| Previous changeset 4:56e104999978 (2017-02-06) Next changeset 6:2119d851a53b (2017-04-11) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b |
|
modified:
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 test-data/callpeak_control_part.bdg test-data/callpeak_part.tabular test-data/callpeak_treatment_part.bdg |
|
added:
test-data/bdgbroadcall_input.bdg test-data/bdgbroadcall_output.bdg test-data/bdgcmp_input_control.bdg test-data/bdgcmp_input_treatment.bdg test-data/bdgcmp_output.bdg test-data/bdgdiff_c1.bdg test-data/bdgdiff_c2.bdg test-data/bdgdiff_t1.bdg test-data/bdgdiff_t2.bdg test-data/bdgpeakcall_input.bdg test-data/bdgpeakcall_output_cutoff.bdg test-data/bdgrandsample_output.bed test-data/refinepeak_bam_input.bam test-data/refinepeak_bed_input.bed test-data/refinepeak_output.bed |
|
removed:
test-data/bdgbroadcall_on_callpeak_treatment.tabular test-data/bdgcmp_on_Control_and_ChIP_slogLR.bdg test-data/callpeak_summits_part.bed test-data/output_extra_files.html tool_dependencies.xml |
| b |
| diff -r 56e104999978 -r beb902da6e5f macs2_bdgbroadcall.xml --- a/macs2_bdgbroadcall.xml Mon Feb 06 02:30:37 2017 -0500 +++ b/macs2_bdgbroadcall.xml Sat Apr 08 08:28:57 2017 -0400 |
| [ |
| @@ -9,49 +9,53 @@ <expand macro="stdio" /> <expand macro="version_command" /> <command> + <![CDATA[ macs2 bdgbroadcall - --ifile "${ infile }" - --cutoff-peak "${ cutoffpeak }" - --cutoff-link "${ cutofflink }" - --min-length "${ minlen }" - --lvl1-max-gap "${ LVL1MAXGAP }" - --lvl2-max-gap "${ LVL2MAXGAP }" + --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" > "${ outfile }" + && + awk '!/^track name/' "macs2_bdgbroadcall.bdg" > '${ outfile }' + ]]> </command> <inputs> - <param name="infile" type="data" format="bedgraph" label="MACS score in bedGraph" /> + <param name="infile" type="data" format="bedgraph" label="bedGraph generated MACS" /> <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)"/> + 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 (--cutoff)"/> <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)"/> + 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." /> + help="It is recommended to set it as d value. Default=200 (--min-length)" /> <param name="LVL1MAXGAP" type="integer" label="Maximum gap between significant peaks" value="30" - help="It is recommended to set it to tag size" /> + help="It is recommended to set it to tag size. Default=30 (--lvl1-max-gap)" /> <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" /> + help="It is recommended to set it to 4 times of d value. Default=800 (--lvl2-max-gap)" /> </inputs> <outputs> - <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" /> + <data name="outfile" format="interval" label="${tool.name} on ${on_string}" /> </outputs> <tests> <test> - <param name="infile" value="callpeak_treatment_part.bdg" ftype="bedgraph" /> + <param name="infile" value="bdgbroadcall_input.bdg" ftype="bedgraph" /> <param name="cutoffpeak" value="2.0"/> <param name="cutofflink" value="1.0"/> <param name="minlen" value="200"/> <param name="LVL1MAXGAP" value="30"/> <param name="LVL2MAXGAP" value="800"/> - <output name="outfile" file="bdgbroadcall_on_callpeak_treatment.tabular"/> + <output name="outfile" file="bdgbroadcall_output.bdg"/> </test> </tests> <help> **What it does** -Call broad peaks from bedGraph output. -bdgbroadcall from macs2 +This is **bdgbroadcall** utility from the MACS2_ Package. It is designed to call broad peaks (e.g., histone) from bedGraph datasets generated with MACS2. + +.. _MACS2: https://github.com/taoliu/MACS + @citation@ </help> |
| b |
| diff -r 56e104999978 -r beb902da6e5f macs2_bdgcmp.xml --- a/macs2_bdgcmp.xml Mon Feb 06 02:30:37 2017 -0500 +++ b/macs2_bdgcmp.xml Sat Apr 08 08:28:57 2017 -0400 |
| [ |
| @@ -7,23 +7,24 @@ <expand macro="stdio" /> <expand macro="version_command" /> <command> + <![CDATA[ macs2 bdgcmp - -t "${ infile_treatment }" - -c "${ infile_control }" + -t '${ infile_treatment }' + -c '${ infile_control }' - -m "${ bdgcmp_options.bdgcmp_options_selector }" + -m '${ bdgcmp_options.bdgcmp_options_selector }' #if str($bdgcmp_options.bdgcmp_options_selector) in ['FE', 'logFE', 'logLR']: - -p "${ bdgcmp_options.pseudocount }" + -p '${ bdgcmp_options.pseudocount }' #end if - -o "${ outfile }" - + -o '${ outfile }' + ]]> </command> <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"> + <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" help="Available choices are: ppois, qpois, subtract, logFE, logLR, and slogLR. They represent Poisson Pvalue (-log10(pvalue) form) using control as lambda and treatment as observation, q-value through a BH process for poisson pvalues, subtraction from treatment, linear scale fold enrichment, log10 fold enrichment(need to set pseudocount), log10 likelihood between ChIP-enriched model and open chromatin model(need to set pseudocount), symmetric log10 likelihood between two ChIP-enrichment models, or maximum value between the two tracks. Default=ppois (--method)."> <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> @@ -33,13 +34,13 @@ <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."/> + <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."/> + <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."/> + <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"/> @@ -52,30 +53,22 @@ </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"/> + <param name="infile_control" value="bdgcmp_input_control.bdg" ftype="bedgraph"/> + <param name="infile_treatment" value="bdgcmp_input_treatment.bdg" ftype="bedgraph"/> + <param name="bdgcmp_options_selector" value="ppois"/> + <output name="outfile" file="bdgcmp_output.bdg"/> </test> </tests> <help> + <![CDATA[ **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 +This is **bdgcmp** utility from the MACS2_ Package. It is designed to deduct noise by comparing two signal tracks in bedGraph. ------- - -**Usage** - -**Compare .bdg files**: Deduct noise by comparing two signal tracks in bedGraph. - +.. _MACS2: https://github.com/taoliu/MACS @citation@ +]]> </help> <expand macro="citations" /> </tool> |
| b |
| diff -r 56e104999978 -r beb902da6e5f macs2_bdgdiff.xml --- a/macs2_bdgdiff.xml Mon Feb 06 02:30:37 2017 -0500 +++ b/macs2_bdgdiff.xml Sat Apr 08 08:28:57 2017 -0400 |
| [ |
| @@ -3,81 +3,83 @@ <macros> <import>macs2_macros.xml</import> </macros> - <expand macro="requirements" /> + <expand macro="requirements"> + <requirement type="package" version="4.1.3">gawk</requirement> + </expand> <expand macro="stdio" /> <expand macro="version_command" /> <command> + <![CDATA[ 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 "${ maxgap }" - --o-prefix MACS2 + --t1 '${ t1 }' + --t2 '${ t2 }' + --c1 '${ c1 }' + --c2 '${ c2 }' + --cutoff '${ cutoff }' + --min-len '${ minlen }' + --depth1 '${ depth.depth1 }' + --depth2 '${ depth.depth2 }' + --max-gap '${ maxgap }' + -o c1.bed c2.bed both.bed && + awk '!/^track name/' "c1.bed" > '${ output_cond1 }' && + awk '!/^track name/' "c2.bed" > '${ output_cond1 }' && + awk '!/^track name/' "both.bed" > '${ output_both }' + + ]]> </command> <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="t1" type="data" format="bedgraph" label="BedGraph for Treatment experiment 1" /> + <param name="t2" type="data" format="bedgraph" label="BedGraph for Treatment experiment 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="c1" type="data" format="bedgraph" label="BedGraph for Control experiment 1" /> + <param name="c2" type="data" format="bedgraph" label="Bedgraph for Control experiment 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="cutoff" type="float" label="Cutoff of log10 likelihood ratio cutoff" value="1.0" help="Default=1.0 correspoinding to likelihood ratio of 1,000 (--cutoff)"/> + <param name="minlen" type="integer" label="Minimum length of differential region" value="200" help=" Try bigger value to remove small regions. Default=200 (--min-len)"/> - <param name="outputs" type="select" display="checkboxes" multiple="True" optional="false" 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> - </param> + <section name="depth" title="Sequencing depth" expanded="True" help="Sequencing depths will be used to calculate scaling factor for each sample, to down-scale larger sample to the level of smaller one. For example, while comparing condition 1 (10 Million reads) and condition 2 (20 million reads), use --depth1 10 --depth2 20, then pileup value in bedGraph for condition 2 will be divided by 2."> + <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)" /> + </section> + <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 (--max-gap)." /> + + </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 ${on_string} (both)"> - <filter>'--ofile-both-conditions' in outputs</filter> - </data> + <data name="output_cond1" format="bed" label="${tool.name} on ${on_string} (Condition 1)"/> + <data name="output_cond2" format="bed" label="${tool.name} on ${on_string} (Condition 2)"/> + <data name="output_both" format="bed" label="${tool.name} on ${on_string} (Common)"/> </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="t1" value="bdgdiff_t1.bdg" ftype="bedgraph"/> + <param name="t2" value="bdgdiff_t2.bdg" ftype="bedgraph"/> + <param name="c1" value="bdgdiff_c1.bdg" ftype="bedgraph"/> + <param name="c2" value="bdgdiff_c2.bdg" ftype="bedgraph"/> <param name="cutoff" value="1.0"/> <param name="minlen" value="200"/> - <param name="depth1" value="1"/> + <param name="depth1" value="10"/> <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=""/> + <output name="output_cond1"> + <assert_contents> + <has_text text="c2.bed1" /> + </assert_contents> + </output> </test> - --> </tests> <help> + <![CDATA[ **What it does** -bdgdiff from macs2 +This is **bdgdiff** utility from the MACS2_ Package. It performs differential peak detection based on paired four bedgraph files. +.. _MACS2: https://github.com/taoliu/MACS @citation@ + ]]> </help> <expand macro="citations" /> </tool> |
| b |
| diff -r 56e104999978 -r beb902da6e5f macs2_bdgpeakcall.xml --- a/macs2_bdgpeakcall.xml Mon Feb 06 02:30:37 2017 -0500 +++ b/macs2_bdgpeakcall.xml Sat Apr 08 08:28:57 2017 -0400 |
| [ |
| @@ -3,58 +3,67 @@ <macros> <import>macs2_macros.xml</import> </macros> - <expand macro="requirements"> - <requirement type="package" version="4.1.0">gnu_awk</requirement> - </expand> + <expand macro="requirements"/> <expand macro="stdio" /> <expand macro="version_command" /> <command> + <![CDATA[ + macs2 bdgpeakcall - --ifile "${ infile }" - --cutoff "${ cutoff }" - --min-length "${ minlen }" - --max-gap "${ maxgap }" - ${ callsummits } + --ifile '${ infile }' + --cutoff '${ cutoff }' + --min-length '${ minlen }' + --max-gap '${ maxgap }' + ${ cutoff_analysis } ${ notrackline } - --ofile "macs2_bdgpeakcall.bdg" - && - awk '!/^track name/' "macs2_bdgpeakcall.bdg" > "${ outfile }" + --ofile '${ outfile }' + + ]]> </command> <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)"/> + 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. Default=200 (--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="cutoff_analysis" type="boolean" truevalue="--cutoff-analysis" falsevalue="" checked="False" label="Perform cutoff analysis" help="While set, bdgpeakcall will analyze number or total length of peaks that can be called by different cutoff then output a summary table to help user decide a better cutoff. Note, --min-len and --max-gap may affect the results. Default=False (--cutoff-analysis)"/> + <param name="notrackline" type="boolean" truevalue="" falsevalue="--no-trackline" checked="False" label="Include trackline into bedGraph output" help="required by UCSC Genome Browser (--no-trackline)"/> </inputs> <outputs> - <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" /> + <data name="outfile" format="bedgraph" label="${tool.name} on ${on_string}" /> </outputs> <tests> <test> - <param name="infile" value="callpeak_treatment_part.bdg" ftype="bedgraph" /> + <param name="infile" value="bdgpeakcall_input.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"/> + <output name="outfile"> + <assert_contents> + <has_text text="chrV" /> + </assert_contents> + </output> + </test> + <test> + <param name="infile" value="bdgpeakcall_input.bdg" ftype="bedgraph" /> + <param name="cutoff" value="5.0"/> + <param name="minlen" value="200"/> + <param name="maxgap" value="30"/> + <param name="cutoff_analysis" value="true" /> + <output name="outfile" file="bdgpeakcall_output_cutoff.bdg"/> </test> </tests> <help> + <![CDATA[ **What it does** -Call peaks from bedGraph output. -bdgpeakcall from macs2 +This is **bdgpeakcall** utility from the MACS2_ Package. It calls peaks from bedGraph output. + +.. _MACS2: https://github.com/taoliu/MACS @citation@ + ]]> </help> <expand macro="citations" /> </tool> |
| b |
| diff -r 56e104999978 -r beb902da6e5f macs2_callpeak.xml --- a/macs2_callpeak.xml Mon Feb 06 02:30:37 2017 -0500 +++ b/macs2_callpeak.xml Sat Apr 08 08:28:57 2017 -0400 |
| [ |
| b'@@ -4,16 +4,15 @@\n <import>macs2_macros.xml</import>\n </macros>\n <expand macro="requirements">\n- <requirement type="package" version="3.1.2">R</requirement>\n- <requirement type="set_environment">MACS2_SCRIPT_PATH</requirement>\n </expand>\n <expand macro="stdio" />\n <expand macro="version_command" />\n <command>\n+ <![CDATA[\n #set $temp_stderr = \'macs2_stderr\'\n (macs2 callpeak\n \n- --name "MACS2"\n+ --name \'MACS2\'\n -t ${ \' \'.join( map( lambda x:\'"%s"\' % ( x ), $input_treatment_file ) ) }\n \n #if str( $input_control_file ) != \'None\':\n@@ -21,7 +20,7 @@\n #end if\n \n #for $ifile in $input_treatment_file:\n- #if $ifile.ext.upper() == \'BAM\' and $bampe:\n+ #if $ifile.ext.upper() == "BAM" and $bampe:\n --format BAMPE\n #else\n --format=\'$ifile.ext.upper()\'\n@@ -30,16 +29,17 @@\n \n @effective_genome_size@\n \n- --bw=\'$band_width\'\n+ --bw \'${$band_width}\'\n+ @mfold_command@\n \n ## advanced options\n- #if $advanced_options.advanced_options_selector == \'on\':\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+ #if $advanced_options.broad_options.broad_options_selector == "broad":\n --broad\n --broad-cutoff=\'${ advanced_options.broad_options.broad_cutoff }\'\n #else:\n@@ -47,73 +47,78 @@\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+ --keep-dup \'${ advanced_options.keep_dup_options.user_keepdup }\'\n #else\n- --keep-dup "${ advanced_options.keep_dup_options.keep_dup_options_selector }"\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+ #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+ #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 #end if\n \n ## model options\n- #if $nomodel_type.nomodel_type_selector == \'nomodel\':\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> $temp_stderr)\n- #if \'peaks_tabular\' in str($outputs).split(\',\'):\n- &&\n- cp MACS2_peaks.xls "${ output_tabular }"\n+ #if "peaks_tabular" in str($outputs).split(\',\'):\n+ &&\n+ cp MACS2_peaks.xls \'${ output_tabular }\'\n #end if\n \n ## run R to create pdf from model script\n- #if $nomodel_type.nomodel_type_selector == \'create_model\' and \'pdf\' in str($outputs).split(\',\'):\n- &a'..b'ame="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_tabular" compare="contains" file="callpeak_part.tabular"/>\n- <output name="output_summits" compare="contains" file="callpeak_summits_part.bed"/>\n+ <param name="lower" value="5" />\n+ <param name="upper" value="50" />\n+ <output name="output_control_lambda" compare="contains" file="callpeak_control_part.bdg" lines_diff="1"/>\n+ <output name="output_treat_pileup" compare="contains" file="callpeak_treatment_part.bdg" lines_diff="1"/>\n+ <output name="output_tabular" compare="contains" file="callpeak_part.tabular" lines_diff="1"/>\n </test>\n <test>\n <param name="input_control_file" value="Control_200K.bed" ftype="bed"/>\n@@ -267,32 +269,37 @@\n <param name="outputs" value="pdf"/>\n <param name="effective_genome_size_options_selector" value="user_defined" />\n <param name="gsize" value="3300000000" />\n+ <param name="lower" value="5" />\n+ <param name="upper" value="50" />\n <output name="output_plot" file="magic.pdf" ftype="pdf" compare="contains" />\n </test>\n </tests>\n <help>\n+ <![CDATA[\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+**callpeak** is the main function of the MACS2_ package. MACS identifies enriched binding sites in ChIP-seq experiments.\n+It captures the influence of genome complexity to evaluate the significance of enriched ChIP regions,\n+and improves the spatial resolution of binding sites through combining the information of both sequencing\n+tag position and orientation. MACS can be used for ChIP-Seq data alone, or with control sample with the\n+increase of specificity (recommended).\n \n-View the original MACS2 documentation: https://github.com/taoliu/MACS/blob/master/README\n-\n-------\n+.. _MACS2: https://github.com/taoliu/MACS\n \n-**Usage**\n-\n-**Peak Calling**: Main MACS2 Function to Call peaks from alignment results.\n+MACS2 performs the following analysis steps:\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+ * Artificially extend reads to expected fragment length, and generate coverage map along genome.\n+ * Assume background reads are Poisson distributed. Mean of the Poisson is locally variable and is estimated from control experiment (if available) in 5Kbp or 10Kbp around examined location.\n+ * For a given location, do we see more reads than we would have expected from the Poisson (p < 0.00005)? If Yes, MACS2 calls a peak. \n \n-**Compare .bdg files**: Deduct noise by comparing two signal tracks in bedGraph.\n+\n+.. class:: warningmark\n+\n+If MACS2 fails, it is usually because it cannot build the model for peaks. You may want to extend **mfold** range by increasing the upper bound or play with **Build model** options.\n \n \n @citation@\n+]]>\n </help>\n <expand macro="citations" />\n </tool>\n' |
| b |
| diff -r 56e104999978 -r beb902da6e5f macs2_filterdup.xml --- a/macs2_filterdup.xml Mon Feb 06 02:30:37 2017 -0500 +++ b/macs2_filterdup.xml Sat Apr 08 08:28:57 2017 -0400 |
| [ |
| @@ -6,29 +6,26 @@ <expand macro="requirements" /> <expand macro="stdio" /> <expand macro="version_command" /> - <command> + <command><![CDATA[ macs2 filterdup - -i "${ infile }" - -o temp_outfile - + -i '${ infile }' + -o '${ outfile }' --format '${ infile.extension.upper() }' @effective_genome_size@ @tag_size@ - --pvalue "${ pvalue }" + --pvalue '${ pvalue }' #if str( $keep_dup_options.keep_dup_options_selector ) == "user": - --keep-dup "${ keep_dup_options.user_keepdup }" + --keep-dup '${ keep_dup_options.user_keepdup }' #else - --keep-dup "${ keep_dup_options.keep_dup_options_selector }" + --keep-dup '${ keep_dup_options.keep_dup_options_selector }' #end if - ; - mv temp_outfile "${ outfile }" + ]]> </command> <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)" /> - + <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> @@ -46,12 +43,15 @@ </test> </tests> <help> +<![CDATA[ **What it does** -Remove duplicate reads at the same position, then convert acceptable format to BED format. -filterdup tool from macs2 +This is **filterdup** utility from the MACS2_ Package. It removes duplicate reads and converts results to BED format. + +.. _MACS2: https://github.com/taoliu/MACS @citation@ +]]> </help> <expand macro="citations" /> </tool> |
| b |
| diff -r 56e104999978 -r beb902da6e5f macs2_macros.xml --- a/macs2_macros.xml Mon Feb 06 02:30:37 2017 -0500 +++ b/macs2_macros.xml Sat Apr 08 08:28:57 2017 -0400 |
| b |
| @@ -1,31 +1,30 @@ <macros> + <token name="@VERSION_STRING@">2.1.1.20160309</token> + <xml name="requirements"> <requirements> - <requirement type="package" version="2.1.0.20151222">macs2</requirement> - <requirement type="package" version="1.7.1">numpy</requirement> - <requirement type="package" version="0.12.0">scipy</requirement> + <requirement type="package" version="@VERSION_STRING@">macs2</requirement> <yield /> </requirements> </xml> - <token name="@VERSION_STRING@">2.1.0.20151222</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> + help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of Ns 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. (--gsize)"> + <option value="2451960000">H. sapiens (2,451,960,000)</option> + <option value="2150570000">M. musculus (2,150,570,000)</option> + <option value="121400000">D. melanogaster (121,400,000)</option> + <option value="93260000">C. elegans (93,260,000)</option> + <option value="12400000">S. cerevisiae (12,400,000)</option> <option value="user_defined">User defined</option> </param> <when value="2451960000" /> <when value="2150570000" /> <when value="121400000" /> <when value="93260000" /> + <when value="12400000" /> <when value="user_defined"> <param name="gsize" type="integer" label="Effective genome size" value=""/> </when> @@ -51,11 +50,22 @@ </conditional> </xml> + <xml name="mfold_options"> + <section name="mfold" title="Mfold settings" expanded="True" help="Select the regions within MFOLD range of highconfidence enrichment ratio against background to build model. Fold-enrichment in regions must be lower than upper limit, and higher than the lower limit. Default is 5 for lower and 50 for upper (--mfold)" > + <param name="lower" type="integer" value="5" label="Set lower mfold bound" /> + <param name="upper" type="integer" value="50" label="Set upper mfold bound" /> + </section> + </xml> + + <token name="@mfold_command@"> + --mfold '${mfold.lower}' '${mfold.upper}' + </token> + <token name="@effective_genome_size@"> - #if $effective_genome_size_options.effective_genome_size_options_selector == 'user_defined': - --gsize "${ effective_genome_size_options.gsize }" + #if $effective_genome_size_options.effective_genome_size_options_selector == "user_defined": + --gsize '${ effective_genome_size_options.gsize }' #else: - --gsize "${ effective_genome_size_options.effective_genome_size_options_selector }" + --gsize '${ effective_genome_size_options.effective_genome_size_options_selector }' #end if </token> @@ -64,16 +74,18 @@ </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)" /> + <param name="tsize" type="integer" label="Tag size" value="" optional="true" + 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)" /> + <param name="band_width" type="integer" value="300" + label="Band width for picking regions to compute fragment size" + help=" You can set this parameter as the medium fragment size expected from sonication or size selection. (--bw)" /> </xml> <token name="@tag_size@"> - #if $tsize == -1.0: - --tsize "${ tsize }" + #if $tsize: + --tsize '${ tsize }' #end if </token> @@ -89,15 +101,13 @@ <token name="@citation@"> ------ -**Citation** +Integration of MACS2 with Galaxy performed by Ziru Zhou and Bjoern Gruening. -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> + <citation type="doi">10.1038/nprot.2012.101</citation> </citations> </xml> </macros> |
| b |
| diff -r 56e104999978 -r beb902da6e5f macs2_predictd.xml --- a/macs2_predictd.xml Mon Feb 06 02:30:37 2017 -0500 +++ b/macs2_predictd.xml Sat Apr 08 08:28:57 2017 -0400 |
| [ |
| @@ -3,40 +3,37 @@ <macros> <import>macs2_macros.xml</import> </macros> - <expand macro="requirements"> - <requirement type="package" version="3.1.2">R</requirement> - <requirement type="package" version="4.1.0">gnu_awk</requirement> - </expand> + <expand macro="requirements"/> <expand macro="stdio" /> <expand macro="version_command" /> <command> + <![CDATA[ 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' + -i ${ ' '.join(["'%s'" % $x for $x in $infiles ]) } + @tag_size@ + @effective_genome_size@ + --bw '${ band_width }' + @mfold_command@ - > "${ outfile }" + ## remove the timepoint and strip the output + 2>&1 | awk -F: '{print $4}' | awk '{$1=$1}1' - && + > '${ outfile }' + + && Rscript predictd + ]]> </command> <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)" /> + <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)"/> - + <expand macro="mfold_options" /> </inputs> <outputs> @@ -48,24 +45,25 @@ <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="tsize" value=""/> <param name="band_width" value="300"/> - <param name="mfoldlo" value="5"/> - <param name="mfoldhi" value="50"/> + <param name="lower" value="5"/> + <param name="upper" 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> +<![CDATA[ **What it does** -predictd from macs2 - +This is **predictd** utility from the MACS2_ Package. It predicts the *d* value or fragment size from alignment results. -Note that pair-end data is not supposed to work with this command. - +.. _MACS2: https://github.com/taoliu/MACS @citation@ +]]> + </help> <expand macro="citations" /> </tool> |
| b |
| diff -r 56e104999978 -r beb902da6e5f macs2_randsample.xml --- a/macs2_randsample.xml Mon Feb 06 02:30:37 2017 -0500 +++ b/macs2_randsample.xml Sat Apr 08 08:28:57 2017 -0400 |
| [ |
| @@ -7,48 +7,62 @@ <expand macro="stdio" /> <expand macro="version_command" /> <command> + <![CDATA[ macs2 randsample - -t "${ infile }" - -o "${ outfile }" + -t '${ infile }' + -o '${ outfile }' + --seed '${ seed }' - --format '${ infile.extension.upper() }' + --format '${ infile.extension.upper() }' - @tag_size@ + @tag_size@ + #if $method_options.method_options_selector == 'percentage': - --percentage "${ method_options.percentage }" + --percentage '${ method_options.percentage }' #else: - --number "${ method_options.number }" + --number '${ method_options.number }' #end if + ]]> </command> <inputs> <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" /> <expand macro="tag_size" /> - <conditional name="method_options"> <param name="method_options_selector" type="select" label="Select action to be performed"> <option value="percentage" selected="true">Percentage</option> <option value="number">Number</option> </param> <when value="percentage"> - <param name="percentage" type="float" value="80.0" label="Pvalue cutoff for binomial distribution test" help="(--percentage)" /> + <param name="percentage" type="float" value="80.0" label="Percentage of tags you want to keep" help="Percentage of tags you want to keep. Input 80.0 for 80%.(--percentage)"/> </when> <when value="number"> <param name="number" type="integer" value="800000" label="Number of tags you want to keep" help="Note that the number of tags in output is approximate as the number specified here (--number)" /> </when> </conditional> + <param name="seed" type="integer" value="1" label="Random seed number" min="0" help="Set the random seed while down sampling data. Must be a positive integer in order to be effective. (--seed)"/> </inputs> <outputs> <data name="outfile" format="bed" label="${tool.name} on ${on_string}" /> </outputs> <tests> - <!-- No test, due to the randomness --> + <test> + <param name="infile" value="ChIP_200K.bed" ftype="bed" /> + <param name="method_options_selector" value="percentage" /> + <param name="percentage" value="80.0" /> + <param name="seed" value="1" /> + <output name="outfile" file="bdgrandsample_output.bed"/> + </test> </tests> <help> + <![CDATA[ **What it does** -randsample tool from macs2 +This is **randsample** utility from the MACS2_ Package. It randomly samples reads by number or percentage from an input file. + +.. _MACS2: https://github.com/taoliu/MACS @citation@ +]]> </help> <expand macro="citations" /> </tool> |
| b |
| diff -r 56e104999978 -r beb902da6e5f macs2_refinepeak.xml --- a/macs2_refinepeak.xml Mon Feb 06 02:30:37 2017 -0500 +++ b/macs2_refinepeak.xml Sat Apr 08 08:28:57 2017 -0400 |
| [ |
| @@ -7,13 +7,15 @@ <expand macro="stdio" /> <expand macro="version_command" /> <command> + <![CDATA[ macs2 refinepeak - -b "${ bed_infile }" - -i "${ infile }" + -b '${ bed_infile }' + -i '${ infile }' --format '${ infile.extension.upper() }' - --cutoff "${ cutoff }" - --window-size "${ winsize }" - --ofile "${ outfile }" + --cutoff '${ cutoff }' + --window-size '${ winsize }' + --ofile '${ outfile }' + ]]> </command> <inputs> <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" /> @@ -27,19 +29,24 @@ </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="infile" value="refinepeak_bam_input.bam" ftype="bam"/> + <param name="bed_infile" value="refinepeak_bed_input.bed" ftype="bed"/> <param name="cutoff" value="5.0"/> <param name="winsize" value="200"/> - <output name="outfile" file="refinepeak_ChIP_and_summits.bed"/> + <output name="outfile" file="refinepeak_output.bed"/> </test> </tests> <help> + <![CDATA[ **What it does** -(Experimental) Take raw reads alignment, refine peak summits and give scores measuring balance of forward- backward tags. Inspired by SPP. +This is **refinepeak** utility from the MACS2_ Package. It is an experimental utility that takes raw read alignments, refines peak summits and gives scores measuring balance of forward- backward tags. Inspired by the SPP_ pipeline. + +.. _MACS2: https://github.com/taoliu/MACS +.. _SPP: http://compbio.med.harvard.edu/Supplements/ChIP-seq/ @citation@ +]]> </help> <expand macro="citations" /> </tool> |
| b |
| diff -r 56e104999978 -r beb902da6e5f test-data/bdgbroadcall_input.bdg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bdgbroadcall_input.bdg Sat Apr 08 08:28:57 2017 -0400 |
| 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 56e104999978 -r beb902da6e5f test-data/bdgbroadcall_on_callpeak_treatment.tabular --- a/test-data/bdgbroadcall_on_callpeak_treatment.tabular Mon Feb 06 02:30:37 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,398 +0,0 @@\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 56e104999978 -r beb902da6e5f test-data/bdgbroadcall_output.bdg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bdgbroadcall_output.bdg Sat Apr 08 08:28:57 2017 -0400 |
| 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 56e104999978 -r beb902da6e5f test-data/bdgcmp_input_control.bdg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bdgcmp_input_control.bdg Sat Apr 08 08:28:57 2017 -0400 |
| b |
| b'@@ -0,0 +1,1000 @@\n+chrX\t0\t64671\t0.01536\n+chrX\t64671\t74671\t0.02540\n+chrX\t74671\t279628\t0.01536\n+chrX\t279628\t280097\t0.02540\n+chrX\t280097\t280556\t0.05080\n+chrX\t280556\t289628\t0.07620\n+chrX\t289628\t290097\t0.05080\n+chrX\t290097\t290556\t0.02540\n+chrX\t290556\t456156\t0.01536\n+chrX\t456156\t466156\t0.02540\n+chrX\t466156\t581983\t0.01536\n+chrX\t581983\t588044\t0.02540\n+chrX\t588044\t591983\t0.05080\n+chrX\t591983\t598044\t0.02540\n+chrX\t598044\t651299\t0.01536\n+chrX\t651299\t661299\t0.02540\n+chrX\t661299\t915309\t0.01536\n+chrX\t915309\t925309\t0.02540\n+chrX\t925309\t943187\t0.01536\n+chrX\t943187\t953187\t0.02540\n+chrX\t953187\t1001805\t0.01536\n+chrX\t1001805\t1011805\t0.02540\n+chrX\t1011805\t1252632\t0.01536\n+chrX\t1252632\t1252813\t0.02540\n+chrX\t1252813\t1252970\t0.05080\n+chrX\t1252970\t1262632\t0.07620\n+chrX\t1262632\t1262813\t0.05080\n+chrX\t1262813\t1262970\t0.02540\n+chrX\t1262970\t1319337\t0.01536\n+chrX\t1319337\t1327580\t0.02540\n+chrX\t1327580\t1329337\t0.05080\n+chrX\t1329337\t1337580\t0.02540\n+chrX\t1337580\t1348039\t0.01536\n+chrX\t1348039\t1358039\t0.02540\n+chrX\t1358039\t1358567\t0.01536\n+chrX\t1358567\t1358859\t0.02540\n+chrX\t1358859\t1361012\t0.05080\n+chrX\t1361012\t1361063\t0.07620\n+chrX\t1361063\t1367998\t0.10160\n+chrX\t1367998\t1368567\t0.12700\n+chrX\t1368567\t1368859\t0.10160\n+chrX\t1368859\t1371012\t0.07620\n+chrX\t1371012\t1371063\t0.05080\n+chrX\t1371063\t1377998\t0.02540\n+chrX\t1377998\t1379092\t0.01536\n+chrX\t1379092\t1389092\t0.02540\n+chrX\t1389092\t1392762\t0.01536\n+chrX\t1392762\t1402762\t0.02540\n+chrX\t1402762\t1425076\t0.01536\n+chrX\t1425076\t1435076\t0.02540\n+chrX\t1435076\t1437229\t0.01536\n+chrX\t1437229\t1437730\t0.02540\n+chrX\t1437730\t1439990\t0.05080\n+chrX\t1439990\t1441470\t0.07620\n+chrX\t1441470\t1447229\t0.10160\n+chrX\t1447229\t1447730\t0.07620\n+chrX\t1447730\t1448397\t0.05080\n+chrX\t1448397\t1449990\t0.07620\n+chrX\t1449990\t1450341\t0.05080\n+chrX\t1450341\t1450707\t0.07620\n+chrX\t1450707\t1451342\t0.10160\n+chrX\t1451342\t1451470\t0.12700\n+chrX\t1451470\t1458397\t0.10160\n+chrX\t1458397\t1460341\t0.07620\n+chrX\t1460341\t1460707\t0.05080\n+chrX\t1460707\t1461342\t0.02540\n+chrX\t1461342\t1501622\t0.01536\n+chrX\t1501622\t1511622\t0.02540\n+chrX\t1511622\t1528881\t0.01536\n+chrX\t1528881\t1534464\t0.02540\n+chrX\t1534464\t1538881\t0.05080\n+chrX\t1538881\t1540410\t0.02540\n+chrX\t1540410\t1544464\t0.05080\n+chrX\t1544464\t1550410\t0.02540\n+chrX\t1550410\t1567536\t0.01536\n+chrX\t1567536\t1568266\t0.02540\n+chrX\t1568266\t1568326\t0.05080\n+chrX\t1568326\t1568387\t0.07620\n+chrX\t1568387\t1568395\t0.10160\n+chrX\t1568395\t1568569\t0.12700\n+chrX\t1568569\t1577536\t0.15240\n+chrX\t1577536\t1578266\t0.12700\n+chrX\t1578266\t1578326\t0.10160\n+chrX\t1578326\t1578387\t0.07620\n+chrX\t1578387\t1578395\t0.05080\n+chrX\t1578395\t1578569\t0.02540\n+chrX\t1578569\t1582508\t0.01536\n+chrX\t1582508\t1592508\t0.02540\n+chrX\t1592508\t1595719\t0.01536\n+chrX\t1595719\t1596104\t0.02540\n+chrX\t1596104\t1597854\t0.05080\n+chrX\t1597854\t1598802\t0.07620\n+chrX\t1598802\t1605719\t0.10160\n+chrX\t1605719\t1606104\t0.07620\n+chrX\t1606104\t1607360\t0.05080\n+chrX\t1607360\t1607854\t0.07620\n+chrX\t1607854\t1608802\t0.05080\n+chrX\t1608802\t1610240\t0.02540\n+chrX\t1610240\t1617360\t0.05080\n+chrX\t1617360\t1620240\t0.02540\n+chrX\t1620240\t1622384\t0.01536\n+chrX\t1622384\t1625646\t0.02540\n+chrX\t1625646\t1631122\t0.05080\n+chrX\t1631122\t1632384\t0.07620\n+chrX\t1632384\t1635646\t0.05080\n+chrX\t1635646\t1641122\t0.02540\n+chrX\t1641122\t1649688\t0.01536\n+chrX\t1649688\t1651379\t0.02540\n+chrX\t1651379\t1651510\t0.05080\n+chrX\t1651510\t1651547\t0.07620\n+chrX\t1651547\t1651577\t0.10160\n+chrX\t1651577\t1659688\t0.12700\n+chrX\t1659688\t1661379\t0.10160\n+chrX\t1661379\t1661510\t0.07620\n+chrX\t1661510\t1661547\t0.05080\n+chrX\t1661547\t1661577\t0.02540\n+chrX\t1661577\t1668614\t0.01536\n+chrX\t1668614\t1673732\t0.02540\n+chrX\t1673732\t1678614\t0.05080\n+chrX\t1678614\t1678727\t0.02540\n+chrX\t1678727\t1683732\t0.05080\n+chrX\t1683732\t1688727\t0.02540\n+chrX\t1688727\t1695130\t0.01536\n+chrX\t1695130\t1697426\t0.02540\n+chrX\t1697426\t1705130\t0.05080\n+chrX\t1705130\t1705407\t0.02540\n+chrX\t1705407\t1707426\t0.05080\n+chrX\t1707426\t1715407\t0.02540\n+chrX\t1715407\t1737824\t0.01536\n+chrX\t1737824\t1747824\t0.02540\n+chrX\t1747824\t1762445\t0.01536\n+chrX\t1762445\t1762467\t0.02540\n+chrX\t1762467\t1762468\t0.05080\n+chrX\t1762468\t1762689\t0.07620\n+chrX\t1762'..b'chrX\t11167356\t11167372\t0.12700\n+chrX\t11167372\t11167591\t0.10160\n+chrX\t11167591\t11167657\t0.07620\n+chrX\t11167657\t11167797\t0.05080\n+chrX\t11167797\t11168444\t0.02540\n+chrX\t11168444\t11280573\t0.01536\n+chrX\t11280573\t11290573\t0.02540\n+chrX\t11290573\t11306409\t0.01536\n+chrX\t11306409\t11316409\t0.02540\n+chrX\t11316409\t11321810\t0.01536\n+chrX\t11321810\t11331810\t0.02540\n+chrX\t11331810\t11345172\t0.01536\n+chrX\t11345172\t11355172\t0.02540\n+chrX\t11355172\t11382894\t0.01536\n+chrX\t11382894\t11392894\t0.02540\n+chrX\t11392894\t11394557\t0.01536\n+chrX\t11394557\t11394731\t0.02540\n+chrX\t11394731\t11404557\t0.05080\n+chrX\t11404557\t11404731\t0.02540\n+chrX\t11404731\t11449031\t0.01536\n+chrX\t11449031\t11459031\t0.02540\n+chrX\t11459031\t11546218\t0.01536\n+chrX\t11546218\t11546222\t0.02540\n+chrX\t11546222\t11546271\t0.05080\n+chrX\t11546271\t11546292\t0.07620\n+chrX\t11546292\t11546297\t0.10160\n+chrX\t11546297\t11546318\t0.12700\n+chrX\t11546318\t11546321\t0.15240\n+chrX\t11546321\t11546339\t0.17780\n+chrX\t11546339\t11546368\t0.20320\n+chrX\t11546368\t11546369\t0.22860\n+chrX\t11546369\t11546411\t0.25400\n+chrX\t11546411\t11546412\t0.27940\n+chrX\t11546412\t11546459\t0.30480\n+chrX\t11546459\t11546460\t0.33020\n+chrX\t11546460\t11546494\t0.35560\n+chrX\t11546494\t11546545\t0.38100\n+chrX\t11546545\t11546550\t0.40640\n+chrX\t11546550\t11546645\t0.43180\n+chrX\t11546645\t11546692\t0.45720\n+chrX\t11546692\t11546843\t0.48260\n+chrX\t11546843\t11554032\t0.50800\n+chrX\t11554032\t11554350\t0.53340\n+chrX\t11554350\t11556218\t0.55880\n+chrX\t11556218\t11556222\t0.53340\n+chrX\t11556222\t11556271\t0.50800\n+chrX\t11556271\t11556292\t0.48260\n+chrX\t11556292\t11556297\t0.45720\n+chrX\t11556297\t11556318\t0.43180\n+chrX\t11556318\t11556321\t0.40640\n+chrX\t11556321\t11556339\t0.38100\n+chrX\t11556339\t11556368\t0.35560\n+chrX\t11556368\t11556369\t0.33020\n+chrX\t11556369\t11556411\t0.30480\n+chrX\t11556411\t11556412\t0.27940\n+chrX\t11556412\t11556459\t0.25400\n+chrX\t11556459\t11556460\t0.22860\n+chrX\t11556460\t11556494\t0.20320\n+chrX\t11556494\t11556545\t0.17780\n+chrX\t11556545\t11556550\t0.15240\n+chrX\t11556550\t11556605\t0.12700\n+chrX\t11556605\t11556645\t0.15240\n+chrX\t11556645\t11556657\t0.12700\n+chrX\t11556657\t11556692\t0.15240\n+chrX\t11556692\t11556843\t0.12700\n+chrX\t11556843\t11562290\t0.10160\n+chrX\t11562290\t11564032\t0.12700\n+chrX\t11564032\t11564350\t0.10160\n+chrX\t11564350\t11566605\t0.07620\n+chrX\t11566605\t11566657\t0.05080\n+chrX\t11566657\t11572290\t0.02540\n+chrX\t11572290\t11572387\t0.01536\n+chrX\t11572387\t11577633\t0.02540\n+chrX\t11577633\t11582387\t0.05080\n+chrX\t11582387\t11587633\t0.02540\n+chrX\t11587633\t11619213\t0.01536\n+chrX\t11619213\t11620198\t0.02540\n+chrX\t11620198\t11623333\t0.05080\n+chrX\t11623333\t11623668\t0.07620\n+chrX\t11623668\t11629213\t0.10160\n+chrX\t11629213\t11630198\t0.07620\n+chrX\t11630198\t11632754\t0.05080\n+chrX\t11632754\t11633333\t0.07620\n+chrX\t11633333\t11633668\t0.05080\n+chrX\t11633668\t11642754\t0.02540\n+chrX\t11642754\t11668544\t0.01536\n+chrX\t11668544\t11677218\t0.02540\n+chrX\t11677218\t11677811\t0.05080\n+chrX\t11677811\t11678544\t0.07620\n+chrX\t11678544\t11680964\t0.05080\n+chrX\t11680964\t11687218\t0.07620\n+chrX\t11687218\t11687811\t0.05080\n+chrX\t11687811\t11690964\t0.02540\n+chrX\t11690964\t11695242\t0.01536\n+chrX\t11695242\t11698876\t0.02540\n+chrX\t11698876\t11705242\t0.05080\n+chrX\t11705242\t11708876\t0.02540\n+chrX\t11708876\t11737517\t0.01536\n+chrX\t11737517\t11737638\t0.02540\n+chrX\t11737638\t11737666\t0.05080\n+chrX\t11737666\t11737761\t0.07620\n+chrX\t11737761\t11737837\t0.10160\n+chrX\t11737837\t11737849\t0.12700\n+chrX\t11737849\t11738131\t0.15240\n+chrX\t11738131\t11747517\t0.17780\n+chrX\t11747517\t11747638\t0.15240\n+chrX\t11747638\t11747666\t0.12700\n+chrX\t11747666\t11747761\t0.10160\n+chrX\t11747761\t11747837\t0.07620\n+chrX\t11747837\t11747849\t0.05080\n+chrX\t11747849\t11748131\t0.02540\n+chrX\t11748131\t11759612\t0.01536\n+chrX\t11759612\t11769612\t0.02540\n+chrX\t11769612\t11769851\t0.01536\n+chrX\t11769851\t11771416\t0.02540\n+chrX\t11771416\t11771448\t0.05080\n+chrX\t11771448\t11771595\t0.07620\n+chrX\t11771595\t11771655\t0.10160\n+chrX\t11771655\t11771751\t0.12700\n+chrX\t11771751\t11771793\t0.15240\n+chrX\t11771793\t11772653\t0.17780\n+chrX\t11772653\t11779851\t0.20320\n+chrX\t11779851\t11780337\t0.17780\n+chrX\t11780337\t11781416\t0.20320\n+chrX\t11781416\t11781448\t0.17780\n' |
| b |
| diff -r 56e104999978 -r beb902da6e5f test-data/bdgcmp_input_treatment.bdg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bdgcmp_input_treatment.bdg Sat Apr 08 08:28:57 2017 -0400 |
| b |
| b'@@ -0,0 +1,1000 @@\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\t1767'..b'573\t1.00000\n+chrX\t11285573\t11311155\t0.00000\n+chrX\t11311155\t11311409\t1.00000\n+chrX\t11311409\t11326556\t0.00000\n+chrX\t11326556\t11326810\t1.00000\n+chrX\t11326810\t11349918\t0.00000\n+chrX\t11349918\t11350172\t1.00000\n+chrX\t11350172\t11387894\t0.00000\n+chrX\t11387894\t11388148\t1.00000\n+chrX\t11388148\t11399557\t0.00000\n+chrX\t11399557\t11399731\t1.00000\n+chrX\t11399731\t11399811\t2.00000\n+chrX\t11399811\t11399985\t1.00000\n+chrX\t11399985\t11454031\t0.00000\n+chrX\t11454031\t11454285\t1.00000\n+chrX\t11454285\t11551114\t0.00000\n+chrX\t11551114\t11551158\t1.00000\n+chrX\t11551158\t11551205\t2.00000\n+chrX\t11551205\t11551218\t3.00000\n+chrX\t11551218\t11551222\t4.00000\n+chrX\t11551222\t11551271\t5.00000\n+chrX\t11551271\t11551291\t6.00000\n+chrX\t11551291\t11551292\t7.00000\n+chrX\t11551292\t11551296\t8.00000\n+chrX\t11551296\t11551297\t9.00000\n+chrX\t11551297\t11551318\t10.00000\n+chrX\t11551318\t11551321\t11.00000\n+chrX\t11551321\t11551339\t12.00000\n+chrX\t11551339\t11551368\t13.00000\n+chrX\t11551368\t11551369\t12.00000\n+chrX\t11551369\t11551391\t13.00000\n+chrX\t11551391\t11551411\t14.00000\n+chrX\t11551411\t11551412\t15.00000\n+chrX\t11551412\t11551438\t14.00000\n+chrX\t11551438\t11551459\t15.00000\n+chrX\t11551459\t11551460\t14.00000\n+chrX\t11551460\t11551472\t15.00000\n+chrX\t11551472\t11551476\t14.00000\n+chrX\t11551476\t11551494\t13.00000\n+chrX\t11551494\t11551525\t14.00000\n+chrX\t11551525\t11551545\t13.00000\n+chrX\t11551545\t11551546\t12.00000\n+chrX\t11551546\t11551550\t11.00000\n+chrX\t11551550\t11551551\t10.00000\n+chrX\t11551551\t11551572\t9.00000\n+chrX\t11551572\t11551575\t8.00000\n+chrX\t11551575\t11551589\t7.00000\n+chrX\t11551589\t11551593\t8.00000\n+chrX\t11551593\t11551623\t7.00000\n+chrX\t11551623\t11551645\t6.00000\n+chrX\t11551645\t11551665\t5.00000\n+chrX\t11551665\t11551692\t4.00000\n+chrX\t11551692\t11551714\t3.00000\n+chrX\t11551714\t11551748\t2.00000\n+chrX\t11551748\t11551843\t1.00000\n+chrX\t11551843\t11559032\t0.00000\n+chrX\t11559032\t11559096\t1.00000\n+chrX\t11559096\t11559286\t2.00000\n+chrX\t11559286\t11559350\t1.00000\n+chrX\t11559350\t11561351\t0.00000\n+chrX\t11561351\t11561403\t1.00000\n+chrX\t11561403\t11561605\t2.00000\n+chrX\t11561605\t11561657\t1.00000\n+chrX\t11561657\t11567036\t0.00000\n+chrX\t11567036\t11567290\t1.00000\n+chrX\t11567290\t11577133\t0.00000\n+chrX\t11577133\t11577387\t1.00000\n+chrX\t11577387\t11582633\t0.00000\n+chrX\t11582633\t11582887\t1.00000\n+chrX\t11582887\t11624213\t0.00000\n+chrX\t11624213\t11624467\t1.00000\n+chrX\t11624467\t11624944\t0.00000\n+chrX\t11624944\t11625198\t1.00000\n+chrX\t11625198\t11628333\t0.00000\n+chrX\t11628333\t11628414\t1.00000\n+chrX\t11628414\t11628587\t2.00000\n+chrX\t11628587\t11628668\t1.00000\n+chrX\t11628668\t11637500\t0.00000\n+chrX\t11637500\t11637754\t1.00000\n+chrX\t11637754\t11673290\t0.00000\n+chrX\t11673290\t11673544\t1.00000\n+chrX\t11673544\t11681964\t0.00000\n+chrX\t11681964\t11682218\t1.00000\n+chrX\t11682218\t11682811\t0.00000\n+chrX\t11682811\t11683065\t1.00000\n+chrX\t11683065\t11685710\t0.00000\n+chrX\t11685710\t11685964\t1.00000\n+chrX\t11685964\t11700242\t0.00000\n+chrX\t11700242\t11700496\t1.00000\n+chrX\t11700496\t11703622\t0.00000\n+chrX\t11703622\t11703876\t1.00000\n+chrX\t11703876\t11742507\t0.00000\n+chrX\t11742507\t11742517\t1.00000\n+chrX\t11742517\t11742583\t2.00000\n+chrX\t11742583\t11742595\t3.00000\n+chrX\t11742595\t11742638\t4.00000\n+chrX\t11742638\t11742666\t5.00000\n+chrX\t11742666\t11742761\t6.00000\n+chrX\t11742761\t11742771\t5.00000\n+chrX\t11742771\t11742837\t4.00000\n+chrX\t11742837\t11742849\t3.00000\n+chrX\t11742849\t11742892\t2.00000\n+chrX\t11742892\t11742920\t1.00000\n+chrX\t11742920\t11743131\t0.00000\n+chrX\t11743131\t11743385\t1.00000\n+chrX\t11743385\t11764612\t0.00000\n+chrX\t11764612\t11764866\t1.00000\n+chrX\t11764866\t11774597\t0.00000\n+chrX\t11774597\t11774851\t1.00000\n+chrX\t11774851\t11776401\t0.00000\n+chrX\t11776401\t11776416\t1.00000\n+chrX\t11776416\t11776448\t2.00000\n+chrX\t11776448\t11776497\t3.00000\n+chrX\t11776497\t11776539\t4.00000\n+chrX\t11776539\t11776595\t5.00000\n+chrX\t11776595\t11776655\t6.00000\n+chrX\t11776655\t11776670\t5.00000\n+chrX\t11776670\t11776702\t4.00000\n+chrX\t11776702\t11776751\t3.00000\n+chrX\t11776751\t11776793\t2.00000\n+chrX\t11776793\t11776849\t1.00000\n+chrX\t11776849\t11777399\t0.00000\n+chrX\t11777399\t11777653\t1.00000\n+chrX\t11777653\t11785083\t0.00000\n+chrX\t11785083\t11785337\t1.00000\n' |
| b |
| diff -r 56e104999978 -r beb902da6e5f test-data/bdgcmp_on_Control_and_ChIP_slogLR.bdg --- a/test-data/bdgcmp_on_Control_and_ChIP_slogLR.bdg Mon Feb 06 02:30:37 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,3162 +0,0 @@\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 56e104999978 -r beb902da6e5f test-data/bdgcmp_output.bdg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bdgcmp_output.bdg Sat Apr 08 08:28:57 2017 -0400 |
| b |
| b'@@ -0,0 +1,1998 @@\n+chrX\t0\t64671\t1.81694\n+chrX\t64671\t69671\t1.60067\n+chrX\t69671\t69925\t3.49871\n+chrX\t69925\t74671\t1.60067\n+chrX\t74671\t279628\t1.81694\n+chrX\t279628\t280097\t1.60067\n+chrX\t280097\t280556\t1.30512\n+chrX\t280556\t284628\t1.13449\n+chrX\t284628\t284843\t2.55911\n+chrX\t284843\t284882\t4.15706\n+chrX\t284882\t285097\t2.55911\n+chrX\t285097\t285556\t1.13449\n+chrX\t285556\t285810\t2.55911\n+chrX\t285810\t289628\t1.13449\n+chrX\t289628\t290097\t1.30512\n+chrX\t290097\t290556\t1.60067\n+chrX\t290556\t456156\t1.81694\n+chrX\t456156\t461156\t1.60067\n+chrX\t461156\t461410\t3.49871\n+chrX\t461410\t466156\t1.60067\n+chrX\t466156\t581983\t1.81694\n+chrX\t581983\t586983\t1.60067\n+chrX\t586983\t587237\t3.49871\n+chrX\t587237\t588044\t1.60067\n+chrX\t588044\t591983\t1.30512\n+chrX\t591983\t593044\t1.60067\n+chrX\t593044\t593298\t3.49871\n+chrX\t593298\t598044\t1.60067\n+chrX\t598044\t651299\t1.81694\n+chrX\t651299\t656045\t1.60067\n+chrX\t656045\t656299\t3.49871\n+chrX\t656299\t661299\t1.60067\n+chrX\t661299\t915309\t1.81694\n+chrX\t915309\t920309\t1.60067\n+chrX\t920309\t920563\t3.49871\n+chrX\t920563\t925309\t1.60067\n+chrX\t925309\t943187\t1.81694\n+chrX\t943187\t947933\t1.60067\n+chrX\t947933\t948187\t3.49871\n+chrX\t948187\t953187\t1.60067\n+chrX\t953187\t1001805\t1.81694\n+chrX\t1001805\t1006805\t1.60067\n+chrX\t1006805\t1007059\t3.49871\n+chrX\t1007059\t1011805\t1.60067\n+chrX\t1011805\t1252632\t1.81694\n+chrX\t1252632\t1252813\t1.60067\n+chrX\t1252813\t1252970\t1.30512\n+chrX\t1252970\t1257632\t1.13449\n+chrX\t1257632\t1257716\t2.55911\n+chrX\t1257716\t1257813\t4.15706\n+chrX\t1257813\t1257886\t5.87883\n+chrX\t1257886\t1257970\t4.15706\n+chrX\t1257970\t1258067\t2.55911\n+chrX\t1258067\t1262632\t1.13449\n+chrX\t1262632\t1262813\t1.30512\n+chrX\t1262813\t1262970\t1.60067\n+chrX\t1262970\t1319337\t1.81694\n+chrX\t1319337\t1324083\t1.60067\n+chrX\t1324083\t1324337\t3.49871\n+chrX\t1324337\t1327580\t1.60067\n+chrX\t1327580\t1329337\t1.30512\n+chrX\t1329337\t1332580\t1.60067\n+chrX\t1332580\t1332834\t3.49871\n+chrX\t1332834\t1337580\t1.60067\n+chrX\t1337580\t1348039\t1.81694\n+chrX\t1348039\t1353039\t1.60067\n+chrX\t1353039\t1353293\t3.49871\n+chrX\t1353293\t1358039\t1.60067\n+chrX\t1358039\t1358567\t1.81694\n+chrX\t1358567\t1358859\t1.60067\n+chrX\t1358859\t1361012\t1.30512\n+chrX\t1361012\t1361063\t1.13449\n+chrX\t1361063\t1363567\t1.01498\n+chrX\t1363567\t1363605\t2.31653\n+chrX\t1363605\t1363821\t3.79048\n+chrX\t1363821\t1363859\t2.31653\n+chrX\t1363859\t1365758\t1.01498\n+chrX\t1365758\t1365809\t2.31653\n+chrX\t1365809\t1366012\t3.79048\n+chrX\t1366012\t1366063\t2.31653\n+chrX\t1366063\t1367998\t1.01498\n+chrX\t1367998\t1368567\t0.92348\n+chrX\t1368567\t1368859\t1.01498\n+chrX\t1368859\t1371012\t1.13449\n+chrX\t1371012\t1371063\t1.30512\n+chrX\t1371063\t1372998\t1.60067\n+chrX\t1372998\t1373252\t3.49871\n+chrX\t1373252\t1377998\t1.60067\n+chrX\t1377998\t1379092\t1.81694\n+chrX\t1379092\t1384092\t1.60067\n+chrX\t1384092\t1384346\t3.49871\n+chrX\t1384346\t1389092\t1.60067\n+chrX\t1389092\t1392762\t1.81694\n+chrX\t1392762\t1397762\t1.60067\n+chrX\t1397762\t1398016\t3.49871\n+chrX\t1398016\t1402762\t1.60067\n+chrX\t1402762\t1425076\t1.81694\n+chrX\t1425076\t1430076\t1.60067\n+chrX\t1430076\t1430330\t3.49871\n+chrX\t1430330\t1435076\t1.60067\n+chrX\t1435076\t1437229\t1.81694\n+chrX\t1437229\t1437730\t1.60067\n+chrX\t1437730\t1439990\t1.30512\n+chrX\t1439990\t1441470\t1.13449\n+chrX\t1441470\t1442229\t1.01498\n+chrX\t1442229\t1442483\t2.31653\n+chrX\t1442483\t1442730\t1.01498\n+chrX\t1442730\t1442984\t2.31653\n+chrX\t1442984\t1444736\t1.01498\n+chrX\t1444736\t1444990\t2.31653\n+chrX\t1444990\t1446470\t1.01498\n+chrX\t1446470\t1446724\t2.31653\n+chrX\t1446724\t1447229\t1.01498\n+chrX\t1447229\t1447730\t1.13449\n+chrX\t1447730\t1448397\t1.30512\n+chrX\t1448397\t1449990\t1.13449\n+chrX\t1449990\t1450341\t1.30512\n+chrX\t1450341\t1450707\t1.13449\n+chrX\t1450707\t1451342\t1.01498\n+chrX\t1451342\t1451470\t0.92348\n+chrX\t1451470\t1453397\t1.01498\n+chrX\t1453397\t1453651\t2.31653\n+chrX\t1453651\t1455341\t1.01498\n+chrX\t1455341\t1455453\t2.31653\n+chrX\t1455453\t1455595\t3.79048\n+chrX\t1455595\t1455707\t2.31653\n+chrX\t1455707\t1456342\t1.01498\n+chrX\t1456342\t1456596\t2.31653\n+chrX\t1456596\t1458397\t1.01498\n+chrX\t1458397\t1460341\t1.13449\n+chrX\t1460341\t1460707\t1.30512\n+chrX\t1460707\t1461342\t1.60067\n+chrX\t1461342\t1501622\t1.81694\n+chrX\t1501622\t1506622\t1.60067\n+chrX\t1506622\t1506876\t3.49871\n+chrX\t1506876\t1511622\t1.'..b'chrX\t11559286\t11559350\t2.31653\n+chrX\t11559350\t11561351\t1.01498\n+chrX\t11561351\t11561403\t2.31653\n+chrX\t11561403\t11561605\t3.79048\n+chrX\t11561605\t11561657\t2.31653\n+chrX\t11561657\t11562290\t1.01498\n+chrX\t11562290\t11564032\t0.92348\n+chrX\t11564032\t11564350\t1.01498\n+chrX\t11564350\t11566605\t1.13449\n+chrX\t11566605\t11566657\t1.30512\n+chrX\t11566657\t11567036\t1.60067\n+chrX\t11567036\t11567290\t3.49871\n+chrX\t11567290\t11572290\t1.60067\n+chrX\t11572290\t11572387\t1.81694\n+chrX\t11572387\t11577133\t1.60067\n+chrX\t11577133\t11577387\t3.49871\n+chrX\t11577387\t11577633\t1.60067\n+chrX\t11577633\t11582387\t1.30512\n+chrX\t11582387\t11582633\t1.60067\n+chrX\t11582633\t11582887\t3.49871\n+chrX\t11582887\t11587633\t1.60067\n+chrX\t11587633\t11619213\t1.81694\n+chrX\t11619213\t11620198\t1.60067\n+chrX\t11620198\t11623333\t1.30512\n+chrX\t11623333\t11623668\t1.13449\n+chrX\t11623668\t11624213\t1.01498\n+chrX\t11624213\t11624467\t2.31653\n+chrX\t11624467\t11624944\t1.01498\n+chrX\t11624944\t11625198\t2.31653\n+chrX\t11625198\t11628333\t1.01498\n+chrX\t11628333\t11628414\t2.31653\n+chrX\t11628414\t11628587\t3.79048\n+chrX\t11628587\t11628668\t2.31653\n+chrX\t11628668\t11629213\t1.01498\n+chrX\t11629213\t11630198\t1.13449\n+chrX\t11630198\t11632754\t1.30512\n+chrX\t11632754\t11633333\t1.13449\n+chrX\t11633333\t11633668\t1.30512\n+chrX\t11633668\t11637500\t1.60067\n+chrX\t11637500\t11637754\t3.49871\n+chrX\t11637754\t11642754\t1.60067\n+chrX\t11642754\t11668544\t1.81694\n+chrX\t11668544\t11673290\t1.60067\n+chrX\t11673290\t11673544\t3.49871\n+chrX\t11673544\t11677218\t1.60067\n+chrX\t11677218\t11677811\t1.30512\n+chrX\t11677811\t11678544\t1.13449\n+chrX\t11678544\t11680964\t1.30512\n+chrX\t11680964\t11681964\t1.13449\n+chrX\t11681964\t11682218\t2.55911\n+chrX\t11682218\t11682811\t1.13449\n+chrX\t11682811\t11683065\t2.55911\n+chrX\t11683065\t11685710\t1.13449\n+chrX\t11685710\t11685964\t2.55911\n+chrX\t11685964\t11687218\t1.13449\n+chrX\t11687218\t11687811\t1.30512\n+chrX\t11687811\t11690964\t1.60067\n+chrX\t11690964\t11695242\t1.81694\n+chrX\t11695242\t11698876\t1.60067\n+chrX\t11698876\t11700242\t1.30512\n+chrX\t11700242\t11700496\t2.90398\n+chrX\t11700496\t11703622\t1.30512\n+chrX\t11703622\t11703876\t2.90398\n+chrX\t11703876\t11705242\t1.30512\n+chrX\t11705242\t11708876\t1.60067\n+chrX\t11708876\t11737517\t1.81694\n+chrX\t11737517\t11737638\t1.60067\n+chrX\t11737638\t11737666\t1.30512\n+chrX\t11737666\t11737761\t1.13449\n+chrX\t11737761\t11737837\t1.01498\n+chrX\t11737837\t11737849\t0.92348\n+chrX\t11737849\t11738131\t0.84969\n+chrX\t11738131\t11742507\t0.78811\n+chrX\t11742507\t11742517\t1.85226\n+chrX\t11742517\t11742583\t3.08601\n+chrX\t11742583\t11742595\t4.44207\n+chrX\t11742595\t11742638\t5.89373\n+chrX\t11742638\t11742666\t7.42382\n+chrX\t11742666\t11742761\t9.02039\n+chrX\t11742761\t11742771\t7.42382\n+chrX\t11742771\t11742837\t5.89373\n+chrX\t11742837\t11742849\t4.44207\n+chrX\t11742849\t11742892\t3.08601\n+chrX\t11742892\t11742920\t1.85226\n+chrX\t11742920\t11743131\t0.78811\n+chrX\t11743131\t11743385\t1.85226\n+chrX\t11743385\t11747517\t0.78811\n+chrX\t11747517\t11747638\t0.84969\n+chrX\t11747638\t11747666\t0.92348\n+chrX\t11747666\t11747761\t1.01498\n+chrX\t11747761\t11747837\t1.13449\n+chrX\t11747837\t11747849\t1.30512\n+chrX\t11747849\t11748131\t1.60067\n+chrX\t11748131\t11759612\t1.81694\n+chrX\t11759612\t11764612\t1.60067\n+chrX\t11764612\t11764866\t3.49871\n+chrX\t11764866\t11769612\t1.60067\n+chrX\t11769612\t11769851\t1.81694\n+chrX\t11769851\t11771416\t1.60067\n+chrX\t11771416\t11771448\t1.30512\n+chrX\t11771448\t11771595\t1.13449\n+chrX\t11771595\t11771655\t1.01498\n+chrX\t11771655\t11771751\t0.92348\n+chrX\t11771751\t11771793\t0.84969\n+chrX\t11771793\t11772653\t0.78811\n+chrX\t11772653\t11774597\t0.73545\n+chrX\t11774597\t11774851\t1.74351\n+chrX\t11774851\t11776401\t0.73545\n+chrX\t11776401\t11776416\t1.74351\n+chrX\t11776416\t11776448\t2.92023\n+chrX\t11776448\t11776497\t4.21887\n+chrX\t11776497\t11776539\t5.61292\n+chrX\t11776539\t11776595\t7.08529\n+chrX\t11776595\t11776655\t8.62407\n+chrX\t11776655\t11776670\t7.08529\n+chrX\t11776670\t11776702\t5.61292\n+chrX\t11776702\t11776751\t4.21887\n+chrX\t11776751\t11776793\t2.92023\n+chrX\t11776793\t11776849\t1.74351\n+chrX\t11776849\t11777399\t0.73545\n+chrX\t11777399\t11777653\t1.74351\n+chrX\t11777653\t11779851\t0.73545\n+chrX\t11779851\t11780337\t0.78811\n+chrX\t11780337\t11781416\t0.73545\n+chrX\t11781416\t11781448\t0.78811\n' |
| b |
| diff -r 56e104999978 -r beb902da6e5f test-data/bdgdiff_c1.bdg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bdgdiff_c1.bdg Sat Apr 08 08:28:57 2017 -0400 |
| b |
| b'@@ -0,0 +1,10000 @@\n+chrV\t0\t60\t1.91100\n+chrV\t60\t70\t2.05800\n+chrV\t70\t102\t2.20500\n+chrV\t102\t103\t2.35200\n+chrV\t103\t110\t2.49900\n+chrV\t110\t114\t2.64600\n+chrV\t114\t287\t2.79300\n+chrV\t287\t288\t3.00000\n+chrV\t288\t300\t4.00000\n+chrV\t300\t322\t5.00000\n+chrV\t322\t324\t6.00000\n+chrV\t324\t325\t7.00000\n+chrV\t325\t327\t8.00000\n+chrV\t327\t331\t9.00000\n+chrV\t331\t333\t10.00000\n+chrV\t333\t334\t11.00000\n+chrV\t334\t335\t12.00000\n+chrV\t335\t431\t13.00000\n+chrV\t431\t432\t12.00000\n+chrV\t432\t434\t11.00000\n+chrV\t434\t435\t10.00000\n+chrV\t435\t447\t9.00000\n+chrV\t447\t469\t8.00000\n+chrV\t469\t471\t7.00000\n+chrV\t471\t472\t6.00000\n+chrV\t472\t474\t5.00000\n+chrV\t474\t478\t4.00000\n+chrV\t478\t480\t3.00000\n+chrV\t480\t528\t2.79300\n+chrV\t528\t529\t3.00000\n+chrV\t529\t536\t4.00000\n+chrV\t536\t540\t5.00000\n+chrV\t540\t634\t6.00000\n+chrV\t634\t644\t5.00000\n+chrV\t644\t675\t4.00000\n+chrV\t675\t676\t3.00000\n+chrV\t676\t857\t2.79300\n+chrV\t857\t858\t2.64600\n+chrV\t858\t860\t2.49900\n+chrV\t860\t861\t2.35200\n+chrV\t861\t873\t2.20500\n+chrV\t873\t896\t2.05800\n+chrV\t896\t898\t1.91100\n+chrV\t898\t899\t1.76400\n+chrV\t899\t901\t1.61700\n+chrV\t901\t905\t1.47000\n+chrV\t905\t907\t1.32300\n+chrV\t907\t908\t1.17600\n+chrV\t908\t909\t1.02900\n+chrV\t909\t1134\t0.88200\n+chrV\t1134\t1158\t0.89670\n+chrV\t1158\t1167\t1.02900\n+chrV\t1167\t1199\t1.17600\n+chrV\t1199\t1200\t1.32300\n+chrV\t1200\t1208\t1.47000\n+chrV\t1208\t1209\t1.61700\n+chrV\t1209\t1223\t1.76400\n+chrV\t1223\t1229\t1.91100\n+chrV\t1229\t1234\t2.05800\n+chrV\t1234\t1241\t2.20500\n+chrV\t1241\t1244\t2.35200\n+chrV\t1244\t1293\t2.64600\n+chrV\t1293\t1533\t2.79300\n+chrV\t1533\t1534\t3.00000\n+chrV\t1534\t1566\t4.00000\n+chrV\t1566\t1572\t5.00000\n+chrV\t1572\t1585\t6.00000\n+chrV\t1585\t1594\t7.00000\n+chrV\t1594\t1625\t8.00000\n+chrV\t1625\t1626\t9.00000\n+chrV\t1626\t1635\t10.00000\n+chrV\t1635\t1650\t12.00000\n+chrV\t1650\t1656\t13.00000\n+chrV\t1656\t1661\t14.00000\n+chrV\t1661\t1667\t15.00000\n+chrV\t1667\t1670\t16.00000\n+chrV\t1670\t1671\t17.00000\n+chrV\t1671\t1677\t18.00000\n+chrV\t1677\t1678\t17.00000\n+chrV\t1678\t1680\t16.00000\n+chrV\t1680\t1681\t15.00000\n+chrV\t1681\t1713\t14.00000\n+chrV\t1713\t1732\t13.00000\n+chrV\t1732\t1741\t12.00000\n+chrV\t1741\t1772\t11.00000\n+chrV\t1772\t1773\t10.00000\n+chrV\t1773\t1782\t9.00000\n+chrV\t1782\t1797\t7.00000\n+chrV\t1797\t1803\t6.00000\n+chrV\t1803\t1808\t5.00000\n+chrV\t1808\t1814\t4.00000\n+chrV\t1814\t1817\t3.00000\n+chrV\t1817\t2017\t2.79300\n+chrV\t2017\t2024\t2.80770\n+chrV\t2024\t2029\t2.82240\n+chrV\t2029\t2031\t2.94000\n+chrV\t2031\t2061\t3.08700\n+chrV\t2061\t2065\t3.23400\n+chrV\t2065\t2066\t3.38100\n+chrV\t2066\t2069\t3.52800\n+chrV\t2069\t2074\t3.67500\n+chrV\t2074\t2079\t3.82200\n+chrV\t2079\t2087\t3.96900\n+chrV\t2087\t2103\t4.11600\n+chrV\t2103\t2104\t3.96900\n+chrV\t2104\t2106\t3.82200\n+chrV\t2106\t2107\t3.67500\n+chrV\t2107\t2140\t3.52800\n+chrV\t2140\t2146\t3.38100\n+chrV\t2146\t2149\t3.26340\n+chrV\t2149\t2152\t3.27810\n+chrV\t2152\t2154\t3.29280\n+chrV\t2154\t2155\t3.30750\n+chrV\t2155\t2159\t3.32220\n+chrV\t2159\t2166\t3.33690\n+chrV\t2166\t2174\t3.35160\n+chrV\t2174\t2178\t3.36630\n+chrV\t2178\t2181\t3.38100\n+chrV\t2181\t2186\t3.39570\n+chrV\t2186\t2188\t3.41040\n+chrV\t2188\t2189\t3.42510\n+chrV\t2189\t2200\t3.43980\n+chrV\t2200\t2203\t3.45450\n+chrV\t2203\t2213\t3.46920\n+chrV\t2213\t2219\t3.48390\n+chrV\t2219\t2220\t3.49860\n+chrV\t2220\t2223\t3.51330\n+chrV\t2223\t2224\t3.52800\n+chrV\t2224\t2227\t3.54270\n+chrV\t2227\t2233\t3.55740\n+chrV\t2233\t2246\t3.57210\n+chrV\t2246\t2247\t3.58680\n+chrV\t2247\t2248\t3.60150\n+chrV\t2248\t2260\t3.61620\n+chrV\t2260\t2263\t3.63090\n+chrV\t2263\t2278\t3.66030\n+chrV\t2278\t2281\t3.67500\n+chrV\t2281\t2286\t3.68970\n+chrV\t2286\t2290\t3.70440\n+chrV\t2290\t2292\t3.71910\n+chrV\t2292\t2297\t3.73380\n+chrV\t2297\t2299\t3.74850\n+chrV\t2299\t2309\t3.76320\n+chrV\t2309\t2310\t3.77790\n+chrV\t2310\t2319\t3.79260\n+chrV\t2319\t2322\t3.80730\n+chrV\t2322\t2324\t3.82200\n+chrV\t2324\t2330\t3.83670\n+chrV\t2330\t2331\t3.85140\n+chrV\t2331\t2332\t3.86610\n+chrV\t2332\t2335\t3.88080\n+chrV\t2335\t2336\t3.89550\n+chrV\t2336\t2356\t3.91020\n+chrV\t2356\t2362\t3.92490\n+chrV\t2362\t2363\t3.93960\n+chrV\t2363\t2369\t3.95430\n+chrV\t2369\t2371\t3.96900\n+chrV\t2371\t2373\t3.98370\n+chrV\t2373\t2374\t3.99840\n+chrV\t2374\t2376\t4.01310\n+chrV\t2376\t2382\t4.02780\n+chrV\t2382\t2383\t4.04250\n+chrV\t2383\t2396\t4.07190\n+chrV\t2396\t2402\t4.08660\n+chrV\t2402\t2411\t4.10130\n+chrV\t2411\t2413\t4.11600\n+chrV\t2413\t2419\t4.13070\n+chrV\t2419\t2427\t4.14540\n+chrV\t2427\t2428\t4.16010\n+chrV'..b'40\n+chrV\t30093\t30094\t37.05870\n+chrV\t30094\t30096\t37.04400\n+chrV\t30096\t30099\t37.02930\n+chrV\t30099\t30100\t37.01460\n+chrV\t30100\t30101\t37.02930\n+chrV\t30101\t30104\t37.04400\n+chrV\t30104\t30105\t37.05870\n+chrV\t30105\t30107\t37.07340\n+chrV\t30107\t30111\t37.08810\n+chrV\t30111\t30113\t37.07340\n+chrV\t30113\t30114\t37.05870\n+chrV\t30114\t30121\t37.04400\n+chrV\t30121\t30122\t37.05870\n+chrV\t30122\t30127\t37.04400\n+chrV\t30127\t30128\t37.01460\n+chrV\t30128\t30130\t37.04400\n+chrV\t30130\t30134\t37.07340\n+chrV\t30134\t30139\t37.08810\n+chrV\t30139\t30140\t37.07340\n+chrV\t30140\t30143\t37.05870\n+chrV\t30143\t30149\t37.04400\n+chrV\t30149\t30152\t37.05870\n+chrV\t30152\t30155\t37.04400\n+chrV\t30155\t30163\t37.02930\n+chrV\t30163\t30165\t37.04400\n+chrV\t30165\t30167\t37.05870\n+chrV\t30167\t30172\t37.04400\n+chrV\t30172\t30173\t37.05870\n+chrV\t30173\t30176\t37.07340\n+chrV\t30176\t30177\t37.08810\n+chrV\t30177\t30178\t37.11750\n+chrV\t30178\t30183\t37.14690\n+chrV\t30183\t30188\t37.16160\n+chrV\t30188\t30195\t37.17630\n+chrV\t30195\t30197\t37.19100\n+chrV\t30197\t30200\t37.17630\n+chrV\t30200\t30201\t37.19100\n+chrV\t30201\t30203\t37.20570\n+chrV\t30203\t30204\t37.22040\n+chrV\t30204\t30206\t37.20570\n+chrV\t30206\t30207\t37.22040\n+chrV\t30207\t30208\t37.23510\n+chrV\t30208\t30212\t37.24980\n+chrV\t30212\t30215\t37.26450\n+chrV\t30215\t30220\t37.27920\n+chrV\t30220\t30225\t37.26450\n+chrV\t30225\t30229\t37.27920\n+chrV\t30229\t30232\t37.29390\n+chrV\t30232\t30233\t37.27920\n+chrV\t30233\t30236\t37.26450\n+chrV\t30236\t30239\t37.27920\n+chrV\t30239\t30240\t37.29390\n+chrV\t30240\t30242\t37.27920\n+chrV\t30242\t30245\t37.26450\n+chrV\t30245\t30247\t37.24980\n+chrV\t30247\t30249\t37.23510\n+chrV\t30249\t30250\t37.20570\n+chrV\t30250\t30253\t37.22040\n+chrV\t30253\t30259\t37.20570\n+chrV\t30259\t30260\t37.22040\n+chrV\t30260\t30264\t37.23510\n+chrV\t30264\t30266\t37.24980\n+chrV\t30266\t30267\t37.23510\n+chrV\t30267\t30268\t37.24980\n+chrV\t30268\t30270\t38.00000\n+chrV\t30270\t30271\t37.24980\n+chrV\t30271\t30273\t37.26450\n+chrV\t30273\t30276\t37.24980\n+chrV\t30276\t30277\t38.00000\n+chrV\t30277\t30280\t39.00000\n+chrV\t30280\t30281\t40.00000\n+chrV\t30281\t30283\t39.00000\n+chrV\t30283\t30288\t38.00000\n+chrV\t30288\t30291\t37.26450\n+chrV\t30291\t30294\t38.00000\n+chrV\t30294\t30296\t37.26450\n+chrV\t30296\t30298\t37.24980\n+chrV\t30298\t30304\t38.00000\n+chrV\t30304\t30308\t39.00000\n+chrV\t30308\t30309\t38.00000\n+chrV\t30309\t30313\t39.00000\n+chrV\t30313\t30315\t37.30860\n+chrV\t30315\t30317\t37.32330\n+chrV\t30317\t30320\t37.30860\n+chrV\t30320\t30321\t38.00000\n+chrV\t30321\t30322\t37.30860\n+chrV\t30322\t30326\t38.00000\n+chrV\t30326\t30328\t37.27920\n+chrV\t30328\t30329\t37.26450\n+chrV\t30329\t30334\t37.27920\n+chrV\t30334\t30339\t37.29390\n+chrV\t30339\t30341\t37.30860\n+chrV\t30341\t30343\t37.32330\n+chrV\t30343\t30344\t37.33800\n+chrV\t30344\t30345\t37.35270\n+chrV\t30345\t30347\t37.36740\n+chrV\t30347\t30348\t37.35270\n+chrV\t30348\t30352\t37.36740\n+chrV\t30352\t30353\t37.35270\n+chrV\t30353\t30356\t37.33800\n+chrV\t30356\t30357\t37.32330\n+chrV\t30357\t30360\t37.33800\n+chrV\t30360\t30361\t37.35270\n+chrV\t30361\t30363\t37.36740\n+chrV\t30363\t30365\t37.38210\n+chrV\t30365\t30366\t37.36740\n+chrV\t30366\t30368\t37.38210\n+chrV\t30368\t30372\t37.36740\n+chrV\t30372\t30376\t37.38210\n+chrV\t30376\t30378\t37.39680\n+chrV\t30378\t30381\t37.38210\n+chrV\t30381\t30383\t37.39680\n+chrV\t30383\t30384\t37.41150\n+chrV\t30384\t30385\t37.42620\n+chrV\t30385\t30387\t37.41150\n+chrV\t30387\t30388\t37.42620\n+chrV\t30388\t30389\t37.44090\n+chrV\t30389\t30391\t37.45560\n+chrV\t30391\t30392\t37.47030\n+chrV\t30392\t30393\t37.48500\n+chrV\t30393\t30396\t37.47030\n+chrV\t30396\t30401\t37.49970\n+chrV\t30401\t30403\t37.48500\n+chrV\t30403\t30411\t37.49970\n+chrV\t30411\t30413\t37.51440\n+chrV\t30413\t30414\t37.49970\n+chrV\t30414\t30415\t37.51440\n+chrV\t30415\t30416\t37.49970\n+chrV\t30416\t30421\t37.51440\n+chrV\t30421\t30423\t37.52910\n+chrV\t30423\t30425\t37.54380\n+chrV\t30425\t30431\t37.55850\n+chrV\t30431\t30434\t37.57320\n+chrV\t30434\t30435\t37.58790\n+chrV\t30435\t30439\t37.60260\n+chrV\t30439\t30440\t37.61730\n+chrV\t30440\t30441\t37.60260\n+chrV\t30441\t30442\t37.58790\n+chrV\t30442\t30444\t37.57320\n+chrV\t30444\t30448\t37.55850\n+chrV\t30448\t30451\t37.57320\n+chrV\t30451\t30452\t37.58790\n+chrV\t30452\t30454\t37.55850\n+chrV\t30454\t30455\t37.54380\n+chrV\t30455\t30458\t37.52910\n+chrV\t30458\t30470\t37.51440\n+chrV\t30470\t30471\t37.52910\n+chrV\t30471\t30473\t37.54380\n' |
| b |
| diff -r 56e104999978 -r beb902da6e5f test-data/bdgdiff_c2.bdg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bdgdiff_c2.bdg Sat Apr 08 08:28:57 2017 -0400 |
| b |
| b'@@ -0,0 +1,10000 @@\n+chrV\t0\t63\t0.29400\n+chrV\t63\t74\t0.44100\n+chrV\t74\t107\t0.58800\n+chrV\t107\t318\t0.73500\n+chrV\t318\t331\t1.00000\n+chrV\t331\t465\t2.00000\n+chrV\t465\t478\t1.00000\n+chrV\t478\t490\t0.73500\n+chrV\t490\t501\t1.00000\n+chrV\t501\t533\t2.00000\n+chrV\t533\t637\t3.00000\n+chrV\t637\t648\t2.00000\n+chrV\t648\t680\t1.00000\n+chrV\t680\t892\t0.73500\n+chrV\t892\t905\t0.58800\n+chrV\t905\t1063\t0.44100\n+chrV\t1063\t1074\t0.29400\n+chrV\t1074\t1086\t0.23520\n+chrV\t1086\t1104\t0.29400\n+chrV\t1104\t1107\t0.44100\n+chrV\t1107\t1158\t0.29400\n+chrV\t1158\t1230\t0.44100\n+chrV\t1230\t1245\t0.58800\n+chrV\t1245\t1253\t0.73500\n+chrV\t1253\t1443\t0.88200\n+chrV\t1443\t1531\t1.02900\n+chrV\t1531\t1585\t2.00000\n+chrV\t1585\t1657\t3.00000\n+chrV\t1657\t1660\t4.00000\n+chrV\t1660\t1671\t3.00000\n+chrV\t1671\t1678\t4.00000\n+chrV\t1678\t1680\t3.00000\n+chrV\t1680\t1732\t4.00000\n+chrV\t1732\t1804\t3.00000\n+chrV\t1804\t1818\t2.00000\n+chrV\t1818\t2062\t1.02900\n+chrV\t2062\t2086\t1.17600\n+chrV\t2086\t2104\t1.02900\n+chrV\t2104\t2158\t0.88200\n+chrV\t2158\t2230\t0.73500\n+chrV\t2230\t2270\t0.66150\n+chrV\t2270\t2316\t0.67620\n+chrV\t2316\t2319\t0.69090\n+chrV\t2319\t2333\t0.70560\n+chrV\t2333\t2365\t0.72030\n+chrV\t2365\t2409\t0.73500\n+chrV\t2409\t2419\t0.74970\n+chrV\t2419\t2446\t0.76440\n+chrV\t2446\t2488\t0.77910\n+chrV\t2488\t2635\t1.00000\n+chrV\t2635\t2644\t0.97020\n+chrV\t2644\t2707\t0.98490\n+chrV\t2707\t2760\t0.99960\n+chrV\t2760\t2798\t1.01430\n+chrV\t2798\t2897\t1.02900\n+chrV\t2897\t2929\t1.04370\n+chrV\t2929\t2947\t1.05840\n+chrV\t2947\t2950\t1.07310\n+chrV\t2950\t2977\t1.08780\n+chrV\t2977\t3025\t1.10250\n+chrV\t3025\t3032\t1.11720\n+chrV\t3032\t3053\t1.13190\n+chrV\t3053\t3077\t1.14660\n+chrV\t3077\t3096\t1.16130\n+chrV\t3096\t3140\t1.17600\n+chrV\t3140\t3148\t1.19070\n+chrV\t3148\t3163\t1.20540\n+chrV\t3163\t3181\t1.22010\n+chrV\t3181\t3214\t1.23480\n+chrV\t3214\t3250\t1.24950\n+chrV\t3250\t3318\t1.26420\n+chrV\t3318\t3321\t1.27890\n+chrV\t3321\t3334\t1.29360\n+chrV\t3334\t3340\t1.30830\n+chrV\t3340\t3342\t1.32300\n+chrV\t3342\t3378\t1.33770\n+chrV\t3378\t3379\t1.35240\n+chrV\t3379\t3398\t1.36710\n+chrV\t3398\t3418\t1.38180\n+chrV\t3418\t3457\t1.39650\n+chrV\t3457\t3472\t1.41120\n+chrV\t3472\t3473\t1.42590\n+chrV\t3473\t3479\t1.44060\n+chrV\t3479\t3481\t1.45530\n+chrV\t3481\t3482\t1.47000\n+chrV\t3482\t3490\t1.48470\n+chrV\t3490\t3502\t1.49940\n+chrV\t3502\t3505\t1.51410\n+chrV\t3505\t3525\t1.52880\n+chrV\t3525\t3586\t1.54350\n+chrV\t3586\t3588\t1.55820\n+chrV\t3588\t3604\t1.57290\n+chrV\t3604\t3605\t1.58760\n+chrV\t3605\t3606\t1.60230\n+chrV\t3606\t3614\t1.61700\n+chrV\t3614\t3615\t1.63170\n+chrV\t3615\t3616\t1.64640\n+chrV\t3616\t3620\t1.66110\n+chrV\t3620\t3664\t1.67580\n+chrV\t3664\t3731\t1.69050\n+chrV\t3731\t3776\t1.70520\n+chrV\t3776\t3787\t1.71990\n+chrV\t3787\t3821\t1.73460\n+chrV\t3821\t3837\t1.74930\n+chrV\t3837\t3838\t1.76400\n+chrV\t3838\t3842\t1.77870\n+chrV\t3842\t3843\t1.79340\n+chrV\t3843\t3847\t1.80810\n+chrV\t3847\t3862\t1.82280\n+chrV\t3862\t3863\t1.83750\n+chrV\t3863\t3925\t1.85220\n+chrV\t3925\t3927\t1.86690\n+chrV\t3927\t3936\t1.88160\n+chrV\t3936\t3938\t1.89630\n+chrV\t3938\t3960\t1.91100\n+chrV\t3960\t4006\t1.92570\n+chrV\t4006\t4015\t1.94040\n+chrV\t4015\t4022\t1.95510\n+chrV\t4022\t4026\t2.00000\n+chrV\t4026\t4156\t3.00000\n+chrV\t4156\t4159\t2.04330\n+chrV\t4159\t4204\t2.05800\n+chrV\t4204\t4235\t2.07270\n+chrV\t4235\t4267\t2.10210\n+chrV\t4267\t4371\t2.11680\n+chrV\t4371\t4382\t2.13150\n+chrV\t4382\t4405\t2.14620\n+chrV\t4405\t4410\t2.16090\n+chrV\t4410\t4463\t2.17560\n+chrV\t4463\t4481\t2.19030\n+chrV\t4481\t4496\t2.20500\n+chrV\t4496\t4508\t2.21970\n+chrV\t4508\t4568\t2.23440\n+chrV\t4568\t4577\t2.24910\n+chrV\t4577\t4599\t2.26380\n+chrV\t4599\t4605\t2.27850\n+chrV\t4605\t4649\t2.29320\n+chrV\t4649\t4666\t2.30790\n+chrV\t4666\t4676\t2.32260\n+chrV\t4676\t4706\t2.33730\n+chrV\t4706\t4710\t2.35200\n+chrV\t4710\t4722\t2.36670\n+chrV\t4722\t4735\t2.38140\n+chrV\t4735\t4755\t2.39610\n+chrV\t4755\t4769\t2.41080\n+chrV\t4769\t4777\t2.42550\n+chrV\t4777\t4822\t2.44020\n+chrV\t4822\t4837\t2.45490\n+chrV\t4837\t4877\t2.46960\n+chrV\t4877\t4949\t2.48430\n+chrV\t4949\t4998\t2.49900\n+chrV\t4998\t5000\t2.52840\n+chrV\t5000\t5006\t2.54310\n+chrV\t5006\t5026\t2.55780\n+chrV\t5026\t5041\t2.57250\n+chrV\t5041\t5058\t2.58720\n+chrV\t5058\t5087\t2.60190\n+chrV\t5087\t5092\t2.61660\n+chrV\t5092\t5095\t2.63130\n+chrV\t5095\t5162\t2.64600\n+chrV\t5162\t5184\t2.66070\n+chrV\t5184\t5208\t2.67540\n+chrV\t5208\t5255\t2.69010\n+chrV\t5255\t5258\t2.70480\n+chrV\t5258\t5299\t2.71950\n+chrV\t5299\t5304\t2.73420\n+chrV\t5304\t5337\t2.74890\n+chrV\t53'..b'5171\t9.33450\n+chrV\t85171\t85176\t9.34920\n+chrV\t85176\t85179\t9.33450\n+chrV\t85179\t85182\t9.34920\n+chrV\t85182\t85199\t9.33450\n+chrV\t85199\t85209\t9.34920\n+chrV\t85209\t85221\t9.36390\n+chrV\t85221\t85227\t9.34920\n+chrV\t85227\t85229\t9.33450\n+chrV\t85229\t85232\t9.34920\n+chrV\t85232\t85251\t9.33450\n+chrV\t85251\t85280\t9.34920\n+chrV\t85280\t85284\t9.33450\n+chrV\t85284\t85299\t9.34920\n+chrV\t85299\t85315\t9.36390\n+chrV\t85315\t85322\t9.34920\n+chrV\t85322\t85340\t9.36390\n+chrV\t85340\t85350\t9.37860\n+chrV\t85350\t85351\t9.36390\n+chrV\t85351\t85380\t9.34920\n+chrV\t85380\t85416\t9.33450\n+chrV\t85416\t85430\t9.34920\n+chrV\t85430\t85431\t9.36390\n+chrV\t85431\t85433\t9.34920\n+chrV\t85433\t85439\t9.33450\n+chrV\t85439\t85448\t9.34920\n+chrV\t85448\t85466\t9.36390\n+chrV\t85466\t85467\t9.37860\n+chrV\t85467\t85472\t9.36390\n+chrV\t85472\t85474\t9.34920\n+chrV\t85474\t85492\t9.36390\n+chrV\t85492\t85496\t9.34920\n+chrV\t85496\t85499\t9.33450\n+chrV\t85499\t85500\t9.34920\n+chrV\t85500\t85501\t9.40800\n+chrV\t85501\t85507\t9.55500\n+chrV\t85507\t85509\t9.70200\n+chrV\t85509\t85515\t9.84900\n+chrV\t85515\t85528\t10.14300\n+chrV\t85528\t85533\t10.29000\n+chrV\t85533\t85536\t10.43700\n+chrV\t85536\t85537\t10.58400\n+chrV\t85537\t85554\t10.43700\n+chrV\t85554\t85564\t10.58400\n+chrV\t85564\t85574\t10.73100\n+chrV\t85574\t85575\t10.87800\n+chrV\t85575\t85576\t11.02500\n+chrV\t85576\t85580\t11.17200\n+chrV\t85580\t85581\t11.31900\n+chrV\t85581\t85584\t11.46600\n+chrV\t85584\t85586\t11.61300\n+chrV\t85586\t85588\t11.76000\n+chrV\t85588\t85589\t11.90700\n+chrV\t85589\t85592\t12.05400\n+chrV\t85592\t85594\t12.20100\n+chrV\t85594\t85596\t12.49500\n+chrV\t85596\t85599\t12.64200\n+chrV\t85599\t85600\t12.78900\n+chrV\t85600\t85610\t12.93600\n+chrV\t85610\t85615\t13.08300\n+chrV\t85615\t85630\t13.23000\n+chrV\t85630\t85632\t13.37700\n+chrV\t85632\t85634\t13.23000\n+chrV\t85634\t85639\t13.37700\n+chrV\t85639\t85642\t13.52400\n+chrV\t85642\t85665\t13.81800\n+chrV\t85665\t85671\t13.96500\n+chrV\t85671\t85682\t14.11200\n+chrV\t85682\t85684\t15.00000\n+chrV\t85684\t85685\t16.00000\n+chrV\t85685\t85689\t17.00000\n+chrV\t85689\t85695\t16.00000\n+chrV\t85695\t85705\t17.00000\n+chrV\t85705\t85707\t18.00000\n+chrV\t85707\t85710\t17.00000\n+chrV\t85710\t85712\t18.00000\n+chrV\t85712\t85713\t20.00000\n+chrV\t85713\t85714\t21.00000\n+chrV\t85714\t85721\t22.00000\n+chrV\t85721\t85722\t23.00000\n+chrV\t85722\t85723\t24.00000\n+chrV\t85723\t85725\t25.00000\n+chrV\t85725\t85733\t26.00000\n+chrV\t85733\t85743\t27.00000\n+chrV\t85743\t85748\t26.00000\n+chrV\t85748\t85749\t27.00000\n+chrV\t85749\t85750\t26.00000\n+chrV\t85750\t85757\t24.00000\n+chrV\t85757\t85758\t25.00000\n+chrV\t85758\t85762\t24.00000\n+chrV\t85762\t85776\t25.00000\n+chrV\t85776\t85777\t24.00000\n+chrV\t85777\t85788\t23.00000\n+chrV\t85788\t85799\t22.00000\n+chrV\t85799\t85802\t23.00000\n+chrV\t85802\t85805\t22.00000\n+chrV\t85805\t85807\t23.00000\n+chrV\t85807\t85809\t22.00000\n+chrV\t85809\t85811\t23.00000\n+chrV\t85811\t85822\t22.00000\n+chrV\t85822\t85824\t23.00000\n+chrV\t85824\t85825\t24.00000\n+chrV\t85825\t85829\t23.00000\n+chrV\t85829\t85831\t22.00000\n+chrV\t85831\t85832\t21.00000\n+chrV\t85832\t85835\t20.00000\n+chrV\t85835\t85842\t21.00000\n+chrV\t85842\t85851\t20.00000\n+chrV\t85851\t85852\t21.00000\n+chrV\t85852\t85857\t20.00000\n+chrV\t85857\t85859\t19.00000\n+chrV\t85859\t85860\t17.00000\n+chrV\t85860\t85861\t16.00000\n+chrV\t85861\t85868\t15.00000\n+chrV\t85868\t85873\t14.25900\n+chrV\t85873\t85885\t14.40600\n+chrV\t85885\t85888\t14.55300\n+chrV\t85888\t85911\t14.70000\n+chrV\t85911\t85914\t14.84700\n+chrV\t85914\t85926\t14.99400\n+chrV\t85926\t85927\t15.00000\n+chrV\t85927\t85934\t16.00000\n+chrV\t85934\t85936\t17.00000\n+chrV\t85936\t85941\t18.00000\n+chrV\t85941\t85942\t19.00000\n+chrV\t85942\t85946\t20.00000\n+chrV\t85946\t85952\t19.00000\n+chrV\t85952\t85955\t18.00000\n+chrV\t85955\t85956\t19.00000\n+chrV\t85956\t85959\t18.00000\n+chrV\t85959\t85963\t19.00000\n+chrV\t85963\t85969\t20.00000\n+chrV\t85969\t85971\t19.00000\n+chrV\t85971\t85980\t18.00000\n+chrV\t85980\t85982\t19.00000\n+chrV\t85982\t85991\t18.00000\n+chrV\t85991\t85998\t19.00000\n+chrV\t85998\t86000\t18.00000\n+chrV\t86000\t86001\t19.00000\n+chrV\t86001\t86002\t20.00000\n+chrV\t86002\t86006\t21.00000\n+chrV\t86006\t86007\t22.00000\n+chrV\t86007\t86010\t23.00000\n+chrV\t86010\t86013\t24.00000\n+chrV\t86013\t86015\t25.00000\n+chrV\t86015\t86016\t26.00000\n+chrV\t86016\t86017\t27.00000\n+chrV\t86017\t86020\t26.00000\n+chrV\t86020\t86021\t27.00000\n+chrV\t86021\t86023\t28.00000\n' |
| b |
| diff -r 56e104999978 -r beb902da6e5f test-data/bdgdiff_t1.bdg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bdgdiff_t1.bdg Sat Apr 08 08:28:57 2017 -0400 |
| b |
| b'@@ -0,0 +1,10000 @@\n+chrV\t0\t248\t0.00000\n+chrV\t248\t253\t0.90636\n+chrV\t253\t254\t1.81272\n+chrV\t254\t255\t2.71907\n+chrV\t255\t256\t3.62543\n+chrV\t256\t257\t4.53179\n+chrV\t257\t260\t5.43815\n+chrV\t260\t269\t6.34450\n+chrV\t269\t353\t7.25086\n+chrV\t353\t355\t8.15722\n+chrV\t355\t363\t9.06358\n+chrV\t363\t366\t9.96994\n+chrV\t366\t368\t10.87629\n+chrV\t368\t375\t11.78265\n+chrV\t375\t395\t12.68901\n+chrV\t395\t400\t11.78265\n+chrV\t400\t401\t10.87629\n+chrV\t401\t402\t9.96994\n+chrV\t402\t403\t9.06358\n+chrV\t403\t404\t8.15722\n+chrV\t404\t407\t7.25086\n+chrV\t407\t416\t6.34450\n+chrV\t416\t457\t5.43815\n+chrV\t457\t500\t6.34450\n+chrV\t500\t502\t5.43815\n+chrV\t502\t510\t4.53179\n+chrV\t510\t513\t3.62543\n+chrV\t513\t515\t2.71907\n+chrV\t515\t522\t1.81272\n+chrV\t522\t560\t0.90636\n+chrV\t560\t561\t1.81272\n+chrV\t561\t566\t2.71907\n+chrV\t566\t604\t3.62543\n+chrV\t604\t707\t2.71907\n+chrV\t707\t708\t1.81272\n+chrV\t708\t713\t0.90636\n+chrV\t713\t999\t0.00000\n+chrV\t999\t1146\t0.90636\n+chrV\t1146\t1479\t0.00000\n+chrV\t1479\t1495\t0.90636\n+chrV\t1495\t1571\t1.81272\n+chrV\t1571\t1600\t2.71907\n+chrV\t1600\t1616\t3.62543\n+chrV\t1616\t1622\t4.53179\n+chrV\t1622\t1626\t5.43815\n+chrV\t1626\t1633\t4.53179\n+chrV\t1633\t1642\t5.43815\n+chrV\t1642\t1644\t4.53179\n+chrV\t1644\t1646\t5.43815\n+chrV\t1646\t1677\t6.34450\n+chrV\t1677\t1718\t7.25086\n+chrV\t1718\t1724\t6.34450\n+chrV\t1724\t1747\t7.25086\n+chrV\t1747\t1754\t6.34450\n+chrV\t1754\t1763\t7.25086\n+chrV\t1763\t1769\t6.34450\n+chrV\t1769\t1780\t5.43815\n+chrV\t1780\t1791\t4.53179\n+chrV\t1791\t1793\t3.62543\n+chrV\t1793\t1824\t2.71907\n+chrV\t1824\t1871\t1.81272\n+chrV\t1871\t1901\t0.90636\n+chrV\t1901\t1943\t0.00000\n+chrV\t1943\t2090\t0.90636\n+chrV\t2090\t2429\t0.00000\n+chrV\t2429\t2436\t0.90636\n+chrV\t2436\t2463\t1.81272\n+chrV\t2463\t2526\t2.71907\n+chrV\t2526\t2538\t3.62543\n+chrV\t2538\t2547\t4.53179\n+chrV\t2547\t2576\t5.43815\n+chrV\t2576\t2583\t4.53179\n+chrV\t2583\t2610\t3.62543\n+chrV\t2610\t2673\t2.71907\n+chrV\t2673\t2685\t1.81272\n+chrV\t2685\t2694\t0.90636\n+chrV\t2694\t3420\t0.00000\n+chrV\t3420\t3423\t0.90636\n+chrV\t3423\t3433\t1.81272\n+chrV\t3433\t3438\t2.71907\n+chrV\t3438\t3531\t3.62543\n+chrV\t3531\t3539\t4.53179\n+chrV\t3539\t3544\t5.43815\n+chrV\t3544\t3567\t6.34450\n+chrV\t3567\t3570\t5.43815\n+chrV\t3570\t3580\t4.53179\n+chrV\t3580\t3585\t3.62543\n+chrV\t3585\t3678\t2.71907\n+chrV\t3678\t3686\t1.81272\n+chrV\t3686\t3691\t0.90636\n+chrV\t3691\t3949\t0.00000\n+chrV\t3949\t3960\t0.90636\n+chrV\t3960\t3968\t1.81272\n+chrV\t3968\t3969\t2.71907\n+chrV\t3969\t3975\t3.62543\n+chrV\t3975\t4058\t4.53179\n+chrV\t4058\t4072\t5.43815\n+chrV\t4072\t4096\t6.34450\n+chrV\t4096\t4107\t5.43815\n+chrV\t4107\t4115\t4.53179\n+chrV\t4115\t4116\t3.62543\n+chrV\t4116\t4122\t2.71907\n+chrV\t4122\t4205\t1.81272\n+chrV\t4205\t4219\t0.90636\n+chrV\t4219\t6132\t0.00000\n+chrV\t6132\t6134\t0.90636\n+chrV\t6134\t6135\t1.81272\n+chrV\t6135\t6137\t2.71907\n+chrV\t6137\t6140\t3.62543\n+chrV\t6140\t6146\t4.53179\n+chrV\t6146\t6147\t5.43815\n+chrV\t6147\t6148\t6.34450\n+chrV\t6148\t6149\t7.25086\n+chrV\t6149\t6150\t8.15722\n+chrV\t6150\t6152\t9.06358\n+chrV\t6152\t6153\t9.96994\n+chrV\t6153\t6154\t10.87629\n+chrV\t6154\t6155\t11.78265\n+chrV\t6155\t6156\t12.68901\n+chrV\t6156\t6157\t13.59537\n+chrV\t6157\t6158\t14.50172\n+chrV\t6158\t6159\t15.40808\n+chrV\t6159\t6160\t16.31444\n+chrV\t6160\t6161\t17.22080\n+chrV\t6161\t6162\t18.12716\n+chrV\t6162\t6163\t19.03351\n+chrV\t6163\t6165\t19.93987\n+chrV\t6165\t6192\t20.84623\n+chrV\t6192\t6194\t21.75259\n+chrV\t6194\t6200\t22.65894\n+chrV\t6200\t6204\t23.56530\n+chrV\t6204\t6209\t24.47166\n+chrV\t6209\t6210\t25.37802\n+chrV\t6210\t6211\t26.28437\n+chrV\t6211\t6212\t27.19073\n+chrV\t6212\t6213\t28.09709\n+chrV\t6213\t6214\t29.00345\n+chrV\t6214\t6216\t29.90981\n+chrV\t6216\t6217\t30.81616\n+chrV\t6217\t6218\t31.72252\n+chrV\t6218\t6220\t32.62888\n+chrV\t6220\t6221\t33.53524\n+chrV\t6221\t6222\t34.44160\n+chrV\t6222\t6223\t35.34795\n+chrV\t6223\t6230\t36.25431\n+chrV\t6230\t6232\t37.16067\n+chrV\t6232\t6233\t38.97338\n+chrV\t6233\t6234\t39.87974\n+chrV\t6234\t6237\t40.78610\n+chrV\t6237\t6238\t41.69246\n+chrV\t6238\t6245\t42.59882\n+chrV\t6245\t6247\t44.41153\n+chrV\t6247\t6249\t45.31789\n+chrV\t6249\t6252\t46.22425\n+chrV\t6252\t6253\t47.13060\n+chrV\t6253\t6254\t48.03696\n+chrV\t6254\t6258\t48.94332\n+chrV\t6258\t6259\t50.75603\n+chrV\t6259\t6261\t51.66239\n+chrV\t6261\t6262\t52.56875\n+chrV\t6262\t6263\t53.47511\n+chrV\t6263\t6265\t54.38147\n+chrV\t6265\t6266\t55.28782\n+chrV\t6266\t6267\t56.19418\n+chrV\t6267\t6268\t57.10054\n+chrV\t6268\t6269\t58.00690\n+chrV\t6269\t6271\t5'..b'82\n+chrV\t33678\t33681\t41.69246\n+chrV\t33681\t33682\t40.78610\n+chrV\t33682\t33683\t41.69246\n+chrV\t33683\t33684\t42.59882\n+chrV\t33684\t33685\t44.41153\n+chrV\t33685\t33686\t45.31789\n+chrV\t33686\t33688\t46.22425\n+chrV\t33688\t33689\t47.13060\n+chrV\t33689\t33690\t48.03696\n+chrV\t33690\t33694\t49.84968\n+chrV\t33694\t33695\t51.66239\n+chrV\t33695\t33703\t53.47511\n+chrV\t33703\t33704\t52.56875\n+chrV\t33704\t33705\t53.47511\n+chrV\t33705\t33707\t54.38147\n+chrV\t33707\t33709\t55.28782\n+chrV\t33709\t33711\t56.19418\n+chrV\t33711\t33712\t57.10054\n+chrV\t33712\t33713\t58.00690\n+chrV\t33713\t33715\t58.91325\n+chrV\t33715\t33717\t59.81961\n+chrV\t33717\t33721\t60.72597\n+chrV\t33721\t33726\t62.53868\n+chrV\t33726\t33727\t61.63233\n+chrV\t33727\t33729\t60.72597\n+chrV\t33729\t33731\t61.63233\n+chrV\t33731\t33734\t62.53868\n+chrV\t33734\t33735\t61.63233\n+chrV\t33735\t33738\t60.72597\n+chrV\t33738\t33740\t59.81961\n+chrV\t33740\t33744\t58.91325\n+chrV\t33744\t33747\t59.81961\n+chrV\t33747\t33749\t58.91325\n+chrV\t33749\t33751\t58.00690\n+chrV\t33751\t33754\t57.10054\n+chrV\t33754\t33756\t58.00690\n+chrV\t33756\t33757\t58.91325\n+chrV\t33757\t33758\t57.10054\n+chrV\t33758\t33759\t56.19418\n+chrV\t33759\t33767\t57.10054\n+chrV\t33767\t33768\t58.00690\n+chrV\t33768\t33770\t57.10054\n+chrV\t33770\t33772\t58.00690\n+chrV\t33772\t33773\t58.91325\n+chrV\t33773\t33775\t59.81961\n+chrV\t33775\t33776\t58.91325\n+chrV\t33776\t33777\t58.00690\n+chrV\t33777\t33779\t59.81961\n+chrV\t33779\t33781\t60.72597\n+chrV\t33781\t33782\t62.53868\n+chrV\t33782\t33783\t63.44505\n+chrV\t33783\t33790\t64.35140\n+chrV\t33790\t33791\t65.25776\n+chrV\t33791\t33796\t66.16412\n+chrV\t33796\t33797\t67.97683\n+chrV\t33797\t33798\t67.07047\n+chrV\t33798\t33800\t67.97683\n+chrV\t33800\t33801\t67.07047\n+chrV\t33801\t33805\t67.97683\n+chrV\t33805\t33808\t68.88319\n+chrV\t33808\t33809\t69.78955\n+chrV\t33809\t33810\t70.69591\n+chrV\t33810\t33811\t71.60226\n+chrV\t33811\t33817\t72.50862\n+chrV\t33817\t33818\t73.41498\n+chrV\t33818\t33820\t72.50862\n+chrV\t33820\t33821\t73.41498\n+chrV\t33821\t33822\t74.32133\n+chrV\t33822\t33823\t76.13405\n+chrV\t33823\t33824\t77.04041\n+chrV\t33824\t33825\t77.94677\n+chrV\t33825\t33826\t78.85313\n+chrV\t33826\t33827\t79.75948\n+chrV\t33827\t33829\t80.66584\n+chrV\t33829\t33830\t79.75948\n+chrV\t33830\t33831\t78.85313\n+chrV\t33831\t33833\t77.04041\n+chrV\t33833\t33835\t76.13405\n+chrV\t33835\t33836\t75.22769\n+chrV\t33836\t33837\t74.32133\n+chrV\t33837\t33841\t72.50862\n+chrV\t33841\t33842\t71.60226\n+chrV\t33842\t33845\t70.69591\n+chrV\t33845\t33846\t71.60226\n+chrV\t33846\t33848\t70.69591\n+chrV\t33848\t33849\t71.60226\n+chrV\t33849\t33850\t72.50862\n+chrV\t33850\t33851\t73.41498\n+chrV\t33851\t33852\t72.50862\n+chrV\t33852\t33854\t71.60226\n+chrV\t33854\t33856\t70.69591\n+chrV\t33856\t33857\t69.78955\n+chrV\t33857\t33859\t68.88319\n+chrV\t33859\t33860\t67.97683\n+chrV\t33860\t33861\t67.07047\n+chrV\t33861\t33862\t67.97683\n+chrV\t33862\t33864\t67.07047\n+chrV\t33864\t33866\t66.16412\n+chrV\t33866\t33868\t67.07047\n+chrV\t33868\t33869\t65.25776\n+chrV\t33869\t33871\t64.35140\n+chrV\t33871\t33872\t65.25776\n+chrV\t33872\t33873\t66.16412\n+chrV\t33873\t33874\t67.07047\n+chrV\t33874\t33876\t66.16412\n+chrV\t33876\t33878\t65.25776\n+chrV\t33878\t33881\t64.35140\n+chrV\t33881\t33882\t63.44505\n+chrV\t33882\t33884\t64.35140\n+chrV\t33884\t33886\t66.16412\n+chrV\t33886\t33891\t67.07047\n+chrV\t33891\t33893\t66.16412\n+chrV\t33893\t33897\t65.25776\n+chrV\t33897\t33898\t66.16412\n+chrV\t33898\t33900\t67.07047\n+chrV\t33900\t33901\t66.16412\n+chrV\t33901\t33903\t65.25776\n+chrV\t33903\t33904\t64.35140\n+chrV\t33904\t33905\t65.25776\n+chrV\t33905\t33908\t66.16412\n+chrV\t33908\t33909\t67.07047\n+chrV\t33909\t33913\t67.97683\n+chrV\t33913\t33915\t68.88319\n+chrV\t33915\t33919\t69.78955\n+chrV\t33919\t33920\t68.88319\n+chrV\t33920\t33921\t67.97683\n+chrV\t33921\t33922\t68.88319\n+chrV\t33922\t33923\t69.78955\n+chrV\t33923\t33924\t70.69591\n+chrV\t33924\t33925\t69.78955\n+chrV\t33925\t33926\t68.88319\n+chrV\t33926\t33927\t67.97683\n+chrV\t33927\t33928\t67.07047\n+chrV\t33928\t33929\t66.16412\n+chrV\t33929\t33930\t64.35140\n+chrV\t33930\t33931\t63.44505\n+chrV\t33931\t33935\t62.53868\n+chrV\t33935\t33937\t63.44505\n+chrV\t33937\t33943\t62.53868\n+chrV\t33943\t33945\t61.63233\n+chrV\t33945\t33947\t60.72597\n+chrV\t33947\t33948\t59.81961\n+chrV\t33948\t33950\t58.91325\n+chrV\t33950\t33951\t58.00690\n+chrV\t33951\t33952\t58.91325\n+chrV\t33952\t33954\t57.10054\n+chrV\t33954\t33955\t56.19418\n+chrV\t33955\t33956\t55.28782\n' |
| b |
| diff -r 56e104999978 -r beb902da6e5f test-data/bdgdiff_t2.bdg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bdgdiff_t2.bdg Sat Apr 08 08:28:57 2017 -0400 |
| b |
| b'@@ -0,0 +1,10000 @@\n+chrV\t0\t253\t0.00000\n+chrV\t253\t261\t0.45810\n+chrV\t261\t363\t0.91619\n+chrV\t363\t366\t1.37429\n+chrV\t366\t373\t1.83239\n+chrV\t373\t400\t2.29048\n+chrV\t400\t408\t1.83239\n+chrV\t408\t510\t1.37429\n+chrV\t510\t513\t0.91619\n+chrV\t513\t520\t0.45810\n+chrV\t520\t1586\t0.00000\n+chrV\t1586\t1597\t0.45810\n+chrV\t1597\t1608\t0.91619\n+chrV\t1608\t1624\t1.37429\n+chrV\t1624\t1633\t1.83239\n+chrV\t1633\t1703\t2.29048\n+chrV\t1703\t1708\t2.74858\n+chrV\t1708\t1733\t3.20667\n+chrV\t1733\t1734\t2.74858\n+chrV\t1734\t1744\t3.20667\n+chrV\t1744\t1755\t2.74858\n+chrV\t1755\t1771\t2.29048\n+chrV\t1771\t1780\t1.83239\n+chrV\t1780\t1850\t1.37429\n+chrV\t1850\t1855\t0.91619\n+chrV\t1855\t1881\t0.45810\n+chrV\t1881\t2538\t0.00000\n+chrV\t2538\t2546\t0.45810\n+chrV\t2546\t2685\t0.91619\n+chrV\t2685\t2693\t0.45810\n+chrV\t2693\t3546\t0.00000\n+chrV\t3546\t3693\t0.45810\n+chrV\t3693\t3954\t0.00000\n+chrV\t3954\t4060\t0.45810\n+chrV\t4060\t4065\t0.91619\n+chrV\t4065\t4071\t1.37429\n+chrV\t4071\t4101\t1.83239\n+chrV\t4101\t4207\t1.37429\n+chrV\t4207\t4212\t0.91619\n+chrV\t4212\t4218\t0.45810\n+chrV\t4218\t6127\t0.00000\n+chrV\t6127\t6128\t0.45810\n+chrV\t6128\t6131\t0.91619\n+chrV\t6131\t6133\t1.37429\n+chrV\t6133\t6135\t1.83239\n+chrV\t6135\t6146\t2.29048\n+chrV\t6146\t6149\t2.74858\n+chrV\t6149\t6150\t3.20667\n+chrV\t6150\t6151\t3.66477\n+chrV\t6151\t6152\t4.12287\n+chrV\t6152\t6153\t4.58096\n+chrV\t6153\t6154\t5.03906\n+chrV\t6154\t6156\t5.49716\n+chrV\t6156\t6160\t5.95525\n+chrV\t6160\t6161\t6.41335\n+chrV\t6161\t6162\t6.87144\n+chrV\t6162\t6192\t7.32954\n+chrV\t6192\t6195\t7.78764\n+chrV\t6195\t6198\t8.24573\n+chrV\t6198\t6200\t8.70383\n+chrV\t6200\t6202\t9.16193\n+chrV\t6202\t6203\t9.62002\n+chrV\t6203\t6208\t10.07812\n+chrV\t6208\t6210\t10.53622\n+chrV\t6210\t6211\t10.99431\n+chrV\t6211\t6212\t11.45241\n+chrV\t6212\t6213\t11.91050\n+chrV\t6213\t6214\t12.36860\n+chrV\t6214\t6217\t12.82670\n+chrV\t6217\t6218\t13.28479\n+chrV\t6218\t6219\t13.74289\n+chrV\t6219\t6222\t14.20099\n+chrV\t6222\t6223\t14.65908\n+chrV\t6223\t6224\t15.11718\n+chrV\t6224\t6231\t15.57528\n+chrV\t6231\t6232\t16.03337\n+chrV\t6232\t6233\t16.49147\n+chrV\t6233\t6234\t16.94956\n+chrV\t6234\t6236\t17.40766\n+chrV\t6236\t6237\t17.86576\n+chrV\t6237\t6238\t18.78195\n+chrV\t6238\t6239\t19.24005\n+chrV\t6239\t6240\t19.69814\n+chrV\t6240\t6245\t20.15624\n+chrV\t6245\t6246\t20.61433\n+chrV\t6246\t6249\t21.07243\n+chrV\t6249\t6252\t21.53053\n+chrV\t6252\t6253\t21.98862\n+chrV\t6253\t6256\t22.44672\n+chrV\t6256\t6260\t22.90482\n+chrV\t6260\t6262\t23.36291\n+chrV\t6262\t6264\t23.82101\n+chrV\t6264\t6266\t24.27911\n+chrV\t6266\t6267\t24.73720\n+chrV\t6267\t6271\t25.19530\n+chrV\t6271\t6278\t25.65339\n+chrV\t6278\t6280\t25.19530\n+chrV\t6280\t6282\t24.73720\n+chrV\t6282\t6283\t24.27911\n+chrV\t6283\t6296\t24.73720\n+chrV\t6296\t6297\t24.27911\n+chrV\t6297\t6299\t23.82101\n+chrV\t6299\t6300\t23.36291\n+chrV\t6300\t6301\t22.90482\n+chrV\t6301\t6302\t22.44672\n+chrV\t6302\t6305\t22.90482\n+chrV\t6305\t6308\t23.36291\n+chrV\t6308\t6309\t22.90482\n+chrV\t6309\t6311\t22.44672\n+chrV\t6311\t6313\t22.90482\n+chrV\t6313\t6322\t23.36291\n+chrV\t6322\t6325\t23.82101\n+chrV\t6325\t6326\t24.73720\n+chrV\t6326\t6328\t25.19530\n+chrV\t6328\t6329\t26.11149\n+chrV\t6329\t6331\t27.02768\n+chrV\t6331\t6333\t27.48578\n+chrV\t6333\t6334\t27.94388\n+chrV\t6334\t6336\t28.40197\n+chrV\t6336\t6337\t28.86007\n+chrV\t6337\t6338\t29.77626\n+chrV\t6338\t6340\t30.23436\n+chrV\t6340\t6341\t30.69245\n+chrV\t6341\t6343\t31.15055\n+chrV\t6343\t6344\t31.60865\n+chrV\t6344\t6346\t32.06674\n+chrV\t6346\t6347\t32.52484\n+chrV\t6347\t6350\t32.06674\n+chrV\t6350\t6351\t31.60865\n+chrV\t6351\t6354\t32.52484\n+chrV\t6354\t6355\t32.98294\n+chrV\t6355\t6357\t32.52484\n+chrV\t6357\t6359\t32.06674\n+chrV\t6359\t6360\t31.60865\n+chrV\t6360\t6362\t31.15055\n+chrV\t6362\t6363\t31.60865\n+chrV\t6363\t6365\t32.06674\n+chrV\t6365\t6366\t31.60865\n+chrV\t6366\t6368\t31.15055\n+chrV\t6368\t6370\t31.60865\n+chrV\t6370\t6371\t31.15055\n+chrV\t6371\t6377\t30.69245\n+chrV\t6377\t6380\t31.15055\n+chrV\t6380\t6382\t30.69245\n+chrV\t6382\t6383\t31.15055\n+chrV\t6383\t6384\t30.69245\n+chrV\t6384\t6385\t29.77626\n+chrV\t6385\t6386\t29.31816\n+chrV\t6386\t6387\t28.86007\n+chrV\t6387\t6389\t28.40197\n+chrV\t6389\t6392\t28.86007\n+chrV\t6392\t6393\t28.40197\n+chrV\t6393\t6394\t27.94388\n+chrV\t6394\t6395\t28.40197\n+chrV\t6395\t6396\t29.31816\n+chrV\t6396\t6398\t28.86007\n+chrV\t6398\t6399\t29.31816\n+chrV\t6399\t6403\t28.86007\n+chrV\t6403\t6407\t28.40197\n+chrV\t6407\t6408\t27.94388\n+chrV\t6408\t6409\t28.40197\n+chrV\t6409\t6411\t27.94388\n+chrV\t6411\t641'..b'\t59837\t59841\t9.16193\n+chrV\t59841\t59842\t8.70383\n+chrV\t59842\t59850\t8.24573\n+chrV\t59850\t59853\t8.70383\n+chrV\t59853\t59854\t8.24573\n+chrV\t59854\t59857\t7.78764\n+chrV\t59857\t59862\t8.24573\n+chrV\t59862\t59865\t7.78764\n+chrV\t59865\t59877\t8.24573\n+chrV\t59877\t59889\t8.70383\n+chrV\t59889\t59893\t9.16193\n+chrV\t59893\t59896\t8.70383\n+chrV\t59896\t59900\t8.24573\n+chrV\t59900\t59906\t7.78764\n+chrV\t59906\t59909\t8.24573\n+chrV\t59909\t59921\t8.70383\n+chrV\t59921\t59922\t8.24573\n+chrV\t59922\t59931\t8.70383\n+chrV\t59931\t59944\t9.16193\n+chrV\t59944\t59945\t8.70383\n+chrV\t59945\t59946\t8.24573\n+chrV\t59946\t59947\t7.78764\n+chrV\t59947\t59956\t8.24573\n+chrV\t59956\t59958\t8.70383\n+chrV\t59958\t59961\t9.16193\n+chrV\t59961\t59962\t8.70383\n+chrV\t59962\t59964\t8.24573\n+chrV\t59964\t59968\t8.70383\n+chrV\t59968\t59970\t8.24573\n+chrV\t59970\t59973\t7.78764\n+chrV\t59973\t59979\t7.32954\n+chrV\t59979\t59984\t6.87144\n+chrV\t59984\t59985\t6.41335\n+chrV\t59985\t59987\t6.87144\n+chrV\t59987\t59990\t7.32954\n+chrV\t59990\t59997\t7.78764\n+chrV\t59997\t59998\t7.32954\n+chrV\t59998\t60004\t7.78764\n+chrV\t60004\t60012\t7.32954\n+chrV\t60012\t60021\t6.87144\n+chrV\t60021\t60024\t7.32954\n+chrV\t60024\t60036\t6.87144\n+chrV\t60036\t60043\t6.41335\n+chrV\t60043\t60053\t6.87144\n+chrV\t60053\t60056\t6.41335\n+chrV\t60056\t60069\t5.95525\n+chrV\t60069\t60075\t5.49716\n+chrV\t60075\t60078\t5.95525\n+chrV\t60078\t60084\t5.49716\n+chrV\t60084\t60087\t5.03906\n+chrV\t60087\t60094\t5.49716\n+chrV\t60094\t60098\t5.03906\n+chrV\t60098\t60100\t5.49716\n+chrV\t60100\t60105\t5.95525\n+chrV\t60105\t60108\t5.49716\n+chrV\t60108\t60114\t5.95525\n+chrV\t60114\t60118\t6.41335\n+chrV\t60118\t60122\t6.87144\n+chrV\t60122\t60131\t7.32954\n+chrV\t60131\t60132\t7.78764\n+chrV\t60132\t60134\t7.32954\n+chrV\t60134\t60137\t6.87144\n+chrV\t60137\t60139\t6.41335\n+chrV\t60139\t60145\t6.87144\n+chrV\t60145\t60161\t6.41335\n+chrV\t60161\t60168\t6.87144\n+chrV\t60168\t60174\t6.41335\n+chrV\t60174\t60179\t6.87144\n+chrV\t60179\t60181\t7.32954\n+chrV\t60181\t60190\t7.78764\n+chrV\t60190\t60212\t7.32954\n+chrV\t60212\t60222\t7.78764\n+chrV\t60222\t60233\t7.32954\n+chrV\t60233\t60234\t7.78764\n+chrV\t60234\t60245\t7.32954\n+chrV\t60245\t60247\t6.87144\n+chrV\t60247\t60249\t6.41335\n+chrV\t60249\t60250\t6.87144\n+chrV\t60250\t60254\t6.41335\n+chrV\t60254\t60255\t6.87144\n+chrV\t60255\t60258\t6.41335\n+chrV\t60258\t60261\t5.95525\n+chrV\t60261\t60265\t5.49716\n+chrV\t60265\t60269\t5.03906\n+chrV\t60269\t60277\t4.58096\n+chrV\t60277\t60278\t5.03906\n+chrV\t60278\t60280\t4.58096\n+chrV\t60280\t60286\t5.03906\n+chrV\t60286\t60308\t4.58096\n+chrV\t60308\t60309\t4.12287\n+chrV\t60309\t60310\t4.58096\n+chrV\t60310\t60317\t5.03906\n+chrV\t60317\t60321\t5.49716\n+chrV\t60321\t60328\t5.03906\n+chrV\t60328\t60330\t4.58096\n+chrV\t60330\t60334\t5.03906\n+chrV\t60334\t60344\t5.49716\n+chrV\t60344\t60350\t5.95525\n+chrV\t60350\t60359\t6.41335\n+chrV\t60359\t60378\t5.95525\n+chrV\t60378\t60380\t6.41335\n+chrV\t60380\t60396\t5.95525\n+chrV\t60396\t60400\t5.49716\n+chrV\t60400\t60401\t5.95525\n+chrV\t60401\t60407\t5.49716\n+chrV\t60407\t60414\t5.95525\n+chrV\t60414\t60417\t6.41335\n+chrV\t60417\t60424\t6.87144\n+chrV\t60424\t60427\t6.41335\n+chrV\t60427\t60431\t5.95525\n+chrV\t60431\t60456\t6.41335\n+chrV\t60456\t60457\t5.95525\n+chrV\t60457\t60464\t5.49716\n+chrV\t60464\t60473\t5.03906\n+chrV\t60473\t60475\t4.58096\n+chrV\t60475\t60477\t5.03906\n+chrV\t60477\t60481\t4.58096\n+chrV\t60481\t60482\t4.12287\n+chrV\t60482\t60484\t4.58096\n+chrV\t60484\t60485\t5.03906\n+chrV\t60485\t60488\t5.49716\n+chrV\t60488\t60491\t5.95525\n+chrV\t60491\t60497\t5.49716\n+chrV\t60497\t60512\t5.03906\n+chrV\t60512\t60519\t5.49716\n+chrV\t60519\t60525\t5.95525\n+chrV\t60525\t60535\t5.49716\n+chrV\t60535\t60547\t6.41335\n+chrV\t60547\t60552\t5.95525\n+chrV\t60552\t60554\t6.41335\n+chrV\t60554\t60559\t5.95525\n+chrV\t60559\t60561\t6.41335\n+chrV\t60561\t60564\t5.95525\n+chrV\t60564\t60578\t5.49716\n+chrV\t60578\t60593\t5.03906\n+chrV\t60593\t60597\t5.49716\n+chrV\t60597\t60603\t5.95525\n+chrV\t60603\t60605\t6.41335\n+chrV\t60605\t60606\t6.87144\n+chrV\t60606\t60612\t7.32954\n+chrV\t60612\t60622\t7.78764\n+chrV\t60622\t60629\t7.32954\n+chrV\t60629\t60631\t6.87144\n+chrV\t60631\t60635\t6.41335\n+chrV\t60635\t60641\t5.95525\n+chrV\t60641\t60659\t6.41335\n+chrV\t60659\t60666\t5.95525\n+chrV\t60666\t60670\t5.49716\n+chrV\t60670\t60675\t5.95525\n+chrV\t60675\t60682\t6.41335\n+chrV\t60682\t60699\t5.49716\n+chrV\t60699\t60706\t5.03906\n+chrV\t60706\t60719\t4.58096\n+chrV\t60719\t60720\t5.03906\n' |
| b |
| diff -r 56e104999978 -r beb902da6e5f test-data/bdgpeakcall_input.bdg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bdgpeakcall_input.bdg Sat Apr 08 08:28:57 2017 -0400 |
| b |
| b'@@ -0,0 +1,10000 @@\n+chrV\t0\t248\t0.00000\n+chrV\t248\t253\t0.90636\n+chrV\t253\t254\t1.81272\n+chrV\t254\t255\t2.71907\n+chrV\t255\t256\t3.62543\n+chrV\t256\t257\t4.53179\n+chrV\t257\t260\t5.43815\n+chrV\t260\t269\t6.34450\n+chrV\t269\t353\t7.25086\n+chrV\t353\t355\t8.15722\n+chrV\t355\t363\t9.06358\n+chrV\t363\t366\t9.96994\n+chrV\t366\t368\t10.87629\n+chrV\t368\t375\t11.78265\n+chrV\t375\t395\t12.68901\n+chrV\t395\t400\t11.78265\n+chrV\t400\t401\t10.87629\n+chrV\t401\t402\t9.96994\n+chrV\t402\t403\t9.06358\n+chrV\t403\t404\t8.15722\n+chrV\t404\t407\t7.25086\n+chrV\t407\t416\t6.34450\n+chrV\t416\t457\t5.43815\n+chrV\t457\t500\t6.34450\n+chrV\t500\t502\t5.43815\n+chrV\t502\t510\t4.53179\n+chrV\t510\t513\t3.62543\n+chrV\t513\t515\t2.71907\n+chrV\t515\t522\t1.81272\n+chrV\t522\t560\t0.90636\n+chrV\t560\t561\t1.81272\n+chrV\t561\t566\t2.71907\n+chrV\t566\t604\t3.62543\n+chrV\t604\t707\t2.71907\n+chrV\t707\t708\t1.81272\n+chrV\t708\t713\t0.90636\n+chrV\t713\t999\t0.00000\n+chrV\t999\t1146\t0.90636\n+chrV\t1146\t1479\t0.00000\n+chrV\t1479\t1495\t0.90636\n+chrV\t1495\t1571\t1.81272\n+chrV\t1571\t1600\t2.71907\n+chrV\t1600\t1616\t3.62543\n+chrV\t1616\t1622\t4.53179\n+chrV\t1622\t1626\t5.43815\n+chrV\t1626\t1633\t4.53179\n+chrV\t1633\t1642\t5.43815\n+chrV\t1642\t1644\t4.53179\n+chrV\t1644\t1646\t5.43815\n+chrV\t1646\t1677\t6.34450\n+chrV\t1677\t1718\t7.25086\n+chrV\t1718\t1724\t6.34450\n+chrV\t1724\t1747\t7.25086\n+chrV\t1747\t1754\t6.34450\n+chrV\t1754\t1763\t7.25086\n+chrV\t1763\t1769\t6.34450\n+chrV\t1769\t1780\t5.43815\n+chrV\t1780\t1791\t4.53179\n+chrV\t1791\t1793\t3.62543\n+chrV\t1793\t1824\t2.71907\n+chrV\t1824\t1871\t1.81272\n+chrV\t1871\t1901\t0.90636\n+chrV\t1901\t1943\t0.00000\n+chrV\t1943\t2090\t0.90636\n+chrV\t2090\t2429\t0.00000\n+chrV\t2429\t2436\t0.90636\n+chrV\t2436\t2463\t1.81272\n+chrV\t2463\t2526\t2.71907\n+chrV\t2526\t2538\t3.62543\n+chrV\t2538\t2547\t4.53179\n+chrV\t2547\t2576\t5.43815\n+chrV\t2576\t2583\t4.53179\n+chrV\t2583\t2610\t3.62543\n+chrV\t2610\t2673\t2.71907\n+chrV\t2673\t2685\t1.81272\n+chrV\t2685\t2694\t0.90636\n+chrV\t2694\t3420\t0.00000\n+chrV\t3420\t3423\t0.90636\n+chrV\t3423\t3433\t1.81272\n+chrV\t3433\t3438\t2.71907\n+chrV\t3438\t3531\t3.62543\n+chrV\t3531\t3539\t4.53179\n+chrV\t3539\t3544\t5.43815\n+chrV\t3544\t3567\t6.34450\n+chrV\t3567\t3570\t5.43815\n+chrV\t3570\t3580\t4.53179\n+chrV\t3580\t3585\t3.62543\n+chrV\t3585\t3678\t2.71907\n+chrV\t3678\t3686\t1.81272\n+chrV\t3686\t3691\t0.90636\n+chrV\t3691\t3949\t0.00000\n+chrV\t3949\t3960\t0.90636\n+chrV\t3960\t3968\t1.81272\n+chrV\t3968\t3969\t2.71907\n+chrV\t3969\t3975\t3.62543\n+chrV\t3975\t4058\t4.53179\n+chrV\t4058\t4072\t5.43815\n+chrV\t4072\t4096\t6.34450\n+chrV\t4096\t4107\t5.43815\n+chrV\t4107\t4115\t4.53179\n+chrV\t4115\t4116\t3.62543\n+chrV\t4116\t4122\t2.71907\n+chrV\t4122\t4205\t1.81272\n+chrV\t4205\t4219\t0.90636\n+chrV\t4219\t6132\t0.00000\n+chrV\t6132\t6134\t0.90636\n+chrV\t6134\t6135\t1.81272\n+chrV\t6135\t6137\t2.71907\n+chrV\t6137\t6140\t3.62543\n+chrV\t6140\t6146\t4.53179\n+chrV\t6146\t6147\t5.43815\n+chrV\t6147\t6148\t6.34450\n+chrV\t6148\t6149\t7.25086\n+chrV\t6149\t6150\t8.15722\n+chrV\t6150\t6152\t9.06358\n+chrV\t6152\t6153\t9.96994\n+chrV\t6153\t6154\t10.87629\n+chrV\t6154\t6155\t11.78265\n+chrV\t6155\t6156\t12.68901\n+chrV\t6156\t6157\t13.59537\n+chrV\t6157\t6158\t14.50172\n+chrV\t6158\t6159\t15.40808\n+chrV\t6159\t6160\t16.31444\n+chrV\t6160\t6161\t17.22080\n+chrV\t6161\t6162\t18.12716\n+chrV\t6162\t6163\t19.03351\n+chrV\t6163\t6165\t19.93987\n+chrV\t6165\t6192\t20.84623\n+chrV\t6192\t6194\t21.75259\n+chrV\t6194\t6200\t22.65894\n+chrV\t6200\t6204\t23.56530\n+chrV\t6204\t6209\t24.47166\n+chrV\t6209\t6210\t25.37802\n+chrV\t6210\t6211\t26.28437\n+chrV\t6211\t6212\t27.19073\n+chrV\t6212\t6213\t28.09709\n+chrV\t6213\t6214\t29.00345\n+chrV\t6214\t6216\t29.90981\n+chrV\t6216\t6217\t30.81616\n+chrV\t6217\t6218\t31.72252\n+chrV\t6218\t6220\t32.62888\n+chrV\t6220\t6221\t33.53524\n+chrV\t6221\t6222\t34.44160\n+chrV\t6222\t6223\t35.34795\n+chrV\t6223\t6230\t36.25431\n+chrV\t6230\t6232\t37.16067\n+chrV\t6232\t6233\t38.97338\n+chrV\t6233\t6234\t39.87974\n+chrV\t6234\t6237\t40.78610\n+chrV\t6237\t6238\t41.69246\n+chrV\t6238\t6245\t42.59882\n+chrV\t6245\t6247\t44.41153\n+chrV\t6247\t6249\t45.31789\n+chrV\t6249\t6252\t46.22425\n+chrV\t6252\t6253\t47.13060\n+chrV\t6253\t6254\t48.03696\n+chrV\t6254\t6258\t48.94332\n+chrV\t6258\t6259\t50.75603\n+chrV\t6259\t6261\t51.66239\n+chrV\t6261\t6262\t52.56875\n+chrV\t6262\t6263\t53.47511\n+chrV\t6263\t6265\t54.38147\n+chrV\t6265\t6266\t55.28782\n+chrV\t6266\t6267\t56.19418\n+chrV\t6267\t6268\t57.10054\n+chrV\t6268\t6269\t58.00690\n+chrV\t6269\t6271\t5'..b'82\n+chrV\t33678\t33681\t41.69246\n+chrV\t33681\t33682\t40.78610\n+chrV\t33682\t33683\t41.69246\n+chrV\t33683\t33684\t42.59882\n+chrV\t33684\t33685\t44.41153\n+chrV\t33685\t33686\t45.31789\n+chrV\t33686\t33688\t46.22425\n+chrV\t33688\t33689\t47.13060\n+chrV\t33689\t33690\t48.03696\n+chrV\t33690\t33694\t49.84968\n+chrV\t33694\t33695\t51.66239\n+chrV\t33695\t33703\t53.47511\n+chrV\t33703\t33704\t52.56875\n+chrV\t33704\t33705\t53.47511\n+chrV\t33705\t33707\t54.38147\n+chrV\t33707\t33709\t55.28782\n+chrV\t33709\t33711\t56.19418\n+chrV\t33711\t33712\t57.10054\n+chrV\t33712\t33713\t58.00690\n+chrV\t33713\t33715\t58.91325\n+chrV\t33715\t33717\t59.81961\n+chrV\t33717\t33721\t60.72597\n+chrV\t33721\t33726\t62.53868\n+chrV\t33726\t33727\t61.63233\n+chrV\t33727\t33729\t60.72597\n+chrV\t33729\t33731\t61.63233\n+chrV\t33731\t33734\t62.53868\n+chrV\t33734\t33735\t61.63233\n+chrV\t33735\t33738\t60.72597\n+chrV\t33738\t33740\t59.81961\n+chrV\t33740\t33744\t58.91325\n+chrV\t33744\t33747\t59.81961\n+chrV\t33747\t33749\t58.91325\n+chrV\t33749\t33751\t58.00690\n+chrV\t33751\t33754\t57.10054\n+chrV\t33754\t33756\t58.00690\n+chrV\t33756\t33757\t58.91325\n+chrV\t33757\t33758\t57.10054\n+chrV\t33758\t33759\t56.19418\n+chrV\t33759\t33767\t57.10054\n+chrV\t33767\t33768\t58.00690\n+chrV\t33768\t33770\t57.10054\n+chrV\t33770\t33772\t58.00690\n+chrV\t33772\t33773\t58.91325\n+chrV\t33773\t33775\t59.81961\n+chrV\t33775\t33776\t58.91325\n+chrV\t33776\t33777\t58.00690\n+chrV\t33777\t33779\t59.81961\n+chrV\t33779\t33781\t60.72597\n+chrV\t33781\t33782\t62.53868\n+chrV\t33782\t33783\t63.44505\n+chrV\t33783\t33790\t64.35140\n+chrV\t33790\t33791\t65.25776\n+chrV\t33791\t33796\t66.16412\n+chrV\t33796\t33797\t67.97683\n+chrV\t33797\t33798\t67.07047\n+chrV\t33798\t33800\t67.97683\n+chrV\t33800\t33801\t67.07047\n+chrV\t33801\t33805\t67.97683\n+chrV\t33805\t33808\t68.88319\n+chrV\t33808\t33809\t69.78955\n+chrV\t33809\t33810\t70.69591\n+chrV\t33810\t33811\t71.60226\n+chrV\t33811\t33817\t72.50862\n+chrV\t33817\t33818\t73.41498\n+chrV\t33818\t33820\t72.50862\n+chrV\t33820\t33821\t73.41498\n+chrV\t33821\t33822\t74.32133\n+chrV\t33822\t33823\t76.13405\n+chrV\t33823\t33824\t77.04041\n+chrV\t33824\t33825\t77.94677\n+chrV\t33825\t33826\t78.85313\n+chrV\t33826\t33827\t79.75948\n+chrV\t33827\t33829\t80.66584\n+chrV\t33829\t33830\t79.75948\n+chrV\t33830\t33831\t78.85313\n+chrV\t33831\t33833\t77.04041\n+chrV\t33833\t33835\t76.13405\n+chrV\t33835\t33836\t75.22769\n+chrV\t33836\t33837\t74.32133\n+chrV\t33837\t33841\t72.50862\n+chrV\t33841\t33842\t71.60226\n+chrV\t33842\t33845\t70.69591\n+chrV\t33845\t33846\t71.60226\n+chrV\t33846\t33848\t70.69591\n+chrV\t33848\t33849\t71.60226\n+chrV\t33849\t33850\t72.50862\n+chrV\t33850\t33851\t73.41498\n+chrV\t33851\t33852\t72.50862\n+chrV\t33852\t33854\t71.60226\n+chrV\t33854\t33856\t70.69591\n+chrV\t33856\t33857\t69.78955\n+chrV\t33857\t33859\t68.88319\n+chrV\t33859\t33860\t67.97683\n+chrV\t33860\t33861\t67.07047\n+chrV\t33861\t33862\t67.97683\n+chrV\t33862\t33864\t67.07047\n+chrV\t33864\t33866\t66.16412\n+chrV\t33866\t33868\t67.07047\n+chrV\t33868\t33869\t65.25776\n+chrV\t33869\t33871\t64.35140\n+chrV\t33871\t33872\t65.25776\n+chrV\t33872\t33873\t66.16412\n+chrV\t33873\t33874\t67.07047\n+chrV\t33874\t33876\t66.16412\n+chrV\t33876\t33878\t65.25776\n+chrV\t33878\t33881\t64.35140\n+chrV\t33881\t33882\t63.44505\n+chrV\t33882\t33884\t64.35140\n+chrV\t33884\t33886\t66.16412\n+chrV\t33886\t33891\t67.07047\n+chrV\t33891\t33893\t66.16412\n+chrV\t33893\t33897\t65.25776\n+chrV\t33897\t33898\t66.16412\n+chrV\t33898\t33900\t67.07047\n+chrV\t33900\t33901\t66.16412\n+chrV\t33901\t33903\t65.25776\n+chrV\t33903\t33904\t64.35140\n+chrV\t33904\t33905\t65.25776\n+chrV\t33905\t33908\t66.16412\n+chrV\t33908\t33909\t67.07047\n+chrV\t33909\t33913\t67.97683\n+chrV\t33913\t33915\t68.88319\n+chrV\t33915\t33919\t69.78955\n+chrV\t33919\t33920\t68.88319\n+chrV\t33920\t33921\t67.97683\n+chrV\t33921\t33922\t68.88319\n+chrV\t33922\t33923\t69.78955\n+chrV\t33923\t33924\t70.69591\n+chrV\t33924\t33925\t69.78955\n+chrV\t33925\t33926\t68.88319\n+chrV\t33926\t33927\t67.97683\n+chrV\t33927\t33928\t67.07047\n+chrV\t33928\t33929\t66.16412\n+chrV\t33929\t33930\t64.35140\n+chrV\t33930\t33931\t63.44505\n+chrV\t33931\t33935\t62.53868\n+chrV\t33935\t33937\t63.44505\n+chrV\t33937\t33943\t62.53868\n+chrV\t33943\t33945\t61.63233\n+chrV\t33945\t33947\t60.72597\n+chrV\t33947\t33948\t59.81961\n+chrV\t33948\t33950\t58.91325\n+chrV\t33950\t33951\t58.00690\n+chrV\t33951\t33952\t58.91325\n+chrV\t33952\t33954\t57.10054\n+chrV\t33954\t33955\t56.19418\n+chrV\t33955\t33956\t55.28782\n' |
| b |
| diff -r 56e104999978 -r beb902da6e5f test-data/bdgpeakcall_output_cutoff.bdg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bdgpeakcall_output_cutoff.bdg Sat Apr 08 08:28:57 2017 -0400 |
| b |
| @@ -0,0 +1,50 @@ +pscore npeaks lpeaks avelpeak +42.15 9 2890 321.00 +41.30 10 3512 351.00 +40.46 10 3709 370.00 +39.62 12 4282 356.00 +38.77 13 4699 361.00 +37.93 16 5998 374.00 +37.09 20 8291 414.00 +36.24 21 9508 452.00 +35.40 21 9508 452.00 +34.56 22 10703 486.00 +33.72 23 11996 521.00 +32.87 25 13676 547.00 +32.03 24 14823 617.00 +31.19 25 16358 654.00 +30.34 26 17951 690.00 +29.50 26 18894 726.00 +28.66 23 19550 850.00 +27.82 21 20518 977.00 +26.97 19 21125 1111.00 +26.13 15 21694 1446.00 +25.29 13 22298 1715.00 +24.44 12 22768 1897.00 +23.60 12 22768 1897.00 +22.76 11 22971 2088.00 +21.92 8 23309 2913.00 +21.07 8 23492 2936.00 +20.23 8 23982 2997.00 +19.39 8 24156 3019.00 +18.54 7 24532 3504.00 +17.70 5 24701 4940.00 +16.86 6 25008 4168.00 +16.01 6 25083 4180.00 +15.17 5 25440 5088.00 +14.33 5 25609 5121.00 +13.49 4 26022 6505.00 +12.64 4 26337 6584.00 +11.80 4 26337 6584.00 +10.96 4 26409 6602.00 +10.11 4 26751 6687.00 +9.27 3 27049 9016.00 +8.43 3 27088 9029.00 +7.59 2 27139 13569.00 +6.74 2 27142 13571.00 +5.90 2 27152 13576.00 +5.06 3 27416 9138.00 +4.22 4 27706 6926.00 +3.37 3 27769 9256.00 +2.53 6 28710 4785.00 +1.69 7 29161 4165.00 |
| b |
| diff -r 56e104999978 -r beb902da6e5f test-data/bdgrandsample_output.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bdgrandsample_output.bed Sat Apr 08 08:28:57 2017 -0400 |
| b |
| b'@@ -0,0 +1,159966 @@\n+chr1\t565533\t565633\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\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\t569553\t569653\t.\t.\t+\n+chr1\t569554\t569654\t.\t.\t+\n+chr1\t569694\t569794\t.\t.\t+\n+chr1\t713744\t713844\t.\t.\t+\n+chr1\t714193\t714293\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\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\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\t1204173\t1204273\t.\t.\t+\n+chr1\t1220903\t1221003\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\t1318226\t1318326\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\t1543963\t1544063\t.\t.\t+\n+chr1\t1555484\t1555584\t.\t.\t+\n+chr1\t1590594\t1590694\t.\t.\t+\n+chr1\t1590667\t1590767\t.\t.\t+\n+chr1\t1655694\t1655794\t.\t.\t+\n+chr1\t1680362\t1680462\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\t1743660\t1743760\t.\t.\t+\n+chr1\t1756325\t1756425\t.\t.\t+\n+chr1\t1759509\t1759609\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\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\t2071198\t2071298\t.\t.\t+\n+chr1\t2090975\t2091075\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\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\t2366865\t2366965\t.\t.\t+\n+chr1\t2416008\t2416108\t.\t.\t+\n+chr1\t2432624\t2432724\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\t2486452\t2486552\t.\t.\t+\n+chr1\t2499013\t2499113\t.\t.\t+\n+chr1\t2510124\t2510224\t.\t.\t+\n+chr1\t2703138\t2703238\t.\t.\t+\n+chr1\t2738710\t2738810\t.\t.\t+\n+chr1\t2914980\t2915080\t.\t.\t+\n+chr1\t2986304\t2986404\t.\t.\t+\n+chr1\t3236562\t3236662\t.\t.\t+\n+chr1\t3274094\t3274194\t.\t.\t+\n+chr1\t3341442\t3341542\t.\t.\t+\n+chr1\t3347962\t3348062\t.\t.\t+\n+chr1\t3369850\t3369950\t.\t.\t+\n+chr1\t3374116\t3374216\t.\t.\t+\n+chr1\t3399056\t3399156\t.\t.\t+\n+chr1\t3399089\t3399189\t.\t.\t+\n+chr1\t3400562\t3400662\t.\t.\t+\n+chr1\t3407788\t3407888\t.\t.\t+\n+chr1\t3407840\t3407940\t.\t.\t+\n+chr1\t3434771\t3434871\t.\t.\t+\n+chr1\t3436993\t3437093\t.\t.\t+\n+chr1\t3446885\t3446985\t.\t.\t+\n+chr1\t3465917\t3466017\t.\t.\t+\n+chr1\t3481629\t3481729\t.\t.\t+\n+chr1\t3481991\t3482091\t.\t.\t+\n+chr1\t3535503\t3535603\t.\t.\t+\n+chr1\t3535567\t3535667\t.\t.\t+\n+chr1\t3535801\t3535901\t.\t.\t+\n+chr1\t3636230\t3636330\t.\t.\t+\n+chr1\t3640837\t3640937\t.\t.\t+\n+chr1\t3640928\t3641028\t.\t.\t+\n+chr1\t3640938\t3641038\t.\t.\t+\n+chr1\t3641104\t3641204\t.\t.\t+\n+chr1\t3641112\t3641212\t.\t.\t+\n+chr1\t3641129\t3641229\t.\t.\t+\n+chr1\t3675588\t3675688\t.\t.\t+\n+chr1\t3689721\t3689821\t.\t.\t+\n+chr1\t3692435\t3692535\t.\t.\t+\n+chr1\t3692611\t3692711\t.\t.\t+\n+chr1\t37'..b'chrX\t149939190\t149939290\t.\t.\t-\n+chrX\t149940748\t149940848\t.\t.\t-\n+chrX\t149940756\t149940856\t.\t.\t-\n+chrX\t150036830\t150036930\t.\t.\t-\n+chrX\t150147948\t150148048\t.\t.\t-\n+chrX\t150172716\t150172816\t.\t.\t-\n+chrX\t150225794\t150225894\t.\t.\t-\n+chrX\t150250953\t150251053\t.\t.\t-\n+chrX\t150320472\t150320572\t.\t.\t-\n+chrX\t150320483\t150320583\t.\t.\t-\n+chrX\t150485146\t150485246\t.\t.\t-\n+chrX\t150528899\t150528999\t.\t.\t-\n+chrX\t150529000\t150529100\t.\t.\t-\n+chrX\t150657246\t150657346\t.\t.\t-\n+chrX\t150849507\t150849607\t.\t.\t-\n+chrX\t150849529\t150849629\t.\t.\t-\n+chrX\t150849577\t150849677\t.\t.\t-\n+chrX\t150849580\t150849680\t.\t.\t-\n+chrX\t150918354\t150918454\t.\t.\t-\n+chrX\t150922098\t150922198\t.\t.\t-\n+chrX\t150958266\t150958366\t.\t.\t-\n+chrX\t150964287\t150964387\t.\t.\t-\n+chrX\t151006096\t151006196\t.\t.\t-\n+chrX\t151008522\t151008622\t.\t.\t-\n+chrX\t151117016\t151117116\t.\t.\t-\n+chrX\t151240666\t151240766\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\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\t152726458\t152726558\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\t152772703\t152772803\t.\t.\t-\n+chrX\t152773255\t152773355\t.\t.\t-\n+chrX\t152820502\t152820602\t.\t.\t-\n+chrX\t152915226\t152915326\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\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\t153396988\t153397088\t.\t.\t-\n+chrX\t153402255\t153402355\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\t153733660\t153733760\t.\t.\t-\n+chrX\t153755437\t153755537\t.\t.\t-\n+chrX\t153763090\t153763190\t.\t.\t-\n+chrX\t153763220\t153763320\t.\t.\t-\n+chrX\t153763239\t153763339\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\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\t154285839\t154285939\t.\t.\t-\n+chrX\t154314834\t154314934\t.\t.\t-\n+chrX\t154331242\t154331342\t.\t.\t-\n+chrX\t154365921\t154366021\t.\t.\t-\n+chrX\t154444870\t154444970\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\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 56e104999978 -r beb902da6e5f test-data/callpeak_control_part.bdg --- a/test-data/callpeak_control_part.bdg Mon Feb 06 02:30:37 2017 -0500 +++ b/test-data/callpeak_control_part.bdg Sat Apr 08 08:28:57 2017 -0400 |
| b |
| b'@@ -98,9903 +98,3 @@\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\t991286\t998793\t0.01536\n-chrX\t998793\t1003293\t0.02536\n-chrX\t1003293\t1003666\t0.25364\n-chrX\t1003666\t1003920\t0.99858\n-chrX\t1003920\t1004293\t0.25364\n-chrX\t1004293\t1008793\t0.02536\n-chrX\t1008793\t1235591\t0.01536\n-chrX\t1235591\t1240091\t0.02536\n-chrX\t1240091\t1240464\t0.25364\n-chrX\t1240464\t1240718\t0.99858\n-chrX\t1240718\t1241091\t0.25364\n-chrX\t1241091\t1245591\t0.02536\n-chrX\t1245591\t1257220\t0.01536\n-chrX\t1257220\t1261720\t0.02536\n-chrX\t1261720\t1262093\t0.25364\n-chrX\t1262093\t1262347\t0.99858\n-chrX\t1262347\t1262720\t0.25364\n-chrX\t1262720\t1267220\t0.02536\n-chrX\t1267220\t1393203\t0.01536\n-chrX\t1393203\t1397703\t0.02536\n-chrX\t1397703\t1398076\t0.25364\n-chrX\t1398076\t1398330\t0.99858\n-chrX\t1398330\t1398703\t0.25364\n-chrX\t1398703\t1403203\t0.02536\n-chrX\t1403203\t1434135\t0.01536\n-chrX\t1434135\t1435030\t0.02536\n-chrX\t1435030\t1438635\t0.05073\n-chrX\t1438635\t1439008\t0.25364\n-chrX\t1439008\t1439262\t0.99858\n-chrX\t1439262\t1439530\t0.25364\n-chrX\t1439530\t1439635\t0.50728\n-chrX\t1439635\t1439903\t0.25364\n-chrX\t1439903\t1440157\t0.99858\n-chrX\t1440157\t1440530\t0.25364\n-chrX\t1440530\t1442001\t0.05073\n-chrX\t1442001\t1444135\t0.07609\n-chrX\t1444135\t1445030\t0.05073\n-chrX\t1445030\t1446501\t0.02536\n-chrX\t1446501\t1446874\t0.25364\n-chrX\t1446874\t1447128\t0.99858\n-chrX\t1447128\t1447501\t0.25364\n-chrX\t1447501\t1452001\t0.02536\n-chrX\t1452001\t1467771\t0.01536\n-chrX\t1467771\t1472271\t0.02536\n-chrX\t1472271\t1472644\t0.25364\n-chrX\t1472644\t1472898\t0.99858\n-chrX\t1472898\t1473271\t0.25364\n-chrX\t1473271\t1473976\t0.02536\n-chrX\t1473976\t1477771\t0.05073\n-chrX\t1477771\t1478476\t0.02536\n-chrX\t1478476\t1478849\t0.25364\n-chrX\t1478849\t1479103\t0.99858\n-chrX\t1479103\t1479476\t0.25364\n-chrX\t1479476\t1483976\t0.02536\n-chrX\t1483976\t1493479\t0.01536\n-chrX\t1493479\t1496314\t0.02536\n-chrX\t1496314\t1497979\t0.05073\n-chrX\t1497979\t1498352\t0.25364\n-chrX\t1498352\t1498606\t0.99858\n-chrX\t1498606\t1498979\t0.25364\n-chrX\t1498979\t1500814\t0.05073\n-chrX\t1500814\t1501187\t0.25364\n-chrX\t1501187\t1501441\t0.99858\n-chrX\t1501441\t1501814\t0.25364\n-chrX\t1501814\t1503479\t0.05073\n-chrX\t1503479\t1506314\t0.02536\n-chrX\t1506314\t1507861\t0.01536\n-chrX\t1507861\t1512361\t0.02536\n-chrX\t1512361\t1512734\t0.25364\n-chrX\t1512734\t1512988\t0.99858\n-chrX\t1512988\t1513361\t0.25364\n-chrX\t1513361\t1517861\t0.02536\n-chrX\t1517861\t1558617\t0.01536\n-chrX\t1558617\t1563117\t0.02536\n-chrX\t1563117\t1563490\t0.25364\n-chrX\t1563490\t1563744\t0.99858\n-chrX\t1563744\t1564117\t0.25364\n-chrX\t1564117\t1566702\t0.05073\n-chrX\t1566702\t1568574\t0.07609\n-chrX\t1568574\t1568947\t0.25364\n-chrX\t1568947\t1569201\t0.99858\n-chrX\t1569201\t1569574\t0.25364\n-chrX\t1569574\t1571202\t0.05073\n-chrX\t1571202\t1571575\t0.25364\n-chrX\t1571575\t1571829\t0.99858\n-chrX\t1571829\t1572202\t0.25364\n-chrX\t1572202\t1574074\t0.05073\n-chrX\t1574074\t1576702\t0.02536\n-chrX\t1576702\t1584817\t0.01536\n-chrX\t1584817\t1585868\t0.02536\n-chrX\t1585868\t1589317'..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 56e104999978 -r beb902da6e5f test-data/callpeak_part.tabular --- a/test-data/callpeak_part.tabular Mon Feb 06 02:30:37 2017 -0500 +++ b/test-data/callpeak_part.tabular Sat Apr 08 08:28:57 2017 -0400 |
| [ |
| b'@@ -1,22 +1,4 @@\n-# effective genome size = 3.30e+09\n-# band width = 300\n-# model fold = [5, 50]\n-# qvalue cutoff = 5.00e-02\n-# Larger dataset will be scaled towards smaller dataset.\n-# Range for calculating regional lambda is: 1000 bps and 10000 bps\n-# Broad region calling is off\n \n-# tag size is determined as 100 bps\n-# total tags in treatment: 199977\n-# tags after filtering in treatment: 199583\n-# maximum duplicate tags at the same position in treatment = 1\n-# Redundant rate in treatment: 0.00\n-# total tags in control: 199978\n-# tags after filtering in control: 199867\n-# maximum duplicate tags at the same position in control = 1\n-# Redundant rate in control: 0.00\n-# d = 254\n-# alternative fragment length(s) may be 254 bps\n chr\tstart\tend\tlength\tabs_summit\tpileup\t-log10(pvalue)\tfold_enrichment\t-log10(qvalue)\tname\n chr1\t840082\t840400\t319\t840240\t4.00\t11.15252\t4.92435\t7.51486\tMACS2_peak_1\n chr1\t919420\t919785\t366\t919550\t5.00\t12.44148\t5.85158\t8.70936\tMACS2_peak_2\n@@ -116,905 +98,3 @@\n chr1\t11002044\t11002404\t361\t11002212\t5.00\t13.74439\t5.90922\t9.80598\tMACS2_peak_96\n chr1\t11021083\t11021336\t254\t11021260\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_97\n chr1\t11346323\t11346576\t254\t11346452\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_98\n-chr1\t11702572\t11702825\t254\t11702694\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_99\n-chr1\t11705668\t11705999\t332\t11705828\t5.00\t13.74439\t5.90922\t9.80598\tMACS2_peak_100\n-chr1\t11724067\t11724385\t319\t11724185\t4.00\t11.15252\t4.92435\t7.51486\tMACS2_peak_101\n-chr1\t11779812\t11780279\t468\t11779934\t5.00\t13.74439\t5.90922\t9.80598\tMACS2_peak_102\n-chr1\t11809339\t11809711\t373\t11809487\t4.00\t11.15252\t4.92435\t7.51486\tMACS2_peak_103\n-chr1\t11898802\t11899083\t282\t11898995\t6.00\t14.88256\t6.82684\t10.84922\tMACS2_peak_104\n-chr1\t12178765\t12179066\t302\t12178873\t4.00\t10.06728\t4.87632\t6.61759\tMACS2_peak_105\n-chr1\t12184738\t12185211\t474\t12184962\t5.00\t13.74439\t5.90922\t9.80598\tMACS2_peak_106\n-chr1\t12268890\t12269328\t439\t12269083\t7.00\t19.11990\t7.87896\t14.58582\tMACS2_peak_107\n-chr1\t12332117\t12332449\t333\t12332281\t4.00\t8.57130\t4.75861\t5.28944\tMACS2_peak_108\n-chr1\t12374347\t12374772\t426\t12374557\t4.00\t10.06728\t4.87632\t6.61759\tMACS2_peak_109\n-chr1\t13038614\t13038867\t254\t13038689\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_110\n-chr1\t13992172\t13992609\t438\t13992379\t7.00\t19.11990\t7.87896\t14.58582\tMACS2_peak_111\n-chr1\t14137710\t14137963\t254\t14137868\t3.00\t7.77216\t3.90105\t4.60940\tMACS2_peak_112\n-chr1\t14286791\t14287044\t254\t14287001\t3.00\t6.57684\t3.80689\t3.50364\tMACS2_peak_113\n-chr1\t14934898\t14935151\t254\t14934985\t3.00\t7.77216\t3.90105\t4.60940\tMACS2_peak_114\n-chr1\t15241996\t15242249\t254\t15242043\t5.00\t8.85741\t5.44734\t5.50533\tMACS2_peak_115\n-chr1\t15354004\t15354257\t254\t15354187\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_116\n-chr1\t15426847\t15427100\t254\t15426945\t3.00\t7.77216\t3.90105\t4.60940\tMACS2_peak_117\n-chr1\t15828065\t15828318\t254\t15828184\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_118\n-chr1\t16067849\t16068158\t310\t16067985\t4.00\t11.15252\t4.92435\t7.51486\tMACS2_peak_119\n-chr1\t16118591\t16118844\t254\t16118671\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_120\n-chr1\t16129826\t16130079\t254\t16129944\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_121\n-chr1\t16142043\t16142296\t254\t16142169\t3.00\t7.77216\t3.90105\t4.60940\tMACS2_peak_122\n-chr1\t16335375\t16335863\t489\t16335619\t8.00\t19.93173\t8.77737\t15.26509\tMACS2_peak_123\n-chr1\t16382535\t16382788\t254\t16382672\t3.00\t7.77216\t3.90105\t4.60940\tMACS2_peak_124\n-chr1\t16400098\t16400352\t255\t16400205\t4.00\t11.15252\t4.92435\t7.51486\tMACS2_peak_125\n-chr1\t16514317\t16514570\t254\t16514372\t5.00\t6.52624\t4.78607\t3.48261\tMACS2_peak_126\n-chr1\t16570996\t16571300\t305\t16571182\t6.00\t14.88256\t6.82684\t10.84922\tMACS2_peak_127\n-chr1\t16689876\t16690294\t419\t16690085\t4.00\t10.06728\t4.87632\t6.61759\tMACS2_peak_128\n-chr1\t16918306\t16918606\t301\t16918413\t8.00\t11.02084\t7.17910\t7.51486\tMACS2_peak_129\n-chr1\t16947523\t16947920\t398\t16947686\t6.00\t11.56197\t6.50502\t7.91704\tMACS2_peak_130\n-chr1\t16951440\t16951826\t387\t16951631\t6.00\t10.69702\t6.35523\t7.22401\tMACS2_peak_131\n-chr1\t16971045\t16971400\t356\t16971235\t4.00\t11.15252\t4.92435\t7.51486\tM'..b'ACS2_peak_953\n-chr1\t167411348\t167411617\t270\t167411508\t9.00\t9.70719\t6.63448\t6.34225\tMACS2_peak_954\n-chr1\t167509677\t167509994\t318\t167509766\t5.00\t13.74439\t5.90922\t9.80598\tMACS2_peak_955\n-chr1\t167606643\t167606904\t262\t167606794\t4.00\t11.15252\t4.92435\t7.51486\tMACS2_peak_956\n-chr1\t167657154\t167657498\t345\t167657336\t7.00\t17.38158\t7.80211\t13.02598\tMACS2_peak_957\n-chr1\t167684256\t167684787\t532\t167684669\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_958\n-chr1\t168051430\t168051903\t474\t168051540\t4.00\t11.15252\t4.92435\t7.51486\tMACS2_peak_959\n-chr1\t168054015\t168054268\t254\t168054128\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_960\n-chr1\t168115055\t168115312\t258\t168115182\t4.00\t11.15252\t4.92435\t7.51486\tMACS2_peak_961\n-chr1\t168312030\t168312283\t254\t168312087\t2.00\t6.22382\t2.95461\t3.18932\tMACS2_peak_962\n-chr1\t168409108\t168409398\t291\t168409236\t5.00\t12.44148\t5.85158\t8.70936\tMACS2_peak_963\n-chr1\t169317676\t169317929\t254\t169317779\t7.00\t9.46957\t6.38142\t6.11149\tMACS2_peak_964\n-chr1\t169435647\t169435900\t254\t169435730\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_965\n-chr1\t169515619\t169516039\t421\t169515830\t6.00\t14.88256\t6.82684\t10.84922\tMACS2_peak_966\n-chr1\t169570239\t169570598\t360\t169570357\t4.00\t11.15252\t4.92435\t7.51486\tMACS2_peak_967\n-chr1\t169681092\t169681643\t552\t169681360\t6.00\t14.88256\t6.82684\t10.84922\tMACS2_peak_968\n-chr1\t169778762\t169779123\t362\t169778927\t6.00\t16.40316\t6.89409\t12.16639\tMACS2_peak_969\n-chr1\t169898085\t169898451\t367\t169898207\t7.00\t17.38158\t7.80211\t13.02598\tMACS2_peak_970\n-chr1\t169979565\t169979919\t355\t169979736\t5.00\t13.74439\t5.90922\t9.80598\tMACS2_peak_971\n-chr1\t170658711\t170659105\t395\t170658858\t4.00\t11.15252\t4.92435\t7.51486\tMACS2_peak_972\n-chr1\t170936228\t170936611\t384\t170936406\t4.00\t11.15252\t4.92435\t7.51486\tMACS2_peak_973\n-chr1\t171157807\t171158175\t369\t171157946\t6.00\t12.78498\t6.66205\t9.02328\tMACS2_peak_974\n-chr1\t171454167\t171454693\t527\t171454409\t5.00\t12.44148\t5.85158\t8.70936\tMACS2_peak_975\n-chr1\t171624734\t171624987\t254\t171624826\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_976\n-chr1\t171770673\t171770926\t254\t171770811\t3.00\t6.57684\t3.80689\t3.50364\tMACS2_peak_977\n-chr1\t171952730\t171952983\t254\t171952866\t3.00\t7.77216\t3.90105\t4.60940\tMACS2_peak_978\n-chr1\t171953941\t171954438\t498\t171954190\t4.00\t10.06728\t4.87632\t6.61759\tMACS2_peak_979\n-chr1\t171971860\t171972280\t421\t171972046\t6.00\t16.40316\t6.89409\t12.16639\tMACS2_peak_980\n-chr1\t172104226\t172104597\t372\t172104448\t4.00\t11.15252\t4.92435\t7.51486\tMACS2_peak_981\n-chr1\t172398515\t172398852\t338\t172398693\t4.00\t10.06728\t4.87632\t6.61759\tMACS2_peak_982\n-chr1\t172688765\t172689204\t440\t172688964\t7.00\t9.46957\t6.38142\t6.11149\tMACS2_peak_983\n-chr1\t172711843\t172712109\t267\t172712013\t4.00\t10.06728\t4.87632\t6.61759\tMACS2_peak_984\n-chr1\t172714121\t172714382\t262\t172714306\t5.00\t12.44148\t5.85158\t8.70936\tMACS2_peak_985\n-chr1\t173171629\t173171882\t254\t173171751\t3.00\t5.88127\t3.71716\t3.00790\tMACS2_peak_986\n-chr1\t173389468\t173389819\t352\t173389640\t8.00\t17.23237\t8.56549\t12.97384\tMACS2_peak_987\n-chr1\t173400335\t173400718\t384\t173400558\t5.00\t12.44148\t5.85158\t8.70936\tMACS2_peak_988\n-chr1\t173684281\t173684534\t254\t173684329\t2.00\t5.57376\t2.92579\t2.70690\tMACS2_peak_989\n-chr1\t173794184\t173794465\t282\t173794324\t4.00\t7.70001\t4.64644\t4.60940\tMACS2_peak_990\n-chr1\t173883386\t173883681\t296\t173883565\t5.00\t13.74439\t5.90922\t9.80598\tMACS2_peak_991\n-chr1\t174084043\t174084320\t278\t174084167\t4.00\t11.15252\t4.92435\t7.51486\tMACS2_peak_992\n-chr1\t174186862\t174187115\t254\t174187033\t9.00\t6.95863\t5.00355\t3.88436\tMACS2_peak_993\n-chr1\t174227189\t174227538\t350\t174227378\t5.00\t12.44148\t5.85158\t8.70936\tMACS2_peak_994\n-chr1\t174695685\t174695942\t258\t174695865\t4.00\t10.06728\t4.87632\t6.61759\tMACS2_peak_995\n-chr1\t174713258\t174713511\t254\t174713320\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_996\n-chr1\t174739199\t174739503\t305\t174739348\t4.00\t8.57130\t4.75861\t5.28944\tMACS2_peak_997\n-chr1\t174967684\t174968030\t347\t174967847\t10.00\t8.00416\t5.50391\t4.83429\tMACS2_peak_998\n-chr1\t174998799\t174999052\t254\t174998982\t3.00\t8.63977\t3.93948\t5.28944\tMACS2_peak_999\n-chr1\t175094596\t175094849\t254\t175094659\t3.00\t7.77216\t3.90105\t4.60940\tMACS2_peak_1000\n' |
| b |
| diff -r 56e104999978 -r beb902da6e5f test-data/callpeak_summits_part.bed --- a/test-data/callpeak_summits_part.bed Mon Feb 06 02:30:37 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,1000 +0,0 @@\n-chr1\t840081\t840400\tMACS2_peak_1\t75\t.\t4.92435\t11.15252\t7.51486\t158\n-chr1\t919419\t919785\tMACS2_peak_2\t87\t.\t5.85158\t12.44148\t8.70936\t130\n-chr1\t937220\t937483\tMACS2_peak_3\t66\t.\t4.87632\t10.06728\t6.61759\t154\n-chr1\t954742\t954996\tMACS2_peak_4\t52\t.\t3.93948\t8.63977\t5.28944\t71\n-chr1\t994762\t995016\tMACS2_peak_5\t52\t.\t3.93948\t8.63977\t5.28944\t143\n-chr1\t1057394\t1057648\tMACS2_peak_6\t52\t.\t3.93948\t8.63977\t5.28944\t114\n-chr1\t1240579\t1241004\tMACS2_peak_7\t46\t.\t3.90105\t7.77216\t4.60940\t197\n-chr1\t1307392\t1307735\tMACS2_peak_8\t87\t.\t5.85158\t12.44148\t8.70936\t208\n-chr1\t1440350\t1440633\tMACS2_peak_9\t75\t.\t4.92435\t11.15252\t7.51486\t111\n-chr1\t1555432\t1555725\tMACS2_peak_10\t75\t.\t4.92435\t11.15252\t7.51486\t138\n-chr1\t1590667\t1590946\tMACS2_peak_11\t66\t.\t4.87632\t10.06728\t6.61759\t172\n-chr1\t1837668\t1838104\tMACS2_peak_12\t108\t.\t6.82684\t14.88256\t10.84922\t217\n-chr1\t1840365\t1840828\tMACS2_peak_13\t98\t.\t5.90922\t13.74439\t9.80598\t181\n-chr1\t1976399\t1976653\tMACS2_peak_14\t52\t.\t3.93948\t8.63977\t5.28944\t69\n-chr1\t2071301\t2071627\tMACS2_peak_15\t75\t.\t4.92435\t11.15252\t7.51486\t121\n-chr1\t2105716\t2106140\tMACS2_peak_16\t46\t.\t4.64644\t7.70001\t4.60940\t202\n-chr1\t2126521\t2126861\tMACS2_peak_17\t66\t.\t4.87632\t10.06728\t6.61759\t126\n-chr1\t2246520\t2246954\tMACS2_peak_18\t62\t.\t5.57573\t9.59761\t6.23289\t191\n-chr1\t2313157\t2313560\tMACS2_peak_19\t98\t.\t5.90922\t13.74439\t9.80598\t195\n-chr1\t2345827\t2346242\tMACS2_peak_20\t130\t.\t7.80211\t17.38158\t13.02598\t200\n-chr1\t2510054\t2510308\tMACS2_peak_21\t52\t.\t3.93948\t8.63977\t5.28944\t158\n-chr1\t3341407\t3341661\tMACS2_peak_22\t46\t.\t3.90105\t7.77216\t4.60940\t53\n-chr1\t3369638\t3369892\tMACS2_peak_23\t52\t.\t3.93948\t8.63977\t5.28944\t224\n-chr1\t3400440\t3400769\tMACS2_peak_24\t75\t.\t4.92435\t11.15252\t7.51486\t169\n-chr1\t3407840\t3408094\tMACS2_peak_25\t52\t.\t3.93948\t8.63977\t5.28944\t134\n-chr1\t3481747\t3482245\tMACS2_peak_26\t75\t.\t4.92435\t11.15252\t7.51486\t115\n-chr1\t3535561\t3535821\tMACS2_peak_27\t52\t.\t3.93948\t8.63977\t5.28944\t101\n-chr1\t3537756\t3538010\tMACS2_peak_28\t52\t.\t3.93948\t8.63977\t5.28944\t203\n-chr1\t3593609\t3593863\tMACS2_peak_29\t46\t.\t3.90105\t7.77216\t4.60940\t228\n-chr1\t3640883\t3641366\tMACS2_peak_30\t249\t.\t12.67843\t30.54970\t24.90331\t250\n-chr1\t3702143\t3702397\tMACS2_peak_31\t46\t.\t3.90105\t7.77216\t4.60940\t116\n-chr1\t3773698\t3774058\tMACS2_peak_32\t145\t.\t7.87896\t19.11990\t14.58582\t177\n-chr1\t3827305\t3827722\tMACS2_peak_33\t98\t.\t5.90922\t13.74439\t9.80598\t219\n-chr1\t4712783\t4713037\tMACS2_peak_34\t52\t.\t3.93948\t8.63977\t5.28944\t120\n-chr1\t4886186\t4886440\tMACS2_peak_35\t46\t.\t3.90105\t7.77216\t4.60940\t139\n-chr1\t5569918\t5570198\tMACS2_peak_36\t75\t.\t4.92435\t11.15252\t7.51486\t137\n-chr1\t5574776\t5575080\tMACS2_peak_37\t52\t.\t3.93948\t8.63977\t5.28944\t61\n-chr1\t5805837\t5806091\tMACS2_peak_38\t31\t.\t2.95461\t6.22382\t3.18932\t127\n-chr1\t5976145\t5976399\tMACS2_peak_39\t52\t.\t3.93948\t8.63977\t5.28944\t89\n-chr1\t6094645\t6094899\tMACS2_peak_40\t31\t.\t2.95461\t6.22382\t3.18932\t32\n-chr1\t6112956\t6113210\tMACS2_peak_41\t35\t.\t3.80689\t6.57684\t3.50364\t178\n-chr1\t6265252\t6265640\tMACS2_peak_42\t79\t.\t6.50502\t11.56197\t7.91704\t184\n-chr1\t6305228\t6305482\tMACS2_peak_43\t52\t.\t3.93948\t8.63977\t5.28944\t70\n-chr1\t6306873\t6307127\tMACS2_peak_44\t52\t.\t3.93948\t8.63977\t5.28944\t139\n-chr1\t6403480\t6403843\tMACS2_peak_45\t121\t.\t6.89409\t16.40316\t12.16639\t198\n-chr1\t6464656\t6465096\tMACS2_peak_46\t79\t.\t6.50502\t11.56197\t7.91704\t212\n-chr1\t6483603\t6483857\tMACS2_peak_47\t52\t.\t3.93948\t8.63977\t5.28944\t135\n-chr1\t6498109\t6498494\tMACS2_peak_48\t108\t.\t6.82684\t14.88256\t10.84922\t148\n-chr1\t6535512\t6535838\tMACS2_peak_49\t98\t.\t5.90922\t13.74439\t9.80598\t78\n-chr1\t6614467\t6614882\tMACS2_peak_50\t66\t.\t4.87632\t10.06728\t6.61759\t240\n-chr1\t6706585\t6706931\tMACS2_peak_51\t98\t.\t5.90922\t13.74439\t9.80598\t157\n-chr1\t6761832\t6762203\tMACS2_peak_52\t109\t.\t7.61377\t14.98313\t10.92185\t206\n-chr1\t6780091\t6780471\tMACS2_peak_53\t121\t.\t6.89409\t16.40316\t12.16639\t237\n-chr1\t6787474\t6787900\tMACS2_peak_54\t145\t.\t7.87896\t19.11990\t14.58582\t229\n-chr1\t6949952\t6950377\tMACS2_peak_55\t71\t.\t5.71033\t10.64473\t7.17293\t200\n-chr1\t7102752\t7103077\tMACS2_peak_56\t75\t.\t4.92435\t11.15252\t7.51486\t162\n-chr1\t7278316\t7278718\tMACS2_peak_57\t121\t.\t6.89409\t16.40316\t12.16639\t166\n-chr1\t7868455\t7868722'..b'947\t46\t.\t3.90105\t7.77216\t4.60940\t55\n-chr1\t166134133\t166134388\tMACS2_peak_948\t66\t.\t4.87632\t10.06728\t6.61759\t208\n-chr1\t166448255\t166448688\tMACS2_peak_949\t108\t.\t6.82684\t14.88256\t10.84922\t215\n-chr1\t167028343\t167028616\tMACS2_peak_950\t47\t.\t5.58374\t7.96913\t4.79957\t215\n-chr1\t167035942\t167036261\tMACS2_peak_951\t66\t.\t4.87632\t10.06728\t6.61759\t95\n-chr1\t167237143\t167237397\tMACS2_peak_952\t35\t.\t3.80689\t6.57684\t3.50364\t152\n-chr1\t167370456\t167370840\tMACS2_peak_953\t66\t.\t4.87632\t10.06728\t6.61759\t230\n-chr1\t167411347\t167411617\tMACS2_peak_954\t63\t.\t6.63448\t9.70719\t6.34225\t160\n-chr1\t167509676\t167509994\tMACS2_peak_955\t98\t.\t5.90922\t13.74439\t9.80598\t89\n-chr1\t167606642\t167606904\tMACS2_peak_956\t75\t.\t4.92435\t11.15252\t7.51486\t151\n-chr1\t167657153\t167657498\tMACS2_peak_957\t130\t.\t7.80211\t17.38158\t13.02598\t182\n-chr1\t167684255\t167684787\tMACS2_peak_958\t52\t.\t3.93948\t8.63977\t5.28944\t413\n-chr1\t168051429\t168051903\tMACS2_peak_959\t75\t.\t4.92435\t11.15252\t7.51486\t110\n-chr1\t168054014\t168054268\tMACS2_peak_960\t52\t.\t3.93948\t8.63977\t5.28944\t113\n-chr1\t168115054\t168115312\tMACS2_peak_961\t75\t.\t4.92435\t11.15252\t7.51486\t127\n-chr1\t168312029\t168312283\tMACS2_peak_962\t31\t.\t2.95461\t6.22382\t3.18932\t57\n-chr1\t168409107\t168409398\tMACS2_peak_963\t87\t.\t5.85158\t12.44148\t8.70936\t128\n-chr1\t169317675\t169317929\tMACS2_peak_964\t61\t.\t6.38142\t9.46957\t6.11149\t103\n-chr1\t169435646\t169435900\tMACS2_peak_965\t52\t.\t3.93948\t8.63977\t5.28944\t83\n-chr1\t169515618\t169516039\tMACS2_peak_966\t108\t.\t6.82684\t14.88256\t10.84922\t211\n-chr1\t169570238\t169570598\tMACS2_peak_967\t75\t.\t4.92435\t11.15252\t7.51486\t118\n-chr1\t169681091\t169681643\tMACS2_peak_968\t108\t.\t6.82684\t14.88256\t10.84922\t268\n-chr1\t169778761\t169779123\tMACS2_peak_969\t121\t.\t6.89409\t16.40316\t12.16639\t165\n-chr1\t169898084\t169898451\tMACS2_peak_970\t130\t.\t7.80211\t17.38158\t13.02598\t122\n-chr1\t169979564\t169979919\tMACS2_peak_971\t98\t.\t5.90922\t13.74439\t9.80598\t171\n-chr1\t170658710\t170659105\tMACS2_peak_972\t75\t.\t4.92435\t11.15252\t7.51486\t147\n-chr1\t170936227\t170936611\tMACS2_peak_973\t75\t.\t4.92435\t11.15252\t7.51486\t178\n-chr1\t171157806\t171158175\tMACS2_peak_974\t90\t.\t6.66205\t12.78498\t9.02328\t139\n-chr1\t171454166\t171454693\tMACS2_peak_975\t87\t.\t5.85158\t12.44148\t8.70936\t242\n-chr1\t171624733\t171624987\tMACS2_peak_976\t52\t.\t3.93948\t8.63977\t5.28944\t92\n-chr1\t171770672\t171770926\tMACS2_peak_977\t35\t.\t3.80689\t6.57684\t3.50364\t138\n-chr1\t171952729\t171952983\tMACS2_peak_978\t46\t.\t3.90105\t7.77216\t4.60940\t136\n-chr1\t171953940\t171954438\tMACS2_peak_979\t66\t.\t4.87632\t10.06728\t6.61759\t249\n-chr1\t171971859\t171972280\tMACS2_peak_980\t121\t.\t6.89409\t16.40316\t12.16639\t186\n-chr1\t172104225\t172104597\tMACS2_peak_981\t75\t.\t4.92435\t11.15252\t7.51486\t222\n-chr1\t172398514\t172398852\tMACS2_peak_982\t66\t.\t4.87632\t10.06728\t6.61759\t178\n-chr1\t172688764\t172689204\tMACS2_peak_983\t61\t.\t6.38142\t9.46957\t6.11149\t199\n-chr1\t172711842\t172712109\tMACS2_peak_984\t66\t.\t4.87632\t10.06728\t6.61759\t170\n-chr1\t172714120\t172714382\tMACS2_peak_985\t87\t.\t5.85158\t12.44148\t8.70936\t185\n-chr1\t173171628\t173171882\tMACS2_peak_986\t30\t.\t3.71716\t5.88127\t3.00790\t122\n-chr1\t173389467\t173389819\tMACS2_peak_987\t129\t.\t8.56549\t17.23237\t12.97384\t172\n-chr1\t173400334\t173400718\tMACS2_peak_988\t87\t.\t5.85158\t12.44148\t8.70936\t223\n-chr1\t173684280\t173684534\tMACS2_peak_989\t27\t.\t2.92579\t5.57376\t2.70690\t48\n-chr1\t173794183\t173794465\tMACS2_peak_990\t46\t.\t4.64644\t7.70001\t4.60940\t140\n-chr1\t173883385\t173883681\tMACS2_peak_991\t98\t.\t5.90922\t13.74439\t9.80598\t179\n-chr1\t174084042\t174084320\tMACS2_peak_992\t75\t.\t4.92435\t11.15252\t7.51486\t124\n-chr1\t174186861\t174187115\tMACS2_peak_993\t38\t.\t5.00355\t6.95863\t3.88436\t171\n-chr1\t174227188\t174227538\tMACS2_peak_994\t87\t.\t5.85158\t12.44148\t8.70936\t189\n-chr1\t174695684\t174695942\tMACS2_peak_995\t66\t.\t4.87632\t10.06728\t6.61759\t180\n-chr1\t174713257\t174713511\tMACS2_peak_996\t52\t.\t3.93948\t8.63977\t5.28944\t62\n-chr1\t174739198\t174739503\tMACS2_peak_997\t52\t.\t4.75861\t8.57130\t5.28944\t149\n-chr1\t174967683\t174968030\tMACS2_peak_998\t48\t.\t5.50391\t8.00416\t4.83429\t163\n-chr1\t174998798\t174999052\tMACS2_peak_999\t52\t.\t3.93948\t8.63977\t5.28944\t183\n-chr1\t175094595\t175094849\tMACS2_peak_1000\t46\t.\t3.90105\t7.77216\t4.60940\t63\n' |
| b |
| diff -r 56e104999978 -r beb902da6e5f test-data/callpeak_treatment_part.bdg --- a/test-data/callpeak_treatment_part.bdg Mon Feb 06 02:30:37 2017 -0500 +++ b/test-data/callpeak_treatment_part.bdg Sat Apr 08 08:28:57 2017 -0400 |
| b |
| b'@@ -98,9903 +98,3 @@\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\t1767468\t1767689\t4.00000\n-chrX\t1767689\t1767699\t3.00000\n-chrX\t1767699\t1767721\t2.00000\n-chrX\t1767721\t1767722\t1.00000\n-chrX\t1767722\t1771093\t0.00000\n-chrX\t1771093\t1771107\t1.00000\n-chrX\t1771107\t1771141\t2.00000\n-chrX\t1771141\t1771263\t3.00000\n-chrX\t1771263\t1771347\t4.00000\n-chrX\t1771347\t1771361\t3.00000\n-chrX\t1771361\t1771395\t2.00000\n-chrX\t1771395\t1771517\t1.00000\n-chrX\t1771517\t1775049\t0.00000\n-chrX\t1775049\t1775303\t1.00000\n-chrX\t1775303\t1776274\t0.00000\n-chrX\t1776274\t1776528\t1.00000\n-chrX\t1776528\t1791977\t0.00000\n-chrX\t1791977\t1792231\t1.00000\n-chrX\t1792231\t1792283\t0.00000\n-chrX\t1792283\t1792290\t1.00000\n-chrX\t1792290\t1792302\t2.00000\n-chrX\t1792302\t1792537\t3.00000\n-chrX\t1792537\t1792544\t2.00000\n-chrX\t1792544\t1792556\t1.00000\n-chrX\t1792556\t1905584\t0.00000\n-chrX\t1905584\t1905838\t1.00000\n-chrX\t1905838\t1934136\t0.00000\n-chrX\t1934136\t1934390\t1.00000\n-chrX\t1934390\t1965862\t0.00000\n-chrX\t1965862\t1966116\t1.00000\n-chrX\t1966116\t1988691\t0.00000\n-chrX\t1988691\t1988945\t1.00000\n-chrX\t1988945\t2127797\t0.00000\n-chrX\t2127797\t2128051\t1.00000\n-chrX\t2128051\t2151050\t0.00000\n-chrX\t2151050\t2151295\t1.00000\n-chrX\t2151295\t2151304\t2.00000\n-chrX\t2151304\t2151348\t1.00000\n-chrX\t2151348\t2151549\t2.00000\n-chrX\t2151549\t2151602\t1.00000\n-chrX\t2151602\t2173736\t0.00000\n-chrX\t2173736\t2173990\t1.00000\n-chrX\t2173990\t2227531\t0.00000\n-chrX\t2227531\t2227785\t1.00000\n-chrX\t2227785\t2247894\t0.00000\n-chrX\t2247894\t2248148\t1.00000\n-chrX\t2248148\t2257982\t0.00000\n-chrX\t2257982\t2258236\t1.00000\n-chrX\t2258236\t2278106\t0.00000\n-chrX\t2278106\t2278360\t1.00000\n-chrX\t2278360\t2418298\t0.00000\n-chrX\t2418298\t2418552\t1.00000\n-chrX\t2418552\t2428648\t0.00000\n-chrX\t2428648\t2428663\t1.00000\n-chrX\t2428663\t2428902\t2.00000\n-chrX\t2428902\t2428917\t1.00000\n-chrX\t2428917\t2432188\t0.00000\n-chrX\t2432188\t2432442\t1.00000\n-chrX\t2432442\t2439562\t0.00000\n-chrX\t2439562\t2439816\t1.00000\n-chrX\t2439816\t2493799\t0.00000\n-chrX\t2493799\t2494053\t1.00000\n-chrX\t2494053\t2495872\t0.00000\n-chrX\t2495872\t2496126\t1.00000\n-chrX\t2496126\t2511222\t0.00000\n-chrX\t2511222\t2511277\t1.00000\n-chrX\t2511277\t2511323\t2.00000\n-chrX\t2511323\t2511409\t3.00000\n-chrX\t2511409\t2511476\t4.00000\n-chrX\t2511476\t2511531\t3.00000\n-chrX\t2511531\t2511577\t2.00000\n-chrX\t2511577\t2511663\t1.00000\n-chrX\t2511663\t2518281\t0.00000\n-chrX\t2518281\t2518535\t1.00000\n-chrX\t2518535\t2529060\t0.00000\n-chrX\t2529060\t2529314\t1.00000\n-chrX\t2529314\t2532872\t0.00000\n-chrX\t2532872\t2533126\t1.00000\n-chrX\t2533126\t2542430\t0.00000\n-chrX\t2542430\t2542684\t1.00000\n-chrX\t2542684\t2549340\t0.00000\n-chrX\t2549340\t2549594\t1.00000\n-chrX\t2549594\t2551070\t0.00000\n-chrX\t2551070\t2551324\t1.00000\n-chrX\t2551324\t2551410\t0.00000\n-chrX\t2551410\t2551497\t1.00000\n-chrX\t2551497\t2551664\t2.00000\n-chrX\t2551664\t2551751\t1.00000\n-chrX\t2551751\t2562595\t0.00000\n-chrX\t2562595\t2562758\t1.00000\n-chrX\t2562758\t2562849\t2.00000\n-chrX\t2562849\t2563012\t1.00000\n-chrX\t2563012\t2565902\t0.00000\n-chrX\t2565902\t2566156\t1.00000\n-chrX\t2566156\t2585188\t0.00000\n-chrX\t2585188\t2585'..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 56e104999978 -r beb902da6e5f test-data/output_extra_files.html --- a/test-data/output_extra_files.html Mon Feb 06 02:30:37 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,22 +0,0 @@ -<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> -<table class="fileList"> -<tr><td class="file"><a href="MACS2_model.pdf">model.pdf</a></td></tr> -<tr><td class="file"><a href="MACS2_summits.bed">summits.bed</a></td></tr> -<tr><td class="file"><a href="MACS2_model.r">model.r</a></td></tr> -<tr><td class="file"><a href="MACS2_peaks.narrowPeak">peaks.narrowPeak</a></td></tr> -<tr><td class="file"><a href="MACS2_model.r.log">model.r.log</a></td></tr> -<tr><td class="file"><a href="MACS2_peaks.xls">peaks.xls</a></td></tr> -</table> -<h3>Messages from MACS2:</h3> -INFO @ Tue, 24 Jan 2017 12:19:10: <br># Command line: callpeak --name MACS2 -t /tmp/tmp1QIUtc/files/000/dataset_1.dat -c /tmp/tmp1QIUtc/files/000/dataset_2.dat --format=BED --gsize 3300000000 --bw=300 --qvalue 0.05<br># ARGUMENTS LIST:<br># name = MACS2<br># format = BED<br># ChIP-seq file = ['/tmp/tmp1QIUtc/files/000/dataset_1.dat']<br># control file = ['/tmp/tmp1QIUtc/files/000/dataset_2.dat']<br># effective genome size = 3.30e+09<br># band width = 300<br># model fold = [5, 50]<br># qvalue cutoff = 5.00e-02<br># Larger dataset will be scaled towards smaller dataset.<br># Range for calculating regional lambda is: 1000 bps and 10000 bps<br># Broad region calling is off<br># Paired-End mode is off<br> <br>INFO @ Tue, 24 Jan 2017 12:19:10: #1 read tag files... <br>INFO @ Tue, 24 Jan 2017 12:19:10: #1 read treatment tags... <br>INFO @ Tue, 24 Jan 2017 12:19:10: #1.2 read input tags... <br>INFO @ Tue, 24 Jan 2017 12:19:10: #1 tag size is determined as 100 bps <br>INFO @ Tue, 24 Jan 2017 12:19:10: #1 tag size = 100 <br>INFO @ Tue, 24 Jan 2017 12:19:10: #1 total tags in treatment: 199977 <br>INFO @ Tue, 24 Jan 2017 12:19:10: #1 user defined the maximum tags... <br>INFO @ Tue, 24 Jan 2017 12:19:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) <br>INFO @ Tue, 24 Jan 2017 12:19:10: #1 tags after filtering in treatment: 199583 <br>INFO @ Tue, 24 Jan 2017 12:19:10: #1 Redundant rate of treatment: 0.00 <br>INFO @ Tue, 24 Jan 2017 12:19:10: #1 total tags in control: 199978 <br>INFO @ Tue, 24 Jan 2017 12:19:10: #1 user defined the maximum tags... <br>INFO @ Tue, 24 Jan 2017 12:19:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) <br>INFO @ Tue, 24 Jan 2017 12:19:10: #1 tags after filtering in control: 199867 <br>INFO @ Tue, 24 Jan 2017 12:19:10: #1 Redundant rate of control: 0.00 <br>INFO @ Tue, 24 Jan 2017 12:19:10: #1 finished! <br>INFO @ Tue, 24 Jan 2017 12:19:10: #2 Build Peak Model... <br>INFO @ Tue, 24 Jan 2017 12:19:10: #2 looking for paired plus/minus strand peaks... <br>INFO @ Tue, 24 Jan 2017 12:19:11: #2 number of paired peaks: 4488 <br>INFO @ Tue, 24 Jan 2017 12:19:11: start model_add_line... <br>INFO @ Tue, 24 Jan 2017 12:19:11: start X-correlation... <br>INFO @ Tue, 24 Jan 2017 12:19:11: end of X-cor <br>INFO @ Tue, 24 Jan 2017 12:19:11: #2 finished! <br>INFO @ Tue, 24 Jan 2017 12:19:11: #2 predicted fragment length is 254 bps <br>INFO @ Tue, 24 Jan 2017 12:19:11: #2 alternative fragment length(s) may be 254 bps <br>INFO @ Tue, 24 Jan 2017 12:19:11: #2.2 Generate R script for model : MACS2_model.r <br>INFO @ Tue, 24 Jan 2017 12:19:11: #3 Call peaks... <br>INFO @ Tue, 24 Jan 2017 12:19:11: #3 Pre-compute pvalue-qvalue table... <br>INFO @ Tue, 24 Jan 2017 12:19:12: #3 Call peaks for each chromosome... <br>INFO @ Tue, 24 Jan 2017 12:19:13: #4 Write output xls file... MACS2_peaks.xls <br>INFO @ Tue, 24 Jan 2017 12:19:13: #4 Write peak in narrowPeak format file... MACS2_peaks.narrowPeak <br>INFO @ Tue, 24 Jan 2017 12:19:13: #4 Write summits bed file... MACS2_summits.bed <br>INFO @ Tue, 24 Jan 2017 12:19:13: Done! <br> -</body> -</html> |
| b |
| diff -r 56e104999978 -r beb902da6e5f test-data/refinepeak_bam_input.bam |
| b |
| Binary file test-data/refinepeak_bam_input.bam has changed |
| b |
| diff -r 56e104999978 -r beb902da6e5f test-data/refinepeak_bed_input.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/refinepeak_bed_input.bed Sat Apr 08 08:28:57 2017 -0400 |
| b |
| @@ -0,0 +1,5 @@ +chrX 60232 60380 MACS2_peak_390 34 . 3.03834 5.42587 3.43119 32 +chrX 68754 69146 MACS2_peak_391 431 . 11.48543 46.83149 43.16708 178 +chrX 79466 79717 MACS2_peak_392 50 . 3.63633 7.17081 5.08198 51 +chrX 83241 83340 MACS2_peak_393 36 . 3.43598 5.63408 3.62981 52 +chrX 90229 90311 MACS2_peak_394 66 . 4.26334 8.78676 6.62347 29 |
| b |
| diff -r 56e104999978 -r beb902da6e5f test-data/refinepeak_output.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/refinepeak_output.bed Sat Apr 08 08:28:57 2017 -0400 |
| b |
| @@ -0,0 +1,5 @@ +chrX 60264 60265 MACS2_peak_390_R 68.31 +chrX 68932 68933 MACS2_peak_391_R 670.30 +chrX 79581 79582 MACS2_peak_392_R 36.82 +chrX 83298 83299 MACS2_peak_393_R 56.71 +chrX 90264 90265 MACS2_peak_394_R 73.71 \ No newline at end of file |
| b |
| diff -r 56e104999978 -r beb902da6e5f tool_dependencies.xml --- a/tool_dependencies.xml Mon Feb 06 02:30:37 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,21 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="numpy" version="1.7.1"> - <repository changeset_revision="300877695495" 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="cfbbe183f8a7" name="package_scipy_0_12" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="R" version="3.1.2"> - <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="gnu_awk" version="4.1.0"> - <repository changeset_revision="f145f856ec57" name="package_gnu_awk_4_1_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="macs2" version="2.1.0.20151222"> - <repository changeset_revision="e1370f7d5e2f" name="package_macs2_2_1_0_20151222" 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> |