| Previous changeset 16:2e615a3f2b07 (2018-02-05) Next changeset 18:eb9fcfcd44a0 (2018-03-02) |
|
Commit message:
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty |
|
modified:
bamCompare.xml deepTools_macros.xml readme.rst test-data/bamPEFragmentSize_histogram_result1.png test-data/bamPEFragmentSize_result1.txt test-data/heatmapper_result1.png test-data/heatmapper_result2.png test-data/multiBamSummary_result1.npz test-data/multiBamSummary_result2.npz test-data/plotCorrelation_result1.tabular test-data/plotCorrelation_result2.png test-data/plotCoverage_result1.png test-data/plotCoverage_result1.tabular test-data/plotEnrichment_output.txt test-data/plotFingerprint_result2.tabular test-data/plotPCA_result1.png test-data/plotPCA_result2.tabular |
|
added:
test-data/alignmentSieve.bam test-data/alignmentSieve.bed test-data/alignmentSieve.txt test-data/alignmentSieve2.bam test-data/alignmentSieve3.bam test-data/bamPEFragmentSize_lengths1.txt test-data/bamPEFragmentSize_table1.txt test-data/estimateReadFiltering.txt test-data/paired_chr2L.cram |
| b |
| diff -r 2e615a3f2b07 -r 2a1b4e95bdf7 bamCompare.xml --- a/bamCompare.xml Mon Feb 05 11:43:36 2018 -0500 +++ b/bamCompare.xml Thu Feb 15 07:48:38 2018 -0500 |
| [ |
| @@ -1,5 +1,5 @@ <tool id="deeptools_bam_compare" name="bamCompare" version="@WRAPPER_VERSION@.0"> - <description>normalizes and compares two BAM files to obtain the ratio, log2ratio or difference between them</description> + <description>normalizes and compares two BAM or CRAM files to obtain the ratio, log2ratio or difference between them</description> <macros> <token name="@BINARY@">bamCompare</token> <import>deepTools_macros.xml</import> @@ -8,9 +8,17 @@ <command> <![CDATA[ ln -s '$bamFile1' one.bam && - ln -s '${bamFile1.metadata.bam_index}' one.bam.bai && + #if $bamFile1.ext == 'bam': + ln -s '${bamFile1.metadata.bam_index}' one.bam.bai && + #else: + ln -s '${bamFile1.metadata.cram_index}' one.bam.crai && + #end if ln -s '$bamFile2' two.bam && - ln -s '${bamFile2.metadata.bam_index}' two.bam.bai && + #if $bamFile2.ext == 'bam': + ln -s '${bamFile2.metadata.bam_index}' two.bam.bai && + #else: + ln -s '${bamFile2.metadata.cram_index}' two.bam.crai && + #end if @BINARY@ @THREADS@ @@ -30,23 +38,16 @@ --scaleFactorsMethod readCount #elif $scaling.method == 'own': --scaleFactors '$scaling.scaleFactor1:$scaling.scaleFactor2' + #elif $scaling.method == 'None': + --scaleFactorsMethod None + #if $scaling.type != '': + --normalizeUsing $scaling.type + #end if #end if - --ratio $comparison.type - - #if $comparison.type == 'subtract': - #if $comparison.normalization.type == 'rpkm': - --normalizeUsingRPKM - #elif $comparison.normalization.type == '1x': + --operation $comparison.type - #if $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize_opt == "specific": - --normalizeTo1x $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize - #else: - --normalizeTo1x $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize_opt - #end if - - #end if - #elif $comparison.type in ['ratio','log2']: + #if $comparison.type in ['ratio','log2']: --pseudocount $comparison.pseudocount #end if @@ -71,14 +72,14 @@ ]]> </command> <inputs> - <param argument="--bamFile1" format="bam" type="data" label="First BAM file (e.g. treated sample)" + <param argument="--bamFile1" format="bam,cram" type="data" label="First BAM/CRAM file (e.g. treated sample)" help=""/> - <param argument="--bamFile2" format="bam" type="data" label="Second BAM file (e.g. control sample)" + <param argument="--bamFile2" format="bam,cram" type="data" label="Second BAM/CRAM file (e.g. control sample)" help=""/> <param argument="--binSize" type="integer" value="50" min="1" label="Bin size in bases" - help="The genome will be divided into bins of the specified size. For each bin, the overlaping number of fragments (or reads) will be reported. + help="The genome will be divided into bins of the specified size. For each bin, the overlapping number of fragments (or reads) will be reported. If only half a fragment overlaps then this fraction will be reported."/> <conditional name="scaling"> @@ -87,6 +88,7 @@ <option value="readCount" selected="true">read count</option> <option value="SES">signal extraction scaling (SES), check with plotFingerprint before using it!</option> <option value="own">enter own scaling factors</option> + <option value="None">Don't scale reads. Samples can instead be normalized using one of the normalization methods</option> </param> <when value="SES"> <param argument="--sampleLength" type="integer" value="1000" min="10" @@ -100,6 +102,14 @@ <when value="own"> <expand macro="scaleFactors" /> </when> + <when value="None"> + <param name="type" type="select" label="Normalization method" > + <option value="RPKM">Normalize to fragments (reads) per kilobase per million (RPKM)</option> + <option value="CPM">Normalize to counts per million (CPM), same as CPM in RNA-seq</option> + <option value="BPM">Normalize to bins per million (BPM), same as TPM in RNA-seq</option> + <option value="">Do not normalize or scale</option> + </param> + </when> </conditional> <conditional name="comparison"> @@ -126,26 +136,13 @@ <expand macro="pseudocount" /> </when> <when value="add" /> + <when value="subtract" /> <when value="mean" /> <when value="first" /> <when value="second" /> <when value="reciprocal_ratio"> <expand macro="pseudocount" /> </when> - <when value="subtract"> - <conditional name="normalization"> - <param name="type" type="select" label="Normalization method" > - <option value="1x">Normalize coverage to 1x</option> - <option value="rpkm">Normalize to fragments (reads) per kilobase per million (RPKM)</option> - <option value="no">Do not normalize or scale</option> - </param> - <when value="rpkm" /> - <when value="no" /> - <when value="1x"> - <expand macro="effectiveGenomeSize" /> - </when> - </conditional> - </when> </conditional> <param name="outFileFormat" type="select" label="Coverage file format"> @@ -211,16 +208,16 @@ What it does ------------- -This tool can be used to generate a bigWig or bedGraph file based on **two BAM** files that are compared to each other while being simultaneously normalized for sequencing depth. +This tool can be used to generate a bigWig or bedGraph file based on **two BAM or CRAM** files that are compared to each other while being simultaneously normalized for sequencing depth. To compare the BAM files to each other, the genome is partitioned into bins of equal size, then the number of reads found in each BAM file is counted per bin, and finally a summary value reported. -This value can be the ratio of the number of reads per bin, the log2 of the ratio, or the difference. -This tool can normalize the number of reads in each BAM file using the SES method proposed in Diaz et al. (2012). "Normalization, bias correction, and peak -calling for ChIP-seq". Statistical applications in genetics and molecular -biology, 11(3). +The tool works in two steps: +1. Scaling : To properly compare samples with different sequencing depth, each bam file can be scaled either using the SES method +(proposed in Diaz et al. (2012). "Normalization, bias correction, and peak calling for ChIP-seq". Statistical applications in genetics and molecular +biology, 11(3).) or total read count. additionally scaling can be turned off and a per-sample normalization can be used (--normalizeUsing RPKM/CPM/BPM) -Normalization based on read counts is also available. +2. Comparison : Two bam files are compared using one of the chosen methods (e.g. add, subtract, mean, log2 ratio etc.) By default, if reads are from a paired-end sequencing run and reads are properly paired, the fragment length reported in the BAM file is used. |
| b |
| diff -r 2e615a3f2b07 -r 2a1b4e95bdf7 deepTools_macros.xml --- a/deepTools_macros.xml Mon Feb 05 11:43:36 2018 -0500 +++ b/deepTools_macros.xml Thu Feb 15 07:48:38 2018 -0500 |
| b |
| b'@@ -1,11 +1,11 @@\n <macros>\n \n <token name="@THREADS@">--numberOfProcessors "\\${GALAXY_SLOTS:-4}"</token>\n- <token name="@WRAPPER_VERSION@">2.5.7</token>\n+ <token name="@WRAPPER_VERSION@">3.0.0</token>\n <xml name="requirements">\n <requirements>\n- <requirement type="package" version="2.5.7">deeptools</requirement>\n- <yield />\n+ <requirement type="package" version="3.0.0">deeptools</requirement>\n+ <requirement type="package" version="1.7">samtools</requirement>\n </requirements>\n <expand macro="stdio" />\n <version_command>@BINARY@ --version</version_command>\n@@ -100,7 +100,7 @@\n <xml name="includeZeros">\n <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""\n label="Include zeros"\n- help="If set, then regions with zero counts for *all* BAM files are included. The default behavior is to ignore such regions." />\n+ help="If set, then regions with zero counts for *all* BAM/CRAM files are included. The default behavior is to ignore such regions." />\n </xml>\n \n <xml name="zMin_zMax">\n@@ -238,7 +238,7 @@\n <xml name="extendReads">\n <conditional name="doExtendCustom">\n <param name="doExtend" type="select" label="Extend reads to the given average fragment size."\n- help="(1) Single-end reads and singletons are extended to match this length. (2) Paired-end reads are extended to match the fragment size, regardless of what is set here.\n+ help="If selected : Single-end reads and singletons are extended to match the given length and Paired-end reads are extended to match the fragment size.\n By default *each* read mate is extended.\n This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate.\n Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value.\n@@ -312,7 +312,7 @@\n <xml name="sortRegions">\n <param argument="--sortRegions" type="select" label="Sort regions"\n help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">\n- <option value="no">no ordering</option>\n+ <option value="no">maintain the same ordering as the input files</option>\n <option value="descend" selected="true">descending order</option>\n <option value="ascend">ascending order</option>\n </param>\n@@ -321,19 +321,19 @@\n <xml name="minMappingQuality">\n <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="0"\n label="Minimum mapping quality"\n- help= "If set, only reads with a mapping quality score higher than this value are considered."/>\n+ help= "If set, only reads with a mapping quality score at least this high are considered."/>\n </xml>\n \n <xml name="skipZeros">\n <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""\n label ="Skip zeros"\n- help ="If set, then zero counts that happen for *all* BAM files given are ignored. This may result in fewer considered regions." />\n+ help ="If set, then zero counts that happen for *all* BAM/CRAM files given are ignored. This may result in fewer considered regions." />\n </xml>\n \n <xml name="fragmentLength">\n- <param argument="--fragmentLength" type="integer" value="300" min="1"\n+ <param argument="--fragmentLength" type="integer" min="1" optional="true"\n label="Fragment length used for the sequencing"\n- help ="If paired-end reads are used, the fragment length is computed from the BAM file, so this is only needed for single-end data."/>\n+ help ="If paired-end reads are'..b'ed="true">hg19 (2451960000)</option>\n- <option value="2150570000">mm9 (2150570000)</option>\n+ <option value="130428560">dm3 (130428560)</option>\n+ <option value="125464728">dm6 (125464728)</option>\n+ <option value="2685511504" selected="true">hg19/GRCh37 (2685511504)</option>\n+ <option value="2701495761">GRCh38/hg38 (2701495761)</option>\n+ <option value="2304947926">GRCm37/mm9 (2304947926)</option>\n+ <option value="2308125349">GRCm38/mm10 (2308125349)</option>\n <option value="specific">user specified</option>\n </param>\n <when value="specific">\n <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size"\n- help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>\n+ help="e.g. ce10: 93260000, dm3: 130428560, hg19: 2685511504, mm9: 2304947926"/>\n </when>\n- <when value="2150570000" />\n- <when value="2451960000" />\n- <when value="121400000" />\n <when value="93260000" />\n+ <when value="130428560" />\n+ <when value="125464728" />\n+ <when value="2685511504" />\n+ <when value="2701495761" />\n+ <when value="2304947926" />\n+ <when value="2308125349" />\n </conditional>\n </xml>\n \n@@ -596,6 +617,7 @@\n <when value="yes">\n <yield />\n <param name="saveSortedRegions" type="boolean"\n+ argument="--outFileSortedRegions"\n label="Save the regions after skipping zeros or min/max threshold values"\n help="The order of the regions in the file follows the sorting order selected. This is useful,\n for example, to generate other heatmaps keeping the sorting of the first heatmap."/>\n@@ -605,11 +627,12 @@\n \n \n <xml name="input_image_file_format">\n- <param argument="--outFileFormat" type="select" label="Image file format">\n+ <param argument="--outFileFormat" type="select" label="Image file format" help="Note that the plotly output can be very large and not all options are supported.">\n <option value="png" selected="true">png</option>\n <option value="pdf">pdf</option>\n <option value="svg">svg</option>\n <option value="eps">eps</option>\n+ <option value="plotly">plotly</option>\n </param>\n </xml>\n \n@@ -624,6 +647,7 @@\n <when input="output.outFileFormat" value="pdf" format="pdf" />\n <when input="output.outFileFormat" value="svg" format="svg" />\n <when input="output.outFileFormat" value="eps" format="eps" />\n+ <when input="output.outFileFormat" value="plotly" format="html" />\n </change_format>\n </data>\n </xml>\n@@ -634,6 +658,7 @@\n <when input="outFileFormat" value="pdf" format="pdf" />\n <when input="outFileFormat" value="svg" format="svg" />\n <when input="outFileFormat" value="eps" format="eps" />\n+ <when input="outFileFormat" value="plotly" format="html" />\n </change_format>\n </data>\n </xml>\n@@ -662,8 +687,7 @@\n \n <xml name="colorMap">\n <param name="colorMap" type="select" label="Color map to use for the heatmap"\n- help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html"\n- multiple="true">\n+ help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html">\n <option value="RdYlBu" selected="true">RdYlBu</option>\n <option value="Accent">Accent</option>\n <option value="Spectral">Spectral</option>\n' |
| b |
| diff -r 2e615a3f2b07 -r 2a1b4e95bdf7 readme.rst --- a/readme.rst Mon Feb 05 11:43:36 2018 -0500 +++ b/readme.rst Thu Feb 15 07:48:38 2018 -0500 |
| b |
| @@ -20,7 +20,7 @@ deeptools is developed under here: - https://github.com/fidelram/deepTools + https://github.com/deeptools/deepTools For support, questions, or feature requests contact: deeptools@googlegroups.com @@ -41,7 +41,7 @@ Citation ======== -deeptools are currently under review. In the meantime please refere to https://github.com/fidelram/deepTools. +deeptools are currently under review. In the meantime please refere to https://github.com/deeptools/deepTools. ======= |
| b |
| diff -r 2e615a3f2b07 -r 2a1b4e95bdf7 test-data/alignmentSieve.bam |
| b |
| Binary file test-data/alignmentSieve.bam has changed |
| b |
| diff -r 2e615a3f2b07 -r 2a1b4e95bdf7 test-data/alignmentSieve.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alignmentSieve.bed Thu Feb 15 07:48:38 2018 -0500 |
| b |
| b'@@ -0,0 +1,4261 @@\n+chr2L\t5093\t5232\n+chr2L\t5101\t5236\n+chr2L\t5105\t5252\n+chr2L\t5108\t5267\n+chr2L\t5105\t5250\n+chr2L\t5108\t5244\n+chr2L\t5108\t5279\n+chr2L\t5105\t5251\n+chr2L\t5105\t5252\n+chr2L\t5105\t5224\n+chr2L\t5108\t5244\n+chr2L\t5108\t5252\n+chr2L\t5108\t5244\n+chr2L\t5108\t5251\n+chr2L\t5105\t5212\n+chr2L\t5105\t5266\n+chr2L\t5108\t5265\n+chr2L\t5106\t5287\n+chr2L\t5106\t5243\n+chr2L\t5106\t5204\n+chr2L\t5109\t5249\n+chr2L\t5109\t5213\n+chr2L\t5106\t5245\n+chr2L\t5118\t5266\n+chr2L\t5116\t5224\n+chr2L\t5117\t5293\n+chr2L\t5117\t5291\n+chr2L\t5120\t5265\n+chr2L\t5117\t5243\n+chr2L\t5122\t5249\n+chr2L\t5119\t5268\n+chr2L\t5119\t5245\n+chr2L\t5123\t5423\n+chr2L\t5120\t5293\n+chr2L\t5120\t5250\n+chr2L\t5123\t5293\n+chr2L\t5129\t5197\n+chr2L\t5129\t5323\n+chr2L\t5130\t5265\n+chr2L\t5127\t5280\n+chr2L\t5127\t5285\n+chr2L\t5133\t5274\n+chr2L\t5138\t5293\n+chr2L\t5141\t5279\n+chr2L\t5138\t5266\n+chr2L\t5141\t5279\n+chr2L\t5152\t5322\n+chr2L\t5149\t5323\n+chr2L\t5149\t5250\n+chr2L\t5149\t5306\n+chr2L\t5152\t5292\n+chr2L\t5152\t5322\n+chr2L\t5149\t5330\n+chr2L\t5151\t5252\n+chr2L\t5154\t5326\n+chr2L\t5154\t5251\n+chr2L\t5153\t5324\n+chr2L\t5154\t5341\n+chr2L\t5157\t5304\n+chr2L\t5157\t5292\n+chr2L\t5159\t5292\n+chr2L\t5156\t5323\n+chr2L\t5160\t5292\n+chr2L\t5157\t5323\n+chr2L\t5160\t5326\n+chr2L\t5160\t5292\n+chr2L\t5161\t5326\n+chr2L\t5167\t5280\n+chr2L\t5168\t5249\n+chr2L\t5168\t5325\n+chr2L\t5165\t5306\n+chr2L\t5166\t5323\n+chr2L\t5166\t5306\n+chr2L\t5171\t5323\n+chr2L\t5181\t5322\n+chr2L\t5179\t5356\n+chr2L\t5179\t5294\n+chr2L\t5179\t5323\n+chr2L\t5182\t5312\n+chr2L\t5185\t5323\n+chr2L\t5197\t5326\n+chr2L\t5206\t5322\n+chr2L\t5207\t5340\n+chr2L\t5207\t5355\n+chr2L\t5211\t5325\n+chr2L\t5212\t5350\n+chr2L\t5212\t5296\n+chr2L\t5209\t5381\n+chr2L\t5219\t5369\n+chr2L\t5216\t5323\n+chr2L\t5219\t5356\n+chr2L\t5216\t5382\n+chr2L\t5219\t5381\n+chr2L\t5219\t5369\n+chr2L\t5224\t5326\n+chr2L\t5221\t5356\n+chr2L\t5224\t5380\n+chr2L\t5224\t5356\n+chr2L\t5224\t5325\n+chr2L\t5224\t5375\n+chr2L\t5225\t5380\n+chr2L\t5225\t5325\n+chr2L\t5225\t5377\n+chr2L\t5225\t5381\n+chr2L\t5225\t5440\n+chr2L\t5225\t5375\n+chr2L\t5225\t5325\n+chr2L\t5225\t5355\n+chr2L\t5225\t5355\n+chr2L\t5227\t5380\n+chr2L\t5226\t5500\n+chr2L\t5230\t5326\n+chr2L\t5231\t5423\n+chr2L\t5228\t5400\n+chr2L\t5236\t5383\n+chr2L\t5256\t5401\n+chr2L\t5253\t5455\n+chr2L\t5257\t5467\n+chr2L\t5257\t5402\n+chr2L\t5261\t5423\n+chr2L\t5258\t5355\n+chr2L\t5261\t5428\n+chr2L\t5264\t5401\n+chr2L\t5264\t5401\n+chr2L\t5261\t5467\n+chr2L\t5261\t5403\n+chr2L\t5265\t5426\n+chr2L\t5265\t5377\n+chr2L\t5262\t5370\n+chr2L\t5262\t5392\n+chr2L\t5265\t5423\n+chr2L\t5265\t5375\n+chr2L\t5265\t5401\n+chr2L\t5265\t5401\n+chr2L\t5262\t5427\n+chr2L\t5274\t5465\n+chr2L\t5276\t5381\n+chr2L\t5279\t5402\n+chr2L\t5281\t5423\n+chr2L\t5281\t5431\n+chr2L\t5288\t5411\n+chr2L\t5289\t5382\n+chr2L\t5288\t5421\n+chr2L\t5288\t5421\n+chr2L\t5291\t5420\n+chr2L\t5288\t5424\n+chr2L\t5289\t5467\n+chr2L\t5302\t5462\n+chr2L\t5303\t5401\n+chr2L\t5300\t5425\n+chr2L\t5303\t5464\n+chr2L\t5300\t5464\n+chr2L\t5300\t5464\n+chr2L\t5306\t5401\n+chr2L\t5303\t5428\n+chr2L\t5303\t5414\n+chr2L\t5303\t5465\n+chr2L\t5304\t5407\n+chr2L\t5311\t5423\n+chr2L\t5310\t5467\n+chr2L\t5313\t5463\n+chr2L\t5313\t5423\n+chr2L\t5310\t5465\n+chr2L\t5313\t5423\n+chr2L\t5313\t5462\n+chr2L\t5317\t5500\n+chr2L\t5328\t5467\n+chr2L\t5331\t5485\n+chr2L\t5334\t5467\n+chr2L\t5334\t5466\n+chr2L\t5334\t5467\n+chr2L\t5331\t5480\n+chr2L\t5332\t5467\n+chr2L\t5335\t5480\n+chr2L\t5332\t5485\n+chr2L\t5332\t5484\n+chr2L\t5332\t5517\n+chr2L\t5335\t5465\n+chr2L\t5335\t5464\n+chr2L\t5335\t5464\n+chr2L\t5332\t5469\n+chr2L\t5335\t5467\n+chr2L\t5333\t5472\n+chr2L\t5337\t5480\n+chr2L\t5334\t5488\n+chr2L\t5337\t5467\n+chr2L\t5334\t5503\n+chr2L\t5337\t5527\n+chr2L\t5337\t5497\n+chr2L\t5334\t5498\n+chr2L\t5334\t5497\n+chr2L\t5337\t5463\n+chr2L\t5337\t5516\n+chr2L\t5334\t5483\n+chr2L\t5337\t5517\n+chr2L\t5337\t5453\n+chr2L\t5337\t5466\n+chr2L\t5337\t5440\n+chr2L\t5334\t5454\n+chr2L\t5339\t5503\n+chr2L\t5343\t5451\n+chr2L\t5340\t5518\n+chr2L\t5350\t5466\n+chr2L\t5352\t5464\n+chr2L\t5349\t5467\n+chr2L\t5352\t5496\n+chr2L\t5352\t5453\n+chr2L\t5361\t5527\n+chr2L\t5365\t5500\n+chr2L\t5362\t5527\n+chr2L\t5365\t5517\n+chr2L\t5362\t5464\n+chr2L\t5362\t5497\n+chr2L\t5368\t5517\n+chr2L\t5368\t5496\n+chr2L\t5378\t5500\n+chr2L\t5378\t5499\n+chr2L\t5375\t5527\n+chr2L\t5385\t5517\n+chr2L\t5385\t5497\n+chr2L\t5387\t5527\n+chr2L\t5390\t5502\n+chr2L\t5387\t5527\n+chr2L\t5390\t5526\n+chr2L\t5394\t5526\n+chr2L\t5391\t5557\n+chr2L\t5395\t5502\n+chr2L\t5395\t5520\n+chr2L\t5392\t5481\n+chr2L\t5392\t5504\n+chr2L\t5395\t5556\n+chr2L\t5394\t5533\n+chr2L\t5395\t5557\n+chr2L\t5398\t5563\n+c'..b'\n+chr2L\t9803\t9973\n+chr2L\t9803\t9959\n+chr2L\t9806\t9946\n+chr2L\t9806\t9949\n+chr2L\t9803\t9891\n+chr2L\t9806\t9958\n+chr2L\t9806\t9958\n+chr2L\t9803\t9942\n+chr2L\t9803\t9949\n+chr2L\t9803\t9956\n+chr2L\t9806\t9948\n+chr2L\t9803\t9942\n+chr2L\t9804\t9954\n+chr2L\t9807\t9958\n+chr2L\t9808\t9953\n+chr2L\t9813\t9912\n+chr2L\t9816\t10018\n+chr2L\t9813\t9950\n+chr2L\t9820\t9978\n+chr2L\t9823\t9949\n+chr2L\t9823\t9975\n+chr2L\t9827\t9949\n+chr2L\t9827\t9955\n+chr2L\t9828\t9936\n+chr2L\t9832\t9954\n+chr2L\t9832\t9971\n+chr2L\t9833\t9942\n+chr2L\t9833\t9953\n+chr2L\t9830\t9942\n+chr2L\t9833\t9973\n+chr2L\t9830\t9950\n+chr2L\t9833\t9942\n+chr2L\t9833\t9932\n+chr2L\t9830\t10006\n+chr2L\t9830\t9974\n+chr2L\t9830\t9946\n+chr2L\t9833\t9971\n+chr2L\t9833\t9932\n+chr2L\t9834\t9960\n+chr2L\t9844\t9953\n+chr2L\t9849\t9973\n+chr2L\t9850\t9974\n+chr2L\t9853\t9972\n+chr2L\t9850\t9955\n+chr2L\t9853\t9997\n+chr2L\t9850\t9972\n+chr2L\t9853\t10029\n+chr2L\t9854\t10017\n+chr2L\t9851\t10003\n+chr2L\t9851\t9938\n+chr2L\t9853\t9959\n+chr2L\t9854\t10005\n+chr2L\t9854\t9973\n+chr2L\t9862\t10010\n+chr2L\t9861\t10031\n+chr2L\t9866\t10039\n+chr2L\t9868\t10017\n+chr2L\t9869\t10018\n+chr2L\t9867\t10011\n+chr2L\t9867\t10022\n+chr2L\t9867\t10025\n+chr2L\t9871\t10024\n+chr2L\t9871\t10075\n+chr2L\t9871\t10004\n+chr2L\t9868\t10025\n+chr2L\t9868\t9959\n+chr2L\t9868\t9957\n+chr2L\t9871\t9975\n+chr2L\t9875\t9961\n+chr2L\t9872\t10030\n+chr2L\t9875\t10009\n+chr2L\t9875\t9961\n+chr2L\t9876\t10017\n+chr2L\t9876\t10024\n+chr2L\t9883\t10018\n+chr2L\t9880\t10025\n+chr2L\t9883\t10004\n+chr2L\t9884\t10046\n+chr2L\t9884\t10030\n+chr2L\t9884\t10144\n+chr2L\t9884\t10018\n+chr2L\t9886\t10017\n+chr2L\t9891\t10018\n+chr2L\t9894\t9972\n+chr2L\t9896\t10054\n+chr2L\t9896\t10050\n+chr2L\t9898\t10077\n+chr2L\t9900\t10050\n+chr2L\t9903\t10055\n+chr2L\t9903\t10049\n+chr2L\t9903\t10056\n+chr2L\t9900\t10064\n+chr2L\t9903\t10067\n+chr2L\t9903\t10067\n+chr2L\t9900\t10076\n+chr2L\t9903\t10062\n+chr2L\t9904\t10018\n+chr2L\t9901\t10030\n+chr2L\t9904\t10063\n+chr2L\t9904\t10073\n+chr2L\t9901\t10019\n+chr2L\t9901\t10018\n+chr2L\t9904\t10046\n+chr2L\t9904\t10055\n+chr2L\t9904\t10072\n+chr2L\t9901\t10051\n+chr2L\t9904\t10029\n+chr2L\t9904\t10017\n+chr2L\t9904\t10068\n+chr2L\t9904\t10050\n+chr2L\t9904\t10072\n+chr2L\t9904\t10049\n+chr2L\t9904\t10067\n+chr2L\t9904\t10049\n+chr2L\t9901\t10047\n+chr2L\t9905\t10050\n+chr2L\t9907\t10049\n+chr2L\t9904\t10047\n+chr2L\t9904\t10030\n+chr2L\t9907\t10067\n+chr2L\t9907\t10036\n+chr2L\t9904\t10026\n+chr2L\t9914\t10068\n+chr2L\t9914\t10017\n+chr2L\t9916\t10048\n+chr2L\t9919\t10068\n+chr2L\t9916\t10064\n+chr2L\t9918\t10019\n+chr2L\t9919\t10068\n+chr2L\t9924\t10069\n+chr2L\t9921\t10056\n+chr2L\t9927\t10019\n+chr2L\t9931\t10067\n+chr2L\t9929\t10090\n+chr2L\t9932\t10072\n+chr2L\t9931\t10089\n+chr2L\t9935\t10100\n+chr2L\t9935\t10072\n+chr2L\t9935\t10067\n+chr2L\t9933\t10089\n+chr2L\t9935\t10088\n+chr2L\t9936\t10045\n+chr2L\t9939\t10094\n+chr2L\t9937\t10030\n+chr2L\t9942\t10135\n+chr2L\t9957\t10049\n+chr2L\t9958\t10095\n+chr2L\t9958\t10106\n+chr2L\t9961\t10088\n+chr2L\t9958\t10086\n+chr2L\t9962\t10089\n+chr2L\t9962\t10100\n+chr2L\t9964\t10108\n+chr2L\t9967\t10088\n+chr2L\t9964\t10073\n+chr2L\t9968\t10134\n+chr2L\t9965\t10068\n+chr2L\t9968\t10107\n+chr2L\t9968\t10067\n+chr2L\t9966\t10089\n+chr2L\t9966\t10074\n+chr2L\t9969\t10089\n+chr2L\t9971\t10089\n+chr2L\t9969\t10103\n+chr2L\t9969\t10142\n+chr2L\t9969\t10094\n+chr2L\t9970\t10106\n+chr2L\t9973\t10132\n+chr2L\t9973\t10121\n+chr2L\t9973\t10116\n+chr2L\t9973\t10095\n+chr2L\t9971\t10280\n+chr2L\t9974\t10113\n+chr2L\t9971\t10088\n+chr2L\t9974\t10116\n+chr2L\t9974\t10088\n+chr2L\t9974\t10117\n+chr2L\t9974\t10134\n+chr2L\t9974\t10104\n+chr2L\t9972\t10141\n+chr2L\t9972\t10073\n+chr2L\t9977\t10101\n+chr2L\t9980\t10118\n+chr2L\t9981\t10125\n+chr2L\t9985\t10135\n+chr2L\t9985\t10134\n+chr2L\t9982\t10133\n+chr2L\t9982\t10237\n+chr2L\t9985\t10113\n+chr2L\t9985\t10134\n+chr2L\t9986\t10362\n+chr2L\t9983\t10146\n+chr2L\t9986\t10132\n+chr2L\t9983\t10141\n+chr2L\t9986\t10149\n+chr2L\t9986\t10141\n+chr2L\t9983\t10142\n+chr2L\t9986\t10100\n+chr2L\t9986\t10134\n+chr2L\t9983\t10136\n+chr2L\t9983\t10108\n+chr2L\t9986\t10141\n+chr2L\t9987\t10121\n+chr2L\t9987\t10134\n+chr2L\t9984\t10141\n+chr2L\t9987\t10089\n+chr2L\t9989\t10171\n+chr2L\t9989\t10099\n+chr2L\t9989\t10141\n+chr2L\t9992\t10134\n+chr2L\t9989\t10158\n+chr2L\t9992\t10150\n+chr2L\t9993\t10147\n+chr2L\t9990\t10108\n+chr2L\t9990\t10142\n+chr2L\t9993\t10170\n+chr2L\t9990\t10135\n+chr2L\t9993\t10091\n+chr2L\t9994\t10135\n+chr2L\t9991\t10145\n+chr2L\t9991\t10101\n+chr2L\t9991\t10145\n+chr2L\t9991\t10133\n+chr2L\t9999\t10134\n+chr2L\t10000\t10173\n' |
| b |
| diff -r 2e615a3f2b07 -r 2a1b4e95bdf7 test-data/alignmentSieve.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alignmentSieve.txt Thu Feb 15 07:48:38 2018 -0500 |
| b |
| @@ -0,0 +1,3 @@ +#bamFilterReads --filterMetrics +#File Reads Remaining Total Initial Reads +paired_chr2L.bam 8440 12644 |
| b |
| diff -r 2e615a3f2b07 -r 2a1b4e95bdf7 test-data/alignmentSieve2.bam |
| b |
| Binary file test-data/alignmentSieve2.bam has changed |
| b |
| diff -r 2e615a3f2b07 -r 2a1b4e95bdf7 test-data/alignmentSieve3.bam |
| b |
| Binary file test-data/alignmentSieve3.bam has changed |
| b |
| diff -r 2e615a3f2b07 -r 2a1b4e95bdf7 test-data/bamPEFragmentSize_histogram_result1.png |
| b |
| Binary file test-data/bamPEFragmentSize_histogram_result1.png has changed |
| b |
| diff -r 2e615a3f2b07 -r 2a1b4e95bdf7 test-data/bamPEFragmentSize_lengths1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bamPEFragmentSize_lengths1.txt Thu Feb 15 07:48:38 2018 -0500 |
| b |
| @@ -0,0 +1,5 @@ +#bamPEFragmentSize +Size Occurrences Sample +241 1 bowtie2 test1.bam +242 1 bowtie2 test1.bam +251 1 bowtie2 test1.bam |
| b |
| diff -r 2e615a3f2b07 -r 2a1b4e95bdf7 test-data/bamPEFragmentSize_result1.txt --- a/test-data/bamPEFragmentSize_result1.txt Mon Feb 05 11:43:36 2018 -0500 +++ b/test-data/bamPEFragmentSize_result1.txt Thu Feb 15 07:48:38 2018 -0500 |
| b |
| @@ -11,8 +11,21 @@ 3rd Qu.: 246.5 Max.: 251.0 Std: 4.496912521077347 +MAD: 1.0 +Len. 10%: 241.20000000000002 +Len. 20%: 241.4 +Len. 30%: 241.6 +Len. 40%: 241.8 +Len. 60%: 243.8 +Len. 70%: 245.6 +Len. 80%: 247.4 +Len. 90%: 249.2 +Len. 99%: 250.82 + Read lengths: +Sample size: 3 + Min.: 251.0 1st Qu.: 251.0 Mean: 251.0 @@ -20,3 +33,14 @@ 3rd Qu.: 251.0 Max.: 251.0 Std: 0.0 +MAD: 0.0 +Len. 10%: 251.0 +Len. 20%: 251.0 +Len. 30%: 251.0 +Len. 40%: 251.0 +Len. 60%: 251.0 +Len. 70%: 251.0 +Len. 80%: 251.0 +Len. 90%: 251.0 +Len. 99%: 251.0 + |
| b |
| diff -r 2e615a3f2b07 -r 2a1b4e95bdf7 test-data/bamPEFragmentSize_table1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bamPEFragmentSize_table1.txt Thu Feb 15 07:48:38 2018 -0500 |
| b |
| @@ -0,0 +1,2 @@ + Frag. Sampled Frag. Len. Min. Frag. Len. 1st. Qu. Frag. Len. Mean Frag. Len. Median Frag. Len. 3rd Qu. Frag. Len. Max Frag. Len. Std. Frag. Med. Abs. Dev. Frag. Len. 10% Frag. Len. 20% Frag. Len. 30% Frag. Len. 40% Frag. Len. 60% Frag. Len. 70% Frag. Len. 80% Frag. Len. 90% Frag. Len. 99% Reads Sampled Read Len. Min. Read Len. 1st. Qu. Read Len. Mean Read Len. Median Read Len. 3rd Qu. Read Len. Max Read Len. Std. Read Med. Abs. Dev. Read Len. 10% Read Len. 20% Read Len. 30% Read Len. 40% Read Len. 60% Read Len. 70% Read Len. 80% Read Len. 90% Read Len. 99% +bowtie2 test1.bam 3 241.0 241.5 244.66666666666666 242.0 246.5 251.0 4.496912521077347 1.0 241.20000000000002 241.4 241.6 241.8 243.8 245.6 247.4 249.2 250.82 3 251.0 251.0 251.0 251.0 251.0 251.0 0.0 0.0 251.0 251.0 251.0 251.0 251.0 251.0 251.0 251.0 251.0 |
| b |
| diff -r 2e615a3f2b07 -r 2a1b4e95bdf7 test-data/estimateReadFiltering.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/estimateReadFiltering.txt Thu Feb 15 07:48:38 2018 -0500 |
| b |
| @@ -0,0 +1,3 @@ +Sample Total Reads Mapped Reads Alignments in blacklisted regions Estimated mapped reads filtered Below MAPQ Missing Flags Excluded Flags Internally-determined Duplicates Marked Duplicates Singletons Wrong strand +paired_chr2L.bam 12644 12589 0 1395.9 4149.0 0.0 0.0 0.0 0.0 55.0 0.0 +paired_chr2L.bam 12644 12589 0 1395.9 4149.0 0.0 0.0 0.0 0.0 55.0 0.0 |
| b |
| diff -r 2e615a3f2b07 -r 2a1b4e95bdf7 test-data/heatmapper_result1.png |
| b |
| Binary file test-data/heatmapper_result1.png has changed |
| b |
| diff -r 2e615a3f2b07 -r 2a1b4e95bdf7 test-data/heatmapper_result2.png |
| b |
| Binary file test-data/heatmapper_result2.png has changed |
| b |
| diff -r 2e615a3f2b07 -r 2a1b4e95bdf7 test-data/multiBamSummary_result1.npz |
| b |
| Binary file test-data/multiBamSummary_result1.npz has changed |
| b |
| diff -r 2e615a3f2b07 -r 2a1b4e95bdf7 test-data/multiBamSummary_result2.npz |
| b |
| Binary file test-data/multiBamSummary_result2.npz has changed |
| b |
| diff -r 2e615a3f2b07 -r 2a1b4e95bdf7 test-data/paired_chr2L.cram |
| b |
| Binary file test-data/paired_chr2L.cram has changed |
| b |
| diff -r 2e615a3f2b07 -r 2a1b4e95bdf7 test-data/plotCorrelation_result1.tabular --- a/test-data/plotCorrelation_result1.tabular Mon Feb 05 11:43:36 2018 -0500 +++ b/test-data/plotCorrelation_result1.tabular Thu Feb 15 07:48:38 2018 -0500 |
| b |
| @@ -1,3 +1,4 @@ +#plotCorrelation --outFileCorMatrix 'bowtie2 test1.bam' 'bowtie2 test1.bam' 'bowtie2 test1.bam' 1.0000 1.0000 'bowtie2 test1.bam' 1.0000 1.0000 |
| b |
| diff -r 2e615a3f2b07 -r 2a1b4e95bdf7 test-data/plotCorrelation_result2.png |
| b |
| Binary file test-data/plotCorrelation_result2.png has changed |
| b |
| diff -r 2e615a3f2b07 -r 2a1b4e95bdf7 test-data/plotCoverage_result1.png |
| b |
| Binary file test-data/plotCoverage_result1.png has changed |
| b |
| diff -r 2e615a3f2b07 -r 2a1b4e95bdf7 test-data/plotCoverage_result1.tabular --- a/test-data/plotCoverage_result1.tabular Mon Feb 05 11:43:36 2018 -0500 +++ b/test-data/plotCoverage_result1.tabular Thu Feb 15 07:48:38 2018 -0500 |
| b |
| @@ -1,3 +1,4 @@ +#plotCoverage --outRawCounts #'chr' 'start' 'end' 'bowtie2 test1.bam' 'bowtie2 test1.bam' chrM 0 1 23.0 23.0 chrM 1 2 35.0 35.0 |
| b |
| diff -r 2e615a3f2b07 -r 2a1b4e95bdf7 test-data/plotEnrichment_output.txt --- a/test-data/plotEnrichment_output.txt Mon Feb 05 11:43:36 2018 -0500 +++ b/test-data/plotEnrichment_output.txt Thu Feb 15 07:48:38 2018 -0500 |
| b |
| @@ -1,5 +1,5 @@ -file featureType percent -bowtie2 test1.bam up 100.00 -bowtie2 test1.bam down 100.00 -bowtie2 test1.bam up 100.00 -bowtie2 test1.bam down 100.00 +file featureType percent featureReadCount totalReadCount +bowtie2 test1.bam up 100.00 47 47 +bowtie2 test1.bam down 100.00 47 47 +bowtie2 test1.bam up 100.00 47 47 +bowtie2 test1.bam down 100.00 47 47 |
| b |
| diff -r 2e615a3f2b07 -r 2a1b4e95bdf7 test-data/plotFingerprint_result2.tabular --- a/test-data/plotFingerprint_result2.tabular Mon Feb 05 11:43:36 2018 -0500 +++ b/test-data/plotFingerprint_result2.tabular Thu Feb 15 07:48:38 2018 -0500 |
| b |
| @@ -1,3 +1,4 @@ +#plotFingerprint --outRawCounts 'bowtie2 test1.bam' 'bowtie2 test1.bam' 1085 1085 1782 1782 |
| b |
| diff -r 2e615a3f2b07 -r 2a1b4e95bdf7 test-data/plotPCA_result1.png |
| b |
| Binary file test-data/plotPCA_result1.png has changed |
| b |
| diff -r 2e615a3f2b07 -r 2a1b4e95bdf7 test-data/plotPCA_result2.tabular --- a/test-data/plotPCA_result2.tabular Mon Feb 05 11:43:36 2018 -0500 +++ b/test-data/plotPCA_result2.tabular Thu Feb 15 07:48:38 2018 -0500 |
| b |
| @@ -1,3 +1,4 @@ +#plotPCA --outFileNameData Component bowtie2-test1.bam bowtie2-test1.bam Eigenvalue -1 -0.7071067811865476 -0.7071067811865475 6.000000000000001 +1 -0.7071067811865476 -0.7071067811865475 4.0 2 -0.7071067811865475 0.7071067811865476 1.2325951644078315e-32 |
