2_peak_42\t7.91704\n+chr1\t6305298\t6305299\tMACS2_peak_43\t5.28945\n+chr1\t6307012\t6307013\tMACS2_peak_44\t5.28945\n+chr1\t6403678\t6403679\tMACS2_peak_45\t12.16639\n+chr1\t6464868\t6464869\tMACS2_peak_46\t7.91704\n+chr1\t6483738\t6483739\tMACS2_peak_47\t5.28945\n+chr1\t6498257\t6498258\tMACS2_peak_48\t10.84923\n+chr1\t6535590\t6535591\tMACS2_peak_49\t9.80599\n+chr1\t6614707\t6614708\tMACS2_peak_50\t6.61760\n+chr1\t6706742\t6706743\tMACS2_peak_51\t9.80599\n+chr1\t6762038\t6762039\tMACS2_peak_52\t10.92185\n+chr1\t6780328\t6780329\tMACS2_peak_53\t12.16639\n+chr1\t6787703\t6787704\tMACS2_peak_54\t14.58582\n+chr1\t6950152\t6950153\tMACS2_peak_55\t7.17294\n+chr1\t7102914\t7102915\tMACS2_peak_56\t7.51487\n+chr1\t7278482\t7278483\tMACS2_peak_57\t12.16639\n+chr1\t7868576\t7868577\tMACS2_peak_58\t7.51487\n+chr1\t7962861\t7962862\tMACS2_peak_59\t4.60941\n+chr1\t8042490\t8042491\tMACS2_peak_60\t10.84923\n+chr1\t8075251\t8075252\tMACS2_peak_61\t9.02328\n+chr1\t8076738\t8076739\tMACS2_peak_62\t5.28945\n+chr1\t8091351\t8091352\tMACS2_peak_63\t7.51487\n+chr1\t8374569\t8374570\tMACS2_peak_64\t12.16639\n+chr1\t8409217\t8409218\tMACS2_peak_65\t7.51487\n+chr1\t8731569\t8731570\tMACS2_peak_66\t6.61760\n+chr1\t8786755\t8786756\tMACS2_peak_67\t8.86076\n+chr1\t8909001\t8909002\tMACS2_peak_68\t2.70691\n+chr1\t8978355\t8978356\tMACS2_peak_69\t9.80599\n+chr1\t9048259\t9048260\tMACS2_peak_70\t5.28945\n+chr1\t9065348\t9065349\tMACS2_peak_71\t9.80599\n+chr1\t9070210\t9070211\tMACS2_peak_72\t7.51487\n+chr1\t9161796\t9161797\tMACS2_peak_73\t7.51487\n+chr1\t9202501\t9202502\tMACS2_peak_74\t17.04807\n+chr1\t9349216\t9349217\tMACS2_peak_75\t9.80599\n+chr1\t9515966\t9515967\tMACS2_peak_76\t8.70937\n+chr1\t9551282\t9551283\tMACS2_peak_77\t15.26510\n+chr1\t9555464\t9555465\tMACS2_peak_78\t5.28945\n+chr1\t9633927\t9633928\tMACS2_peak_79\t7.51487\n+chr1\t9687168\t9687169\tMACS2_peak_80\t17.04807\n+chr1\t9785326\t9785327\tMACS2_peak_81\t7.51487\n+chr1\t9844799\t9844800\tMACS2_peak_82\t13.02599\n+chr1\t9927731\t9927732\tMACS2_peak_83\t12.16639\n+chr1\t9935117\t9935118\tMACS2_peak_84\t22.22259\n+chr1\t10002611\t10002612\tMACS2_peak_85\t10.84923\n+chr1\t10094708\t10094709\tMACS2_peak_86\t4.60941\n+chr1\t10213169\t10213170\tMACS2_peak_87\t5.28945\n+chr1\t10270453\t10270454\tMACS2_peak_88\t4.60941\n+chr1\t10398241\t10398242\tMACS2_peak_89\t5.28945\n+chr1\t10437671\t10437672\tMACS2_peak_90\t6.61760\n+chr1\t10'..b'ak_919\t4.60941\n+chr1\t161617363\t161617364\tMACS2_peak_920\t6.61760\n+chr1\t161708708\t161708709\tMACS2_peak_921\t14.96855\n+chr1\t161875153\t161875154\tMACS2_peak_922\t7.51487\n+chr1\t162035334\t162035335\tMACS2_peak_923\t4.60941\n+chr1\t162362094\t162362095\tMACS2_peak_924\t5.28945\n+chr1\t162597769\t162597770\tMACS2_peak_925\t4.60941\n+chr1\t162817776\t162817777\tMACS2_peak_926\t6.61760\n+chr1\t162824188\t162824189\tMACS2_peak_927\t4.79957\n+chr1\t162847902\t162847903\tMACS2_peak_928\t2.70691\n+chr1\t163041843\t163041844\tMACS2_peak_929\t3.50365\n+chr1\t163285733\t163285734\tMACS2_peak_930\t7.51487\n+chr1\t163329105\t163329106\tMACS2_peak_931\t7.51487\n+chr1\t163531543\t163531544\tMACS2_peak_932\t5.28945\n+chr1\t164587198\t164587199\tMACS2_peak_933\t5.28945\n+chr1\t164756743\t164756744\tMACS2_peak_934\t6.61760\n+chr1\t165098959\t165098960\tMACS2_peak_935\t7.51487\n+chr1\t165112930\t165112931\tMACS2_peak_936\t5.28945\n+chr1\t165114234\t165114235\tMACS2_peak_937\t9.80599\n+chr1\t165227511\t165227512\tMACS2_peak_938\t4.60941\n+chr1\t165338549\t165338550\tMACS2_peak_939\t3.18933\n+chr1\t165362290\t165362291\tMACS2_peak_940\t12.97385\n+chr1\t165562320\t165562321\tMACS2_peak_941\t13.02599\n+chr1\t165571060\t165571061\tMACS2_peak_942\t7.51487\n+chr1\t165687394\t165687395\tMACS2_peak_943\t8.70937\n+chr1\t165883679\t165883680\tMACS2_peak_944\t17.04807\n+chr1\t165894119\t165894120\tMACS2_peak_945\t12.16639\n+chr1\t165897513\t165897514\tMACS2_peak_946\t12.16639\n+chr1\t166102578\t166102579\tMACS2_peak_947\t4.60941\n+chr1\t166134341\t166134342\tMACS2_peak_948\t6.61760\n+chr1\t166448470\t166448471\tMACS2_peak_949\t10.84923\n+chr1\t167028558\t167028559\tMACS2_peak_950\t4.79957\n+chr1\t167036037\t167036038\tMACS2_peak_951\t6.61760\n+chr1\t167237295\t167237296\tMACS2_peak_952\t3.50365\n+chr1\t167370686\t167370687\tMACS2_peak_953\t6.61760\n+chr1\t167411507\t167411508\tMACS2_peak_954\t6.34225\n+chr1\t167509765\t167509766\tMACS2_peak_955\t9.80599\n+chr1\t167606793\t167606794\tMACS2_peak_956\t7.51487\n+chr1\t167657335\t167657336\tMACS2_peak_957\t13.02599\n+chr1\t167684668\t167684669\tMACS2_peak_958\t5.28945\n+chr1\t168051539\t168051540\tMACS2_peak_959\t7.51487\n+chr1\t168054127\t168054128\tMACS2_peak_960\t5.28945\n+chr1\t168115181\t168115182\tMACS2_peak_961\t7.51487\n+chr1\t168312086\t168312087\tMACS2_peak_962\t3.18933\n+chr1\t168409235\t168409236\tMACS2_peak_963\t8.70937\n+chr1\t169317778\t169317779\tMACS2_peak_964\t6.11150\n+chr1\t169435729\t169435730\tMACS2_peak_965\t5.28945\n+chr1\t169515829\t169515830\tMACS2_peak_966\t10.84923\n+chr1\t169570356\t169570357\tMACS2_peak_967\t7.51487\n+chr1\t169681359\t169681360\tMACS2_peak_968\t10.84923\n+chr1\t169778926\t169778927\tMACS2_peak_969\t12.16639\n+chr1\t169898206\t169898207\tMACS2_peak_970\t13.02599\n+chr1\t169979735\t169979736\tMACS2_peak_971\t9.80599\n+chr1\t170658857\t170658858\tMACS2_peak_972\t7.51487\n+chr1\t170936405\t170936406\tMACS2_peak_973\t7.51487\n+chr1\t171157945\t171157946\tMACS2_peak_974\t9.02328\n+chr1\t171454408\t171454409\tMACS2_peak_975\t8.70937\n+chr1\t171624825\t171624826\tMACS2_peak_976\t5.28945\n+chr1\t171770810\t171770811\tMACS2_peak_977\t3.50365\n+chr1\t171952865\t171952866\tMACS2_peak_978\t4.60941\n+chr1\t171954189\t171954190\tMACS2_peak_979\t6.61760\n+chr1\t171972045\t171972046\tMACS2_peak_980\t12.16639\n+chr1\t172104447\t172104448\tMACS2_peak_981\t7.51487\n+chr1\t172398692\t172398693\tMACS2_peak_982\t6.61760\n+chr1\t172688963\t172688964\tMACS2_peak_983\t6.11150\n+chr1\t172712012\t172712013\tMACS2_peak_984\t6.61760\n+chr1\t172714305\t172714306\tMACS2_peak_985\t8.70937\n+chr1\t173171750\t173171751\tMACS2_peak_986\t3.00791\n+chr1\t173389639\t173389640\tMACS2_peak_987\t12.97385\n+chr1\t173400557\t173400558\tMACS2_peak_988\t8.70937\n+chr1\t173684328\t173684329\tMACS2_peak_989\t2.70691\n+chr1\t173794323\t173794324\tMACS2_peak_990\t4.60941\n+chr1\t173883564\t173883565\tMACS2_peak_991\t9.80599\n+chr1\t174084166\t174084167\tMACS2_peak_992\t7.51487\n+chr1\t174187032\t174187033\tMACS2_peak_993\t3.88437\n+chr1\t174227377\t174227378\tMACS2_peak_994\t8.70937\n+chr1\t174695864\t174695865\tMACS2_peak_995\t6.61760\n+chr1\t174713319\t174713320\tMACS2_peak_996\t5.28945\n+chr1\t174739347\t174739348\tMACS2_peak_997\t5.28945\n+chr1\t174967846\t174967847\tMACS2_peak_998\t4.83430\n+chr1\t174998981\t174998982\tMACS2_peak_999\t5.28945\n+chr1\t175094658\t175094659\tMACS2_peak_1000\t4.60941\n' |
| b |
| diff -r 000000000000 -r fe62ba547975 test-data/callpeak_treatment_part.bdg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/callpeak_treatment_part.bdg Wed Feb 11 10:18:02 2015 -0500 |
| b |
| b'@@ -0,0 +1,10000 @@\n+chrX\t0\t69671\t0.00000\n+chrX\t69671\t69925\t1.00000\n+chrX\t69925\t284628\t0.00000\n+chrX\t284628\t284843\t1.00000\n+chrX\t284843\t284882\t2.00000\n+chrX\t284882\t285097\t1.00000\n+chrX\t285097\t285556\t0.00000\n+chrX\t285556\t285810\t1.00000\n+chrX\t285810\t461156\t0.00000\n+chrX\t461156\t461410\t1.00000\n+chrX\t461410\t586983\t0.00000\n+chrX\t586983\t587237\t1.00000\n+chrX\t587237\t593044\t0.00000\n+chrX\t593044\t593298\t1.00000\n+chrX\t593298\t656045\t0.00000\n+chrX\t656045\t656299\t1.00000\n+chrX\t656299\t920309\t0.00000\n+chrX\t920309\t920563\t1.00000\n+chrX\t920563\t947933\t0.00000\n+chrX\t947933\t948187\t1.00000\n+chrX\t948187\t1006805\t0.00000\n+chrX\t1006805\t1007059\t1.00000\n+chrX\t1007059\t1257632\t0.00000\n+chrX\t1257632\t1257716\t1.00000\n+chrX\t1257716\t1257813\t2.00000\n+chrX\t1257813\t1257886\t3.00000\n+chrX\t1257886\t1257970\t2.00000\n+chrX\t1257970\t1258067\t1.00000\n+chrX\t1258067\t1324083\t0.00000\n+chrX\t1324083\t1324337\t1.00000\n+chrX\t1324337\t1332580\t0.00000\n+chrX\t1332580\t1332834\t1.00000\n+chrX\t1332834\t1353039\t0.00000\n+chrX\t1353039\t1353293\t1.00000\n+chrX\t1353293\t1363567\t0.00000\n+chrX\t1363567\t1363605\t1.00000\n+chrX\t1363605\t1363821\t2.00000\n+chrX\t1363821\t1363859\t1.00000\n+chrX\t1363859\t1365758\t0.00000\n+chrX\t1365758\t1365809\t1.00000\n+chrX\t1365809\t1366012\t2.00000\n+chrX\t1366012\t1366063\t1.00000\n+chrX\t1366063\t1372998\t0.00000\n+chrX\t1372998\t1373252\t1.00000\n+chrX\t1373252\t1384092\t0.00000\n+chrX\t1384092\t1384346\t1.00000\n+chrX\t1384346\t1397762\t0.00000\n+chrX\t1397762\t1398016\t1.00000\n+chrX\t1398016\t1430076\t0.00000\n+chrX\t1430076\t1430330\t1.00000\n+chrX\t1430330\t1442229\t0.00000\n+chrX\t1442229\t1442483\t1.00000\n+chrX\t1442483\t1442730\t0.00000\n+chrX\t1442730\t1442984\t1.00000\n+chrX\t1442984\t1444736\t0.00000\n+chrX\t1444736\t1444990\t1.00000\n+chrX\t1444990\t1446470\t0.00000\n+chrX\t1446470\t1446724\t1.00000\n+chrX\t1446724\t1453397\t0.00000\n+chrX\t1453397\t1453651\t1.00000\n+chrX\t1453651\t1455341\t0.00000\n+chrX\t1455341\t1455453\t1.00000\n+chrX\t1455453\t1455595\t2.00000\n+chrX\t1455595\t1455707\t1.00000\n+chrX\t1455707\t1456342\t0.00000\n+chrX\t1456342\t1456596\t1.00000\n+chrX\t1456596\t1506622\t0.00000\n+chrX\t1506622\t1506876\t1.00000\n+chrX\t1506876\t1533627\t0.00000\n+chrX\t1533627\t1533881\t1.00000\n+chrX\t1533881\t1539210\t0.00000\n+chrX\t1539210\t1539464\t1.00000\n+chrX\t1539464\t1545156\t0.00000\n+chrX\t1545156\t1545410\t1.00000\n+chrX\t1545410\t1572536\t0.00000\n+chrX\t1572536\t1572790\t1.00000\n+chrX\t1572790\t1573012\t0.00000\n+chrX\t1573012\t1573072\t1.00000\n+chrX\t1573072\t1573141\t2.00000\n+chrX\t1573141\t1573266\t3.00000\n+chrX\t1573266\t1573315\t2.00000\n+chrX\t1573315\t1573326\t3.00000\n+chrX\t1573326\t1573387\t2.00000\n+chrX\t1573387\t1573395\t3.00000\n+chrX\t1573395\t1573569\t2.00000\n+chrX\t1573569\t1573641\t1.00000\n+chrX\t1573641\t1587254\t0.00000\n+chrX\t1587254\t1587508\t1.00000\n+chrX\t1587508\t1600719\t0.00000\n+chrX\t1600719\t1600850\t1.00000\n+chrX\t1600850\t1600973\t2.00000\n+chrX\t1600973\t1601104\t1.00000\n+chrX\t1601104\t1602854\t0.00000\n+chrX\t1602854\t1603108\t1.00000\n+chrX\t1603108\t1603548\t0.00000\n+chrX\t1603548\t1603802\t1.00000\n+chrX\t1603802\t1612360\t0.00000\n+chrX\t1612360\t1612614\t1.00000\n+chrX\t1612614\t1614986\t0.00000\n+chrX\t1614986\t1615240\t1.00000\n+chrX\t1615240\t1627130\t0.00000\n+chrX\t1627130\t1627384\t1.00000\n+chrX\t1627384\t1630646\t0.00000\n+chrX\t1630646\t1630900\t1.00000\n+chrX\t1630900\t1636122\t0.00000\n+chrX\t1636122\t1636376\t1.00000\n+chrX\t1636376\t1654688\t0.00000\n+chrX\t1654688\t1654942\t1.00000\n+chrX\t1654942\t1656256\t0.00000\n+chrX\t1656256\t1656323\t1.00000\n+chrX\t1656323\t1656379\t2.00000\n+chrX\t1656379\t1656510\t3.00000\n+chrX\t1656510\t1656547\t2.00000\n+chrX\t1656547\t1656577\t3.00000\n+chrX\t1656577\t1656633\t2.00000\n+chrX\t1656633\t1656801\t1.00000\n+chrX\t1656801\t1673614\t0.00000\n+chrX\t1673614\t1673868\t1.00000\n+chrX\t1673868\t1678732\t0.00000\n+chrX\t1678732\t1678986\t1.00000\n+chrX\t1678986\t1683727\t0.00000\n+chrX\t1683727\t1683981\t1.00000\n+chrX\t1683981\t1700130\t0.00000\n+chrX\t1700130\t1700384\t1.00000\n+chrX\t1700384\t1702172\t0.00000\n+chrX\t1702172\t1702426\t1.00000\n+chrX\t1702426\t1710407\t0.00000\n+chrX\t1710407\t1710661\t1.00000\n+chrX\t1710661\t1742824\t0.00000\n+chrX\t1742824\t1743078\t1.00000\n+chrX\t1743078\t1767435\t0.00000\n+chrX\t1767435\t1767445\t1.00000\n+chrX\t1767445\t1767467\t2.00000\n+chrX\t1767467\t1767468\t3.00000\n+chrX\t176'..b'88\t119384485\t0.00000\n+chrX\t119384485\t119384739\t1.00000\n+chrX\t119384739\t119384889\t0.00000\n+chrX\t119384889\t119385143\t1.00000\n+chrX\t119385143\t119397246\t0.00000\n+chrX\t119397246\t119397500\t1.00000\n+chrX\t119397500\t119433740\t0.00000\n+chrX\t119433740\t119433994\t1.00000\n+chrX\t119433994\t119443366\t0.00000\n+chrX\t119443366\t119443387\t1.00000\n+chrX\t119443387\t119443398\t2.00000\n+chrX\t119443398\t119443484\t3.00000\n+chrX\t119443484\t119443620\t4.00000\n+chrX\t119443620\t119443641\t3.00000\n+chrX\t119443641\t119443652\t2.00000\n+chrX\t119443652\t119443738\t1.00000\n+chrX\t119443738\t119453196\t0.00000\n+chrX\t119453196\t119453450\t1.00000\n+chrX\t119453450\t119496500\t0.00000\n+chrX\t119496500\t119496754\t1.00000\n+chrX\t119496754\t119499109\t0.00000\n+chrX\t119499109\t119499118\t1.00000\n+chrX\t119499118\t119499322\t2.00000\n+chrX\t119499322\t119499363\t3.00000\n+chrX\t119499363\t119499372\t2.00000\n+chrX\t119499372\t119499576\t1.00000\n+chrX\t119499576\t119584005\t0.00000\n+chrX\t119584005\t119584138\t1.00000\n+chrX\t119584138\t119584233\t2.00000\n+chrX\t119584233\t119584259\t3.00000\n+chrX\t119584259\t119584392\t2.00000\n+chrX\t119584392\t119584487\t1.00000\n+chrX\t119584487\t119586039\t0.00000\n+chrX\t119586039\t119586293\t1.00000\n+chrX\t119586293\t119608806\t0.00000\n+chrX\t119608806\t119609060\t1.00000\n+chrX\t119609060\t119609317\t0.00000\n+chrX\t119609317\t119609354\t1.00000\n+chrX\t119609354\t119609375\t2.00000\n+chrX\t119609375\t119609397\t3.00000\n+chrX\t119609397\t119609437\t4.00000\n+chrX\t119609437\t119609571\t5.00000\n+chrX\t119609571\t119609608\t4.00000\n+chrX\t119609608\t119609629\t3.00000\n+chrX\t119609629\t119609651\t2.00000\n+chrX\t119609651\t119609681\t1.00000\n+chrX\t119609681\t119609691\t2.00000\n+chrX\t119609691\t119609935\t1.00000\n+chrX\t119609935\t119619999\t0.00000\n+chrX\t119619999\t119620043\t1.00000\n+chrX\t119620043\t119620253\t2.00000\n+chrX\t119620253\t119620297\t1.00000\n+chrX\t119620297\t119631826\t0.00000\n+chrX\t119631826\t119631922\t1.00000\n+chrX\t119631922\t119631946\t2.00000\n+chrX\t119631946\t119631960\t3.00000\n+chrX\t119631960\t119632001\t4.00000\n+chrX\t119632001\t119632026\t5.00000\n+chrX\t119632026\t119632080\t6.00000\n+chrX\t119632080\t119632176\t5.00000\n+chrX\t119632176\t119632200\t4.00000\n+chrX\t119632200\t119632214\t3.00000\n+chrX\t119632214\t119632255\t2.00000\n+chrX\t119632255\t119632280\t1.00000\n+chrX\t119632280\t119640766\t0.00000\n+chrX\t119640766\t119641020\t1.00000\n+chrX\t119641020\t119668285\t0.00000\n+chrX\t119668285\t119668539\t1.00000\n+chrX\t119668539\t119680122\t0.00000\n+chrX\t119680122\t119680376\t1.00000\n+chrX\t119680376\t119728234\t0.00000\n+chrX\t119728234\t119728488\t1.00000\n+chrX\t119728488\t119737495\t0.00000\n+chrX\t119737495\t119737749\t1.00000\n+chrX\t119737749\t119758695\t0.00000\n+chrX\t119758695\t119758949\t1.00000\n+chrX\t119758949\t119762376\t0.00000\n+chrX\t119762376\t119762630\t1.00000\n+chrX\t119762630\t119769884\t0.00000\n+chrX\t119769884\t119770138\t1.00000\n+chrX\t119770138\t119826519\t0.00000\n+chrX\t119826519\t119826773\t1.00000\n+chrX\t119826773\t119864257\t0.00000\n+chrX\t119864257\t119864511\t1.00000\n+chrX\t119864511\t119883657\t0.00000\n+chrX\t119883657\t119883911\t1.00000\n+chrX\t119883911\t119887334\t0.00000\n+chrX\t119887334\t119887390\t1.00000\n+chrX\t119887390\t119887515\t2.00000\n+chrX\t119887515\t119887588\t3.00000\n+chrX\t119887588\t119887644\t2.00000\n+chrX\t119887644\t119887769\t1.00000\n+chrX\t119887769\t119903862\t0.00000\n+chrX\t119903862\t119903877\t1.00000\n+chrX\t119903877\t119903925\t2.00000\n+chrX\t119903925\t119904116\t3.00000\n+chrX\t119904116\t119904131\t2.00000\n+chrX\t119904131\t119904179\t1.00000\n+chrX\t119904179\t119904260\t0.00000\n+chrX\t119904260\t119904514\t1.00000\n+chrX\t119904514\t119923853\t0.00000\n+chrX\t119923853\t119923868\t1.00000\n+chrX\t119923868\t119923897\t2.00000\n+chrX\t119923897\t119923935\t3.00000\n+chrX\t119923935\t119924010\t4.00000\n+chrX\t119924010\t119924026\t5.00000\n+chrX\t119924026\t119924071\t6.00000\n+chrX\t119924071\t119924107\t7.00000\n+chrX\t119924107\t119924122\t6.00000\n+chrX\t119924122\t119924151\t5.00000\n+chrX\t119924151\t119924189\t4.00000\n+chrX\t119924189\t119924198\t3.00000\n+chrX\t119924198\t119924264\t4.00000\n+chrX\t119924264\t119924280\t3.00000\n+chrX\t119924280\t119924325\t2.00000\n+chrX\t119924325\t119924452\t1.00000\n+chrX\t119924452\t119931658\t0.00000\n+chrX\t119931658\t119931912\t1.00000\n' |
| b |
| diff -r 000000000000 -r fe62ba547975 test-data/filterdup_on_ChIP_200K_w_dups.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filterdup_on_ChIP_200K_w_dups.bed Wed Feb 11 10:18:02 2015 -0500 |
| b |
| @@ -0,0 +1,10 @@ +chr1 564917 565017 . . + +chr1 565533 565633 . . + +chr1 565844 565944 . . + +chr1 565858 565958 . . + +chr1 566132 566232 . . + +chr1 566212 566312 . . + +chr1 566736 566836 . . + +chr1 566976 567076 . . + +chr1 567211 567311 . . + +chr1 567320 567420 . . + |
| b |
| diff -r 000000000000 -r fe62ba547975 test-data/predictd_on_ChIP_200K_and_Control_200K.pdf |
| b |
| Binary file test-data/predictd_on_ChIP_200K_and_Control_200K.pdf has changed |
| b |
| diff -r 000000000000 -r fe62ba547975 test-data/predictd_on_ChIP_200K_and_Control_200K.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/predictd_on_ChIP_200K_and_Control_200K.txt Wed Feb 11 10:18:02 2015 -0500 |
| b |
| @@ -0,0 +1,16 @@ +# read alignment files... +# read treatment tags... +Detected format is +Detected format is +tag size is determined as 86 bps +# tag size = 86 +# total tags in alignment file +# Build Peak Model... +#2 number of paired peaks +start model_add_line... +start X-correlation... +end of X-cor +# finished! +# predicted fragment length is 284 bps +# alternative fragment length(s) may be 284 bps +# Generate R script for model |
| b |
| diff -r 000000000000 -r fe62ba547975 test-data/refinepeak_ChIP_and_summits.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/refinepeak_ChIP_and_summits.bed Wed Feb 11 10:18:02 2015 -0500 |
| b |
| b'@@ -0,0 +1,1000 @@\n+chr1\t840148\t840149\tMACS2_peak_1_F\t3.46\n+chr1\t919487\t919488\tMACS2_peak_2_F\t2.46\n+chr1\t937350\t937351\tMACS2_peak_3_F\t2.83\n+chr1\t954797\t954798\tMACS2_peak_4_F\t2.83\n+chr1\t994890\t994891\tMACS2_peak_5_F\t2.83\n+chr1\t1057493\t1057494\tMACS2_peak_6_F\t2.83\n+chr1\t1240751\t1240752\tMACS2_peak_7_F\t1.83\n+chr1\t1307482\t1307483\tMACS2_peak_8_F\t4.00\n+chr1\t1440462\t1440463\tMACS2_peak_9_F\t1.83\n+chr1\t1555487\t1555488\tMACS2_peak_10_F\t4.00\n+chr1\t1590693\t1590694\tMACS2_peak_11_F\t0.00\n+chr1\t1837880\t1837881\tMACS2_peak_12_F\t4.90\n+chr1\t1840575\t1840576\tMACS2_peak_13_F\t4.00\n+chr1\t1976454\t1976455\tMACS2_peak_14_F\t2.00\n+chr1\t2071222\t2071223\tMACS2_peak_15_F\t0.00\n+chr1\t2105890\t2105891\tMACS2_peak_16_F\t0.00\n+chr1\t2126608\t2126609\tMACS2_peak_17_F\t3.46\n+chr1\t2246764\t2246765\tMACS2_peak_18_F\t2.83\n+chr1\t2313333\t2313334\tMACS2_peak_19_F\t3.46\n+chr1\t2346010\t2346011\tMACS2_peak_20_R\t5.66\n+chr1\t2510125\t2510126\tMACS2_peak_21_F\t2.83\n+chr1\t3341443\t3341444\tMACS2_peak_22_F\t0.00\n+chr1\t3369851\t3369852\tMACS2_peak_23_F\t2.83\n+chr1\t3400563\t3400564\tMACS2_peak_24_F\t3.46\n+chr1\t3407907\t3407908\tMACS2_peak_25_F\t0.00\n+chr1\t3481992\t3481993\tMACS2_peak_26_F\t4.00\n+chr1\t3535802\t3535803\tMACS2_peak_27_F\t2.00\n+chr1\t3537759\t3537760\tMACS2_peak_28_F\t0.00\n+chr1\t3593823\t3593824\tMACS2_peak_29_F\t2.83\n+chr1\t3641130\t3641131\tMACS2_peak_30_R\t10.00\n+chr1\t3702198\t3702199\tMACS2_peak_31_F\t2.83\n+chr1\t3773867\t3773868\tMACS2_peak_32_R\t6.32\n+chr1\t3827469\t3827470\tMACS2_peak_33_F\t4.00\n+chr1\t4712838\t4712839\tMACS2_peak_34_F\t2.83\n+chr1\t4886247\t4886248\tMACS2_peak_35_F\t2.83\n+chr1\t5570049\t5570050\tMACS2_peak_36_F\t4.00\n+chr1\t5574872\t5574873\tMACS2_peak_37_F\t0.00\n+chr1\t5805892\t5805893\tMACS2_peak_38_F\t2.00\n+chr1\t5976034\t5976035\tMACS2_peak_39_F\t0.00\n+chr1\t6094646\t6094647\tMACS2_peak_40_F\t0.00\n+chr1\t6113105\t6113106\tMACS2_peak_41_F\t2.00\n+chr1\t6265402\t6265403\tMACS2_peak_42_F\t4.00\n+chr1\t6305237\t6305238\tMACS2_peak_43_F\t2.83\n+chr1\t6307000\t6307001\tMACS2_peak_44_F\t2.83\n+chr1\t6403590\t6403591\tMACS2_peak_45_F\t3.46\n+chr1\t6464859\t6464860\tMACS2_peak_46_F\t3.46\n+chr1\t6483666\t6483667\tMACS2_peak_47_F\t2.83\n+chr1\t6498287\t6498288\tMACS2_peak_48_F\t4.90\n+chr1\t6535636\t6535637\tMACS2_peak_49_F\t3.46\n+chr1\t6614629\t6614630\tMACS2_peak_50_F\t2.83\n+chr1\t6706734\t6706735\tMACS2_peak_51_F\t4.90\n+chr1\t6762004\t6762005\tMACS2_peak_52_R\t5.66\n+chr1\t6780313\t6780314\tMACS2_peak_53_F\t4.00\n+chr1\t6787701\t6787702\tMACS2_peak_54_R\t5.93\n+chr1\t6950124\t6950125\tMACS2_peak_55_F\t3.46\n+chr1\t7102878\t7102879\tMACS2_peak_56_F\t3.46\n+chr1\t7278465\t7278466\tMACS2_peak_57_F\t0.00\n+chr1\t7868491\t7868492\tMACS2_peak_58_F\t3.46\n+chr1\t7962955\t7962956\tMACS2_peak_59_F\t2.83\n+chr1\t8042484\t8042485\tMACS2_peak_60_F\t2.83\n+chr1\t8075252\t8075253\tMACS2_peak_61_F\t2.83\n+chr1\t8076699\t8076700\tMACS2_peak_62_F\t2.83\n+chr1\t8091311\t8091312\tMACS2_peak_63_F\t3.46\n+chr1\t8374548\t8374549\tMACS2_peak_64_R\t5.66\n+chr1\t8409017\t8409018\tMACS2_peak_65_F\t0.00\n+chr1\t8731538\t8731539\tMACS2_peak_66_F\t3.46\n+chr1\t8786749\t8786750\tMACS2_peak_67_F\t2.83\n+chr1\t8908916\t8908917\tMACS2_peak_68_F\t0.00\n+chr1\t8978341\t8978342\tMACS2_peak_69_F\t4.90\n+chr1\t9048203\t9048204\tMACS2_peak_70_F\t4.00\n+chr1\t9065293\t9065294\tMACS2_peak_71_F\t2.83\n+chr1\t9070176\t9070177\tMACS2_peak_72_F\t4.00\n+chr1\t9161596\t9161597\tMACS2_peak_73_F\t0.00\n+chr1\t9202486\t9202487\tMACS2_peak_74_R\t7.75\n+chr1\t9349202\t9349203\tMACS2_peak_75_F\t4.00\n+chr1\t9515932\t9515933\tMACS2_peak_76_F\t4.00\n+chr1\t9551230\t9551231\tMACS2_peak_77_R\t6.93\n+chr1\t9555264\t9555265\tMACS2_peak_78_F\t0.00\n+chr1\t9633882\t9633883\tMACS2_peak_79_F\t0.00\n+chr1\t9687165\t9687166\tMACS2_peak_80_F\t4.93\n+chr1\t9785291\t9785292\tMACS2_peak_81_F\t3.00\n+chr1\t9844724\t9844725\tMACS2_peak_82_F\t4.90\n+chr1\t9927686\t9927687\tMACS2_peak_83_R\t6.00\n+chr1\t9935064\t9935065\tMACS2_peak_84_R\t7.75\n+chr1\t10002555\t10002556\tMACS2_peak_85_F\t4.90\n+chr1\t10094682\t10094683\tMACS2_peak_86_F\t2.83\n+chr1\t10213135\t10213136\tMACS2_peak_87_F\t2.83\n+chr1\t10270427\t10270428\tMACS2_peak_88_F\t2.00\n+chr1\t10398178\t10398179\tMACS2_peak_89_F\t2.83\n+chr1\t10437670\t10437671\tMACS2_peak_90_F\t3.46\n+chr1\t10488229\t10488230\tMACS2_peak_91_F\t4.00\n+chr1\t10490426\t10490427\tMACS2_peak_92_F\t2.83\n+chr1\t10555245\t10555246\tMA'..b'0\t161456991\tMACS2_peak_918_F\t4.00\n+chr1\t161612655\t161612656\tMACS2_peak_919_F\t2.83\n+chr1\t161617349\t161617350\tMACS2_peak_920_F\t0.00\n+chr1\t161708692\t161708693\tMACS2_peak_921_F\t0.00\n+chr1\t161875128\t161875129\tMACS2_peak_922_F\t4.00\n+chr1\t162035218\t162035219\tMACS2_peak_923_F\t0.00\n+chr1\t162362068\t162362069\tMACS2_peak_924_F\t2.83\n+chr1\t162597675\t162597676\tMACS2_peak_925_F\t2.83\n+chr1\t162817576\t162817577\tMACS2_peak_926_F\t0.00\n+chr1\t162824184\t162824185\tMACS2_peak_927_F\t4.90\n+chr1\t162847869\t162847870\tMACS2_peak_928_F\t2.00\n+chr1\t163041747\t163041748\tMACS2_peak_929_F\t0.00\n+chr1\t163285697\t163285698\tMACS2_peak_930_F\t3.46\n+chr1\t163329077\t163329078\tMACS2_peak_931_F\t4.00\n+chr1\t163531411\t163531412\tMACS2_peak_932_F\t2.00\n+chr1\t164587179\t164587180\tMACS2_peak_933_F\t2.83\n+chr1\t164756700\t164756701\tMACS2_peak_934_F\t2.00\n+chr1\t165098934\t165098935\tMACS2_peak_935_F\t4.00\n+chr1\t165112852\t165112853\tMACS2_peak_936_F\t2.83\n+chr1\t165114261\t165114262\tMACS2_peak_937_F\t4.00\n+chr1\t165227504\t165227505\tMACS2_peak_938_F\t0.00\n+chr1\t165338349\t165338350\tMACS2_peak_939_F\t0.00\n+chr1\t165362267\t165362268\tMACS2_peak_940_R\t5.29\n+chr1\t165562310\t165562311\tMACS2_peak_941_R\t6.93\n+chr1\t165570860\t165570861\tMACS2_peak_942_F\t0.00\n+chr1\t165687301\t165687302\tMACS2_peak_943_F\t2.83\n+chr1\t165883663\t165883664\tMACS2_peak_944_F\t3.47\n+chr1\t165894112\t165894113\tMACS2_peak_945_R\t5.66\n+chr1\t165897514\t165897515\tMACS2_peak_946_F\t3.46\n+chr1\t166102578\t166102579\tMACS2_peak_947_F\t2.83\n+chr1\t166134141\t166134142\tMACS2_peak_948_F\t0.00\n+chr1\t166448381\t166448382\tMACS2_peak_949_F\t3.46\n+chr1\t167028502\t167028503\tMACS2_peak_950_F\t4.00\n+chr1\t167036032\t167036033\tMACS2_peak_951_F\t4.00\n+chr1\t167237272\t167237273\tMACS2_peak_952_F\t2.83\n+chr1\t167370701\t167370702\tMACS2_peak_953_F\t0.00\n+chr1\t167411459\t167411460\tMACS2_peak_954_R\t7.48\n+chr1\t167509745\t167509746\tMACS2_peak_955_F\t4.00\n+chr1\t167606712\t167606713\tMACS2_peak_956_F\t0.00\n+chr1\t167657299\t167657300\tMACS2_peak_957_F\t4.90\n+chr1\t167684581\t167684582\tMACS2_peak_958_F\t0.00\n+chr1\t168051650\t168051651\tMACS2_peak_959_F\t1.83\n+chr1\t168054094\t168054095\tMACS2_peak_960_F\t2.83\n+chr1\t168114981\t168114982\tMACS2_peak_961_F\t0.00\n+chr1\t168312030\t168312031\tMACS2_peak_962_F\t2.00\n+chr1\t168409222\t168409223\tMACS2_peak_963_F\t4.00\n+chr1\t169317755\t169317756\tMACS2_peak_964_R\t5.66\n+chr1\t169435717\t169435718\tMACS2_peak_965_F\t2.83\n+chr1\t169515822\t169515823\tMACS2_peak_966_F\t2.83\n+chr1\t169570156\t169570157\tMACS2_peak_967_F\t0.00\n+chr1\t169681329\t169681330\tMACS2_peak_968_F\t3.90\n+chr1\t169778870\t169778871\tMACS2_peak_969_F\t4.00\n+chr1\t169898139\t169898140\tMACS2_peak_970_F\t4.00\n+chr1\t169979682\t169979683\tMACS2_peak_971_F\t4.47\n+chr1\t170658657\t170658658\tMACS2_peak_972_F\t0.00\n+chr1\t170936375\t170936376\tMACS2_peak_973_F\t3.46\n+chr1\t171157922\t171157923\tMACS2_peak_974_F\t0.00\n+chr1\t171454456\t171454457\tMACS2_peak_975_F\t4.90\n+chr1\t171624794\t171624795\tMACS2_peak_976_F\t2.83\n+chr1\t171770610\t171770611\tMACS2_peak_977_F\t0.00\n+chr1\t171952803\t171952804\tMACS2_peak_978_F\t2.83\n+chr1\t171954349\t171954350\tMACS2_peak_979_F\t0.00\n+chr1\t171972029\t171972030\tMACS2_peak_980_R\t6.00\n+chr1\t172104344\t172104345\tMACS2_peak_981_F\t2.00\n+chr1\t172398492\t172398493\tMACS2_peak_982_F\t0.00\n+chr1\t172688955\t172688956\tMACS2_peak_983_F\t4.90\n+chr1\t172711856\t172711857\tMACS2_peak_984_F\t0.00\n+chr1\t172714264\t172714265\tMACS2_peak_985_F\t4.00\n+chr1\t173171741\t173171742\tMACS2_peak_986_F\t2.83\n+chr1\t173389620\t173389621\tMACS2_peak_987_R\t8.00\n+chr1\t173400465\t173400466\tMACS2_peak_988_F\t4.90\n+chr1\t173684281\t173684282\tMACS2_peak_989_F\t0.00\n+chr1\t173794123\t173794124\tMACS2_peak_990_F\t0.00\n+chr1\t173883547\t173883548\tMACS2_peak_991_F\t4.00\n+chr1\t174084082\t174084083\tMACS2_peak_992_F\t0.00\n+chr1\t174186991\t174186992\tMACS2_peak_993_R\t8.00\n+chr1\t174227339\t174227340\tMACS2_peak_994_F\t4.00\n+chr1\t174695830\t174695831\tMACS2_peak_995_F\t4.00\n+chr1\t174713262\t174713263\tMACS2_peak_996_F\t0.00\n+chr1\t174739304\t174739305\tMACS2_peak_997_F\t2.00\n+chr1\t174967837\t174967838\tMACS2_peak_998_R\t7.80\n+chr1\t174998966\t174998967\tMACS2_peak_999_F\t0.00\n+chr1\t175094596\t175094597\tMACS2_peak_1000_F\t2.00\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r fe62ba547975 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Feb 11 10:18:02 2015 -0500 |
| b |
| @@ -0,0 +1,21 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="numpy" version="1.7.1"> + <repository changeset_revision="ef12a3a11d5b" name="package_numpy_1_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="scipy" version="0.12.0"> + <repository changeset_revision="336aead68607" name="package_scipy_0_12" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="R_3_0_1" version="3.0.1"> + <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="gnu_awk" version="4.1.0"> + <repository changeset_revision="52a8268bb49f" name="package_gnu_awk_4_1_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="macs2" version="2.1.0"> + <repository changeset_revision="4d7ef54c3fa4" name="package_macs2_2_1_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <set_environment version="1.0"> + <environment_variable action="set_to" name="MACS2_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable> + </set_environment> +</tool_dependency> |