Mercurial > repos > bgruening > deeptools_bam_compare
changeset 17:2a1b4e95bdf7 draft
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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--- 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.
--- a/deepTools_macros.xml Mon Feb 05 11:43:36 2018 -0500 +++ b/deepTools_macros.xml Thu Feb 15 07:48:38 2018 -0500 @@ -1,11 +1,11 @@ <macros> <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> - <token name="@WRAPPER_VERSION@">2.5.7</token> + <token name="@WRAPPER_VERSION@">3.0.0</token> <xml name="requirements"> <requirements> - <requirement type="package" version="2.5.7">deeptools</requirement> - <yield /> + <requirement type="package" version="3.0.0">deeptools</requirement> + <requirement type="package" version="1.7">samtools</requirement> </requirements> <expand macro="stdio" /> <version_command>@BINARY@ --version</version_command> @@ -100,7 +100,7 @@ <xml name="includeZeros"> <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue="" label="Include zeros" - help="If set, then regions with zero counts for *all* BAM files are included. The default behavior is to ignore such regions." /> + help="If set, then regions with zero counts for *all* BAM/CRAM files are included. The default behavior is to ignore such regions." /> </xml> <xml name="zMin_zMax"> @@ -238,7 +238,7 @@ <xml name="extendReads"> <conditional name="doExtendCustom"> <param name="doExtend" type="select" label="Extend reads to the given average fragment size." - 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. + 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. By default *each* read mate is extended. This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate. Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value. @@ -312,7 +312,7 @@ <xml name="sortRegions"> <param argument="--sortRegions" type="select" label="Sort regions" help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region."> - <option value="no">no ordering</option> + <option value="no">maintain the same ordering as the input files</option> <option value="descend" selected="true">descending order</option> <option value="ascend">ascending order</option> </param> @@ -321,19 +321,19 @@ <xml name="minMappingQuality"> <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="0" label="Minimum mapping quality" - help= "If set, only reads with a mapping quality score higher than this value are considered."/> + help= "If set, only reads with a mapping quality score at least this high are considered."/> </xml> <xml name="skipZeros"> <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue="" label ="Skip zeros" - help ="If set, then zero counts that happen for *all* BAM files given are ignored. This may result in fewer considered regions." /> + help ="If set, then zero counts that happen for *all* BAM/CRAM files given are ignored. This may result in fewer considered regions." /> </xml> <xml name="fragmentLength"> - <param argument="--fragmentLength" type="integer" value="300" min="1" + <param argument="--fragmentLength" type="integer" min="1" optional="true" label="Fragment length used for the sequencing" - 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."/> + help ="If paired-end reads are used, the fragment length is computed from the BAM/CRAM file, so this is only needed for single-end data."/> </xml> <xml name="scaleFactor"> @@ -390,13 +390,13 @@ <option value="Yes">Yes</option> </param> <when value="No"> - <param argument="--bamfiles" type="data" format="bam" min="@MIN@" - label="Bam file" multiple="true" + <param argument="--bamfiles" type="data" format="bam,cram" min="@MIN@" + label="BAM/CRAM file" multiple="true" help=""/> </when> <when value="Yes"> - <repeat name="multibam_repeats" min="@MIN@" title="BAM Files"> - <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" /> + <repeat name="multibam_repeats" min="@MIN@" title="BAM/CRAM Files"> + <param argument="--bamfiles" type="data" format="bam,cram" label="BAM/CRAM file" help="" /> </repeat> </when> </conditional> @@ -404,7 +404,7 @@ <xml name="multiple_input_bigwigs" tokens="MIN,LABEL,TITLE"> <conditional name="multibigwig_conditional"> - <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples + <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples is vital to you, select Yes below."> <option value="No" selected="true">No</option> <option value="Yes">Yes</option> @@ -412,11 +412,11 @@ <when value="No"> <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="@MIN@" label="@LABEL@" - help="You can generate a bigWig file from a BAM file using the bamCoverage tool."/> + help="You can generate a bigWig file from a BAM/CRAM file using the bamCoverage tool."/> </when> <when value="Yes"> <repeat name="multibigwig_repeats" min="@MIN@" title="@TITLE@"> - <param argument="--bigwigfiles" type="data" format="bigwig" label="@LABEL@" help="You can generate a bigWig file from a BAM file using the bamCoverage tool."/> + <param argument="--bigwigfiles" type="data" format="bigwig" label="@LABEL@" help="You can generate a bigWig file from a BAM/CRAM file using the bamCoverage tool."/> </repeat> </when> </conditional> @@ -428,6 +428,12 @@ help="Title of the plot, to be printed on top of the generated image." /> </xml> + <xml name="labelRotation"> + <param argument="--labelRotation" type="integer" value="0" + label="Rotation of the X-axis labels (in degrees)" + help="The rotation of things like TSS or TES on the X-axis of profile plots in both plotHeatmap and plotProfile. The default is 0, positive values denome a counter-clockwise rotation." /> + </xml> + <token name="@multiple_input_bams@"> <![CDATA[ @@ -438,8 +444,12 @@ #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles): #set identifier = re.sub('[^\.\s\w\-]', '_', str($bamfile.element_identifier)) ln -s "${bamfile}" "./${counter}.bam" && - ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" && - #silent $files.append('%s.bam' % $counter) + #if $bamfile.ext == 'bam': + ln -s '${bamfile.metadata.bam_index}' './${counter}.bam.bai' && + #else: + ln -s '${bamfile.metadata.cram_index}' './${counter}.bam.crai' && + #end if + #silent $files.append("'%s.bam'" % $counter) #silent $labels.append("'%s'" % identifier) #end for #else: @@ -447,7 +457,12 @@ #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier)) ln -s "${f.bamfiles}" "./${counter}.bam" && ln -s "${f.bamfiles.metadata.bam_index}" "./${counter}.bam.bai" && - #silent $files.append('%s.bam' % $counter) + #if $f.bamfiles.ext == 'bam': + ln -s '${f.bamfiles.metadata.bam_index}' './${counter}.bam.bai' && + #else: + ln -s '${f.bamfiles.metadata.cram_index}' './${counter}.bam.crai' && + #end if + #silent $files.append("'%s.bam'" % $counter) #silent $labels.append("'%s'" % $identifier) #end for #end if @@ -463,14 +478,14 @@ #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles): #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier)) ln -f -s "${bigwig}" "${identifier}_${counter}.bw" && - #silent $files.append('%s_%s.bw' % ($identifier, $counter)) + #silent $files.append("'%s_%s.bw'" % ($identifier, $counter)) #silent $labels.append("'%s'" % $identifier) #end for #else: #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats): #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier)) ln -f -s "${f.bigwigfiles}" "${identifier}_${counter}.bw" && - #silent $files.append('%s_%s.bw' % ($identifier, $counter)) + #silent $files.append("'%s_%s.bw'" % ($identifier, $counter)) #silent $labels.append("'%s'" % $identifier) #end for #end if @@ -494,7 +509,7 @@ --blackListFileName #echo ' '.join($blfiles)# #end if #end if -]]> +]]> </token> <xml name="multiple_bed"> @@ -515,7 +530,7 @@ --BED #echo ' '.join($files)# --regionLabels #echo ' '.join($labels)# #end if -]]> +]]> </token> <xml name="reference_genome_source"> @@ -551,21 +566,27 @@ <param name="effectiveGenomeSize_opt" 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."> + We provide a table of useful sizes here: http://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html"> <option value="93260000">ce10 (93260000)</option> - <option value="121400000">dm3 (121400000)</option> - <option value="2451960000" selected="true">hg19 (2451960000)</option> - <option value="2150570000">mm9 (2150570000)</option> + <option value="130428560">dm3 (130428560)</option> + <option value="125464728">dm6 (125464728)</option> + <option value="2685511504" selected="true">hg19/GRCh37 (2685511504)</option> + <option value="2701495761">GRCh38/hg38 (2701495761)</option> + <option value="2304947926">GRCm37/mm9 (2304947926)</option> + <option value="2308125349">GRCm38/mm10 (2308125349)</option> <option value="specific">user specified</option> </param> <when value="specific"> <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size" - help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/> + help="e.g. ce10: 93260000, dm3: 130428560, hg19: 2685511504, mm9: 2304947926"/> </when> - <when value="2150570000" /> - <when value="2451960000" /> - <when value="121400000" /> <when value="93260000" /> + <when value="130428560" /> + <when value="125464728" /> + <when value="2685511504" /> + <when value="2701495761" /> + <when value="2304947926" /> + <when value="2308125349" /> </conditional> </xml> @@ -596,6 +617,7 @@ <when value="yes"> <yield /> <param name="saveSortedRegions" type="boolean" + argument="--outFileSortedRegions" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/> @@ -605,11 +627,12 @@ <xml name="input_image_file_format"> - <param argument="--outFileFormat" type="select" label="Image file format"> + <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."> <option value="png" selected="true">png</option> <option value="pdf">pdf</option> <option value="svg">svg</option> <option value="eps">eps</option> + <option value="plotly">plotly</option> </param> </xml> @@ -624,6 +647,7 @@ <when input="output.outFileFormat" value="pdf" format="pdf" /> <when input="output.outFileFormat" value="svg" format="svg" /> <when input="output.outFileFormat" value="eps" format="eps" /> + <when input="output.outFileFormat" value="plotly" format="html" /> </change_format> </data> </xml> @@ -634,6 +658,7 @@ <when input="outFileFormat" value="pdf" format="pdf" /> <when input="outFileFormat" value="svg" format="svg" /> <when input="outFileFormat" value="eps" format="eps" /> + <when input="outFileFormat" value="plotly" format="html" /> </change_format> </data> </xml> @@ -662,8 +687,7 @@ <xml name="colorMap"> <param name="colorMap" type="select" label="Color map to use for the heatmap" - help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html" - multiple="true"> + help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html"> <option value="RdYlBu" selected="true">RdYlBu</option> <option value="Accent">Accent</option> <option value="Spectral">Spectral</option>
--- a/readme.rst Mon Feb 05 11:43:36 2018 -0500 +++ b/readme.rst Thu Feb 15 07:48:38 2018 -0500 @@ -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. =======
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alignmentSieve.bed Thu Feb 15 07:48:38 2018 -0500 @@ -0,0 +1,4261 @@ +chr2L 5093 5232 +chr2L 5101 5236 +chr2L 5105 5252 +chr2L 5108 5267 +chr2L 5105 5250 +chr2L 5108 5244 +chr2L 5108 5279 +chr2L 5105 5251 +chr2L 5105 5252 +chr2L 5105 5224 +chr2L 5108 5244 +chr2L 5108 5252 +chr2L 5108 5244 +chr2L 5108 5251 +chr2L 5105 5212 +chr2L 5105 5266 +chr2L 5108 5265 +chr2L 5106 5287 +chr2L 5106 5243 +chr2L 5106 5204 +chr2L 5109 5249 +chr2L 5109 5213 +chr2L 5106 5245 +chr2L 5118 5266 +chr2L 5116 5224 +chr2L 5117 5293 +chr2L 5117 5291 +chr2L 5120 5265 +chr2L 5117 5243 +chr2L 5122 5249 +chr2L 5119 5268 +chr2L 5119 5245 +chr2L 5123 5423 +chr2L 5120 5293 +chr2L 5120 5250 +chr2L 5123 5293 +chr2L 5129 5197 +chr2L 5129 5323 +chr2L 5130 5265 +chr2L 5127 5280 +chr2L 5127 5285 +chr2L 5133 5274 +chr2L 5138 5293 +chr2L 5141 5279 +chr2L 5138 5266 +chr2L 5141 5279 +chr2L 5152 5322 +chr2L 5149 5323 +chr2L 5149 5250 +chr2L 5149 5306 +chr2L 5152 5292 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alignmentSieve.txt Thu Feb 15 07:48:38 2018 -0500 @@ -0,0 +1,3 @@ +#bamFilterReads --filterMetrics +#File Reads Remaining Total Initial Reads +paired_chr2L.bam 8440 12644
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bamPEFragmentSize_lengths1.txt Thu Feb 15 07:48:38 2018 -0500 @@ -0,0 +1,5 @@ +#bamPEFragmentSize +Size Occurrences Sample +241 1 bowtie2 test1.bam +242 1 bowtie2 test1.bam +251 1 bowtie2 test1.bam
--- 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 @@ -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 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bamPEFragmentSize_table1.txt Thu Feb 15 07:48:38 2018 -0500 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/estimateReadFiltering.txt Thu Feb 15 07:48:38 2018 -0500 @@ -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
--- 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 @@ -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
--- 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 @@ -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
--- 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 @@ -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
--- 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 @@ -1,3 +1,4 @@ +#plotFingerprint --outRawCounts 'bowtie2 test1.bam' 'bowtie2 test1.bam' 1085 1085 1782 1782
--- 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 @@ -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