| Previous changeset 17:424aefbd7777 (2019-04-25) Next changeset 19:86e2413cf3f8 (2023-10-16) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e8307adcc6ee9245fa2bb9ecb6de1cbe008dc2c3" |
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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/bdgbroadcall_output.bdg test-data/bdgpeakcall_output_cutoff.bdg test-data/callpeak_bampe_narrow.bed test-data/callpeak_control_part.bdg test-data/callpeak_part.tabular test-data/callpeak_treatment_part.bdg test-data/filterdup_on_ChIP_200K_w_dups.bed test-data/magic.pdf test-data/predictd_on_ChIP_200K_and_Control_200K.pdf |
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removed:
test-data/bdgrandsample_output.bed |
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| diff -r 424aefbd7777 -r 640d3af5d833 macs2_bdgbroadcall.xml --- a/macs2_bdgbroadcall.xml Thu Apr 25 17:49:05 2019 -0400 +++ b/macs2_bdgbroadcall.xml Sat Apr 02 21:37:38 2022 +0000 |
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| @@ -1,5 +1,6 @@ -<tool id="macs2_bdgbroadcall" name="MACS2 bdgbroadcall" version="@VERSION_STRING@.0"> +<tool id="macs2_bdgbroadcall" name="MACS2 bdgbroadcall" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> <description>Call broad peaks from bedGraph output</description> + <expand macro="bio_tools"/> <macros> <import>macs2_macros.xml</import> </macros> |
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| diff -r 424aefbd7777 -r 640d3af5d833 macs2_bdgcmp.xml --- a/macs2_bdgcmp.xml Thu Apr 25 17:49:05 2019 -0400 +++ b/macs2_bdgcmp.xml Sat Apr 02 21:37:38 2022 +0000 |
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| @@ -1,5 +1,6 @@ -<tool id="macs2_bdgcmp" name="MACS2 bdgcmp" version="@VERSION_STRING@.0"> +<tool id="macs2_bdgcmp" name="MACS2 bdgcmp" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> <description>Deduct noise by comparing two signal tracks in bedGraph</description> + <expand macro="bio_tools"/> <macros> <import>macs2_macros.xml</import> </macros> |
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| diff -r 424aefbd7777 -r 640d3af5d833 macs2_bdgdiff.xml --- a/macs2_bdgdiff.xml Thu Apr 25 17:49:05 2019 -0400 +++ b/macs2_bdgdiff.xml Sat Apr 02 21:37:38 2022 +0000 |
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| @@ -1,5 +1,6 @@ -<tool id="macs2_bdgdiff" name="MACS2 bdgdiff" version="@VERSION_STRING@.1" profile="17.09"> +<tool id="macs2_bdgdiff" name="MACS2 bdgdiff" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> <description>Differential peak detection based on paired four bedgraph files</description> + <expand macro="bio_tools"/> <macros> <import>macs2_macros.xml</import> </macros> |
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| diff -r 424aefbd7777 -r 640d3af5d833 macs2_bdgpeakcall.xml --- a/macs2_bdgpeakcall.xml Thu Apr 25 17:49:05 2019 -0400 +++ b/macs2_bdgpeakcall.xml Sat Apr 02 21:37:38 2022 +0000 |
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| @@ -1,5 +1,6 @@ -<tool id="macs2_bdgpeakcall" name="MACS2 bdgpeakcall" version="@VERSION_STRING@.0"> +<tool id="macs2_bdgpeakcall" name="MACS2 bdgpeakcall" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> <description>Call peaks from bedGraph output</description> + <expand macro="bio_tools"/> <macros> <import>macs2_macros.xml</import> </macros> |
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| diff -r 424aefbd7777 -r 640d3af5d833 macs2_callpeak.xml --- a/macs2_callpeak.xml Thu Apr 25 17:49:05 2019 -0400 +++ b/macs2_callpeak.xml Sat Apr 02 21:37:38 2022 +0000 |
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| @@ -1,5 +1,6 @@ -<tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.6" profile="17.09"> +<tool id="macs2_callpeak" name="MACS2 callpeak" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> <description>Call peaks from alignment results</description> + <expand macro="bio_tools"/> <macros> <import>macs2_macros.xml</import> </macros> @@ -72,6 +73,8 @@ --keep-dup '${ advanced_options.keep_dup_options.keep_dup_options_selector }' #end if + --d-min $advanced_options.d_min + --buffer-size $advanced_options.buffer_size ## With --bdg two additional output files will be generated. #if "bdg" in str($outputs).split(','): @@ -246,6 +249,8 @@ </when> </conditional> <expand macro="keep_duplicates" /> + <expand macro="fragment_size"/> + <expand macro="buffer_size"/> </section> </inputs> <outputs> @@ -310,6 +315,10 @@ <param name="gsize" value="3300000000" /> <param name="lower" value="5" /> <param name="upper" value="50" /> + <assert_command> + <has_text text="--buffer-size"/> + <has_text text="--d-min"/> + </assert_command> <output name="output_control_lambda" compare="contains" file="callpeak_control_part.bdg" lines_diff="1"/> <output name="output_treat_pileup" compare="contains" file="callpeak_treatment_part.bdg" lines_diff="1"/> <output name="output_tabular" compare="contains" file="callpeak_part.tabular" lines_diff="3"/> @@ -333,7 +342,7 @@ <param name="gsize" value="3300000000" /> <param name="lower" value="5" /> <param name="upper" value="50" /> - <output name="output_plot" file="magic.pdf" ftype="pdf" compare="contains" /> + <output name="output_plot" file="magic.pdf" compare="sim_size" ftype="pdf"/> </test> <!-- Ensure BAMPE works --> <test expect_num_outputs="1"> |
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| diff -r 424aefbd7777 -r 640d3af5d833 macs2_filterdup.xml --- a/macs2_filterdup.xml Thu Apr 25 17:49:05 2019 -0400 +++ b/macs2_filterdup.xml Sat Apr 02 21:37:38 2022 +0000 |
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| @@ -1,5 +1,6 @@ -<tool id="macs2_filterdup" name="MACS2 filterdup" version="@VERSION_STRING@.1"> +<tool id="macs2_filterdup" name="MACS2 filterdup" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> <description>Remove duplicate reads at the same position</description> + <expand macro="bio_tools"/> <macros> <import>macs2_macros.xml</import> </macros> @@ -20,6 +21,7 @@ #else --keep-dup '${ keep_dup_options.keep_dup_options_selector }' #end if + @buffer_size@ ]]> </command> <inputs> @@ -28,7 +30,7 @@ <expand macro="tag_size" /> <param name="pvalue" type="text" value="1e-5" label="Pvalue cutoff for binomial distribution test" help="Default=1e-5 (--pvalue)" /> <expand macro="keep_duplicates" /> - + <expand macro="buffer_size"/> </inputs> <outputs> <data name="outfile" format="bed" label="${tool.name} on ${on_string}" /> |
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| diff -r 424aefbd7777 -r 640d3af5d833 macs2_macros.xml --- a/macs2_macros.xml Thu Apr 25 17:49:05 2019 -0400 +++ b/macs2_macros.xml Sat Apr 02 21:37:38 2022 +0000 |
| [ |
| @@ -1,14 +1,18 @@ <macros> - <token name="@VERSION_STRING@">2.1.1.20160309</token> - + <token name="@TOOL_VERSION@">2.2.7.1</token> + <token name="@VERSION_SUFFIX@">0</token> <xml name="requirements"> <requirements> - <requirement type="package" version="@VERSION_STRING@">macs2</requirement> + <requirement type="package" version="@TOOL_VERSION@">macs2</requirement> <requirement type="package" version="3.4">r-base</requirement> <yield /> </requirements> </xml> - + <xml name="bio_tools"> + <xrefs> + <xref type="bio.tools">macs</xref> + </xrefs> + </xml> <token name="@home_dir@"><![CDATA[ export PYTHON_EGG_CACHE=`pwd` && ]]></token> @@ -54,7 +58,8 @@ </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)" > + <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" > <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> @@ -72,13 +77,24 @@ #end if </token> + <xml name="buffer_size"> + <param argument="--buffer-size" type="integer" min="0" value="100000" label="Buffer size" + help="Buffer size for incrementally increasing internal array size to store reads alignment information. In most cases, you don't have to change this parameter. + However, if there are large number of chromosomes/contigs/scaffolds in your alignment, it's recommended to specify a smaller buffer size in order to + decrease memory usage (but it will take longer time to read alignment files)." /> + </xml> + + <token name="@buffer_size@"> + --buffer-size $buffer_size + </token> + <xml name="version_command"> <version_command>macs2 --version</version_command> </xml> <xml name="tag_size"> - <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)" /> + <param argument="--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 " /> </xml> <xml name="band_width"> <param name="band_width" type="integer" value="300" @@ -86,6 +102,12 @@ help=" You can set this parameter as the medium fragment size expected from sonication or size selection. (--bw)" /> </xml> + <xml name="fragment_size"> + <param argument="--d-min" type="integer" value="20" + label="Minimum fragment size in basepair" + help="Any predicted fragment size less than this will be excluded."/> + </xml> + <token name="@tag_size@"> #if $tsize: --tsize '${ tsize }' |
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| diff -r 424aefbd7777 -r 640d3af5d833 macs2_predictd.xml --- a/macs2_predictd.xml Thu Apr 25 17:49:05 2019 -0400 +++ b/macs2_predictd.xml Sat Apr 02 21:37:38 2022 +0000 |
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| @@ -1,5 +1,6 @@ -<tool id="macs2_predictd" name="MACS2 predictd" version="@VERSION_STRING@.1"> +<tool id="macs2_predictd" name="MACS2 predictd" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> <description>Predict 'd' or fragment size from alignment results</description> + <expand macro="bio_tools"/> <macros> <import>macs2_macros.xml</import> </macros> @@ -15,6 +16,8 @@ @effective_genome_size@ --bw '${ band_width }' @mfold_command@ + --d-min $d_min + @buffer_size@ ## remove the timepoint and strip the output 2>&1 | awk -F: '{print $4}' | awk '{$1=$1}1' @@ -33,6 +36,8 @@ <expand macro="tag_size" /> <expand macro="band_width" /> <expand macro="mfold_options" /> + <expand macro="fragment_size"/> + <expand macro="buffer_size"/> </inputs> <outputs> @@ -48,12 +53,16 @@ <param name="band_width" value="300"/> <param name="lower" value="5"/> <param name="upper" value="50"/> + <assert_command> + <has_text text="--buffer-size"/> + <has_text text="--d-min"/> + </assert_command> <output name="outfile"> <assert_contents> <has_line line="# predicted fragment length is 284 bps" /> </assert_contents> </output> - <output name="outfile_image" file="predictd_on_ChIP_200K_and_Control_200K.pdf" compare="sim_size"/> + <output name="outfile_image" file="predictd_on_ChIP_200K_and_Control_200K.pdf" compare="sim_size" ftype="pdf"/> </test> </tests> <help> |
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| diff -r 424aefbd7777 -r 640d3af5d833 macs2_randsample.xml --- a/macs2_randsample.xml Thu Apr 25 17:49:05 2019 -0400 +++ b/macs2_randsample.xml Sat Apr 02 21:37:38 2022 +0000 |
| [ |
| @@ -1,5 +1,6 @@ -<tool id="macs2_randsample" name="MACS2 randsample" version="@VERSION_STRING@.1"> +<tool id="macs2_randsample" name="MACS2 randsample" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> <description>Randomly sample number or percentage of total reads</description> + <expand macro="bio_tools"/> <macros> <import>macs2_macros.xml</import> </macros> @@ -9,7 +10,7 @@ <command><![CDATA[ @home_dir@ macs2 randsample - -t '${ infile }' + -i '${ infile }' -o '${ outfile }' --seed '${ seed }' @@ -49,8 +50,14 @@ <param name="method_options_selector" value="percentage" /> <param name="percentage" value="80.0" /> <param name="seed" value="1" /> - <output name="outfile" file="bdgrandsample_output.bed"/> - </test> + <output name="outfile"> + <assert_contents> + <has_text text="27179762" /> + <has_text text="4441986" /> + <has_size value="4787911" delta="500"/> + </assert_contents> + </output> + </test> </tests> <help> <![CDATA[ |
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| diff -r 424aefbd7777 -r 640d3af5d833 macs2_refinepeak.xml --- a/macs2_refinepeak.xml Thu Apr 25 17:49:05 2019 -0400 +++ b/macs2_refinepeak.xml Sat Apr 02 21:37:38 2022 +0000 |
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| @@ -1,5 +1,6 @@ -<tool id="macs2_refinepeak" name="MACS2 refinepeak" version="@VERSION_STRING@.1"> +<tool id="macs2_refinepeak" name="MACS2 refinepeak" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> <description>Refine peak summits and give scores measuring balance of forward- backward tags (Experimental)</description> + <expand macro="bio_tools"/> <macros> <import>macs2_macros.xml</import> </macros> @@ -15,12 +16,14 @@ --cutoff '${ cutoff }' --window-size '${ winsize }' --ofile '${ outfile }' + @buffer_size@ ]]></command> <inputs> <param name="infile" type="data" format="bam,bed" label="Sequencing alignment file" /> <param name="bed_infile" type="data" format="bed" label="Candidate peak file in BED format" /> <param name="cutoff" type="float" label="Cutoff" value="5.0" help="default: 5.0 (--cutoff)"/> <param name="winsize" type="integer" value="200" label="Scan window size on both side of the summit" help="default: 200bp (--window-size)" /> + <expand macro="buffer_size"/> </inputs> <outputs> |
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| diff -r 424aefbd7777 -r 640d3af5d833 test-data/bdgbroadcall_output.bdg --- a/test-data/bdgbroadcall_output.bdg Thu Apr 25 17:49:05 2019 -0400 +++ b/test-data/bdgbroadcall_output.bdg Sat Apr 02 21:37:38 2022 +0000 |
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| b'@@ -1,398 +1,3346 @@\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_bro'..b'dgbroadcall.bdg_broadRegion3311\t10\t.\t119219691\t119219945\t0\t2\t1,1\t0,253\t0\t0\t0\n+chrX\t119224194\t119224448\tmacs2_bdgbroadcall.bdg_broadRegion3312\t10\t.\t119224194\t119224448\t0\t2\t1,1\t0,253\t0\t0\t0\n+chrX\t119270090\t119270344\tmacs2_bdgbroadcall.bdg_broadRegion3313\t10\t.\t119270090\t119270344\t0\t2\t1,1\t0,253\t0\t0\t0\n+chrX\t119274283\t119274537\tmacs2_bdgbroadcall.bdg_broadRegion3314\t10\t.\t119274283\t119274537\t0\t2\t1,1\t0,253\t0\t0\t0\n+chrX\t119279664\t119279918\tmacs2_bdgbroadcall.bdg_broadRegion3315\t10\t.\t119279664\t119279918\t0\t2\t1,1\t0,253\t0\t0\t0\n+chrX\t119347622\t119348131\tmacs2_bdgbroadcall.bdg_broadRegion3316\t20\t.\t119347622\t119348131\t0\t3\t1,254,1\t0,45,508\t0\t0\t0\n+chrX\t119349399\t119349653\tmacs2_bdgbroadcall.bdg_broadRegion3317\t10\t.\t119349399\t119349653\t0\t2\t1,1\t0,253\t0\t0\t0\n+chrX\t119350590\t119350844\tmacs2_bdgbroadcall.bdg_broadRegion3318\t10\t.\t119350590\t119350844\t0\t2\t1,1\t0,253\t0\t0\t0\n+chrX\t119377334\t119377588\tmacs2_bdgbroadcall.bdg_broadRegion3319\t10\t.\t119377334\t119377588\t0\t2\t1,1\t0,253\t0\t0\t0\n+chrX\t119384485\t119385143\tmacs2_bdgbroadcall.bdg_broadRegion3320\t10\t.\t119384485\t119385143\t0\t2\t1,1\t0,657\t0\t0\t0\n+chrX\t119397246\t119397500\tmacs2_bdgbroadcall.bdg_broadRegion3321\t10\t.\t119397246\t119397500\t0\t2\t1,1\t0,253\t0\t0\t0\n+chrX\t119433740\t119433994\tmacs2_bdgbroadcall.bdg_broadRegion3322\t10\t.\t119433740\t119433994\t0\t2\t1,1\t0,253\t0\t0\t0\n+chrX\t119443366\t119443738\tmacs2_bdgbroadcall.bdg_broadRegion3323\t40\t.\t119443366\t119443738\t0\t3\t1,265,1\t0,21,371\t0\t0\t0\n+chrX\t119453196\t119453450\tmacs2_bdgbroadcall.bdg_broadRegion3324\t10\t.\t119453196\t119453450\t0\t2\t1,1\t0,253\t0\t0\t0\n+chrX\t119496500\t119496754\tmacs2_bdgbroadcall.bdg_broadRegion3325\t10\t.\t119496500\t119496754\t0\t2\t1,1\t0,253\t0\t0\t0\n+chrX\t119499109\t119499576\tmacs2_bdgbroadcall.bdg_broadRegion3326\t30\t.\t119499109\t119499576\t0\t3\t1,254,1\t0,9,466\t0\t0\t0\n+chrX\t119584005\t119584487\tmacs2_bdgbroadcall.bdg_broadRegion3327\t30\t.\t119584005\t119584487\t0\t3\t1,254,1\t0,133,481\t0\t0\t0\n+chrX\t119586039\t119586293\tmacs2_bdgbroadcall.bdg_broadRegion3328\t10\t.\t119586039\t119586293\t0\t2\t1,1\t0,253\t0\t0\t0\n+chrX\t119608806\t119609935\tmacs2_bdgbroadcall.bdg_broadRegion3329\t50\t.\t119608806\t119609935\t0\t3\t1,337,1\t0,548,1128\t0\t0\t0\n+chrX\t119619999\t119620297\tmacs2_bdgbroadcall.bdg_broadRegion3330\t20\t.\t119619999\t119620297\t0\t3\t1,210,1\t0,44,297\t0\t0\t0\n+chrX\t119631826\t119632280\tmacs2_bdgbroadcall.bdg_broadRegion3331\t60\t.\t119631826\t119632280\t0\t3\t1,333,1\t0,96,453\t0\t0\t0\n+chrX\t119640766\t119641020\tmacs2_bdgbroadcall.bdg_broadRegion3332\t10\t.\t119640766\t119641020\t0\t2\t1,1\t0,253\t0\t0\t0\n+chrX\t119668285\t119668539\tmacs2_bdgbroadcall.bdg_broadRegion3333\t10\t.\t119668285\t119668539\t0\t2\t1,1\t0,253\t0\t0\t0\n+chrX\t119680122\t119680376\tmacs2_bdgbroadcall.bdg_broadRegion3334\t10\t.\t119680122\t119680376\t0\t2\t1,1\t0,253\t0\t0\t0\n+chrX\t119728234\t119728488\tmacs2_bdgbroadcall.bdg_broadRegion3335\t10\t.\t119728234\t119728488\t0\t2\t1,1\t0,253\t0\t0\t0\n+chrX\t119737495\t119737749\tmacs2_bdgbroadcall.bdg_broadRegion3336\t10\t.\t119737495\t119737749\t0\t2\t1,1\t0,253\t0\t0\t0\n+chrX\t119758695\t119758949\tmacs2_bdgbroadcall.bdg_broadRegion3337\t10\t.\t119758695\t119758949\t0\t2\t1,1\t0,253\t0\t0\t0\n+chrX\t119762376\t119762630\tmacs2_bdgbroadcall.bdg_broadRegion3338\t10\t.\t119762376\t119762630\t0\t2\t1,1\t0,253\t0\t0\t0\n+chrX\t119769884\t119770138\tmacs2_bdgbroadcall.bdg_broadRegion3339\t10\t.\t119769884\t119770138\t0\t2\t1,1\t0,253\t0\t0\t0\n+chrX\t119826519\t119826773\tmacs2_bdgbroadcall.bdg_broadRegion3340\t10\t.\t119826519\t119826773\t0\t2\t1,1\t0,253\t0\t0\t0\n+chrX\t119864257\t119864511\tmacs2_bdgbroadcall.bdg_broadRegion3341\t10\t.\t119864257\t119864511\t0\t2\t1,1\t0,253\t0\t0\t0\n+chrX\t119883657\t119883911\tmacs2_bdgbroadcall.bdg_broadRegion3342\t10\t.\t119883657\t119883911\t0\t2\t1,1\t0,253\t0\t0\t0\n+chrX\t119887334\t119887769\tmacs2_bdgbroadcall.bdg_broadRegion3343\t30\t.\t119887334\t119887769\t0\t3\t1,254,1\t0,56,434\t0\t0\t0\n+chrX\t119903862\t119904514\tmacs2_bdgbroadcall.bdg_broadRegion3344\t30\t.\t119903862\t119904514\t0\t3\t1,254,1\t0,15,651\t0\t0\t0\n+chrX\t119923853\t119924452\tmacs2_bdgbroadcall.bdg_broadRegion3345\t70\t.\t119923853\t119924452\t0\t3\t1,457,1\t0,15,598\t0\t0\t0\n+chrX\t119931658\t119931912\tmacs2_bdgbroadcall.bdg_broadRegion3346\t10\t.\t119931658\t119931912\t0\t2\t1,1\t0,253\t0\t0\t0\n' |
| b |
| diff -r 424aefbd7777 -r 640d3af5d833 test-data/bdgpeakcall_output_cutoff.bdg --- a/test-data/bdgpeakcall_output_cutoff.bdg Thu Apr 25 17:49:05 2019 -0400 +++ b/test-data/bdgpeakcall_output_cutoff.bdg Sat Apr 02 21:37:38 2022 +0000 |
| b |
| @@ -1,50 +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 +42.15 9 2890 321.11 +41.30 10 3512 351.20 +40.46 10 3709 370.90 +39.62 12 4282 356.83 +38.77 13 4699 361.46 +37.93 16 5998 374.88 +37.09 20 8291 414.55 +36.24 21 9508 452.76 +35.40 21 9508 452.76 +34.56 22 10703 486.50 +33.72 23 11996 521.57 +32.87 25 13676 547.04 +32.03 24 14823 617.62 +31.19 25 16358 654.32 +30.34 26 17951 690.42 +29.50 26 18894 726.69 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 +27.82 21 20518 977.05 +26.97 19 21125 1111.84 +26.13 15 21694 1446.27 +25.29 13 22298 1715.23 +24.44 12 22768 1897.33 +23.60 12 22768 1897.33 +22.76 11 22971 2088.27 +21.92 8 23309 2913.62 +21.07 8 23492 2936.50 +20.23 8 23982 2997.75 +19.39 8 24156 3019.50 +18.54 7 24532 3504.57 +17.70 5 24701 4940.20 16.86 6 25008 4168.00 -16.01 6 25083 4180.00 +16.01 6 25083 4180.50 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 +14.33 5 25609 5121.80 +13.49 4 26022 6505.50 +12.64 4 26337 6584.25 +11.80 4 26337 6584.25 +10.96 4 26409 6602.25 +10.11 4 26751 6687.75 +9.27 3 27049 9016.33 +8.43 3 27088 9029.33 +7.59 2 27139 13569.50 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 +5.06 3 27416 9138.67 +4.22 4 27706 6926.50 +3.37 3 27769 9256.33 2.53 6 28710 4785.00 -1.69 7 29161 4165.00 +1.69 7 29161 4165.86 |
| b |
| diff -r 424aefbd7777 -r 640d3af5d833 test-data/bdgrandsample_output.bed --- a/test-data/bdgrandsample_output.bed Thu Apr 25 17:49:05 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,159966 +0,0 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|
| b |
| diff -r 424aefbd7777 -r 640d3af5d833 test-data/callpeak_bampe_narrow.bed --- a/test-data/callpeak_bampe_narrow.bed Thu Apr 25 17:49:05 2019 -0400 +++ b/test-data/callpeak_bampe_narrow.bed Sat Apr 02 21:37:38 2022 +0000 |
| b |
| @@ -1,1 +1,1 @@ -gi|251831106|ref|NC_012920.1| 0 251 bwa-mem-test1_bam_peak_1 3056 . 44.99989 308.04297 305.64328 56 +gi|251831106|ref|NC_012920.1| 0 251 bwa-mem-test1_bam_peak_1 3056 . 44.9999 308.043 305.643 56 |
| b |
| diff -r 424aefbd7777 -r 640d3af5d833 test-data/callpeak_control_part.bdg --- a/test-data/callpeak_control_part.bdg Thu Apr 25 17:49:05 2019 -0400 +++ b/test-data/callpeak_control_part.bdg Sat Apr 02 21:37:38 2022 +0000 |
| b |
| b'@@ -1,100 +1,1000 @@\n-chrX\t0\t173099\t0.01536\n-chrX\t173099\t177599\t0.02536\n-chrX\t177599\t177972\t0.25364\n-chrX\t177972\t178226\t0.99858\n-chrX\t178226\t178599\t0.25364\n-chrX\t178599\t183099\t0.02536\n-chrX\t183099\t196237\t0.01536\n-chrX\t196237\t200737\t0.02536\n-chrX\t200737\t201110\t0.25364\n-chrX\t201110\t201364\t0.99858\n-chrX\t201364\t201737\t0.25364\n-chrX\t201737\t205373\t0.02536\n-chrX\t205373\t206237\t0.05073\n-chrX\t206237\t209873\t0.02536\n-chrX\t209873\t210246\t0.25364\n-chrX\t210246\t210500\t0.99858\n-chrX\t210500\t210873\t0.25364\n-chrX\t210873\t215373\t0.02536\n-chrX\t215373\t222667\t0.01536\n-chrX\t222667\t227167\t0.02536\n-chrX\t227167\t227540\t0.25364\n-chrX\t227540\t227794\t0.99858\n-chrX\t227794\t228167\t0.25364\n-chrX\t228167\t232667\t0.02536\n-chrX\t232667\t342891\t0.01536\n-chrX\t342891\t347391\t0.02536\n-chrX\t347391\t347764\t0.25364\n-chrX\t347764\t348018\t0.99858\n-chrX\t348018\t348391\t0.25364\n-chrX\t348391\t350176\t0.02536\n-chrX\t350176\t352891\t0.05073\n-chrX\t352891\t354676\t0.02536\n-chrX\t354676\t355049\t0.25364\n-chrX\t355049\t355303\t0.99858\n-chrX\t355303\t355676\t0.25364\n-chrX\t355676\t359696\t0.05073\n-chrX\t359696\t360069\t0.25364\n-chrX\t360069\t360323\t0.99858\n-chrX\t360323\t360696\t0.25364\n-chrX\t360696\t365196\t0.02536\n-chrX\t365196\t435810\t0.01536\n-chrX\t435810\t440310\t0.02536\n-chrX\t440310\t440683\t0.25364\n-chrX\t440683\t440937\t0.99858\n-chrX\t440937\t441310\t0.25364\n-chrX\t441310\t445810\t0.02536\n-chrX\t445810\t479224\t0.01536\n-chrX\t479224\t483724\t0.02536\n-chrX\t483724\t484097\t0.25364\n-chrX\t484097\t484351\t0.99858\n-chrX\t484351\t484724\t0.25364\n-chrX\t484724\t489224\t0.02536\n-chrX\t489224\t582624\t0.01536\n-chrX\t582624\t586422\t0.02536\n-chrX\t586422\t587124\t0.05073\n-chrX\t587124\t587497\t0.25364\n-chrX\t587497\t587751\t0.99858\n-chrX\t587751\t588124\t0.25364\n-chrX\t588124\t590922\t0.05073\n-chrX\t590922\t591295\t0.25364\n-chrX\t591295\t591549\t0.99858\n-chrX\t591549\t591922\t0.25364\n-chrX\t591922\t592624\t0.05073\n-chrX\t592624\t594385\t0.02536\n-chrX\t594385\t596422\t0.05073\n-chrX\t596422\t598885\t0.02536\n-chrX\t598885\t599258\t0.25364\n-chrX\t599258\t599512\t0.99858\n-chrX\t599512\t599885\t0.25364\n-chrX\t599885\t604385\t0.02536\n-chrX\t604385\t620365\t0.01536\n-chrX\t620365\t624865\t0.02536\n-chrX\t624865\t625238\t0.25364\n-chrX\t625238\t625492\t0.99858\n-chrX\t625492\t625865\t0.25364\n-chrX\t625865\t630365\t0.02536\n-chrX\t630365\t636674\t0.01536\n-chrX\t636674\t641174\t0.02536\n-chrX\t641174\t641547\t0.25364\n-chrX\t641547\t641801\t0.99858\n-chrX\t641801\t642174\t0.25364\n-chrX\t642174\t646674\t0.02536\n-chrX\t646674\t654813\t0.01536\n-chrX\t654813\t659313\t0.02536\n-chrX\t659313\t659686\t0.25364\n-chrX\t659686\t659940\t0.99858\n-chrX\t659940\t660313\t0.25364\n-chrX\t660313\t664813\t0.02536\n-chrX\t664813\t707545\t0.01536\n-chrX\t707545\t712045\t0.02536\n-chrX\t712045\t712418\t0.25364\n-chrX\t712418\t712672\t0.99858\n-chrX\t712672\t713045\t0.25364\n-chrX\t713045\t717545\t0.02536\n-chrX\t717545\t756774\t0.01536\n-chrX\t756774\t761274\t0.02536\n-chrX\t761274\t761647\t0.25364\n-chrX\t761647\t761901\t0.99858\n-chrX\t761901\t762274\t0.25364\n-chrX\t762274\t766774\t0.02536\n+chr1\t0\t559459\t0.01536\n+chr1\t559459\t559461\t0.02536\n+chr1\t559461\t559482\t0.05073\n+chr1\t559482\t559484\t0.07609\n+chr1\t559484\t559489\t0.10146\n+chr1\t559489\t559494\t0.12682\n+chr1\t559494\t559505\t0.15218\n+chr1\t559505\t559517\t0.17755\n+chr1\t559517\t559521\t0.20291\n+chr1\t559521\t559526\t0.22828\n+chr1\t559526\t559530\t0.25364\n+chr1\t559530\t559542\t0.27900\n+chr1\t559542\t559548\t0.30437\n+chr1\t559548\t559555\t0.32973\n+chr1\t559555\t559558\t0.35509\n+chr1\t559558\t559590\t0.38046\n+chr1\t559590\t559591\t0.40582\n+chr1\t559591\t559597\t0.43119\n+chr1\t559597\t559600\t0.45655\n+chr1\t559600\t559623\t0.48191\n+chr1\t559623\t559629\t0.50728\n+chr1\t559629\t559643\t0.53264\n+chr1\t559643\t559645\t0.55801\n+chr1\t559645\t559665\t0.58337\n+chr1\t559665\t559671\t0.60873\n+chr1\t559671\t559676\t0.63410\n+chr1\t559676\t559716\t0.65946\n+chr1\t559716\t559718\t0.68483\n+chr1\t559718\t559724\t0.71019\n+chr1\t559724\t559736\t0.73555\n+chr1\t559736\t559741\t0.76092\n+chr1\t559741\t559747\t0.78628\n+chr1\t559747\t559748\t0.81165\n+chr1\t559748\t559753\t0.83701\n+chr1\t559753\t559756\t0.86237\n+chr1\t559756\t559758\t0.88774\n+chr1\t559758\t559759\t0.91310\n+chr1\t559759\t559764\t0.93846\n+chr1\t559764\t559769\t0.96383\n+chr1\t559769\t559782\t0.98919\n+chr1\t559782\t559784\t1.01456\n+chr1\t559784\t559796\t1.03992\n+chr1\t559796'..b'r1\t563916\t563917\t23.23334\n+chr1\t563917\t563918\t23.25870\n+chr1\t563918\t563924\t23.28407\n+chr1\t563924\t563925\t23.30943\n+chr1\t563925\t563930\t23.33479\n+chr1\t563930\t563934\t23.36016\n+chr1\t563934\t563935\t23.38552\n+chr1\t563935\t563939\t23.41089\n+chr1\t563939\t563954\t23.43625\n+chr1\t563954\t563955\t23.46161\n+chr1\t563955\t563956\t23.48698\n+chr1\t563956\t563961\t23.51234\n+chr1\t563961\t563965\t23.53771\n+chr1\t563965\t563969\t23.56307\n+chr1\t563969\t563970\t23.58843\n+chr1\t563970\t563972\t23.61380\n+chr1\t563972\t563989\t23.63916\n+chr1\t563989\t563993\t23.66453\n+chr1\t563993\t563997\t23.68989\n+chr1\t563997\t564045\t23.71525\n+chr1\t564045\t564052\t23.74062\n+chr1\t564052\t564054\t23.76598\n+chr1\t564054\t564058\t23.81671\n+chr1\t564058\t564064\t23.84207\n+chr1\t564064\t564073\t23.86744\n+chr1\t564073\t564105\t23.89280\n+chr1\t564105\t564106\t23.91817\n+chr1\t564106\t564112\t23.94353\n+chr1\t564112\t564125\t23.99426\n+chr1\t564125\t564126\t24.01962\n+chr1\t564126\t564132\t24.04498\n+chr1\t564132\t564134\t24.07035\n+chr1\t564134\t564139\t24.09571\n+chr1\t564139\t564142\t24.12108\n+chr1\t564142\t564147\t24.14644\n+chr1\t564147\t564148\t24.19717\n+chr1\t564148\t564151\t24.22253\n+chr1\t564151\t564153\t24.24790\n+chr1\t564153\t564156\t24.29862\n+chr1\t564156\t564163\t24.32399\n+chr1\t564163\t564165\t24.34935\n+chr1\t564165\t564169\t24.37471\n+chr1\t564169\t564173\t24.40008\n+chr1\t564173\t564176\t24.42544\n+chr1\t564176\t564179\t24.45081\n+chr1\t564179\t564190\t24.47617\n+chr1\t564190\t564205\t24.50153\n+chr1\t564205\t564243\t24.52690\n+chr1\t564243\t564251\t24.55226\n+chr1\t564251\t564252\t24.57763\n+chr1\t564252\t564256\t24.60299\n+chr1\t564256\t564262\t24.62835\n+chr1\t564262\t564264\t24.65372\n+chr1\t564264\t564266\t24.67908\n+chr1\t564266\t564268\t24.70444\n+chr1\t564268\t564270\t24.72981\n+chr1\t564270\t564272\t24.75517\n+chr1\t564272\t564276\t24.78054\n+chr1\t564276\t564283\t24.80590\n+chr1\t564283\t564284\t24.83126\n+chr1\t564284\t564286\t24.85663\n+chr1\t564286\t564290\t24.88199\n+chr1\t564290\t564293\t24.90736\n+chr1\t564293\t564295\t24.93272\n+chr1\t564295\t564308\t24.95808\n+chr1\t564308\t564312\t24.98345\n+chr1\t564312\t564313\t25.00881\n+chr1\t564313\t564316\t25.03418\n+chr1\t564316\t564317\t25.05954\n+chr1\t564317\t564324\t25.08490\n+chr1\t564324\t564331\t25.11027\n+chr1\t564331\t564334\t25.13563\n+chr1\t564334\t564346\t25.16100\n+chr1\t564346\t564353\t25.18636\n+chr1\t564353\t564356\t25.21172\n+chr1\t564356\t564366\t25.23709\n+chr1\t564366\t564367\t25.26245\n+chr1\t564367\t564368\t25.28782\n+chr1\t564368\t564370\t25.33854\n+chr1\t564370\t564375\t25.36391\n+chr1\t564375\t564378\t25.38927\n+chr1\t564378\t564383\t25.41463\n+chr1\t564383\t564386\t25.44000\n+chr1\t564386\t564390\t25.46536\n+chr1\t564390\t564393\t25.49073\n+chr1\t564393\t564402\t25.51609\n+chr1\t564402\t564412\t25.54145\n+chr1\t564412\t564413\t25.56682\n+chr1\t564413\t564419\t25.59218\n+chr1\t564419\t564425\t25.61755\n+chr1\t564425\t564426\t25.66827\n+chr1\t564426\t564428\t25.71900\n+chr1\t564428\t564433\t25.74437\n+chr1\t564433\t564434\t25.76973\n+chr1\t564434\t564442\t25.79509\n+chr1\t564442\t564447\t25.82046\n+chr1\t564447\t564448\t25.87119\n+chr1\t564448\t564449\t25.89655\n+chr1\t564449\t564451\t25.92191\n+chr1\t564451\t564452\t25.94728\n+chr1\t564452\t564456\t25.97264\n+chr1\t564456\t564459\t25.99800\n+chr1\t564459\t564460\t26.02337\n+chr1\t564460\t564464\t26.04873\n+chr1\t564464\t564475\t26.07410\n+chr1\t564475\t564484\t26.09946\n+chr1\t564484\t564485\t26.12482\n+chr1\t564485\t564489\t26.15019\n+chr1\t564489\t564492\t26.17555\n+chr1\t564492\t564494\t26.20092\n+chr1\t564494\t564495\t26.22628\n+chr1\t564495\t564496\t26.25164\n+chr1\t564496\t564498\t26.27701\n+chr1\t564498\t564500\t26.30237\n+chr1\t564500\t564504\t26.32774\n+chr1\t564504\t564509\t26.35310\n+chr1\t564509\t564512\t26.37846\n+chr1\t564512\t564518\t26.40383\n+chr1\t564518\t564519\t26.42919\n+chr1\t564519\t564521\t26.45456\n+chr1\t564521\t564524\t26.47992\n+chr1\t564524\t564529\t26.50528\n+chr1\t564529\t564530\t26.53065\n+chr1\t564530\t564533\t26.55601\n+chr1\t564533\t564550\t26.58138\n+chr1\t564550\t564554\t26.60674\n+chr1\t564554\t564559\t26.63210\n+chr1\t564559\t564564\t26.65747\n+chr1\t564564\t564565\t26.68283\n+chr1\t564565\t564570\t26.70819\n+chr1\t564570\t564575\t26.73356\n+chr1\t564575\t564577\t26.75892\n+chr1\t564577\t564581\t26.78429\n+chr1\t564581\t564586\t26.80965\n+chr1\t564586\t564590\t26.83501\n+chr1\t564590\t564594\t26.88574\n+chr1\t564594\t564604\t27.13938\n+chr1\t564604\t564610\t27.39302\n' |
| b |
| diff -r 424aefbd7777 -r 640d3af5d833 test-data/callpeak_part.tabular --- a/test-data/callpeak_part.tabular Thu Apr 25 17:49:05 2019 -0400 +++ b/test-data/callpeak_part.tabular Sat Apr 02 21:37:38 2022 +0000 |
| [ |
| b'@@ -1,14 +1,16 @@\n-# This file is generated by MACS version 2.1.1.20160309\n-# Command line: callpeak -t /private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmptu7iXI/files/000/dataset_8.dat --name ChIP_200K_bed -c /private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmptu7iXI/files/000/dataset_9.dat --format BED --gsize 3300000000 --keep-dup 1 --qvalue 0.05 --mfold 5 50 --bw 300\n+# This file is generated by MACS version 2.2.7.1\n+# Command line: callpeak -t /tmp/tmpnaqc0336/files/3/f/0/dataset_3f02f858-205a-41bb-bfbc-712b99093ecb.dat --name ChIP_200K_bed -c /tmp/tmpnaqc0336/files/e/4/5/dataset_e45de785-43dc-44da-badd-fd49fc164b85.dat --format BED --gsize 3300000000 --keep-dup 1 --d-min 20 --buffer-size 100000 --bdg --qvalue 0.05 --mfold 5 50 --bw 300\n # ARGUMENTS LIST:\n # name = ChIP_200K_bed\n # format = BED\n-# ChIP-seq file = [\'/private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmptu7iXI/files/000/dataset_8.dat\']\n-# control file = [\'/private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmptu7iXI/files/000/dataset_9.dat\']\n+# ChIP-seq file = [\'/tmp/tmpnaqc0336/files/3/f/0/dataset_3f02f858-205a-41bb-bfbc-712b99093ecb.dat\']\n+# control file = [\'/tmp/tmpnaqc0336/files/e/4/5/dataset_e45de785-43dc-44da-badd-fd49fc164b85.dat\']\n # effective genome size = 3.30e+09\n # band width = 300\n # model fold = [5, 50]\n # qvalue cutoff = 5.00e-02\n+# The maximum gap between significant sites is assigned as the read length/tag size.\n+# The minimum length of peaks is assigned as the predicted fragment length "d".\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@@ -26,75 +28,973 @@\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\tChIP_200K_bed_peak_1\n-chr1\t919420\t919785\t366\t919550\t5.00\t12.44148\t5.85158\t8.70936\tChIP_200K_bed_peak_2\n-chr1\t937221\t937483\t263\t937375\t4.00\t10.06728\t4.87632\t6.61759\tChIP_200K_bed_peak_3\n-chr1\t954743\t954996\t254\t954814\t3.00\t8.63977\t3.93948\t5.28944\tChIP_200K_bed_peak_4\n-chr1\t994763\t995016\t254\t994906\t3.00\t8.63977\t3.93948\t5.28944\tChIP_200K_bed_peak_5\n-chr1\t1057395\t1057648\t254\t1057509\t3.00\t8.63977\t3.93948\t5.28944\tChIP_200K_bed_peak_6\n-chr1\t1240580\t1241004\t425\t1240777\t3.00\t7.77216\t3.90105\t4.60940\tChIP_200K_bed_peak_7\n-chr1\t1307393\t1307735\t343\t1307601\t5.00\t12.44148\t5.85158\t8.70936\tChIP_200K_bed_peak_8\n-chr1\t1440351\t1440633\t283\t1440462\t4.00\t11.15252\t4.92435\t7.51486\tChIP_200K_bed_peak_9\n-chr1\t1555433\t1555725\t293\t1555571\t4.00\t11.15252\t4.92435\t7.51486\tChIP_200K_bed_peak_10\n-chr1\t1590668\t1590946\t279\t1590840\t4.00\t10.06728\t4.87632\t6.61759\tChIP_200K_bed_peak_11\n-chr1\t1837669\t1838104\t436\t1837886\t6.00\t14.88256\t6.82684\t10.84922\tChIP_200K_bed_peak_12\n-chr1\t1840366\t1840828\t463\t1840547\t5.00\t13.74439\t5.90922\t9.80598\tChIP_200K_bed_peak_13\n-chr1\t1976400\t1976653\t254\t1976469\t3.00\t8.63977\t3.93948\t5.28944\tChIP_200K_bed_peak_14\n-chr1\t2071302\t2071627\t326\t2071423\t4.00\t11.15252\t4.92435\t7.51486\tChIP_200K_bed_peak_15\n-chr1\t2105717\t2106140\t424\t2105919\t4.00\t7.70001\t4.64644\t4.60940\tChIP_200K_bed_peak_16\n-chr1\t2126522\t2126861\t340\t2126648\t4.00\t10.06728\t4.87632\t6.61759\tChIP_200K_bed_peak_17\n-chr1\t2246521\t2246954\t434\t2246712\t5.00\t9.59761\t5.57573\t6.23289\tChIP_200K_bed_peak_18\n-chr1\t2313158\t2313560\t403\t2313353\t5.00\t13.74439\t5.90922\t9.80598\tChIP_200K_bed_peak_19\n-chr1\t2345828\t2346242\t415\t2346028\t7.00\t17.38158\t7.80211\t13.02598\tChIP_200K_bed_peak_20\n-chr1\t2510055\t2510308\t254\t2510213\t3.00\t8.63977\t3.93948\t5.28944\tChIP_200K_bed_peak_21\n-chr1\t3341408\t3341661\t254\t3341461\t3.00\t7.77216\t3.90105\t4.60940\tChIP_200K_bed_peak_22\n-chr1\t3369639\t3369892\t254\t3369863\t3.00\t8.63977\t3.93948\t5.28944\tChIP_200K_bed_peak_23\n-chr1\t3400441\t3400769\t329\t3400610\t4.00\t11.15252\t4.92435\t7.51486\tChIP_200K_bed_peak_24\n-chr1\t3407841\t3408094\t254\t3407975\t3.00\t8.63977\t3.93948\t5.28944\tChIP_200K_bed_peak_25\n-chr1\t3481748\t3482245\t'..b'k_925\n+chr1\t162817657\t162817932\t276\t162817777\t4\t10.0673\t4.87632\t6.6176\tChIP_200K_bed_peak_926\n+chr1\t162823938\t162824385\t448\t162824189\t6\t7.96913\t5.58374\t4.79957\tChIP_200K_bed_peak_927\n+chr1\t162847869\t162848122\t254\t162847903\t2\t5.57376\t2.92579\t2.7069\tChIP_200K_bed_peak_928\n+chr1\t163041739\t163041992\t254\t163041844\t3\t6.57684\t3.80689\t3.50364\tChIP_200K_bed_peak_929\n+chr1\t163285588\t163285879\t292\t163285734\t4\t11.1525\t4.92435\t7.51486\tChIP_200K_bed_peak_930\n+chr1\t163328972\t163329300\t329\t163329106\t4\t11.1525\t4.92435\t7.51486\tChIP_200K_bed_peak_931\n+chr1\t163531411\t163531664\t254\t163531544\t3\t8.63977\t3.93948\t5.28944\tChIP_200K_bed_peak_932\n+chr1\t164587080\t164587333\t254\t164587199\t3\t8.63977\t3.93948\t5.28944\tChIP_200K_bed_peak_933\n+chr1\t164756530\t164756953\t424\t164756744\t4\t10.0673\t4.87632\t6.6176\tChIP_200K_bed_peak_934\n+chr1\t165098799\t165099130\t332\t165098960\t4\t11.1525\t4.92435\t7.51486\tChIP_200K_bed_peak_935\n+chr1\t165112798\t165113051\t254\t165112931\t3\t8.63977\t3.93948\t5.28944\tChIP_200K_bed_peak_936\n+chr1\t165114156\t165114464\t309\t165114235\t5\t13.7444\t5.90922\t9.80598\tChIP_200K_bed_peak_937\n+chr1\t165227445\t165227698\t254\t165227512\t3\t7.77216\t3.90105\t4.6094\tChIP_200K_bed_peak_938\n+chr1\t165338430\t165338683\t254\t165338550\t2\t6.22382\t2.95461\t3.18932\tChIP_200K_bed_peak_939\n+chr1\t165362099\t165362474\t376\t165362291\t8\t17.2324\t8.56549\t12.9738\tChIP_200K_bed_peak_940\n+chr1\t165562233\t165562516\t284\t165562321\t7\t17.3816\t7.80211\t13.026\tChIP_200K_bed_peak_941\n+chr1\t165570813\t165571309\t497\t165571061\t4\t11.1525\t4.92435\t7.51486\tChIP_200K_bed_peak_942\n+chr1\t165687191\t165687500\t310\t165687395\t5\t12.4415\t5.85158\t8.70937\tChIP_200K_bed_peak_943\n+chr1\t165883472\t165884023\t552\t165883680\t8\t21.8878\t8.86384\t17.0481\tChIP_200K_bed_peak_944\n+chr1\t165893926\t165894290\t365\t165894120\t6\t16.4032\t6.89409\t12.1664\tChIP_200K_bed_peak_945\n+chr1\t165897288\t165897729\t442\t165897514\t6\t16.4032\t6.89409\t12.1664\tChIP_200K_bed_peak_946\n+chr1\t166102524\t166102777\t254\t166102579\t3\t7.77216\t3.90105\t4.6094\tChIP_200K_bed_peak_947\n+chr1\t166134134\t166134388\t255\t166134342\t4\t10.0673\t4.87632\t6.6176\tChIP_200K_bed_peak_948\n+chr1\t166448256\t166448688\t433\t166448471\t6\t14.8826\t6.82684\t10.8492\tChIP_200K_bed_peak_949\n+chr1\t167028344\t167028616\t273\t167028559\t6\t7.96913\t5.58374\t4.79957\tChIP_200K_bed_peak_950\n+chr1\t167035943\t167036261\t319\t167036038\t4\t10.0673\t4.87632\t6.6176\tChIP_200K_bed_peak_951\n+chr1\t167237144\t167237397\t254\t167237296\t3\t6.57684\t3.80689\t3.50364\tChIP_200K_bed_peak_952\n+chr1\t167370457\t167370840\t384\t167370687\t4\t10.0673\t4.87632\t6.6176\tChIP_200K_bed_peak_953\n+chr1\t167411348\t167411617\t270\t167411508\t9\t9.70719\t6.63448\t6.34225\tChIP_200K_bed_peak_954\n+chr1\t167509677\t167509994\t318\t167509766\t5\t13.7444\t5.90922\t9.80598\tChIP_200K_bed_peak_955\n+chr1\t167606643\t167606904\t262\t167606794\t4\t11.1525\t4.92435\t7.51486\tChIP_200K_bed_peak_956\n+chr1\t167657154\t167657498\t345\t167657336\t7\t17.3816\t7.80211\t13.026\tChIP_200K_bed_peak_957\n+chr1\t167684256\t167684787\t532\t167684669\t3\t8.63977\t3.93948\t5.28944\tChIP_200K_bed_peak_958\n+chr1\t168051430\t168051903\t474\t168051540\t4\t11.1525\t4.92435\t7.51486\tChIP_200K_bed_peak_959\n+chr1\t168054015\t168054268\t254\t168054128\t3\t8.63977\t3.93948\t5.28944\tChIP_200K_bed_peak_960\n+chr1\t168115055\t168115312\t258\t168115182\t4\t11.1525\t4.92435\t7.51486\tChIP_200K_bed_peak_961\n+chr1\t168312030\t168312283\t254\t168312087\t2\t6.22382\t2.95461\t3.18932\tChIP_200K_bed_peak_962\n+chr1\t168409108\t168409398\t291\t168409236\t5\t12.4415\t5.85158\t8.70937\tChIP_200K_bed_peak_963\n+chr1\t169317676\t169317929\t254\t169317779\t7\t9.46957\t6.38142\t6.1115\tChIP_200K_bed_peak_964\n+chr1\t169435647\t169435900\t254\t169435730\t3\t8.63977\t3.93948\t5.28944\tChIP_200K_bed_peak_965\n+chr1\t169515619\t169516039\t421\t169515830\t6\t14.8826\t6.82684\t10.8492\tChIP_200K_bed_peak_966\n+chr1\t169570239\t169570598\t360\t169570357\t4\t11.1525\t4.92435\t7.51486\tChIP_200K_bed_peak_967\n+chr1\t169681092\t169681643\t552\t169681360\t6\t14.8826\t6.82684\t10.8492\tChIP_200K_bed_peak_968\n+chr1\t169778762\t169779123\t362\t169778927\t6\t16.4032\t6.89409\t12.1664\tChIP_200K_bed_peak_969\n+chr1\t169898085\t169898451\t367\t169898207\t7\t17.3816\t7.80211\t13.026\tChIP_200K_bed_peak_970\n' |
| b |
| diff -r 424aefbd7777 -r 640d3af5d833 test-data/callpeak_treatment_part.bdg --- a/test-data/callpeak_treatment_part.bdg Thu Apr 25 17:49:05 2019 -0400 +++ b/test-data/callpeak_treatment_part.bdg Sat Apr 02 21:37:38 2022 +0000 |
| b |
| b'@@ -1,100 +1,1000 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|
| b |
| diff -r 424aefbd7777 -r 640d3af5d833 test-data/filterdup_on_ChIP_200K_w_dups.bed --- a/test-data/filterdup_on_ChIP_200K_w_dups.bed Thu Apr 25 17:49:05 2019 -0400 +++ b/test-data/filterdup_on_ChIP_200K_w_dups.bed Sat Apr 02 21:37:38 2022 +0000 |
| b |
| @@ -1,10 +1,1 @@ chr1 564917 565017 . . + -chr1 565533 565633 . . + -chr1 565844 565944 . . + -chr1 565858 565958 . . + -chr1 566132 566232 . . + -chr1 566212 566312 . . + -chr1 566736 566836 . . + -chr1 566976 567076 . . + -chr1 567211 567311 . . + -chr1 567320 567420 . . + |
| b |
| diff -r 424aefbd7777 -r 640d3af5d833 test-data/magic.pdf |
| b |
| Binary file test-data/magic.pdf has changed |
| b |
| diff -r 424aefbd7777 -r 640d3af5d833 test-data/predictd_on_ChIP_200K_and_Control_200K.pdf |
| b |
| Binary file test-data/predictd_on_ChIP_200K_and_Control_200K.pdf has changed |