Repository 'deeptools_bam_coverage'
hg clone https://toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage

Changeset 17:f024daeffbed (2018-02-15)
Previous changeset 16:77e1664d66cd (2018-02-05) Next changeset 18:609399927ca5 (2018-03-02)
Commit message:
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
modified:
bamCoverage.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 77e1664d66cd -r f024daeffbed bamCoverage.xml
--- a/bamCoverage.xml Mon Feb 05 11:45:28 2018 -0500
+++ b/bamCoverage.xml Thu Feb 15 15:13:44 2018 -0500
[
@@ -1,5 +1,5 @@
 <tool id="deeptools_bam_coverage" name="bamCoverage" version="@WRAPPER_VERSION@.0">
-    <description>generates a coverage bigWig file from a given BAM file</description>
+    <description>generates a coverage bigWig file from a given BAM or CRAM file</description>
     <macros>
         <token name="@BINARY@">bamCoverage</token>
         <import>deepTools_macros.xml</import>
@@ -8,7 +8,11 @@
     <command>
 <![CDATA[
         ln -s '$bamInput' one.bam &&
-        ln -s '${bamInput.metadata.bam_index}' one.bam.bai &&
+        #if $bamInput.ext == 'bam':
+            ln -s '${bamInput.metadata.bam_index}' one.bam.bai &&
+        #else:
+            ln -s '${bamInput.metadata.cram_index}' one.bam.crai &&
+        #end if
 
         @BINARY@
             @THREADS@
@@ -20,12 +24,17 @@
             --binSize $binSize
 
             #if $scaling.type=='rpkm':
-                --normalizeUsingRPKM
+                --normalizeUsing RPKM
+            #elif $scaling.type=='cpm':
+                --normalizeUsing CPM
+            #elif $scaling.type=='bpm':
+                --normalizeUsing BPM
             #elif $scaling.type=='1x':
+                --normalizeUsing RPGC
                 #if $scaling.effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
-                    --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize
+                    --effectiveGenomeSize $scaling.effectiveGenomeSize.effectiveGenomeSize
                 #else:
-                    --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize_opt
+                    --effectiveGenomeSize $scaling.effectiveGenomeSize.effectiveGenomeSize_opt
                 #end if
             #end if
 
@@ -63,7 +72,7 @@
     </command>
 
     <inputs>
-        <param name="bamInput" format="bam" type="data" label="BAM file"
+        <param name="bamInput" format="bam,cram" type="data" label="BAM/CRAM file"
             help=""/>
 
         <param name="binSize" type="integer" value="50" min="1"
@@ -73,10 +82,14 @@
         <conditional name="scaling">
             <param name="type" type="select" label="Scaling/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="rpkm">Normalize to 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="no">Do not normalize or scale</option>
             </param>
             <when value="rpkm"/>
+            <when value="cpm"/>
+            <when value="bpm"/>
             <when value="no"/>
             <when value="1x">
                 <expand macro="effectiveGenomeSize" />
@@ -129,7 +142,7 @@
                         --Offset 5 -1 will result in the 5th through last position being used, which
                         is equivalent to trimming 4 bases from the 5-prime end of alignments." />
 
-                <param argument="filterRNAstrand" type="select" label="Only include reads originating from fragments from the forward or reverse strand." 
+                <param argument="filterRNAstrand" type="select" label="Only include reads originating from fragments from the forward or reverse strand."
                     help="By default (the no option), all reads are processed, regardless of the strand they originated from. For RNAseq, it can be useful to separately create bigWig files for the forward or reverse strands.
                           Note that this tools assumes that a dUTP-based method was used, so fragments will be assigned to the reverse strand if the second read in a pair is reverse complemented.">
                     <option value="no" selected="true">no</option>
@@ -162,6 +175,8 @@
             <param name="bamInput" value="bowtie2 test1.bam" ftype="bam" />
             <param name="outFileFormat" value="bigwig" />
             <param name="showAdvancedOpt" value="no" />
+            <param name="effectiveGenomeSize_opt" value="specific" />
+            <param name="effectiveGenomeSize" value="2451960000" />
             <param name="binSize" value="10" />
             <output name="outFileName" file="bamCoverage_result2.bw" ftype="bigwig" />
         </test>
@@ -169,6 +184,8 @@
             <param name="bamInput" value="bowtie2 test1.bam" ftype="bam" />
             <param name="outFileFormat" value="bedgraph" />
             <param name="showAdvancedOpt" value="no" />
+            <param name="effectiveGenomeSize_opt" value="specific" />
+            <param name="effectiveGenomeSize" value="2451960000" />
             <param name="binSize" value="10" />
             <output name="outFileName" file="bamCoverage_result3.bg" ftype="bedgraph" />
         </test>
@@ -176,6 +193,8 @@
             <param name="bamInput" value="phiX.bam" ftype="bam" />
             <param name="outFileFormat" value="bigwig" />
             <param name="showAdvancedOpt" value="no" />
+            <param name="effectiveGenomeSize_opt" value="specific" />
+            <param name="effectiveGenomeSize" value="2451960000" />
             <param name="binSize" value="10" />
             <output name="outFileName" file="bamCoverage_result4.bw" ftype="bigwig" />
         </test>
@@ -183,6 +202,8 @@
             <param name="bamInput" value="phiX.bam" ftype="bam" />
             <param name="outFileFormat" value="bedgraph" />
             <param name="showAdvancedOpt" value="yes" />
+            <param name="effectiveGenomeSize_opt" value="specific" />
+            <param name="effectiveGenomeSize" value="2451960000" />
             <param name="binSize" value="10" />
             <output name="outFileName" file="bamCoverage_result4.bg" ftype="bedgraph" />
         </test>
@@ -191,6 +212,8 @@
             <param name="outFileFormat" value="bigwig" />
             <param name="showAdvancedOpt" value="yes" />
             <param name="filterRNAstrand" value="reverse" />
+            <param name="effectiveGenomeSize_opt" value="specific" />
+            <param name="effectiveGenomeSize" value="2451960000" />
             <param name="binSize" value="10" />
             <output name="outFileName" file="bamCoverage_result5.bw" ftype="bigwig" />
         </test>
@@ -215,9 +238,14 @@
 Given a BAM file, this tool generates a bigWig or bedGraph file of fragment or
 read coverages. The way the method works is by first calculating all the
 number of reads (either extended to match the fragment length or not) that
-overlap each bin in the genome. The resulting read counts can be normalized
-using either a given scaling factor, the RPKM formula or to get a 1x depth of
-coverage (RPGC). In the case of paired-end mapping, each read mate is treated
+overlap each bin in the genome. Various options are available to normalize the reads:
+1) using a given scaling factor
+2) RPKM (reads per kilobase per million) : RPKM (per bin) =  number of reads per bin / ( number of mapped reads (in millions) * bin length (kb) ).
+3) CPM (counts per million) : CPM (per bin) =  number of reads per bin / number of mapped reads (in millions).
+4) BPM (bins per million) :  BPM (per bin) =  number of reads per bin / sum of all reads per bin (in millions).
+5) RPGC (1x sequencing depth ) : number of reads per bin /(total number of mapped reads * fragment length / effective genome size)
+
+In the case of paired-end mapping, each read mate is treated
 independently to avoid a bias when a mixture of concordant and discordant
 pairs is present. This means that *each end* will be extended to match the
 fragment length.
b
diff -r 77e1664d66cd -r f024daeffbed deepTools_macros.xml
--- a/deepTools_macros.xml Mon Feb 05 11:45:28 2018 -0500
+++ b/deepTools_macros.xml Thu Feb 15 15:13:44 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 77e1664d66cd -r f024daeffbed readme.rst
--- a/readme.rst Mon Feb 05 11:45:28 2018 -0500
+++ b/readme.rst Thu Feb 15 15:13:44 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 77e1664d66cd -r f024daeffbed test-data/alignmentSieve.bam
b
Binary file test-data/alignmentSieve.bam has changed
b
diff -r 77e1664d66cd -r f024daeffbed test-data/alignmentSieve.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alignmentSieve.bed Thu Feb 15 15:13:44 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 77e1664d66cd -r f024daeffbed test-data/alignmentSieve.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alignmentSieve.txt Thu Feb 15 15:13:44 2018 -0500
b
@@ -0,0 +1,3 @@
+#bamFilterReads --filterMetrics
+#File Reads Remaining Total Initial Reads
+paired_chr2L.bam 8440 12644
b
diff -r 77e1664d66cd -r f024daeffbed test-data/alignmentSieve2.bam
b
Binary file test-data/alignmentSieve2.bam has changed
b
diff -r 77e1664d66cd -r f024daeffbed test-data/alignmentSieve3.bam
b
Binary file test-data/alignmentSieve3.bam has changed
b
diff -r 77e1664d66cd -r f024daeffbed test-data/bamPEFragmentSize_histogram_result1.png
b
Binary file test-data/bamPEFragmentSize_histogram_result1.png has changed
b
diff -r 77e1664d66cd -r f024daeffbed test-data/bamPEFragmentSize_lengths1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bamPEFragmentSize_lengths1.txt Thu Feb 15 15:13:44 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 77e1664d66cd -r f024daeffbed test-data/bamPEFragmentSize_result1.txt
--- a/test-data/bamPEFragmentSize_result1.txt Mon Feb 05 11:45:28 2018 -0500
+++ b/test-data/bamPEFragmentSize_result1.txt Thu Feb 15 15:13:44 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 77e1664d66cd -r f024daeffbed test-data/bamPEFragmentSize_table1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bamPEFragmentSize_table1.txt Thu Feb 15 15:13:44 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 77e1664d66cd -r f024daeffbed test-data/estimateReadFiltering.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/estimateReadFiltering.txt Thu Feb 15 15:13:44 2018 -0500
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+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
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diff -r 77e1664d66cd -r f024daeffbed test-data/heatmapper_result1.png
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diff -r 77e1664d66cd -r f024daeffbed test-data/heatmapper_result2.png
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diff -r 77e1664d66cd -r f024daeffbed test-data/multiBamSummary_result1.npz
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diff -r 77e1664d66cd -r f024daeffbed test-data/multiBamSummary_result2.npz
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diff -r 77e1664d66cd -r f024daeffbed test-data/paired_chr2L.cram
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diff -r 77e1664d66cd -r f024daeffbed test-data/plotCorrelation_result1.tabular
--- a/test-data/plotCorrelation_result1.tabular Mon Feb 05 11:45:28 2018 -0500
+++ b/test-data/plotCorrelation_result1.tabular Thu Feb 15 15:13:44 2018 -0500
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+#plotCorrelation --outFileCorMatrix
  'bowtie2 test1.bam' 'bowtie2 test1.bam'
 'bowtie2 test1.bam' 1.0000 1.0000
 'bowtie2 test1.bam' 1.0000 1.0000
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diff -r 77e1664d66cd -r f024daeffbed test-data/plotCorrelation_result2.png
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diff -r 77e1664d66cd -r f024daeffbed test-data/plotCoverage_result1.png
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diff -r 77e1664d66cd -r f024daeffbed test-data/plotCoverage_result1.tabular
--- a/test-data/plotCoverage_result1.tabular Mon Feb 05 11:45:28 2018 -0500
+++ b/test-data/plotCoverage_result1.tabular Thu Feb 15 15:13:44 2018 -0500
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@@ -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
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diff -r 77e1664d66cd -r f024daeffbed test-data/plotEnrichment_output.txt
--- a/test-data/plotEnrichment_output.txt Mon Feb 05 11:45:28 2018 -0500
+++ b/test-data/plotEnrichment_output.txt Thu Feb 15 15:13:44 2018 -0500
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@@ -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
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diff -r 77e1664d66cd -r f024daeffbed test-data/plotFingerprint_result2.tabular
--- a/test-data/plotFingerprint_result2.tabular Mon Feb 05 11:45:28 2018 -0500
+++ b/test-data/plotFingerprint_result2.tabular Thu Feb 15 15:13:44 2018 -0500
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@@ -1,3 +1,4 @@
+#plotFingerprint --outRawCounts
 'bowtie2 test1.bam' 'bowtie2 test1.bam'
 1085 1085
 1782 1782
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diff -r 77e1664d66cd -r f024daeffbed test-data/plotPCA_result1.png
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diff -r 77e1664d66cd -r f024daeffbed test-data/plotPCA_result2.tabular
--- a/test-data/plotPCA_result2.tabular Mon Feb 05 11:45:28 2018 -0500
+++ b/test-data/plotPCA_result2.tabular Thu Feb 15 15:13:44 2018 -0500
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+#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