Mercurial > repos > bgruening > deeptools_bam_compare

changeset 17:2a1b4e95bdf7 draft

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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
author bgruening
date Thu, 15 Feb 2018 07:48:38 -0500
parents 2e615a3f2b07
children eb9fcfcd44a0
files bamCompare.xml deepTools_macros.xml readme.rst test-data/alignmentSieve.bam test-data/alignmentSieve.bed test-data/alignmentSieve.txt test-data/alignmentSieve2.bam test-data/alignmentSieve3.bam test-data/bamPEFragmentSize_histogram_result1.png test-data/bamPEFragmentSize_lengths1.txt test-data/bamPEFragmentSize_result1.txt test-data/bamPEFragmentSize_table1.txt test-data/estimateReadFiltering.txt test-data/heatmapper_result1.png test-data/heatmapper_result2.png test-data/multiBamSummary_result1.npz test-data/multiBamSummary_result2.npz test-data/paired_chr2L.cram 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
diffstat 26 files changed, 4406 insertions(+), 83 deletions(-) [+]
line wrap: on
line diff
--- 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.
 
 
 =======
Binary file test-data/alignmentSieve.bam has changed
--- /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
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+chr2L	9884	10144
+chr2L	9884	10018
+chr2L	9886	10017
+chr2L	9891	10018
+chr2L	9894	9972
+chr2L	9896	10054
+chr2L	9896	10050
+chr2L	9898	10077
+chr2L	9900	10050
+chr2L	9903	10055
+chr2L	9903	10049
+chr2L	9903	10056
+chr2L	9900	10064
+chr2L	9903	10067
+chr2L	9903	10067
+chr2L	9900	10076
+chr2L	9903	10062
+chr2L	9904	10018
+chr2L	9901	10030
+chr2L	9904	10063
+chr2L	9904	10073
+chr2L	9901	10019
+chr2L	9901	10018
+chr2L	9904	10046
+chr2L	9904	10055
+chr2L	9904	10072
+chr2L	9901	10051
+chr2L	9904	10029
+chr2L	9904	10017
+chr2L	9904	10068
+chr2L	9904	10050
+chr2L	9904	10072
+chr2L	9904	10049
+chr2L	9904	10067
+chr2L	9904	10049
+chr2L	9901	10047
+chr2L	9905	10050
+chr2L	9907	10049
+chr2L	9904	10047
+chr2L	9904	10030
+chr2L	9907	10067
+chr2L	9907	10036
+chr2L	9904	10026
+chr2L	9914	10068
+chr2L	9914	10017
+chr2L	9916	10048
+chr2L	9919	10068
+chr2L	9916	10064
+chr2L	9918	10019
+chr2L	9919	10068
+chr2L	9924	10069
+chr2L	9921	10056
+chr2L	9927	10019
+chr2L	9931	10067
+chr2L	9929	10090
+chr2L	9932	10072
+chr2L	9931	10089
+chr2L	9935	10100
+chr2L	9935	10072
+chr2L	9935	10067
+chr2L	9933	10089
+chr2L	9935	10088
+chr2L	9936	10045
+chr2L	9939	10094
+chr2L	9937	10030
+chr2L	9942	10135
+chr2L	9957	10049
+chr2L	9958	10095
+chr2L	9958	10106
+chr2L	9961	10088
+chr2L	9958	10086
+chr2L	9962	10089
+chr2L	9962	10100
+chr2L	9964	10108
+chr2L	9967	10088
+chr2L	9964	10073
+chr2L	9968	10134
+chr2L	9965	10068
+chr2L	9968	10107
+chr2L	9968	10067
+chr2L	9966	10089
+chr2L	9966	10074
+chr2L	9969	10089
+chr2L	9971	10089
+chr2L	9969	10103
+chr2L	9969	10142
+chr2L	9969	10094
+chr2L	9970	10106
+chr2L	9973	10132
+chr2L	9973	10121
+chr2L	9973	10116
+chr2L	9973	10095
+chr2L	9971	10280
+chr2L	9974	10113
+chr2L	9971	10088
+chr2L	9974	10116
+chr2L	9974	10088
+chr2L	9974	10117
+chr2L	9974	10134
+chr2L	9974	10104
+chr2L	9972	10141
+chr2L	9972	10073
+chr2L	9977	10101
+chr2L	9980	10118
+chr2L	9981	10125
+chr2L	9985	10135
+chr2L	9985	10134
+chr2L	9982	10133
+chr2L	9982	10237
+chr2L	9985	10113
+chr2L	9985	10134
+chr2L	9986	10362
+chr2L	9983	10146
+chr2L	9986	10132
+chr2L	9983	10141
+chr2L	9986	10149
+chr2L	9986	10141
+chr2L	9983	10142
+chr2L	9986	10100
+chr2L	9986	10134
+chr2L	9983	10136
+chr2L	9983	10108
+chr2L	9986	10141
+chr2L	9987	10121
+chr2L	9987	10134
+chr2L	9984	10141
+chr2L	9987	10089
+chr2L	9989	10171
+chr2L	9989	10099
+chr2L	9989	10141
+chr2L	9992	10134
+chr2L	9989	10158
+chr2L	9992	10150
+chr2L	9993	10147
+chr2L	9990	10108
+chr2L	9990	10142
+chr2L	9993	10170
+chr2L	9990	10135
+chr2L	9993	10091
+chr2L	9994	10135
+chr2L	9991	10145
+chr2L	9991	10101
+chr2L	9991	10145
+chr2L	9991	10133
+chr2L	9999	10134
+chr2L	10000	10173
--- /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
Binary file test-data/alignmentSieve2.bam has changed
Binary file test-data/alignmentSieve3.bam has changed
Binary file test-data/bamPEFragmentSize_histogram_result1.png has changed
--- /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
Binary file test-data/heatmapper_result1.png has changed
Binary file test-data/heatmapper_result2.png has changed
Binary file test-data/multiBamSummary_result1.npz has changed
Binary file test-data/multiBamSummary_result2.npz has changed
Binary file test-data/paired_chr2L.cram has changed
--- 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
Binary file test-data/plotCorrelation_result2.png has changed
Binary file test-data/plotCoverage_result1.png has changed
--- 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
Binary file test-data/plotPCA_result1.png has changed
--- 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