changeset 4:f4d018471628 draft default tip

Uploaded
author jpruab
date Tue, 13 Aug 2013 12:09:14 -0400
parents 08b477977410
children
files picard_AddOrReplaceReadGroups.xml picard_BamIndexStats.xml picard_FastqToSam.xml picard_ReorderSam.xml picard_ReplaceSamHeader.xml picard_SamToFastq.xml picard_SamToFastq_wrapper.py picard_wrapper.py rgPicardASMetrics.xml rgPicardFixMate.xml rgPicardGCBiasMetrics.xml rgPicardHsMetrics.xml rgPicardInsertSize.xml rgPicardLibComplexity.xml rgPicardMarkDups.xml test-data/bfast_out1.sam test-data/bwa_wrapper_in2.fastqsanger test-data/bwa_wrapper_in3.fastqsanger test-data/bwa_wrapper_out3.sam test-data/phiX.fasta test-data/picard_ARRG_input1.bam test-data/picard_ARRG_input1.sam test-data/picard_ARRG_input2.sam test-data/picard_ARRG_output1.sam test-data/picard_ARRG_output2.bam test-data/picard_ARRG_output2.sam test-data/picard_ARRG_output3.bam test-data/picard_ARRG_output3.bam.bai test-data/picard_ARRG_output3.sam test-data/picard_BIS_input1.bam test-data/picard_BIS_input1.sam test-data/picard_BIS_output1.txt test-data/picard_BIS_output2.txt test-data/picard_MD_output1.txt test-data/picard_MD_output2.bam test-data/picard_MD_output3.txt test-data/picard_MD_output4.sam test-data/picard_RSH_input1.bam test-data/picard_RSH_input1.sam test-data/picard_RSH_output1.sam test-data/picard_RSH_output2.bam test-data/picard_RSH_output2.sam test-data/picard_RS_input1.bam test-data/picard_RS_input2.sam test-data/picard_RS_input3.bam test-data/picard_RS_input3.sam test-data/picard_RS_input4.fasta test-data/picard_RS_output1.bam test-data/picard_RS_output2.sam test-data/picard_RS_output3.sam test-data/picard_fastq_to_sam_out1.bam test-data/picard_fastq_to_sam_out1.bam.bai test-data/picard_fastq_to_sam_out2.bam test-data/picard_fastq_to_sam_out2.bam.bai test-data/picard_input_bait.bed test-data/picard_input_coordinate_sorted.bam test-data/picard_input_hg18.trimmed.fasta test-data/picard_input_sorted_pair.bam test-data/picard_input_sorted_pair.sam test-data/picard_input_summary_alignment_stats.sam test-data/picard_input_tiny.sam test-data/picard_input_tiny_coord.bam test-data/picard_input_tiny_coord.sam test-data/picard_output_AsMetrics_indexed_hg18_sorted_pair.html test-data/picard_output_GcBias_uploaded_hg18_summary_alignment_stats.html test-data/picard_output_alignment_summary_metrics.html test-data/picard_output_collect_AS_sorted_pair.txt test-data/picard_output_estlibcomplexity_tinysam.html test-data/picard_output_fixmate_sorted_pair.bam test-data/picard_output_fixmate_sorted_pair.sam test-data/picard_output_fixmate_tiny.bam test-data/picard_output_gc_summary_alignment_stats.pdf test-data/picard_output_gc_summary_alignment_stats.txt test-data/picard_output_hs_transposed_summary_alignment_stats.html test-data/picard_output_insertsize_tinysam.html test-data/picard_output_markdups_remdupes.bam test-data/picard_output_markdups_sortedpairsam.bam test-data/picard_output_markdups_sortedpairsam.html test-data/picard_output_markdups_sortedpairsam.sam test-data/picard_output_validate_tiny_sam.html test-data/picard_summary_alignment_stats.sam test-data/random_phiX_1.fastqsanger tool-data/picard_index.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml
diffstat 85 files changed, 5991 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/picard_AddOrReplaceReadGroups.xml	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,205 @@
+<tool name="Add or Replace Groups" id="picard_ARRG" version="1.56.0">
+  <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
+  <command interpreter="python">
+    picard_wrapper.py
+      --input="${inputFile}"
+      --rg-lb="${rglb}"
+      --rg-pl="${rgpl}"
+      --rg-pu="${rgpu}"
+      --rg-sm="${rgsm}"
+      --rg-id="${rgid}"
+      --rg-opts="${readGroupOpts.rgOpts}"
+      #if $readGroupOpts.rgOpts == "full"
+        --rg-cn="${readGroupOpts.rgcn}"
+        --rg-ds="${readGroupOpts.rgds}"
+      #end if
+      --output-format="${outputFormat}"
+      --output="${outFile}"
+      -j "\$JAVA_JAR_PATH/AddOrReplaceReadGroups.jar"
+      --tmpdir "${__new_file_path__}" 
+  </command>
+  <inputs>
+    <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to add or replace read groups in"
+      help="If empty, upload or import a SAM/BAM dataset." />
+    <param name="rgid" value="1" type="text" label="Read group ID (ID tag)" help="The most important read group tag. Galaxy will use a value of '1' if nothing provided." />
+    <param name="rgsm" value="" type="text" label="Read group sample name (SM tag)" />
+    <param name="rglb" value="" type="text" label="Read group library (LB tag)" />
+    <param name="rgpl" value="" type="text" label="Read group platform (PL tag)" help="illumina, solid, 454, pacbio, helicos" />
+    <param name="rgpu" value="" type="text" label="Read group platform unit" help="like run barcode, etc." />
+    <conditional name="readGroupOpts">
+      <param name="rgOpts" type="select" label="Specify additional (optional) arguments" help="Allows you to set RGCN and RGDS.">
+        <option value="preSet">Use pre-set defaults</option>
+        <option value="full">Set optional arguments</option>
+      </param>
+      <when value="preSet" />
+      <when value="full">
+        <param name="rgcn" value="" type="text" label="Read group sequencing center name" help="Leave set to &lt;null&gt; for default (none)" />
+        <param name="rgds" value="" type="text" label="Read group description" help="Leave set to &lt;null&gt; for default (none)" />
+      </when>
+    </conditional>
+    <param name="outputFormat" type="boolean" checked="True" truevalue="bam" falsevalue="sam" label="Output bam instead of sam" help="Uncheck for sam output" />
+  </inputs>
+  <outputs>
+    <data name="outFile" format="bam" label="${tool.name} on ${on_string}: ${outputFormat} with read groups replaced">
+      <change_format>
+        <when input="outputFormat" value="sam" format="sam" />
+      </change_format>
+    </data>
+  </outputs>
+  <tests>
+    <test>
+      <!-- Command for replacing read groups in bam:
+      java -jar AddOrReplaceReadGroups.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_ARRG_input1.bam O=picard_ARRG_output1.sam RGID=one RGLB=lib RGPL=illumina RGPU=peaewe RGSM=sam1
+      -->
+      <param name="inputFile" value="picard_ARRG_input1.bam" />
+      <param name="rglb" value="lib" />
+      <param name="rgpl" value="illumina" />
+      <param name="rgpu" value="peaewe" />
+      <param name="rgsm" value="sam1" />
+      <param name="rgid" value="one" />
+      <param name="rgOpts" value="preSet" />
+      <param name="outputFormat" value="False" />
+      <output name="outFile" file="picard_ARRG_output1.sam" ftype="sam" />
+    </test>
+    <test>
+      <!-- Command for replacing read groups in sam:
+      java -jar AddOrReplaceReadGroups.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_ARRG_input1.sam O=picard_ARRG_output2.sam RGLB=LIB RGPL=IL RGPU=PLAT RGSM=smp RGID=M5 RGCN=FamousCenter RGDS="description with spaces"
+      picard_ARRG_input1.bam can be created from picard_ARRG_input1.sam
+      -->
+      <param name="inputFile" value="picard_ARRG_input1.sam" />
+      <param name="rglb" value="LIB" />
+      <param name="rgpl" value="IL" />
+      <param name="rgpu" value="PLAT" />
+      <param name="rgsm" value="smp" />
+      <param name="rgid" value="M5" />
+      <param name="rgOpts" value="full" />
+      <param name="rgcn" value="FamousCenter" />
+      <param name="rgds" value="description with spaces" />
+      <param name="outputFormat" value="False" />
+      <output name="outFile" file="picard_ARRG_output2.sam" ftype="sam" />
+    </test>
+    <test>
+      <!-- Command for adding read groups in sam:
+      java -jar AddOrReplaceReadGroups.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_ARRG_input2.sam O=picard_ARRG_output3.bam RGID=M6 RGLB=LIB RGPL=IL RGPU=PLAT RGSM=smp1
+      -->
+      <param name="inputFile" value="picard_ARRG_input2.sam" />
+      <param name="rglb" value="LIB" />
+      <param name="rgpl" value="IL" />
+      <param name="rgpu" value="PLAT" />
+      <param name="rgsm" value="smp1" />
+      <param name="rgid" value="M6" />
+      <param name="rgOpts" value="preSet" />
+      <param name="outputFormat" value="True" />
+      <output name="outFile" file="picard_ARRG_output3.bam" ftype="bam" />
+    </test>
+  </tests>
+  <help>
+
+.. class:: infomark
+
+**Purpose**
+
+Add or Replace Read Groups in an input BAM or SAM file.
+
+**Read Groups are Important!**
+
+Many downstream analysis tools (such as GATK, for example) require BAM datasets to contain read groups. Even if you are not going to use GATK, setting read groups correctly from the start will simplify your life greatly. Below we provide an explanation of read groups fields taken from GATK FAQ webpage:
+
+.. csv-table::
+   :header-rows: 1
+    
+    Tag,Importance,Definition,Meaning
+    "ID","Required","Read group identifier. Each @RG line must have a unique ID. The value of ID is used in the RG tags of alignment records. Must be unique among all read groups in header section. Read group IDs may be modified when merging SAM files in order to handle collisions.","Ideally, this should be a globally unique identify across all sequencing data in the world, such as the Illumina flowcell + lane name and number.  Will be referenced by each read with the RG:Z field, allowing tools to determine the read group information associated with each read, including the sample from which the read came.  Also, a read group is effectively treated as a separate run of the NGS instrument in tools like base quality score recalibration (a GATK component) -- all reads within a read group are assumed to come from the same instrument run and to therefore share the same error model."
+    "SM","Sample. Use pool name where a pool is being sequenced.","Required.  As important as ID.","The name of the sample sequenced in this read group.  GATK tools treat all read groups with the same SM value as containing sequencing data for the same sample.  Therefore it's critical that the SM field be correctly specified, especially when using multi-sample tools like the Unified Genotyper (a GATK component)."
+    "PL","Platform/technology used to produce the read. Valid values: ILLUMINA, SOLID, LS454, HELICOS and PACBIO.","Important.  Not currently used in the GATK, but was in the past, and may return.  The only way to known the sequencing technology used to generate the sequencing data","It's a good idea to use this field."
+    "LB","DNA preparation library identify","Essential for MarkDuplicates","MarkDuplicates uses the LB field to determine which read groups might contain molecular duplicates, in case the same DNA library was sequenced on multiple lanes."
+
+**Example of Read Group usage**
+
+Support we have a trio of samples: MOM, DAD, and KID.  Each has two DNA libraries prepared, one with 400 bp inserts and another with 200 bp inserts.  Each of these libraries is run on two lanes of an illumina hiseq, requiring 3 x 2 x 2 = 12 lanes of data.  When the data come off the sequencer, we would create 12 BAM files, with the following @RG fields in the header::
+
+ Dad's data:
+ @RG     ID:FLOWCELL1.LANE1      PL:illumina     LB:LIB-DAD-1 SM:DAD      PI:200
+ @RG     ID:FLOWCELL1.LANE2      PL:illumina     LB:LIB-DAD-1 SM:DAD      PI:200
+ @RG     ID:FLOWCELL1.LANE3      PL:illumina     LB:LIB-DAD-2 SM:DAD      PI:400
+ @RG     ID:FLOWCELL1.LANE4      PL:illumina     LB:LIB-DAD-2 SM:DAD      PI:400
+  
+ Mom's data:
+ @RG     ID:FLOWCELL1.LANE5      PL:illumina     LB:LIB-MOM-1 SM:MOM      PI:200
+ @RG     ID:FLOWCELL1.LANE6      PL:illumina     LB:LIB-MOM-1 SM:MOM      PI:200
+ @RG     ID:FLOWCELL1.LANE7      PL:illumina     LB:LIB-MOM-2 SM:MOM      PI:400
+ @RG     ID:FLOWCELL1.LANE8      PL:illumina     LB:LIB-MOM-2 SM:MOM      PI:400
+ 
+ Kid's data:
+ @RG     ID:FLOWCELL2.LANE1      PL:illumina     LB:LIB-KID-1 SM:KID      PI:200
+ @RG     ID:FLOWCELL2.LANE2      PL:illumina     LB:LIB-KID-1 SM:KID      PI:200
+ @RG     ID:FLOWCELL2.LANE3      PL:illumina     LB:LIB-KID-2 SM:KID      PI:400
+ @RG     ID:FLOWCELL2.LANE4      PL:illumina     LB:LIB-KID-2 SM:KID      PI:400
+
+Note the hierarchical relationship between read groups (unique for each lane) to libraries (sequenced on two lanes) and samples (across four lanes, two lanes for each library).
+
+**Picard documentation**
+
+This is a Galaxy wrapper for AddOrReplaceReadGroups, a part of the external package Picard-tools_.
+
+ .. _Picard-tools: http://www.google.com/search?q=picard+samtools
+
+------
+
+.. class:: infomark
+
+**Inputs, outputs, and parameters**
+
+Either a sam file or a bam file must be supplied. If a bam file is used, it must
+be coordinate-sorted. Galaxy currently coordinate-sorts all bam files.
+
+The output file is either bam (the default) or sam, according to user selection,
+and contains the same information as the input file except for the appropraite
+additional (or modified) read group tags. Bam is recommended since it is smaller.
+
+From the Picard documentation.
+
+AddOrReplaceReadGroups REQUIRED parameters::
+
+  Option (Type)    Description
+  
+  RGLB=String      Read Group Library
+  RGPL=String      Read Group platform (e.g. illumina, solid)
+  RGPU=String      Read Group platform unit (eg. run barcode)
+  RGSM=String      Read Group sample name
+  RGID=String      Read Group ID; Default value: null (empty)
+
+AddOrReplaceReadGroups OPTIONAL parameters::
+
+  Option (Type)    Description
+  
+  RGCN=String      Read Group sequencing center name; Default value: null (empty)
+  RGDS=String      Read Group description Default value: null (empty)
+
+One parameter that Picard's AddOrReplaceReadGroups offers that is automatically
+set by Galaxy is the SORT_ORDER, which is set to coordinate.
+
+.. class:: warningmark
+
+**Warning on SAM/BAM quality**
+
+Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT**
+flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears
+to be the only way to deal with SAM/BAM that cannot be parsed.
+
+
+
+  </help>
+</tool>
+
+
+
+
+
+
+
+
+
+
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/picard_BamIndexStats.xml	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,118 @@
+<tool name="BAM Index Statistics" id="picard_BamIndexStats" version="1.56.0">
+  <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
+  <command interpreter="python">
+    picard_wrapper.py
+      --input "${input_file}"
+      --bai-file "${input_file.metadata.bam_index}"
+      -t "${htmlfile}"
+      -d "${htmlfile.files_path}"
+      -j "\$JAVA_JAR_PATH/BamIndexStats.jar"
+      --tmpdir "${__new_file_path__}" 
+  </command>
+  <inputs>
+    <param format="bam" name="input_file" type="data"  label="BAM dataset to generate statistics for"
+      help="If empty, upload or import a BAM dataset" />
+  </inputs>
+  <outputs>
+    <data format="html" name="htmlfile" label="${tool.name}_on_${on_string}.html" />
+  </outputs>
+  <tests>
+    <test>
+      <!-- Command
+      java -jar BamIndexStats.jar I=test-data/picard_input_tiny_coord.bam > picard_BIS_output1.txt
+      picard_input_tiny_coord.bam can be created from picard_input_tiny_coord.sam
+      -->
+      <param name="input_file" value="picard_input_tiny_coord.bam" ftype="bam" />
+      <output name="htmlfile" file="picard_BIS_output1.txt" ftype="html" compare="contains" lines_diff="12"/>
+    </test>
+    <test>
+      <!-- Command
+      java -jar BamIndexStats.jar I=test-data/picard_BIS_input1.bam > picard_BIS_output2.txt
+      picard_BIS_input1.bam can be created from picard_BIS_input1.sam
+      -->
+      <param name="input_file" value="picard_BIS_input1.bam" ftype="bam" />
+      <output name="htmlfile" file="picard_BIS_output2.txt" ftype="html" compare="contains" lines_diff="12" />
+    </test>
+  </tests>
+  <help>
+
+.. class:: infomark
+
+**Purpose**
+
+Generate Bam Index Stats for a provided BAM file.
+
+**Picard documentation**
+
+This is a Galaxy wrapper for BamIndexStats, a part of the external package Picard-tools_.
+
+ .. _Picard-tools: http://www.google.com/search?q=picard+samtools
+
+------
+
+.. class:: infomark
+
+**Inputs and outputs**
+
+The only input is the BAM file you wish to obtain statistics for, which is required.
+Note that it must be coordinate-sorted. Galaxy currently coordinate-sorts all BAM files.
+
+This tool outputs an HTML file that contains links to the actual metrics results, as well
+as a log file with info on the exact command run.
+
+.. class:: warningmark
+
+**Warning on SAM/BAM quality**
+
+Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT**
+flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears
+to be the only way to deal with SAM/BAM that cannot be parsed.
+
+------
+
+**Example**
+
+Given a BAM file created from the following::
+
+  @HD    VN:1.0     SO:coordinate
+  @SQ    SN:chr1    LN:101
+  @SQ    SN:chr7    LN:404
+  @SQ    SN:chr8    LN:202
+  @SQ    SN:chr10   LN:303
+  @SQ    SN:chr14   LN:505
+  @RG    ID:0       SM:Hi,Mom!
+  @RG    ID:1       SM:samplesample    DS:ClearDescription
+  @PG    ID:1       PN:Hey!   VN:2.0
+  @CO    Just a generic comment to make the header longer
+  read1     83    chr7      1    255    101M             =       302     201    CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN    )'.*.+2,))II'I*/)-I*-)I.-)I)I),/-II..)./.,.).*II,I.II-)III0*IIIIIIII/32/,01460II/6/*0*/2/283//36868/I    RG:Z:0
+  read2     89    chr7      1    255    101M             *         0       0    CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN    )'.*.+2,))II'I*/)-I*-)I.-)I)I),/-II..)./.,.).*II,I.II-)III0*IIIIIIII/32/,01460II/6/*0*/2/283//36868/I    RG:Z:0
+  read3     83    chr7      1    255    101M             =       302     201    CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN    )'.*.+2,))II'I*/)-I*-)I.-)I)I),/-II..)./.,.).*II,I.II-)III0*IIIIIIII/32/,01460II/6/*0*/2/283//36868/I    RG:Z:0
+  read4    147    chr7     16    255    101M             =        21     -96    CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN    )'.*.+2,))II'I*/)-I*-)I.-)I)I),/-II..)./.,.).*II,I.II-)III0*IIIIIIII/32/,01460II/6/*0*/2/283//36868/I    RG:Z:0
+  read5     99    chr7     21    255    101M             =        16      96    CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN    )'.*.+2,))II'I*/)-I*-)I.-)I)I),/-II..)./.,.).*II,I.II-)III0*IIIIIIII/32/,01460II/6/*0*/2/283//36868/I    RG:Z:0
+  read6    163    chr7    302    255    101M             =         1    -201    NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA    I/15445666651/566666553+2/14/I/555512+3/)-'/-I-'*+))*''13+3)'//++''/'))/3+I*5++)I'2+I+/*I-II*)I-./1'1    RG:Z:0
+  read7    163    chr7    302    255    10M1D10M5I76M    =         1    -201    NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA    I/15445666651/566666553+2/14/I/555512+3/)-'/-I-'*+))*''13+3)'//++''/'))/3+I*5++)I'2+I+/*I-II*)I-./1'1    RG:Z:0
+  read8    165       *      0      0    *                chr7      1       0    NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA    I/15445666651/566666553+2/14/I/555512+3/)-'/-I-'*+))*''13+3)'//++''/'))/3+I*5++)I'2+I+/*I-II*)I-./1'1    RG:Z:0
+
+The following metrics file will be produced::
+
+  chr1 length=    101    Aligned= 0    Unaligned= 0
+  chr7 length=    404    Aligned= 7    Unaligned= 0
+  chr8 length=    202    Aligned= 0    Unaligned= 0
+  chr10 length=   303    Aligned= 0    Unaligned= 0
+  chr14 length=   505    Aligned= 0    Unaligned= 0
+  NoCoordinateCount= 1
+
+  </help>
+</tool>
+
+
+
+
+
+
+
+
+
+
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/picard_FastqToSam.xml	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,145 @@
+<tool id="picard_FastqToSam" name="FASTQ to BAM" version="1.56.0">
+  <description>creates an unaligned BAM file</description>
+  <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
+  <!-- Dan Blankenberg -->
+  <command>java  -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC
+    -jar "\$JAVA_JAR_PATH/FastqToSam.jar"
+    FASTQ="${input_fastq1}"
+    #if str( $input_fastq2) != "None":
+        FASTQ2="${input_fastq2}"
+    #end if
+    QUALITY_FORMAT="${ dict( fastqsanger='Standard', fastqcssanger='Standard', fastqillumina='Illumina', fastqsolexa='Solexa' )[ $input_fastq1.ext ] }" ##Solexa, Illumina, Standard
+    OUTPUT="${output_bam}"
+    READ_GROUP_NAME="${read_group_name}"
+    SAMPLE_NAME="${sample_name}" 
+    #if $param_type.param_type_selector == "advanced":
+        #if str( $param_type.library_name ) != "":
+            LIBRARY_NAME="${param_type.library_name}" 
+        #end if
+        #if str( $param_type.platform_unit ) != "":
+            PLATFORM_UNIT="${param_type.platform_unit}"
+        #end if
+        #if str( $param_type.platform ) != "":
+            PLATFORM="${param_type.platform}"
+        #end if 
+        #if str( $param_type.sequencing_center ) != "":
+            SEQUENCING_CENTER="${param_type.sequencing_center}"
+        #end if 
+        #if str( $param_type.predicted_insert_size ) != "":
+            PREDICTED_INSERT_SIZE="${param_type.predicted_insert_size}"
+        #end if 
+        #if str( $param_type.description.value ) != "":
+            DESCRIPTION="${param_type.description}"
+        #end if 
+        #if str( $param_type.run_date ) != "":
+            RUN_DATE="${param_type.run_date}"
+        #end if
+        #if str( $param_type.min_q ) != "":
+            MIN_Q="${param_type.min_q}"
+        #end if
+        #if str( $param_type.max_q ) != "":
+            MAX_Q="${param_type.max_q}"
+        #end if
+        SORT_ORDER="${param_type.sort_order}"
+    #else:
+        SORT_ORDER=coordinate ##unsorted, queryname, coordinate; always use coordinate
+    #end if
+  2&gt;&amp;1 
+  || echo "Error running Picard FastqToSAM" >&amp;2
+  </command>
+  <inputs>
+    <param name="input_fastq1" type="data" format="fastqsanger,fastqillumina,fastqsolexa,fastqcssanger" label="FASTQ file" /> <!-- confirm that fastqcssanger also works -->
+    <param name="input_fastq2" type="data" format="fastqsanger,fastqillumina,fastqsolexa,fastqcssanger" optional="True" label="Second FASTQ of paired end data" help="Only needed when using paired end data." >
+      <options options_filter_attribute="ext" from_parameter="tool.app.datatypes_registry.datatypes_by_extension" transform_lines="obj.keys()">
+        <column name="name" index="0"/>
+        <column name="value" index="0"/>
+        <filter type="param_value" ref="input_fastq1" ref_attribute="ext" column="0"/> 
+      </options>
+    </param>
+    <param name="read_group_name" type="text" value="A" label="Read Group Name" />
+    <param name="sample_name" type="text" value="unknown sample" label="Sample Name" />
+    <conditional name="param_type">
+      <param name="param_type_selector" type="select" label="Basic or Advanced options">
+        <option value="basic" selected="True">Basic</option>
+        <option value="advanced">Advanced</option>
+      </param>
+      <when value="basic">
+        <!-- Do nothing here -->
+      </when>
+      <when value="advanced">
+        <param name="library_name" type="text" value="" label="Library Name" />
+        <param name="platform_unit" type="text" value="" label="Platform Unit" />
+        <param name="platform" type="text" value="" label="Platform" />
+        <param name="sequencing_center" type="text" value="" label="Sequencing Center" />
+        <param name="predicted_insert_size" type="integer" value="" optional="True" label="Predicted Insert Size" />
+        <param name="description" type="text" value="" label="Description" />
+        <param name="run_date" type="text" value="" label="Run Date" />
+        <param name="min_q" type="integer" optional="True" value="0" label="Min Q" />
+        <param name="max_q" type="integer" optional="True" value="93" label="Max Q" />
+        <param name="sort_order" type="select" label="Sort order">
+          <option value="coordinate" selected="True">coordinate</option>
+          <option value="queryname">queryname</option>
+          <option value="unsorted">unsorted</option>
+        </param>
+      </when>
+    </conditional>
+  </inputs>
+  <outputs>
+    <data format="bam" name="output_bam" />
+  </outputs>
+  <tests>
+      <test>
+          <param name="input_fastq1" value="bwa_wrapper_in2.fastqsanger" ftype="fastqsanger" />
+          <param name="input_fastq2" />
+          <param name="read_group_name" value="A" />
+          <param name="sample_name" value="unknown sample" />
+          <param name="param_type_selector" value="basic" />
+          <output name="output_bam" file="picard_fastq_to_sam_out1.bam" ftype="bam"/> 
+      </test>
+      <test>
+          <param name="input_fastq1" value="bwa_wrapper_in2.fastqsanger" ftype="fastqsanger" />
+          <param name="input_fastq2" value="bwa_wrapper_in3.fastqsanger" ftype="fastqsanger" />
+          <param name="read_group_name" value="A" />
+          <param name="sample_name" value="unknown sample" />
+          <param name="param_type_selector" value="basic" />
+          <output name="output_bam" file="picard_fastq_to_sam_out2.bam" ftype="bam"/> 
+      </test>
+  </tests>
+  <help>
+**What it does**
+
+Picard: FastqToSam converts FASTQ files to unaligned BAM files.
+
+------
+
+Please cite the website "http://picard.sourceforge.net".
+
+------
+
+
+**Input formats**
+
+FastqToSam accepts FASTQ input files. If using paired-end data, you should select two FASTQ files.
+
+------
+
+**Outputs**
+
+The output is in BAM format, see http://samtools.sourceforge.net for more details.
+
+-------
+
+**FastqToSam settings**
+
+This is list of FastqToSam options::
+
+ READ_GROUP_NAME=String	Read group name Default value: A. This option can be set to 'null' to clear the default value.
+ SAMPLE_NAME=String	Sample name to insert into the read group header Required.
+ LIBRARY_NAME=String	The library name to place into the LB attribute in the read group header Default value: null.
+ PLATFORM_UNIT=String	The platform unit (often run_barcode.lane) to insert into the read group header Default value: null.
+ PLATFORM=String	The platform type (e.g. illumina, solid) to insert into the read group header Default value: null.
+ SEQUENCING_CENTER=String	The sequencing center from which the data originated Default value: null.
+ PREDICTED_INSERT_SIZE=Integer	Predicted median insert size, to insert into the read group header Default value: null.
+ DESCRIPTION=String	Inserted into the read group header Default value: null. 
+  </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/picard_ReorderSam.xml	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,166 @@
+<tool name="Reorder SAM/BAM" id="picard_ReorderSam" version="1.56.0">
+  <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
+  <command interpreter="python">
+    picard_wrapper.py
+      --input="${inputFile}"
+      #if $source.indexSource == "built-in"
+        --ref="${source.ref.fields.path}"
+      #else
+        --ref-file="${refFile}"
+        --species-name="${source.speciesName}"
+        --build-name="${source.buildName}"
+        --trunc-names="${source.truncateSeqNames}"
+      #end if
+      --allow-inc-dict-concord="${allowIncDictConcord}"
+      --allow-contig-len-discord="${allowContigLenDiscord}"
+      --output-format="${outputFormat}"
+      --output="${outFile}"
+      --tmpdir "${__new_file_path__}" 
+      -j "\$JAVA_JAR_PATH/ReorderSam.jar"
+  </command>
+  <inputs>
+    <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to be reordered"
+           help="If empty, upload or import a SAM/BAM dataset." />
+    <conditional name="source">
+      <param name="indexSource" type="select" label="Select Reference Genome" help="This tool will re-order SAM/BAM in the same order as reference selected below.">
+        <option value="built-in">Locally cached</option>
+        <option value="history">History</option>
+      </param>
+      <when value="built-in">
+        <param name="ref" type="select" label="Select a reference genome">
+          <options from_data_table="picard_indexes" />
+        </param>
+      </when>
+      <when value="history">
+        <param name="refFile" type="data" format="fasta" metadata_name="dbkey" label="Using reference file" />
+        <param name="speciesName" type="text" value="" label="Species name" />
+        <param name="buildName" type="text" value="" label="Build name" />
+        <param name="truncateSeqNames" type="boolean" checked="False" truevalue="true" falsevalue="false" label="Truncate sequence names after first whitespace" />
+      </when>
+    </conditional>
+    <param name="allowIncDictConcord" type="boolean" checked="False" truevalue="true" falsevalue="false" label="Allow incomplete dict concordance?" help="Allows a partial overlap of the BAM contigs with the new reference sequence contigs." />
+    <param name="allowContigLenDiscord" type="boolean" checked="False" truevalue="true" falsevalue="false" label="Allow contig length discordance?" help="This is dangerous--don't check it unless you know exactly what you're doing!" />
+    <param name="outputFormat" type="boolean" checked="True" truevalue="bam" falsevalue="sam" label="Output BAM instead of SAM" help="Uncheck for SAM output" />
+  </inputs>
+  <outputs>
+    <data name="outFile" format="bam" label="${tool.name} on ${on_string}: reordered ${outputFormat}">
+      <change_format>
+        <when input="outputFormat" value="sam" format="sam" />
+      </change_format>
+    </data>
+  </outputs>
+  <tests>
+    <test>
+      <!-- Commands:
+      cp test-data/phiX.fasta .
+      samtools faidx phiX.fasta
+      java -jar CreateSequenceDictionary.jar R=phiX.fasta O=phiX.dict URI=phiX.fasta TRUNCATE_NAMES_AT_WHITESPACE=false SPECIES=phiX174
+      java -jar ReorderSam.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_RS_input1.bam O=picard_RS_output1.bam REFERENCE=phiX.fasta ALLOW_INCOMPLETE_DICT_CONCORDANCE=false ALLOW_CONTIG_LENGTH_DISCORDANCE=false
+    -->
+      <param name="inputFile" value="picard_RS_input1.bam" />
+      <param name="indexSource" value="history" />
+      <param name="refFile" value="phiX.fasta" />
+      <param name="speciesName" value="phiX174" />
+      <param name="buildName" value="" />
+      <param name="truncateSeqNames" value="false" />
+      <param name="allowIncDictConcord" value="false" />
+      <param name="allowContigLenDiscord" value="false" />
+      <param name="outputFormat" value="True" />
+      <output name="outFile" file="picard_RS_output1.bam" ftype="bam" lines_diff="4" compare="contains" />
+    </test>
+    <test>
+      <!-- Command:
+      java -jar ReorderSam.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_RS_input2.sam O=picard_RS_output2.sam REFERENCE=/path/to/phiX/picard_index/phiX.fa ALLOW_INCOMPLETE_DICT_CONCORDANCE=false ALLOW_CONTIG_LENGTH_DISCORDANCE=false
+      /path/to/phiX/srma_index/phiX.fa is path to phiX.fa, phiX.fa.fai, and phiX.dict
+      -->
+      <param name="inputFile" value="picard_RS_input2.sam" />
+      <param name="indexSource" value="built-in" />
+      <param name="ref" value="phiX" />
+      <param name="allowIncDictConcord" value="false" />
+      <param name="allowContigLenDiscord" value="false" />
+      <param name="outputFormat" value="False" />
+      <output name="outFile" file="picard_RS_output2.sam" ftype="sam" lines_diff="4" sort="True" />
+    </test>
+    <test>
+      <!-- Commands:
+      cp test-data/picard_RS_input4.fasta .
+      samtools faidx picard_RS_input4.fasta
+      java -jar CreateSequenceDictionary.jar R=picard_RS_input4.fasta O=picard_RS_input4.dict URI=picard_RS_input4.fasta TRUNCATE_NAMES_AT_WHITESPACE=true SPECIES=phiX174 GENOME_ASSEMBLY=phiX_buildBlah1.1
+      java -jar ReorderSam.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_RS_input3.bam O=picard_RS_output3.sam REFERENCE=picard_RS_input4.fasta ALLOW_INCOMPLETE_DICT_CONCORDANCE=true ALLOW_CONTIG_LENGTH_DISCORDANCE=false
+      picard_RS_input3.bam can be made from picard_RS_input3.sam
+      -->
+      <param name="inputFile" value="picard_RS_input3.bam" />
+      <param name="indexSource" value="history" />
+      <param name="refFile" value="picard_RS_input4.fasta" />
+      <param name="speciesName" value="phiX174" />
+      <param name="buildName" value="phiX_buildBlah1.1" />
+      <param name="truncateSeqNames" value="true" />
+      <param name="allowIncDictConcord" value="true" />
+      <param name="allowContigLenDiscord" value="false" />
+      <param name="outputFormat" value="False" />
+      <output name="outFile" file="picard_RS_output3.sam" ftype="sam" lines_diff="12" sort="True" />
+    </test>
+  </tests>
+  <help>
+
+.. class:: infomark
+
+**Purpose**
+
+Reorder SAM/BAM to match contig ordering in a particular reference file. Note that this is
+not the same as sorting as done by the SortSam tool, which sorts by either coordinate
+values or query name. The ordering in ReorderSam is based on exact name matching of
+contigs/chromosomes. Reads that are mapped to a contig that is not in the new reference file are
+not included in the output.
+
+**Picard documentation**
+
+This is a Galaxy wrapper for ReorderSam, a part of the external package Picard-tools_.
+
+ .. _Picard-tools: http://www.google.com/search?q=picard+samtools
+
+------
+
+.. class:: infomark 
+
+**Inputs, outputs, and parameters**
+
+For the file that needs to be reordered, either a sam file or a bam file must be supplied.
+If a bam file is used, it must be coordinate-sorted. A reference file is also required,
+so either a fasta file should be supplied or a built-in reference can be selected.
+
+The output contains the same reads as the input file but the reads have been rearranged so
+they appear in the same order as the provided reference file. The tool will output either
+bam (the default) or sam, according to user selection. Bam is recommended since it is smaller.
+
+The only extra parameters that can be set are flags for allowing incomplete dict concordance
+and allowing contig length discordance. If incomplete dict concordance is allowed, only a
+partial overlap of the bam contigs with the new reference sequence contigs is required. By
+default it is off, requiring a corresponding contig in the new reference for each read contig.
+If contig length discordance is allowed, contig names that are the same between a read and the
+new reference contig are allowed even if they have different lengths. This is usually not a
+good idea, unless you know exactly what you're doing. It's off by default.
+
+.. class:: warningmark
+
+**Warning on SAM/BAM quality**
+
+Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT**
+flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears
+to be the only way to deal with SAM/BAM that cannot be parsed.
+
+
+  </help>
+</tool>
+
+
+
+
+
+
+
+
+
+
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/picard_ReplaceSamHeader.xml	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,115 @@
+<tool name="Replace SAM/BAM Header" id="picard_ReplaceSamHeader" version="1.56.0">
+  <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
+  <command interpreter="python">
+    picard_wrapper.py
+      --input "${inputFile}"
+      -o "${outFile}"
+      --header-file "${headerFile}"
+      --output-format "${outputFormat}"
+      -j "\$JAVA_JAR_PATH/ReplaceSamHeader.jar"
+      --tmpdir "${__new_file_path__}" 
+  </command>
+  <inputs>
+    <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to replace header in (TARGET)"
+      help="If empty, upload or import a SAM/BAM dataset." />
+    <param format="bam,sam" name="headerFile" type="data" label="SAM/BAM to reader header from (SOURCE)"
+      help="If empty, upload or import a SAM/BAM dataset." />
+    <param name="outputFormat" type="boolean" checked="True" truevalue="bam" falsevalue="sam" label="Output BAM instead of SAM" help="Uncheck for SAM output" />
+  </inputs>
+  <outputs>
+    <data name="outFile" format="bam" label="${tool.name} on ${on_string}: ${outputFormat} with replaced header">
+      <change_format>
+        <when input="outputFormat" value="sam" format="sam" />
+      </change_format>
+    </data>
+  </outputs>
+  <tests>
+    <test>
+      <!-- Command:
+      java -jar ReplaceSamHeader.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_input_tiny_coord.bam HEADER=test-data/picard_RSH_input1.bam O=picard_RSH_output1.sam
+      picard_RSH_input1.bam can be made from picard_RSH_input1.sam
+      -->
+      <param name="inputFile" value="picard_input_tiny_coord.bam" ftype="bam" />
+      <param name="headerFile" value="picard_RSH_input1.bam" ftype="bam" />
+      <param name="outputFormat" value="False" />
+      <output name="outFile" file="picard_RSH_output1.sam" ftype="sam" />
+    </test>
+    <test>
+      <!-- Command:
+      java -jar ReplaceSamHeader.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_input_tiny_coord.sam HEADER=test-data/picard_RSH_input1.bam O=picard_RSH_output2.sam
+      picard_RSH_input1.bam can be made from picard_RSH_input1.sam
+      -->
+      <param name="inputFile" value="picard_input_tiny_coord.sam" ftype="sam" />
+      <param name="headerFile" value="picard_RSH_input1.bam" ftype="bam" />
+      <param name="outputFormat" value="False" />
+      <output name="outFile" file="picard_RSH_output2.sam" ftype="sam" />
+    </test>
+    <test>
+      <!-- Command:
+      java -jar ReplaceSamHeader.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_input_tiny_coord.sam HEADER=test-data/picard_RSH_input1.sam O=picard_RSH_output2.bam
+      -->
+      <param name="inputFile" value="picard_input_tiny_coord.sam" ftype="sam" />
+      <param name="headerFile" value="picard_RSH_input1.sam" ftype="sam" />
+      <param name="outputFormat" value="True" />
+      <output name="outFile" file="picard_RSH_output2.bam" ftype="bam" />
+    </test>
+  </tests>
+  <help>
+
+
+.. class:: infomark
+
+**Purpose**
+
+Replace Sam Header with the header from another sam file. The tool does not do any
+significant validation, so it's up to the user to make sure that the elements in
+the header are relevant and that the new header has all the required things.
+
+Replace the SAMFileHeader in a SAM file with the given header. Validation is
+minimal. It is up to the user to ensure that all the elements referred to in the
+SAMRecords are present in the new header. Sort order of the two input files must
+be the same.
+
+**Picard documentation**
+
+This is a Galaxy wrapper for ReplaceSamHeader, a part of the external package Picard-tools_.
+
+ .. _Picard-tools: http://www.google.com/search?q=picard+samtools
+
+------
+
+.. class:: infomark
+
+**Inputs and outputs**
+
+Either a sam file or a bam file is required as the file whose header will be replaced.
+The header file is also required and can also be either sam or bam (it does not have
+to be the same type as the other file). In both cases, if a bam file is used, it must
+be coordinate-sorted. Galaxy currently coordinate-sorts all bam files.
+
+The tool will output either bam (the default) or sam. Bam is recommended since it is smaller.
+
+.. class:: warningmark
+
+**Warning on SAM/BAM quality**
+
+Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT**
+flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears
+to be the only way to deal with SAM/BAM that cannot be parsed.
+
+
+
+  </help>
+</tool>
+
+
+
+
+
+
+
+
+
+
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/picard_SamToFastq.xml	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,189 @@
+<tool id="picard_SamToFastq" name="SAM to FASTQ" version="1.56.1" force_history_refresh="True">
+  <description>creates a FASTQ file</description>
+  <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
+  <!-- Dan Blankenberg -->
+  <command interpreter="python">picard_SamToFastq_wrapper.py
+    -p '
+    java -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC
+    -jar "\$JAVA_JAR_PATH/SamToFastq.jar"
+    INPUT="${input_sam}"
+    VALIDATION_STRINGENCY="LENIENT"
+    RE_REVERSE="${re_reverse}"
+    INCLUDE_NON_PF_READS="${include_non_pf_reads}"
+    #if str( $clipping_attribute ):
+        CLIPPING_ATTRIBUTE="${clipping_attribute}"
+    #end if
+    #if str( $clipping_action ):
+        CLIPPING_ACTION="${clipping_action}"
+    #end if
+    #if str( $read1_trim ):
+        READ1_TRIM="${read1_trim}"
+    #end if
+    #if str( $read1_max_bases_to_write ):
+        READ1_MAX_BASES_TO_WRITE="${read1_max_bases_to_write}"
+    #end if
+    INCLUDE_NON_PRIMARY_ALIGNMENTS="${include_non_primary_alignments}"
+    
+    #if str( $output_per_read_group_selector ) == 'per_sam_file':
+        ##OUTPUT_PER_RG=false
+        FASTQ="${output_fastq1}"
+        
+        #if str( $single_paired_end_type.single_paired_end_type_selector ) == 'paired':
+            SECOND_END_FASTQ="${output_fastq2}"
+            #if str( $single_paired_end_type.read2_trim ): 
+                READ2_TRIM="${single_paired_end_type.read2_trim}"
+            #end if
+            #if str( $single_paired_end_type.read2_max_bases_to_write ):
+                READ2_MAX_BASES_TO_WRITE="${single_paired_end_type.read2_max_bases_to_write}"
+            #end if
+        #end if
+        '
+    #else:
+        OUTPUT_PER_RG=true
+        #if str( $single_paired_end_type.single_paired_end_type_selector ) == 'paired':
+            ' 
+            --read_group_file_2 "${output_fastq2}"
+            --file_id_2 "${output_fastq2.id}"
+            -p '
+            #if str( $single_paired_end_type.read2_trim ): 
+                READ2_TRIM="${single_paired_end_type.read2_trim}"
+            #end if
+            #if str( $single_paired_end_type.read2_max_bases_to_write ):
+                READ2_MAX_BASES_TO_WRITE="${single_paired_end_type.read2_max_bases_to_write}"
+            #end if
+        #end if
+        '
+        --read_group_file_1 "${output_fastq1}"
+        --new_files_path "${__new_file_path__}"
+        --file_id_1 "${output_fastq1.id}"
+    #end if
+  </command>
+  <inputs>
+    <param name="input_sam" type="data" format="sam,bam" label="BAM/SAM file" />
+    <param name="read1_trim" type="integer" value="" optional="True" label="The number of bases to trim from the beginning of read 1." />
+    <param name="read1_max_bases_to_write" type="integer" optional="True" value="" label="The maximum number of bases to write from read 1 after trimming." />
+    <param name="output_per_read_group_selector" type="select" label="Output per read group">
+      <option value="per_sam_file" selected="True">Per BAM/SAM file</option>
+      <option value="per_read_group">Per Read Group</option>
+    </param>
+    <conditional name="single_paired_end_type">
+      <param name="single_paired_end_type_selector" type="select" label="Single or Paired end">
+        <option value="single" selected="True">Single</option>
+        <option value="paired">Paired end</option>
+      </param>
+      <when value="single">
+        <!-- nothing yet -->
+      </when>
+      <when value="paired">
+        <param name="read2_trim" type="integer" value="" optional="True" label="The number of bases to trim from the beginning of read 2." />
+        <param name="read2_max_bases_to_write" type="integer" optional="True" value="" label="The maximum number of bases to write from read 2 after trimming." />
+      </when>
+    </conditional>
+    <param name="re_reverse" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Re-reverse bases and qualities of reads on negative strand"/>
+    <param name="include_non_pf_reads" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Include non-PF reads from the SAM file into the output FASTQ files."/>
+    <param name="clipping_attribute" type="text" value="" label="The attribute that stores the position at which the SAM record should be clipped" help="Leave blank for null" />
+    <param name="clipping_action" type="text" value="" label="The action that should be taken with clipped reads" help="'X' means the reads and qualities should be trimmed at the clipped position; 'N' means the bases should be changed to Ns in the clipped region; and any integer means that the base qualities should be set to that value in the clipped region. Leave blank for null" />
+    <param name="include_non_primary_alignments" type="boolean" truevalue="true" falsevalue="false" checked="False" label="If true, include non-primary alignments in the output." help="Support of non-primary alignments in SamToFastq is not comprehensive, so there may be exceptions if this is set to true and there are paired reads with non-primary alignments."/>
+    
+  </inputs>
+  <outputs>
+    <data format="fastqsanger" name="output_fastq1" label="${tool.name} on ${on_string}: FASTQ 1" />
+    <data format="fastqsanger" name="output_fastq2" label="${tool.name} on ${on_string}: FASTQ 2" >
+        <filter>single_paired_end_type['single_paired_end_type_selector'] == 'paired'</filter>
+    </data>
+  </outputs>
+  <tests>
+      <test>
+          <param name="input_sam" value="bfast_out1.sam" ftype="sam" />
+          <param name="output_per_read_group_selector" value="per_sam_file" />
+          <param name="single_paired_end_type_selector" value="single" />
+          <param name="read1_trim" value="" />
+          <param name="read1_max_bases_to_write" value="" />
+          <param name="re_reverse" value="True" />
+          <param name="include_non_pf_reads" value="False" />
+          <param name="clipping_action" value="" />
+          <param name="clipping_attribute" value="" />
+          <param name="include_non_primary_alignments" value="False" />
+          <output name="output_fastq1" file="random_phiX_1.fastqsanger"/> 
+      </test>
+      <test>
+          <param name="input_sam" value="bwa_wrapper_out3.sam" ftype="sam" />
+          <param name="output_per_read_group_selector" value="per_sam_file" />
+          <param name="single_paired_end_type_selector" value="paired" />
+          <param name="read1_trim" value="" />
+          <param name="read1_max_bases_to_write" value="" />
+          <param name="read2_trim" value="" />
+          <param name="read2_max_bases_to_write" value="" />
+          <param name="re_reverse" value="True" />
+          <param name="include_non_pf_reads" value="False" />
+          <param name="clipping_action" value="" />
+          <param name="clipping_attribute" value="" />
+          <param name="include_non_primary_alignments" value="False" />
+          <output name="output_fastq1" file="bwa_wrapper_in2.fastqsanger" lines_diff="64"/> <!-- 16 unaligned fastq blocks not present in original sam file -->
+          <output name="output_fastq2" file="bwa_wrapper_in3.fastqsanger" lines_diff="64"/> <!-- 16 unaligned fastq blocks not present in original sam file -->
+      </test>
+      <test>
+          <param name="input_sam" value="bwa_wrapper_out3.sam" ftype="sam" />
+          <param name="output_per_read_group_selector" value="per_read_group" />
+          <param name="single_paired_end_type_selector" value="paired" />
+          <param name="read1_trim" value="" />
+          <param name="read1_max_bases_to_write" value="" />
+          <param name="read2_trim" value="" />
+          <param name="read2_max_bases_to_write" value="" />
+          <param name="re_reverse" value="True" />
+          <param name="include_non_pf_reads" value="False" />
+          <param name="clipping_action" value="" />
+          <param name="clipping_attribute" value="" />
+          <param name="include_non_primary_alignments" value="False" />
+          <output name="output_fastq1" file="bwa_wrapper_in2.fastqsanger" lines_diff="64"/> <!-- 16 unaligned fastq blocks not present in original sam file -->
+          <output name="output_fastq2" file="bwa_wrapper_in3.fastqsanger" lines_diff="64"/> <!-- 16 unaligned fastq blocks not present in original sam file -->
+      </test>
+  </tests>
+  <help>
+**What it does**
+
+Picard: SamToFastq converts SAM files to FASTQ files.
+
+Extracts read sequences and qualities from the input SAM/BAM file and writes them into the output file in Sanger fastq format. In the RC mode (default is True), if the read is aligned and the alignment is to the reverse strand on the genome, the read's sequence from input SAM file will be reverse-complemented prior to writing it to fastq in order restore correctly the original read sequence as it was generated by the sequencer.
+
+------
+
+Please cite the website "http://picard.sourceforge.net".
+
+------
+
+
+**Input formats**
+
+FastqToSam accepts SAM input files, see http://samtools.sourceforge.net for more details.
+
+------
+
+**Outputs**
+
+The output is in FASTQ format. If using Paired end data, 2 fastq files are created.
+
+-------
+
+**FastqToSam settings**
+
+This is list of SamToFastq options::
+  
+  INPUT=File	Input SAM/BAM file to extract reads from Required.
+  FASTQ=File	Output fastq file (single-end fastq or, if paired, first end of the pair fastq). Required. Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG)
+  SECOND_END_FASTQ=File	Output fastq file (if paired, second end of the pair fastq). Default value: null. Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG)
+  OUTPUT_PER_RG=Boolean	Output a fastq file per read group (two fastq files per read group if the group is paired). Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false} Cannot be used in conjuction with option(s) SECOND_END_FASTQ (F2) FASTQ (F)
+  OUTPUT_DIR=File	Directory in which to output the fastq file(s). Used only when OUTPUT_PER_RG is true. Default value: null.
+  RE_REVERSE=Boolean	Re-reverse bases and qualities of reads with negative strand flag set before writing them to fastq Default value: true. This option can be set to 'null' to clear the default value. Possible values: {true, false}
+  INCLUDE_NON_PF_READS=Boolean	Include non-PF reads from the SAM file into the output FASTQ files. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
+  CLIPPING_ATTRIBUTE=String	The attribute that stores the position at which the SAM record should be clipped Default value: null.
+  CLIPPING_ACTION=String	The action that should be taken with clipped reads: 'X' means the reads and qualities should be trimmed at the clipped position; 'N' means the bases should be changed to Ns in the clipped region; and any integer means that the base qualities should be set to that value in the clipped region. Default value: null.
+  READ1_TRIM=Integer	The number of bases to trim from the beginning of read 1. Default value: 0. This option can be set to 'null' to clear the default value.
+  READ1_MAX_BASES_TO_WRITE=Integer	The maximum number of bases to write from read 1 after trimming. If there are fewer than this many bases left after trimming, all will be written. If this value is null then all bases left after trimming will be written. Default value: null.
+  READ2_TRIM=Integer	The number of bases to trim from the beginning of read 2. Default value: 0. This option can be set to 'null' to clear the default value.
+  READ2_MAX_BASES_TO_WRITE=Integer	The maximum number of bases to write from read 2 after trimming. If there are fewer than this many bases left after trimming, all will be written. If this value is null then all bases left after trimming will be written. Default value: null.
+  INCLUDE_NON_PRIMARY_ALIGNMENTS=Boolean	If true, include non-primary alignments in the output. Support of non-primary alignments in SamToFastq is not comprehensive, so there may be exceptions if this is set to true and there are paired reads with non-primary alignments. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false} 
+
+
+  </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/picard_SamToFastq_wrapper.py	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,93 @@
+#!/usr/bin/env python
+#Dan Blankenberg
+
+"""
+A wrapper script for running the Picard SamToFastq command. Allows parsing read groups into separate files.
+"""
+
+import sys, optparse, os, tempfile, subprocess, shutil
+
+CHUNK_SIZE = 2**20 #1mb
+
+
+def cleanup_before_exit( tmp_dir ):
+    if tmp_dir and os.path.exists( tmp_dir ):
+        shutil.rmtree( tmp_dir )
+
+def open_file_from_option( filename, mode = 'rb' ):
+    if filename:
+        return open( filename, mode = mode )
+    return None
+
+def __main__():
+    #Parse Command Line
+    parser = optparse.OptionParser()
+    parser.add_option( '-p', '--pass_through', dest='pass_through_options', action='append', type="string", help='These options are passed through directly to PICARD, without any modification.' )
+    parser.add_option( '-1', '--read_group_file_1', dest='read_group_file_1', action='store', type="string", default=None, help='Read Group 1 output file, when using multiple readgroups' )
+    parser.add_option( '-2', '--read_group_file_2', dest='read_group_file_2', action='store', type="string", default=None, help='Read Group 2 output file, when using multiple readgroups and paired end' )
+    parser.add_option( '', '--stdout', dest='stdout', action='store', type="string", default=None, help='If specified, the output of stdout will be written to this file.' )
+    parser.add_option( '', '--stderr', dest='stderr', action='store', type="string", default=None, help='If specified, the output of stderr will be written to this file.' )
+    parser.add_option( '-n', '--new_files_path', dest='new_files_path', action='store', type="string", default=None, help='new_files_path')
+    parser.add_option( '-i', '--file_id_1', dest='file_id_1', action='store', type="string", default=None, help='file_id_1')
+    parser.add_option( '-f', '--file_id_2', dest='file_id_2', action='store', type="string", default=None, help='file_id_2')
+    (options, args) = parser.parse_args()
+    
+    tmp_dir = tempfile.mkdtemp( prefix='tmp-picard-' )
+    if options.pass_through_options:
+        cmd = ' '.join( options.pass_through_options )
+    else:
+        cmd = ''
+    if options.new_files_path is not None:
+        print 'Creating FASTQ files by Read Group'
+        assert None not in [ options.read_group_file_1, options.new_files_path, options.file_id_1 ], 'When using read group aware, you need to specify --read_group_file_1, --read_group_file_2 (when paired end), --new_files_path, and --file_id'
+        cmd = '%s OUTPUT_DIR="%s"' % ( cmd,  tmp_dir)
+    #set up stdout and stderr output options
+    stdout = open_file_from_option( options.stdout, mode = 'wb' )
+    if stdout is None:
+        stdout = sys.stdout
+    stderr = open_file_from_option( options.stderr, mode = 'wb' )
+    #if no stderr file is specified, we'll use our own
+    if stderr is None:
+        stderr = tempfile.NamedTemporaryFile( prefix="picard-stderr-", dir=tmp_dir )
+    
+    proc = subprocess.Popen( args=cmd, stdout=stdout, stderr=stderr, shell=True, cwd=tmp_dir )
+    return_code = proc.wait()
+    
+    if return_code:
+        stderr_target = sys.stderr
+    else:
+        stderr_target = sys.stdout
+    stderr.flush()
+    stderr.seek(0)
+    while True:
+        chunk = stderr.read( CHUNK_SIZE )
+        if chunk:
+            stderr_target.write( chunk )
+        else:
+            break
+    stderr.close()
+    #if rg aware, put files where they belong
+    if options.new_files_path is not None:
+        fastq_1_name = options.read_group_file_1
+        fastq_2_name = options.read_group_file_2
+        file_id_1 = options.file_id_1
+        file_id_2 = options.file_id_2
+        if file_id_2 is None:
+            file_id_2 = file_id_1
+        for filename in sorted( os.listdir( tmp_dir ) ):
+            if filename.endswith( '_1.fastq' ):
+                if fastq_1_name:
+                    shutil.move( os.path.join( tmp_dir, filename ), fastq_1_name )
+                    fastq_1_name = None
+                else:
+                    shutil.move( os.path.join( tmp_dir, filename ), os.path.join( options.new_files_path, 'primary_%s_%s - 1_visible_fastqsanger' % ( file_id_1, filename[:-len( '_1.fastq' )] ) ) )
+            elif filename.endswith( '_2.fastq' ):
+                if fastq_2_name:
+                    shutil.move( os.path.join( tmp_dir, filename ), fastq_2_name )
+                    fastq_2_name = None
+                else:
+                    shutil.move( os.path.join( tmp_dir, filename ), os.path.join( options.new_files_path, 'primary_%s_%s - 2_visible_fastqsanger' % ( file_id_2, filename[:-len( '_2.fastq' )] ) ) )
+    
+    cleanup_before_exit( tmp_dir )
+
+if __name__=="__main__": __main__()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/picard_wrapper.py	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,776 @@
+#!/usr/bin/env python
+"""
+Originally written by Kelly Vincent
+pretty output and additional picard wrappers by Ross Lazarus for rgenetics
+Runs all available wrapped Picard tools.
+usage: picard_wrapper.py [options]
+code Ross wrote licensed under the LGPL
+see http://www.gnu.org/copyleft/lesser.html
+"""
+
+import optparse, os, sys, subprocess, tempfile, shutil, time, logging
+
+galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<meta name="generator" content="Galaxy %s tool output - see http://getgalaxy.org/" />
+<title></title>
+<link rel="stylesheet" href="/static/style/base.css" type="text/css" />
+</head>
+<body>
+<div class="document">
+"""
+galhtmlattr = """Galaxy tool %s run at %s</b><br/>"""
+galhtmlpostfix = """</div></body></html>\n"""
+
+
+def stop_err( msg ):
+    sys.stderr.write( '%s\n' % msg )
+    sys.exit()
+    
+
+def timenow():
+    """return current time as a string
+    """
+    return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
+
+
+class PicardBase():
+    """
+    simple base class with some utilities for Picard
+    adapted and merged with Kelly Vincent's code april 2011 Ross
+    lots of changes...
+    """
+    
+    def __init__(self, opts=None,arg0=None):
+        """ common stuff needed at init for a picard tool
+        """
+        assert opts <> None, 'PicardBase needs opts at init'
+        self.opts = opts
+        if self.opts.outdir == None:
+             self.opts.outdir = os.getcwd() # fixmate has no html file eg so use temp dir
+        assert self.opts.outdir <> None,'## PicardBase needs a temp directory if no output directory passed in'
+        self.picname = self.baseName(opts.jar)
+        if self.picname.startswith('picard'):
+            self.picname = opts.picard_cmd # special case for some tools like replaceheader?
+        self.progname = self.baseName(arg0)
+        self.version = '0.002'
+        self.delme = [] # list of files to destroy
+        self.title = opts.title
+        self.inputfile = opts.input
+        try:
+            os.makedirs(opts.outdir)
+        except:
+            pass
+        try:
+            os.makedirs(opts.tmpdir)
+        except:
+            pass
+        self.log_filename = os.path.join(self.opts.outdir,'%s.log' % self.picname)
+        self.metricsOut =  os.path.join(opts.outdir,'%s.metrics.txt' % self.picname)
+        self.setLogging(logfname=self.log_filename)
+ 
+    def baseName(self,name=None):
+        return os.path.splitext(os.path.basename(name))[0]
+
+    def setLogging(self,logfname="picard_wrapper.log"):
+        """setup a logger
+        """
+        logging.basicConfig(level=logging.INFO,
+                    filename=logfname,
+                    filemode='a')
+
+
+    def readLarge(self,fname=None):
+        """ read a potentially huge file.
+        """
+        try:
+            # get stderr, allowing for case where it's very large
+            tmp = open( fname, 'rb' )
+            s = ''
+            buffsize = 1048576
+            try:
+                while True:
+                    more = tmp.read( buffsize )
+                    if len(more) > 0:
+                        s += more
+                    else:
+                        break
+            except OverflowError:
+                pass
+            tmp.close()
+        except Exception, e:
+            stop_err( 'Read Large Exception : %s' % str( e ) )   
+        return s
+    
+    def runCL(self,cl=None,output_dir=None):
+        """ construct and run a command line
+        we have galaxy's temp path as opt.temp_dir so don't really need isolation
+        sometimes stdout is needed as the output - ugly hacks to deal with potentially vast artifacts
+        """
+        assert cl <> None, 'PicardBase runCL needs a command line as cl'
+        if output_dir == None:
+            output_dir = self.opts.outdir
+        if type(cl) == type([]):
+            cl = ' '.join(cl)
+        fd,templog = tempfile.mkstemp(dir=output_dir,suffix='rgtempRun.txt')
+        tlf = open(templog,'wb')
+        fd,temperr = tempfile.mkstemp(dir=output_dir,suffix='rgtempErr.txt')
+        tef = open(temperr,'wb')
+        process = subprocess.Popen(cl, shell=True, stderr=tef, stdout=tlf, cwd=output_dir)
+        rval = process.wait()
+        tlf.close()
+        tef.close()
+        stderrs = self.readLarge(temperr)
+        stdouts = self.readLarge(templog)        
+        if rval > 0:
+            s = '## executing %s returned status %d and stderr: \n%s\n' % (cl,rval,stderrs)
+            stdouts = '%s\n%s' % (stdouts,stderrs)
+        else:
+            s = '## executing %s returned status %d and nothing on stderr\n' % (cl,rval)
+        logging.info(s)
+        os.unlink(templog) # always
+        os.unlink(temperr) # always
+        return s, stdouts, rval  # sometimes s is an output
+    
+    def runPic(self, jar, cl):
+        """
+        cl should be everything after the jar file name in the command
+        """
+        runme = ['java -Xmx%s' % self.opts.maxjheap]
+        runme.append(" -Djava.io.tmpdir='%s' " % self.opts.tmpdir)
+        runme.append('-jar %s' % jar)
+        runme += cl
+        s,stdouts,rval = self.runCL(cl=runme, output_dir=self.opts.outdir)
+        return stdouts,rval
+
+    def samToBam(self,infile=None,outdir=None):
+        """
+        use samtools view to convert sam to bam
+        """
+        fd,tempbam = tempfile.mkstemp(dir=outdir,suffix='rgutilsTemp.bam')
+        cl = ['samtools view -h -b -S -o ',tempbam,infile]
+        tlog,stdouts,rval = self.runCL(cl,outdir)
+        return tlog,tempbam,rval
+
+    def sortSam(self, infile=None,outfile=None,outdir=None):
+        """
+        """
+        print '## sortSam got infile=%s,outfile=%s,outdir=%s' % (infile,outfile,outdir)
+        cl = ['samtools sort',infile,outfile]
+        tlog,stdouts,rval = self.runCL(cl,outdir)
+        return tlog
+
+    def cleanup(self):
+        for fname in self.delme:
+            try:
+                os.unlink(fname)
+            except:
+                pass
+                    
+    def prettyPicout(self,transpose,maxrows):
+        """organize picard outpouts into a report html page
+        """
+        res = []
+        try:
+            r = open(self.metricsOut,'r').readlines()
+        except:
+            r = []        
+        if len(r) > 0:
+            res.append('<b>Picard on line resources</b><ul>\n')
+            res.append('<li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li>\n')
+            res.append('<li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/>\n')
+            if transpose:
+                res.append('<b>Picard output (transposed to make it easier to see)</b><hr/>\n')       
+            else:
+                res.append('<b>Picard output</b><hr/>\n')  
+            res.append('<table cellpadding="3" >\n')
+            dat = []
+            heads = []
+            lastr = len(r) - 1
+            # special case for estimate library complexity hist
+            thist = False
+            for i,row in enumerate(r):
+                if row.strip() > '':
+                    srow = row.split('\t')
+                    if row.startswith('#'):
+                        heads.append(row.strip()) # want strings
+                    else:
+                        dat.append(srow) # want lists
+                    if row.startswith('## HISTOGRAM'):
+                        thist = True
+            if len(heads) > 0:
+                hres = ['<tr class="d%d"><td colspan="2">%s</td></tr>' % (i % 2,x) for i,x in enumerate(heads)]
+                res += hres
+                heads = []
+            if len(dat) > 0:
+                if transpose and not thist:
+                    tdat = map(None,*dat) # transpose an arbitrary list of lists
+                    tdat = ['<tr class="d%d"><td>%s</td><td>%s&nbsp;</td></tr>\n' % ((i+len(heads)) % 2,x[0],x[1]) for i,x in enumerate(tdat)] 
+                else:
+                    tdat = ['\t'.join(x).strip() for x in dat] # back to strings :(
+                    tdat = ['<tr class="d%d"><td colspan="2">%s</td></tr>\n' % ((i+len(heads)) % 2,x) for i,x in enumerate(tdat)]
+                res += tdat
+                dat = []
+            res.append('</table>\n')   
+        return res
+
+    def fixPicardOutputs(self,transpose,maxloglines):
+        """
+        picard produces long hard to read tab header files
+        make them available but present them transposed for readability
+        """
+        logging.shutdown()
+        self.cleanup() # remove temp files stored in delme
+        rstyle="""<style type="text/css">
+        tr.d0 td {background-color: oldlace; color: black;}
+        tr.d1 td {background-color: aliceblue; color: black;}
+        </style>"""    
+        res = [rstyle,]
+        res.append(galhtmlprefix % self.progname)   
+        res.append(galhtmlattr % (self.picname,timenow()))
+        flist = [x for x in os.listdir(self.opts.outdir) if not x.startswith('.')] 
+        pdflist = [x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf']
+        if len(pdflist) > 0: # assumes all pdfs come with thumbnail .jpgs
+            for p in pdflist:
+                pbase = os.path.splitext(p)[0] # removes .pdf
+                imghref = '%s.jpg' % pbase
+                mimghref = '%s-0.jpg' % pbase # multiple pages pdf -> multiple thumbnails without asking!
+                if mimghref in flist:
+                    imghref=mimghref # only one for thumbnail...it's a multi page pdf
+                res.append('<table cellpadding="10"><tr><td>\n')
+                res.append('<a href="%s"><img src="%s" title="Click image preview for a print quality PDF version" hspace="10" align="middle"></a>\n' % (p,imghref)) 
+                res.append('</tr></td></table>\n')   
+        if len(flist) > 0:
+            res.append('<b>The following output files were created (click the filename to view/download a copy):</b><hr/>')
+            res.append('<table>\n')
+            for i,f in enumerate(flist):
+                fn = os.path.split(f)[-1]
+                res.append('<tr><td><a href="%s">%s</a></td></tr>\n' % (fn,fn))
+            res.append('</table><p/>\n') 
+        pres = self.prettyPicout(transpose,maxloglines)
+        if len(pres) > 0:
+            res += pres
+        l = open(self.log_filename,'r').readlines()
+        llen = len(l)
+        if llen > 0: 
+            res.append('<b>Picard Tool Run Log</b><hr/>\n') 
+            rlog = ['<pre>',]
+            if llen > maxloglines:
+                n = min(50,int(maxloglines/2))
+                rlog += l[:n]
+                rlog.append('------------ ## %d rows deleted ## --------------\n' % (llen-maxloglines))
+                rlog += l[-n:]
+            else:
+                rlog += l
+            rlog.append('</pre>')
+            if llen > maxloglines:
+                rlog.append('\n<b>## WARNING - %d log lines truncated - <a href="%s">%s</a> contains entire output</b>' % (llen - maxloglines,self.log_filename,self.log_filename))
+            res += rlog
+        else:
+            res.append("### Odd, Picard left no log file %s - must have really barfed badly?\n" % self.log_filename)
+        res.append('<hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> \n') 
+        res.append( 'generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool')   
+        res.append(galhtmlpostfix) 
+        outf = open(self.opts.htmlout,'w')
+        outf.write(''.join(res))   
+        outf.write('\n')
+        outf.close()
+
+    def makePicInterval(self,inbed=None,outf=None):
+        """
+        picard wants bait and target files to have the same header length as the incoming bam/sam 
+        a meaningful (ie accurate) representation will fail because of this - so this hack
+        it would be far better to be able to supply the original bed untouched
+        Additional checking added Ross Lazarus Dec 2011 to deal with two 'bug' reports on the list
+        """
+        assert inbed <> None
+        bed = open(inbed,'r').readlines()
+        sbed = [x.split('\t') for x in bed] # lengths MUST be 5
+        lens = [len(x) for x in sbed]
+        strands = [x[3] for x in sbed if not x[3] in ['+','-']]
+        maxl = max(lens)
+        minl = min(lens)
+        e = []
+        if maxl <> minl:
+            e.append("## Input error: Inconsistent field count in %s - please read the documentation on bait/target format requirements, fix and try again" % inbed)
+        if maxl <> 5:
+            e.append("## Input error: %d fields found in %s, 5 required - please read the warning and documentation on bait/target format requirements, fix and try again" % (maxl,inbed))
+        if len(strands) > 0:
+            e.append("## Input error: Fourth column in %s is not the required strand (+ or -) - please read the warning and documentation on bait/target format requirements, fix and try again" % (inbed))
+        if len(e) > 0: # write to stderr and quit
+            print >> sys.stderr, '\n'.join(e)
+            sys.exit(1)
+        thead = os.path.join(self.opts.outdir,'tempSamHead.txt')
+        if self.opts.datatype == 'sam':
+            cl = ['samtools view -H -S',self.opts.input,'>',thead]
+        else:
+            cl = ['samtools view -H',self.opts.input,'>',thead]
+        self.runCL(cl=cl,output_dir=self.opts.outdir)
+        head = open(thead,'r').readlines()
+        s = '## got %d rows of header\n' % (len(head))
+        logging.info(s)
+        o = open(outf,'w')
+        o.write(''.join(head))
+        o.write(''.join(bed))
+        o.close()
+        return outf
+
+    def cleanSam(self, insam=None, newsam=None, picardErrors=[],outformat=None):
+        """
+        interesting problem - if paired, must remove mate pair of errors too or we have a new set of errors after cleaning - missing mate pairs!
+        Do the work of removing all the error sequences
+        pysam is cool
+        infile = pysam.Samfile( "-", "r" )
+        outfile = pysam.Samfile( "-", "w", template = infile )
+        for s in infile: outfile.write(s)
+
+        errors from ValidateSameFile.jar look like
+        WARNING: Record 32, Read name SRR006041.1202260, NM tag (nucleotide differences) is missing
+        ERROR: Record 33, Read name SRR006041.1042721, Empty sequence dictionary.
+        ERROR: Record 33, Read name SRR006041.1042721, RG ID on SAMRecord not found in header: SRR006041
+
+        """
+        assert os.path.isfile(insam), 'rgPicardValidate cleansam needs an input sam file - cannot find %s' % insam
+        assert newsam <> None, 'rgPicardValidate cleansam needs an output new sam file path'
+        removeNames = [x.split(',')[1].replace(' Read name ','') for x in picardErrors if len(x.split(',')) > 2]
+        remDict = dict(zip(removeNames,range(len(removeNames))))
+        infile = pysam.Samfile(insam,'rb')
+        info = 'found %d error sequences in picardErrors, %d unique' % (len(removeNames),len(remDict))
+        if len(removeNames) > 0:
+            outfile = pysam.Samfile(newsam,'wb',template=infile) # template must be an open file
+            i = 0
+            j = 0
+            for row in infile:
+                dropme = remDict.get(row.qname,None) # keep if None
+                if not dropme:
+                    outfile.write(row)
+                    j += 1
+                else: # discard
+                    i += 1
+            info = '%s\n%s' % (info, 'Discarded %d lines writing %d to %s from %s' % (i,j,newsam,insam))
+            outfile.close()
+            infile.close()
+        else: # we really want a nullop or a simple pointer copy
+            infile.close()
+            if newsam:
+                shutil.copy(insam,newsam)
+        logging.info(info)
+                
+
+
+def __main__():
+    doFix = False # tools returning htmlfile don't need this
+    doTranspose = True # default
+    maxloglines = 100 # default 
+    #Parse Command Line
+    op = optparse.OptionParser()
+    # All tools
+    op.add_option('-i', '--input', dest='input', help='Input SAM or BAM file' )
+    op.add_option('-e', '--inputext', default=None)
+    op.add_option('-o', '--output', default=None)
+    op.add_option('-n', '--title', default="Pick a Picard Tool")
+    op.add_option('-t', '--htmlout', default=None)
+    op.add_option('-d', '--outdir', default=None)
+    op.add_option('-x', '--maxjheap', default='4g')
+    op.add_option('-b', '--bisulphite', default='false')
+    op.add_option('-s', '--sortorder', default='query')     
+    op.add_option('','--tmpdir', default='/tmp')
+    op.add_option('-j','--jar',default='')    
+    op.add_option('','--picard-cmd',default=None)    
+    # Many tools
+    op.add_option( '', '--output-format', dest='output_format', help='Output format' )
+    op.add_option( '', '--bai-file', dest='bai_file', help='The path to the index file for the input bam file' )
+    op.add_option( '', '--ref', dest='ref', help='Built-in reference with fasta and dict file', default=None )
+    # CreateSequenceDictionary
+    op.add_option( '', '--ref-file', dest='ref_file', help='Fasta to use as reference', default=None )
+    op.add_option( '', '--species-name', dest='species_name', help='Species name to use in creating dict file from fasta file' )
+    op.add_option( '', '--build-name', dest='build_name', help='Name of genome assembly to use in creating dict file from fasta file' )
+    op.add_option( '', '--trunc-names', dest='trunc_names', help='Truncate sequence names at first whitespace from fasta file' )
+    # MarkDuplicates
+    op.add_option( '', '--remdups', default='true', help='Remove duplicates from output file' )
+    op.add_option( '', '--optdupdist', default="100", help='Maximum pixels between two identical sequences in order to consider them optical duplicates.' )
+    # CollectInsertSizeMetrics
+    op.add_option('', '--taillimit', default="0")
+    op.add_option('', '--histwidth', default="0")
+    op.add_option('', '--minpct', default="0.01")
+    op.add_option('', '--malevel', default='')
+    op.add_option('', '--deviations', default="0.0")
+    # CollectAlignmentSummaryMetrics
+    op.add_option('', '--maxinsert', default="20")
+    op.add_option('', '--adaptors', default='')
+    # FixMateInformation and validate
+    # CollectGcBiasMetrics
+    op.add_option('', '--windowsize', default='100')
+    op.add_option('', '--mingenomefrac', default='0.00001')    
+    # AddOrReplaceReadGroups
+    op.add_option( '', '--rg-opts', dest='rg_opts', help='Specify extra (optional) arguments with full, otherwise preSet' )
+    op.add_option( '', '--rg-lb', dest='rg_library', help='Read Group Library' )
+    op.add_option( '', '--rg-pl', dest='rg_platform', help='Read Group platform (e.g. illumina, solid)' )
+    op.add_option( '', '--rg-pu', dest='rg_plat_unit', help='Read Group platform unit (eg. run barcode) ' )
+    op.add_option( '', '--rg-sm', dest='rg_sample', help='Read Group sample name' )
+    op.add_option( '', '--rg-id', dest='rg_id', help='Read Group ID' )
+    op.add_option( '', '--rg-cn', dest='rg_seq_center', help='Read Group sequencing center name' )
+    op.add_option( '', '--rg-ds', dest='rg_desc', help='Read Group description' )
+    # ReorderSam
+    op.add_option( '', '--allow-inc-dict-concord', dest='allow_inc_dict_concord', help='Allow incomplete dict concordance' )
+    op.add_option( '', '--allow-contig-len-discord', dest='allow_contig_len_discord', help='Allow contig length discordance' )
+    # ReplaceSamHeader
+    op.add_option( '', '--header-file', dest='header_file', help='sam or bam file from which header will be read' )
+
+    op.add_option('','--assumesorted', default='true') 
+    op.add_option('','--readregex', default="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*")
+    #estimatelibrarycomplexity
+    op.add_option('','--minid', default="5")
+    op.add_option('','--maxdiff', default="0.03")
+    op.add_option('','--minmeanq', default="20")
+    #hsmetrics
+    op.add_option('','--baitbed', default=None)
+    op.add_option('','--targetbed', default=None)
+    #validate
+    op.add_option('','--ignoreflags', action='append', type="string")
+    op.add_option('','--maxerrors', default=None)
+    op.add_option('','--datatype', default=None)
+    op.add_option('','--bamout', default=None)
+    op.add_option('','--samout', default=None)
+
+    opts, args = op.parse_args()
+    opts.sortme = opts.assumesorted == 'false'
+    assert opts.input <> None
+    # need to add
+    # instance that does all the work
+    pic = PicardBase(opts,sys.argv[0])
+
+    tmp_dir = opts.outdir
+    haveTempout = False # we use this where sam output is an option
+    rval = 0
+    stdouts = 'Not run yet'
+    # set ref and dict files to use (create if necessary)
+    ref_file_name = opts.ref
+    if opts.ref_file <> None:
+        csd = 'CreateSequenceDictionary'
+        realjarpath = os.path.split(opts.jar)[0]
+        jarpath = os.path.join(realjarpath,'%s.jar' % csd) # for refseq
+        tmp_ref_fd, tmp_ref_name = tempfile.mkstemp( dir=opts.tmpdir , prefix = pic.picname)
+        ref_file_name = '%s.fasta' % tmp_ref_name
+        # build dict
+        dict_file_name = '%s.dict' % tmp_ref_name
+        os.symlink( opts.ref_file, ref_file_name )
+        cl = ['REFERENCE=%s' % ref_file_name]
+        cl.append('OUTPUT=%s' % dict_file_name)
+        cl.append('URI=%s' % os.path.basename( opts.ref_file ))
+        cl.append('TRUNCATE_NAMES_AT_WHITESPACE=%s' % opts.trunc_names)
+        if opts.species_name:
+            cl.append('SPECIES=%s' % opts.species_name)
+        if opts.build_name:
+            cl.append('GENOME_ASSEMBLY=%s' % opts.build_name)
+        pic.delme.append(dict_file_name)
+        pic.delme.append(ref_file_name)
+        pic.delme.append(tmp_ref_name)
+        stdouts,rval = pic.runPic(jarpath, cl)
+        # run relevant command(s)
+
+    # define temporary output
+    # if output is sam, it must have that extension, otherwise bam will be produced
+    # specify sam or bam file with extension
+    if opts.output_format == 'sam':
+        suff = '.sam'
+    else:
+        suff = ''
+    tmp_fd, tempout = tempfile.mkstemp( dir=opts.tmpdir, suffix=suff )
+
+    cl = ['VALIDATION_STRINGENCY=LENIENT',]
+
+    if pic.picname == 'AddOrReplaceReadGroups':
+        # sort order to match Galaxy's default
+        cl.append('SORT_ORDER=coordinate')
+        # input
+        cl.append('INPUT=%s' % opts.input)
+        # outputs
+        cl.append('OUTPUT=%s' % tempout)
+        # required read groups
+        cl.append('RGLB="%s"' % opts.rg_library)
+        cl.append('RGPL="%s"' % opts.rg_platform)
+        cl.append('RGPU="%s"' % opts.rg_plat_unit)
+        cl.append('RGSM="%s"' % opts.rg_sample)
+        if opts.rg_id:
+            cl.append('RGID="%s"' % opts.rg_id)
+        # optional read groups
+        if opts.rg_seq_center:
+            cl.append('RGCN="%s"' % opts.rg_seq_center)
+        if opts.rg_desc:
+            cl.append('RGDS="%s"' % opts.rg_desc)
+        stdouts,rval = pic.runPic(opts.jar, cl)
+        haveTempout = True
+
+    elif pic.picname == 'BamIndexStats':
+        tmp_fd, tmp_name = tempfile.mkstemp( dir=tmp_dir )
+        tmp_bam_name = '%s.bam' % tmp_name
+        tmp_bai_name = '%s.bai' % tmp_bam_name
+        os.symlink( opts.input, tmp_bam_name )
+        os.symlink( opts.bai_file, tmp_bai_name )
+        cl.append('INPUT=%s' % ( tmp_bam_name ))
+        pic.delme.append(tmp_bam_name)
+        pic.delme.append(tmp_bai_name)
+        pic.delme.append(tmp_name)
+        stdouts,rval = pic.runPic( opts.jar, cl )
+        f = open(pic.metricsOut,'a')
+        f.write(stdouts) # got this on stdout from runCl
+        f.write('\n')
+        f.close()
+        doTranspose = False # but not transposed
+
+    elif pic.picname == 'EstimateLibraryComplexity':
+        cl.append('I=%s' % opts.input)
+        cl.append('O=%s' % pic.metricsOut)
+        if float(opts.minid) > 0:
+            cl.append('MIN_IDENTICAL_BASES=%s' % opts.minid)
+        if float(opts.maxdiff) > 0.0:
+            cl.append('MAX_DIFF_RATE=%s' % opts.maxdiff)
+        if float(opts.minmeanq) > 0:
+            cl.append('MIN_MEAN_QUALITY=%s' % opts.minmeanq)
+        if opts.readregex > '':
+            cl.append('READ_NAME_REGEX="%s"' % opts.readregex)
+        if float(opts.optdupdist) > 0:
+            cl.append('OPTICAL_DUPLICATE_PIXEL_DISTANCE=%s' % opts.optdupdist)
+        stdouts,rval = pic.runPic(opts.jar, cl)
+
+    elif pic.picname == 'CollectAlignmentSummaryMetrics':
+        # Why do we do this fakefasta thing? 
+        # Because we need NO fai to be available or picard barfs unless it matches the input data.
+        # why? Dunno Seems to work without complaining if the .bai file is AWOL....
+        fakefasta = os.path.join(opts.outdir,'%s_fake.fasta' % os.path.basename(ref_file_name))
+        try:
+            os.symlink(ref_file_name,fakefasta)
+        except:
+            s = '## unable to symlink %s to %s - different devices? Will shutil.copy'
+            info = s
+            shutil.copy(ref_file_name,fakefasta)
+        pic.delme.append(fakefasta)
+        cl.append('ASSUME_SORTED=true')
+        adaptlist = opts.adaptors.split(',')
+        adaptorseqs = ['ADAPTER_SEQUENCE=%s' % x for x in adaptlist]
+        cl += adaptorseqs
+        cl.append('IS_BISULFITE_SEQUENCED=%s' % opts.bisulphite)
+        cl.append('MAX_INSERT_SIZE=%s' % opts.maxinsert)
+        cl.append('OUTPUT=%s' % pic.metricsOut)
+        cl.append('R=%s' % fakefasta)
+        cl.append('TMP_DIR=%s' % opts.tmpdir)
+        if not opts.assumesorted.lower() == 'true': # we need to sort input
+            sortedfile = '%s.sorted' % os.path.basename(opts.input)
+            if opts.datatype == 'sam': # need to work with a bam 
+                tlog,tempbam,trval = pic.samToBam(opts.input,opts.outdir)
+                pic.delme.append(tempbam)
+                try:
+                    tlog = pic.sortSam(tempbam,sortedfile,opts.outdir)
+                except:
+                    print '## exception on sorting sam file %s' % opts.input
+            else: # is already bam
+                try:
+                    tlog = pic.sortSam(opts.input,sortedfile,opts.outdir)
+                except : # bug - [bam_sort_core] not being ignored - TODO fixme
+                    print '## exception %s on sorting bam file %s' % (sys.exc_info()[0],opts.input)
+            cl.append('INPUT=%s.bam' % os.path.abspath(os.path.join(opts.outdir,sortedfile)))
+            pic.delme.append(os.path.join(opts.outdir,sortedfile))
+        else:
+            cl.append('INPUT=%s' % os.path.abspath(opts.input)) 
+        stdouts,rval = pic.runPic(opts.jar, cl)
+       
+        
+    elif pic.picname == 'CollectGcBiasMetrics':
+        assert os.path.isfile(ref_file_name),'PicardGC needs a reference sequence - cannot read %s' % ref_file_name
+        # sigh. Why do we do this fakefasta thing? Because we need NO fai to be available or picard barfs unless it has the same length as the input data.
+        # why? Dunno 
+        fakefasta = os.path.join(opts.outdir,'%s_fake.fasta' % os.path.basename(ref_file_name))
+        try:
+            os.symlink(ref_file_name,fakefasta)
+        except:
+            s = '## unable to symlink %s to %s - different devices? May need to replace with shutil.copy'
+            info = s
+            shutil.copy(ref_file_name,fakefasta)
+        pic.delme.append(fakefasta)
+        x = 'rgPicardGCBiasMetrics'
+        pdfname = '%s.pdf' % x
+        jpgname = '%s.jpg' % x
+        tempout = os.path.join(opts.outdir,'rgPicardGCBiasMetrics.out')
+        temppdf = os.path.join(opts.outdir,pdfname)
+        cl.append('R=%s' % fakefasta)
+        cl.append('WINDOW_SIZE=%s' % opts.windowsize)
+        cl.append('MINIMUM_GENOME_FRACTION=%s' % opts.mingenomefrac)
+        cl.append('INPUT=%s' % opts.input)
+        cl.append('OUTPUT=%s' % tempout)
+        cl.append('TMP_DIR=%s' % opts.tmpdir)
+        cl.append('CHART_OUTPUT=%s' % temppdf)
+        cl.append('SUMMARY_OUTPUT=%s' % pic.metricsOut)
+        stdouts,rval = pic.runPic(opts.jar, cl)
+        if os.path.isfile(temppdf):
+            cl2 = ['convert','-resize x400',temppdf,os.path.join(opts.outdir,jpgname)] # make the jpg for fixPicardOutputs to find
+            s,stdouts,rval = pic.runCL(cl=cl2,output_dir=opts.outdir)
+        else:
+            s='### runGC: Unable to find pdf %s - please check the log for the causal problem\n' % temppdf
+        lf = open(pic.log_filename,'a')
+        lf.write(s)
+        lf.write('\n')
+        lf.close()
+        
+    elif pic.picname == 'CollectInsertSizeMetrics':
+        """ <command interpreter="python">
+   picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --deviations "$deviations"
+   --histwidth "$histWidth" --minpct "$minPct" --malevel "$malevel"
+   -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/CollectInsertSizeMetrics.jar" -d "$html_file.files_path" -t "$html_file"
+  </command>
+        """
+        isPDF = 'InsertSizeHist.pdf'
+        pdfpath = os.path.join(opts.outdir,isPDF)
+        histpdf = 'InsertSizeHist.pdf'
+        cl.append('I=%s' % opts.input)
+        cl.append('O=%s' % pic.metricsOut)
+        cl.append('HISTOGRAM_FILE=%s' % histpdf)
+        #if opts.taillimit <> '0': # this was deprecated although still mentioned in the docs at 1.56
+        #    cl.append('TAIL_LIMIT=%s' % opts.taillimit)
+        if  opts.histwidth <> '0':
+            cl.append('HISTOGRAM_WIDTH=%s' % opts.histwidth)
+        if float( opts.minpct) > 0.0:
+            cl.append('MINIMUM_PCT=%s' % opts.minpct)
+        if float(opts.deviations) > 0.0:
+            cl.append('DEVIATIONS=%s' % opts.deviations)
+        if opts.malevel:
+            malists = opts.malevel.split(',')
+            malist = ['METRIC_ACCUMULATION_LEVEL=%s' % x for x in malists]
+            cl += malist
+        stdouts,rval = pic.runPic(opts.jar, cl)
+        if os.path.exists(pdfpath): # automake thumbnail - will be added to html 
+            cl2 = ['mogrify', '-format jpg -resize x400 %s' % pdfpath]
+            pic.runCL(cl=cl2,output_dir=opts.outdir)
+        else:
+            s = 'Unable to find expected pdf file %s<br/>\n' % pdfpath
+            s += 'This <b>always happens if single ended data was provided</b> to this tool,\n'
+            s += 'so please double check that your input data really is paired-end NGS data.<br/>\n'
+            s += 'If your input was paired data this may be a bug worth reporting to the galaxy-bugs list\n<br/>'
+            logging.info(s)
+        if len(stdouts) > 0:
+           logging.info(stdouts)
+        
+    elif pic.picname == 'MarkDuplicates':
+        # assume sorted even if header says otherwise
+        cl.append('ASSUME_SORTED=%s' % (opts.assumesorted))
+        # input
+        cl.append('INPUT=%s' % opts.input)
+        # outputs
+        cl.append('OUTPUT=%s' % opts.output) 
+        cl.append('METRICS_FILE=%s' % pic.metricsOut )
+        # remove or mark duplicates
+        cl.append('REMOVE_DUPLICATES=%s' % opts.remdups)
+        # the regular expression to be used to parse reads in incoming SAM file
+        cl.append('READ_NAME_REGEX="%s"' % opts.readregex)
+        # maximum offset between two duplicate clusters
+        cl.append('OPTICAL_DUPLICATE_PIXEL_DISTANCE=%s' % opts.optdupdist)
+        stdouts,rval = pic.runPic(opts.jar, cl)
+
+    elif pic.picname == 'FixMateInformation':
+        cl.append('I=%s' % opts.input)
+        cl.append('O=%s' % tempout)
+        cl.append('SORT_ORDER=%s' % opts.sortorder)
+        stdouts,rval = pic.runPic(opts.jar,cl)
+        haveTempout = True
+        
+    elif pic.picname == 'ReorderSam':
+        # input
+        cl.append('INPUT=%s' % opts.input)
+        # output
+        cl.append('OUTPUT=%s' % tempout)
+        # reference
+        cl.append('REFERENCE=%s' % ref_file_name)
+        # incomplete dict concordance
+        if opts.allow_inc_dict_concord == 'true':
+            cl.append('ALLOW_INCOMPLETE_DICT_CONCORDANCE=true')
+        # contig length discordance
+        if opts.allow_contig_len_discord == 'true':
+            cl.append('ALLOW_CONTIG_LENGTH_DISCORDANCE=true')
+        stdouts,rval = pic.runPic(opts.jar, cl)
+        haveTempout = True
+
+    elif pic.picname == 'ReplaceSamHeader':
+        cl.append('INPUT=%s' % opts.input)
+        cl.append('OUTPUT=%s' % tempout)
+        cl.append('HEADER=%s' % opts.header_file)
+        stdouts,rval = pic.runPic(opts.jar, cl)
+        haveTempout = True
+
+    elif pic.picname == 'CalculateHsMetrics':
+        maxloglines = 100
+        baitfname = os.path.join(opts.outdir,'rgPicardHsMetrics.bait')
+        targetfname = os.path.join(opts.outdir,'rgPicardHsMetrics.target')
+        baitf = pic.makePicInterval(opts.baitbed,baitfname)
+        if opts.targetbed == opts.baitbed: # same file sometimes
+            targetf = baitf
+        else:
+            targetf = pic.makePicInterval(opts.targetbed,targetfname)   
+        cl.append('BAIT_INTERVALS=%s' % baitf)
+        cl.append('TARGET_INTERVALS=%s' % targetf)
+        cl.append('INPUT=%s' % os.path.abspath(opts.input))
+        cl.append('OUTPUT=%s' % pic.metricsOut)
+        cl.append('TMP_DIR=%s' % opts.tmpdir)
+        stdouts,rval = pic.runPic(opts.jar,cl)
+           
+    elif pic.picname == 'ValidateSamFile':
+        import pysam
+        doTranspose = False
+        sortedfile = os.path.join(opts.outdir,'rgValidate.sorted')
+        stf = open(pic.log_filename,'w')
+        tlog = None
+        if opts.datatype == 'sam': # need to work with a bam 
+            tlog,tempbam,rval = pic.samToBam(opts.input,opts.outdir)
+            try:
+                tlog = pic.sortSam(tempbam,sortedfile,opts.outdir)
+            except:
+                print '## exception on sorting sam file %s' % opts.input
+        else: # is already bam
+            try:
+                tlog = pic.sortSam(opts.input,sortedfile,opts.outdir)
+            except: # bug - [bam_sort_core] not being ignored - TODO fixme
+                print '## exception on sorting bam file %s' % opts.input
+        if tlog:
+            print '##tlog=',tlog
+            stf.write(tlog)
+            stf.write('\n')
+        sortedfile = '%s.bam' % sortedfile # samtools does that      
+        cl.append('O=%s' % pic.metricsOut)
+        cl.append('TMP_DIR=%s' % opts.tmpdir)
+        cl.append('I=%s' % sortedfile)
+        opts.maxerrors = '99999999'
+        cl.append('MAX_OUTPUT=%s' % opts.maxerrors)
+        if opts.ignoreflags[0] <> 'None': # picard error values to ignore
+            igs = ['IGNORE=%s' % x for x in opts.ignoreflags if x <> 'None']
+            cl.append(' '.join(igs))
+        if opts.bisulphite.lower() <> 'false':
+            cl.append('IS_BISULFITE_SEQUENCED=true')
+        if opts.ref <> None or opts.ref_file <> None:
+            cl.append('R=%s' %  ref_file_name)
+        stdouts,rval = pic.runPic(opts.jar,cl)
+        if opts.datatype == 'sam':
+            pic.delme.append(tempbam)
+        newsam = opts.output
+        outformat = 'bam'
+        pe = open(pic.metricsOut,'r').readlines()
+        pic.cleanSam(insam=sortedfile, newsam=newsam, picardErrors=pe,outformat=outformat)
+        pic.delme.append(sortedfile) # not wanted
+        stf.close()
+        pic.cleanup()
+    else:
+        print >> sys.stderr,'picard.py got an unknown tool name - %s' % pic.picname
+        sys.exit(1)
+    if haveTempout:
+        # Some Picard tools produced a potentially intermediate bam file. 
+        # Either just move to final location or create sam
+        if os.path.exists(tempout):
+            shutil.move(tempout, os.path.abspath(opts.output))
+    if opts.htmlout <> None or doFix: # return a pretty html page
+        pic.fixPicardOutputs(transpose=doTranspose,maxloglines=maxloglines)
+    if rval <> 0:
+        print >> sys.stderr, '## exit code=%d; stdout=%s' % (rval,stdouts)
+        # signal failure
+if __name__=="__main__": __main__()
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rgPicardASMetrics.xml	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,162 @@
+<tool name="SAM/BAM Alignment Summary Metrics" id="PicardASMetrics" version="1.56.0">
+  <command interpreter="python">
+    picard_wrapper.py -i "${input_file}" -d "${html_file.files_path}" -t "${html_file}"
+    --assumesorted "${sorted}" -b "${bisulphite}" --adaptors "${adaptors}" --maxinsert "${maxinsert}" -n "${out_prefix}" --datatype "${input_file.ext}"
+    -j \$JAVA_JAR_PATH/CollectAlignmentSummaryMetrics.jar  --tmpdir "${__new_file_path__}" 
+#if $genomeSource.refGenomeSource == "history":
+    --ref-file "${genomeSource.ownFile}"
+#else
+    --ref "${genomeSource.index.fields.path}"
+#end if
+  </command>
+  <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
+  <inputs>
+    <param format="sam,bam" name="input_file" type="data" label="SAM/BAM dataset to generate statistics for"
+      help="If empty, upload or import a SAM/BAM dataset."/>
+    <param name="out_prefix" value="Picard Alignment Summary Metrics" type="text"
+      label="Title for the output file" help="Use this remind you what the job was for." size="80" />
+
+      <conditional name="genomeSource">
+    
+      <param name="refGenomeSource" type="select" label="Select Reference Genome">
+        <option value="default" selected="true">Use the assigned data genome/build</option>
+        <option value="indexed">Select a different built-in genome</option>
+        <option value="history">Use a genome (fasta format) from my history</option>
+      </param>
+      <when value="default">
+        <param name="index" type="select" label="Check the assigned reference genome" help="Galaxy thinks that the reads in you dataset were aligned against this reference. If this is not correct, use the 'Select a build-in reference genome' option of the 'Select Reference Genome' dropdown to select approprtiate Reference.">
+          <options from_data_table="all_fasta">
+          <filter type="data_meta" ref="input_file" key="dbkey" column="dbkey" multiple="True" separator="," />
+          <validator type="no_options" message="No reference build available for selected input" /> 
+          </options>
+        </param>
+      </when>
+      <when value="indexed">
+        <param name="index" type="select" label="Select a built-in reference genome" help="This list contains genomes cached at this Galaxy instance. If your genome of interest is not present here request it by using 'Help' link at the top of Galaxy interface or use the 'Use a genome (fasta format) from my history' option of the 'Select Reference Genome' dropdown.">
+          <options from_data_table="all_fasta">
+          </options>
+        </param>
+      </when>
+      <when value="history">
+        <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference genome from history" help="This option works best for relatively small genomes. If you are working with large human-sized genomes, send request to Galaxy team for adding your reference to this Galaxy instance by using 'Help' link at the top of Galaxy interface."/>
+      </when>
+    </conditional>
+    <param name="sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false"/>
+    <param name="bisulphite" type="boolean" label="Input file contains Bisulphite sequenced reads" checked="false" falsevalue="false" truevalue="true" />
+    <param name="adaptors" value="" type="text" area="true" label="Adapter sequences" help="One per line if multiple" size="5x120" />
+    <param name="maxinsert" value="100000" type="integer" label="Larger paired end reads and inter-chromosomal pairs considered chimeric " size="20" />
+  </inputs>
+  <outputs>
+    <data format="html" name="html_file"  label="${out_prefix}.html" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="out_prefix" value="AsMetrics" />
+      <param name="bisulphite" value="false" />
+      <param name="sorted" value="true" />
+      <param name="adaptors" value="" />
+      <param name="maxinsert" value="100000" />
+      <param name="refGenomeSource" value="history" />
+      <param name="ownFile" value="picard_input_hg18.trimmed.fasta" />
+      <param name="input_file" value="picard_input_tiny.sam" dbkey="hg18" />
+      <output name="html_file" file="picard_output_alignment_summary_metrics.html" ftype="html" lines_diff="55"/>
+    </test>
+    <test>
+      <param name="out_prefix" value="AsMetricsIndexed" />
+      <param name="bisulphite" value="false" />
+      <param name="sorted" value="true" />
+      <param name="adaptors" value="" />
+      <param name="maxinsert" value="100000" />
+      <param name="refGenomeSource" value="indexed" />
+      <param name="index" value="hg19" />
+      <param name="input_file" value="picard_input_sorted_pair.sam" dbkey="hg19" />
+      <output name="html_file" file="picard_output_AsMetrics_indexed_hg18_sorted_pair.html" ftype="html" lines_diff="50"/>
+    </test>
+  </tests>
+  <help>
+
+.. class:: infomark
+
+**Summary**
+
+This Galaxy tool uses Picard to report high-level measures of alignment based on a provided sam or bam file.
+
+**Picard documentation**
+
+This is a Galaxy wrapper for CollectAlignmentSummaryMetrics, a part of the external package Picard-tools_.
+
+ .. _Picard-tools: http://www.google.com/search?q=picard+samtools
+
+-----
+
+.. class:: infomark
+
+**Syntax**
+
+- **Input** - SAM/BAM format aligned short read data in your current history
+- **Title** - the title to use for all output files from this job - use it for high level metadata
+- **Reference Genome** - Galaxy (and Picard) needs to know which genomic reference was used to generate alignemnts within the input SAM/BAM dataset. Here you have three choices:
+
+  - *Assigned data genome/build* - a genome specified for this dataset. If you your SAM/BAM dataset has an assigned reference genome it will be displayed below this dropdown. If it does not -> use one of the following two options.
+  - *Select a different built-in genome* - this option will list all reference genomes presently cached at this instance of Galaxy.
+  - *Select a reference genome from history* - alternatively you can upload your own version of reference genome into your history and use it with this option. This is however not advisable with large human-sized genomes. If your genome is large contact Galaxy team using "Help" link at the top of the interface and provide exact details on where we can download sequences you would like to use as the refenece. We will then install them as a part of locally cached genomic references.
+  
+- **Assume Sorted** - saves sorting time - but only if true!
+- **Bisulphite data** - see Picard documentation http://picard.sourceforge.net/command-line-overview.shtml#CollectAlignmentSummaryMetrics
+- **Maximum acceptable insertion length** - see Picard documentation at http://picard.sourceforge.net/command-line-overview.shtml#CollectAlignmentSummaryMetrics
+
+-----
+
+.. class:: infomark
+
+**Inputs, outputs, and parameters**
+
+The Picard documentation (reformatted for Galaxy) says:
+
+.. csv-table:: 
+   :header-rows: 1
+
+    Option,Description
+    "INPUT=File","SAM or BAM file Required."
+    "OUTPUT=File","File to write insert size metrics to Required."
+    "REFERENCE_SEQUENCE=File","Reference sequence file Required."
+    "ASSUME_SORTED=Boolean","If true (default), unsorted SAM/BAM files will be considerd coordinate sorted "
+    "MAX_INSERT_SIZE=Integer","Paired end reads above this insert size will be considered chimeric along with inter-chromosomal pairs. Default value: 100000."
+    "ADAPTER_SEQUENCE=String","This option may be specified 0 or more times. "
+    "IS_BISULFITE_SEQUENCED=Boolean","Whether the SAM or BAM file consists of bisulfite sequenced reads. Default value: false. "
+    "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created."
+
+The output produced by the tool has the following columns::
+
+  1. CATEGORY: One of either UNPAIRED (for a fragment run), FIRST_OF_PAIR when metrics are for only the first read in a paired run, SECOND_OF_PAIR when the metrics are for only the second read in a paired run or PAIR when the metrics are aggregeted for both first and second reads in a pair.
+  2. TOTAL_READS: The total number of reads including all PF and non-PF reads. When CATEGORY equals PAIR this value will be 2x the number of clusters.
+  3. PF_READS: The number of PF reads where PF is defined as passing Illumina's filter.
+  4. PCT_PF_READS: The percentage of reads that are PF (PF_READS / TOTAL_READS)
+  5. PF_NOISE_READS: The number of PF reads that are marked as noise reads. A noise read is one which is composed entirey of A bases and/or N bases. These reads are marked as they are usually artifactual and are of no use in downstream analysis.
+  6. PF_READS_ALIGNED: The number of PF reads that were aligned to the reference sequence. This includes reads that aligned with low quality (i.e. their alignments are ambiguous).
+  7. PCT_PF_READS_ALIGNED: The percentage of PF reads that aligned to the reference sequence. PF_READS_ALIGNED / PF_READS
+  8. PF_HQ_ALIGNED_READS: The number of PF reads that were aligned to the reference sequence with a mapping quality of Q20 or higher signifying that the aligner estimates a 1/100 (or smaller) chance that the alignment is wrong.
+  9. PF_HQ_ALIGNED_BASES: The number of bases aligned to the reference sequence in reads that were mapped at high quality. Will usually approximate PF_HQ_ALIGNED_READS * READ_LENGTH but may differ when either mixed read lengths are present or many reads are aligned with gaps.
+ 10. PF_HQ_ALIGNED_Q20_BASES: The subest of PF_HQ_ALIGNED_BASES where the base call quality was Q20 or higher.
+ 11. PF_HQ_MEDIAN_MISMATCHES: The median number of mismatches versus the reference sequence in reads that were aligned to the reference at high quality (i.e. PF_HQ_ALIGNED READS).
+ 12. PF_HQ_ERROR_RATE: The percentage of bases that mismatch the reference in PF HQ aligned reads.
+ 13. MEAN_READ_LENGTH: The mean read length of the set of reads examined. When looking at the data for a single lane with equal length reads this number is just the read length. When looking at data for merged lanes with differing read lengths this is the mean read length of all reads.
+ 14. READS_ALIGNED_IN_PAIRS: The number of aligned reads who's mate pair was also aligned to the reference.
+ 15. PCT_READS_ALIGNED_IN_PAIRS: The percentage of reads who's mate pair was also aligned to the reference. READS_ALIGNED_IN_PAIRS / PF_READS_ALIGNED
+ 16. BAD_CYCLES: The number of instrument cycles in which 80% or more of base calls were no-calls.
+ 17. STRAND_BALANCE: The number of PF reads aligned to the positive strand of the genome divided by the number of PF reads aligned to the genome.
+ 18. PCT_CHIMERAS: The percentage of reads that map outside of a maximum insert size (usually 100kb) or that have the two ends mapping to different chromosomes.
+ 19. PCT_ADAPTER: The percentage of PF reads that are unaligned and match to a known adapter sequence right from the start of the read.
+
+.. class:: warningmark
+
+**Warning on SAM/BAM quality**
+
+Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT**
+flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears
+to be the only way to deal with SAM/BAM that cannot be parsed.
+
+
+  </help>
+</tool>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rgPicardFixMate.xml	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,107 @@
+<tool name="Paired Read Mate Fixer" id="rgPicFixMate" version="1.56.0">
+  <description>for paired data</description>
+  <command interpreter="python">
+   picard_wrapper.py -i "${input_file}" -o "${out_file}" --tmpdir "${__new_file_path__}" -n "${out_prefix}" 
+   --output-format "${outputFormat}" -j "\$JAVA_JAR_PATH/FixMateInformation.jar" --sortorder "${sortOrder}"
+  </command>
+  <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
+  <inputs>
+    <param format="bam,sam" name="input_file" type="data" label="SAM/BAM dataset to fix"
+      help="If empty, upload or import a SAM/BAM dataset."/>
+      <param name="sortOrder" type="select" help="If in doubt, leave as default and read Picard/Samtools documentation"
+         label="Sort order">
+        <option value="coordinate" selected ="true">Coordinate sort</option>
+        <option value="queryname">Query name sort</option>
+        <option value="unsorted">Unsorted - docs not clear if this means unchanged or not</option>
+      </param>
+    <param name="out_prefix" value="Fix Mate" type="text"
+      label="Title for the output file" help="Use this remind you what the job was for." size="80" />
+    <param name="outputFormat" type="boolean" checked="True" truevalue="bam" falsevalue="sam" label="Output BAM instead of SAM" help="Uncheck for SAM output" />
+  </inputs>
+  <outputs>
+    <data format="bam" name="out_file" label="${tool.name} on ${on_string}: ${outputFormat} with fixed mates">
+    <change_format>
+     <when input="outputFormat" value="sam" format="sam" />
+    </change_format> 
+    </data>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input_file" value="picard_input_sorted_pair.sam" />
+      <param name="sortOrder" value="coordinate" />
+      <param name="outputFormat" value="True" />
+      <param name="out_prefix" value="Test FixMate" />
+      <output name="out_file" file="picard_output_fixmate_sorted_pair.bam" ftype="bam" />
+    </test>
+    <test>
+      <param name="input_file" value="picard_input_sorted_pair.sam" />
+      <param name="sortOrder" value="coordinate" />
+      <param name="outputFormat" value="False" />
+      <param name="out_prefix" value="Test FixMate" />
+      <output name="out_file" file="picard_output_fixmate_sorted_pair.sam" ftype="sam" />
+    </test>
+  </tests>
+  <help>
+
+
+.. class:: infomark
+
+**Purpose**
+
+Ensure that all mate-pair information is in sync between each read and it's mate pair.
+
+**Picard documentation**
+
+This is a Galaxy wrapper for FixMateInformation, a part of the external package Picard-tools_.
+
+ .. _Picard-tools: http://www.google.com/search?q=picard+samtools
+
+.. class:: warningmark
+
+**Useful for paired data only**
+
+Likely won't do anything helpful for single end sequence data
+Currently, Galaxy doesn't distinguish paired from single ended SAM/BAM so make sure
+the data you choose are valid (paired end) SAM or BAM data - unless you trust this
+tool not to harm your data.
+
+-----
+
+.. class:: infomark
+
+**Syntax**
+
+- **Input** - a paired read sam/bam format aligned short read data in your current history
+- **Sort order** - can be used to adjust the ordering of reads 
+- **Title** - the title to use for all output files from this job - use it for high level metadata
+- **Output Format** - either SAM or compressed as BAM
+
+-----
+
+.. class:: infomark
+
+**Inputs, outputs, and parameters**
+
+.. csv-table::
+
+   :header-rows: 1
+
+  Option,Description
+  "INPUT=File","The input file to fix. This option may be specified 0 or more times."
+  "OUTPUT=File","The output file to write to"
+  "SORT_ORDER=SortOrder","Optional sort order if the OUTPUT file should be sorted differently than the INPUT file. Default value: null. Possible values: {unsorted, queryname, coordinate}"
+  "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created. Default value: false"
+
+.. class:: warningmark
+
+**Warning on SAM/BAM quality**
+
+Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT**
+flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears
+to be the only way to deal with SAM/BAM that cannot be parsed.
+
+
+  </help>
+</tool>
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rgPicardGCBiasMetrics.xml	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,150 @@
+<tool name="SAM/BAM GC Bias Metrics" id="PicardGCBiasMetrics" version="1.56.0">
+  <command interpreter="python">
+    picard_wrapper.py -i "${input_file}" -d "${html_file.files_path}" -t "${html_file}"
+    --windowsize "${windowsize}" --mingenomefrac "${mingenomefrac}" -n "${out_prefix}" --tmpdir "${__new_file_path__}"
+    -j "\$JAVA_JAR_PATH/CollectGcBiasMetrics.jar"
+#if $genomeSource.refGenomeSource == "history":
+ --ref-file "${genomeSource.ownFile}"
+#else:
+ --ref "${genomeSource.index.fields.path}"
+#end if
+  </command>
+  <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
+  <inputs>
+    <param format="sam,bam" name="input_file" type="data" label="SAM/BAM dataset to generateGC bias metrics"
+      help="If empty, upload or import a SAM/BAM dataset."/>
+    <param name="out_prefix" value="Short Read GC Bias Metrics" type="text"
+      label="Title for the output file" help="Use this remind you what the job was for." size="80" />
+    <conditional name="genomeSource"> 
+      <param name="refGenomeSource" type="select" label="Select Reference Genome">
+        <option value="default" selected="true">Use the assigned data genome/build</option>
+        <option value="indexed">Select a different built-in genome</option>
+        <option value="history">Use a genome (fasta format) from my history</option>
+      </param>
+      <when value="default">
+        <param name="index" type="select" label="Check the assigned reference genome" help="Galaxy thinks that the reads in you dataset were aligned against this reference. If this is not correct, use the 'Select a build-in reference genome' option of the 'Select Reference Genome' dropdown to select approprtiate Reference.">
+          <options from_data_table="all_fasta">
+          <filter type="data_meta" ref="input_file" key="dbkey" column="dbkey" multiple="True" separator=","/>
+          <validator type="no_options" message="No reference build available for the selected input data" />
+          </options>
+        </param>
+      </when>
+      <when value="indexed">
+        <param name="index" type="select" label="Select a built-in reference genome" help="This list contains genomes cached at this Galaxy instance. If your genome of interest is not present here request it by using 'Help' link at the top of Galaxy interface or use the 'Use a genome (fasta format) from my history' option of the 'Select Reference Genome' dropdown.">
+          <options from_data_table="all_fasta"/>
+        </param>
+      </when>
+      <when value="history">
+        <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference genome from history" help="This option works best for relatively small genomes. If you are working with large human-sized genomes, send request to Galaxy team for adding your reference to this Galaxy instance by using 'Help' link at the top of Galaxy interface."/>
+      </when>
+    </conditional>
+    <param name="windowsize" type="integer" label="GC minimum window size" value="100"
+    help="The size of windows on the genome that are used to bin reads. Default value: 100."/>
+    <param name="mingenomefrac" value="0.00001" type="float" label="Minimum Genome Fraction"
+    help="For summary metrics, exclude GC windows that include less than this fraction of the genome. Default value: 1.0E-5." />
+    <!--
+    
+    Users can be enabled to set Java heap size by uncommenting this option and adding '-x "$maxheap"' to the <command> tag.
+    If commented out the heapsize defaults to the value specified within picard_wrapper.py
+    
+    <param name="maxheap" type="select" help="If in doubt, choose 8G and read Picard documentation please"
+     label="Java heap size">
+    <option value="1G">1GB: very small data</option>
+    <option value="2G" selected="true">2GB</option>
+    <option value="4G">4GB for larger datasets </option>
+    <option value="8G" >8GB use if 4GB fails</option>
+    <option value="16G">16GB - try this if 8GB fails</option>
+    </param>
+    
+    -->
+
+  </inputs>
+  <outputs>
+    <data format="html" name="html_file"  label="${out_prefix}.html"/>
+  </outputs>
+  <tests>
+    <test>
+      <!-- Uncomment this if maxheap is enabled above
+      <param name="maxheap" value="8G" />
+      -->
+      <param name="out_prefix" value="CollectGCBias" />
+      <param name="windowsize" value="100" />
+      <param name="mingenomefrac" value="0.00001" />
+      <param name="refGenomeSource" value="history" />
+      <param name="ownFile" value="picard_input_hg18.trimmed.fasta" dbkey="hg18" />      
+      <param name="input_file" value="picard_input_summary_alignment_stats.sam" ftype="sam" dbkey="hg18"/>
+      <output name="html_file" file="picard_output_GcBias_uploaded_hg18_summary_alignment_stats.html" ftype="html" lines_diff="50"/>
+    </test>
+  </tests>
+  <help>
+
+
+.. class:: infomark
+
+**Summary**
+
+This Galaxy tool uses Picard to report detailed metrics about reads that fall within windows of a certain GC bin on the reference genome.
+
+**Picard documentation**
+
+This is a Galaxy wrapper for CollectGcBiasMetrics, a part of the external package Picard-tools_.
+
+ .. _Picard-tools: http://www.google.com/search?q=picard+samtools
+
+-----
+
+.. class:: infomark
+
+**Syntax**
+
+- **Input** - SAM/BAM format aligned short read data in your current history
+- **Title** - the title to use for all output files from this job - use it for high level metadata
+- **Reference Genome** - Galaxy (and Picard) needs to know which genomic reference was used to generate alignemnts within the input SAM/BAM dataset. Here you have three choices:
+
+  - *Assigned data genome/build* - a genome specified for this dataset. If you your SAM/BAM dataset has an assigned reference genome it will be displayed below this dropdown. If it does not -> use one of the following two options.
+  - *Select a different built-in genome* - this option will list all reference genomes presently cached at this instance of Galaxy.
+  - *Select a reference genome from history* - alternatively you can upload your own version of reference genome into your history and use it with this option. This is however not advisable with large human-sized genomes. If your genome is large contact Galaxy team using "Help" link at the top of the interface and provide exact details on where we can download sequences you would like to use as the refenece. We will then install them as a part of locally cached genomic references.
+  
+- **Window Size** see Picard documentation http://picard.sourceforge.net/command-line-overview.shtml#CollectGCBiasMetrics
+- **Minimum Genome Fraction** See Picard documentation at http://picard.sourceforge.net/command-line-overview.shtml#CollectGCBiasMetrics
+
+-----
+
+.. class:: infomark
+
+**Inputs, outputs, and parameters**
+
+The Picard documentation (reformatted for Galaxy) says:
+
+.. csv-table::
+   :header-rows: 1
+
+    Option,Description
+    "REFERENCE_SEQUENCE=File","The reference sequence fasta file. Required."
+    "INPUT=File","The BAM or SAM file containing aligned reads. Required."
+    "OUTPUT=File","The text file to write the metrics table to. Required."
+    "CHART_OUTPUT=File","The PDF file to render the chart to. Required."
+    "SUMMARY_OUTPUT=File","The text file to write summary metrics to. Default value: null."
+    "WINDOW_SIZE=Integer","The size of windows on the genome that are used to bin reads. Default value: 100."
+    "MINIMUM_GENOME_FRACTION=Double","For summary metrics, exclude GC windows that include less than this fraction of the genome. Default value: 1.0E-5."
+    "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created. Default value: false."
+
+The output produced by the tool has the following columns::
+
+ 1. GC: The G+C content of the reference sequence represented by this bin. Values are from 0% to 100%
+ 2. WINDOWS: The number of windows on the reference genome that have this G+C content.
+ 3. READ_STARTS: The number of reads who's start position is at the start of a window of this GC.
+ 4. MEAN_BASE_QUALITY: The mean quality (determined via the error rate) of all bases of all reads that are assigned to windows of this GC.
+ 5. NORMALIZED_COVERAGE: The ration of "coverage" in this GC bin vs. the mean coverage of all GC bins. A number of 1 represents mean coverage, a number less than one represents lower than mean coverage (e.g. 0.5 means half as much coverage as average) while a number greater than one represents higher than mean coverage (e.g. 3.1 means this GC bin has 3.1 times more reads per window than average).
+ 6. ERROR_BAR_WIDTH: The radius of error bars in this bin based on the number of observations made. For example if the normalized coverage is 0.75 and the error bar width is 0.1 then the error bars would be drawn from 0.65 to 0.85.
+
+.. class:: warningmark
+
+**Warning on SAM/BAM quality**
+
+Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT**
+flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears
+to be the only way to deal with SAM/BAM that cannot be parsed.
+
+  </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rgPicardHsMetrics.xml	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,156 @@
+<tool name="SAM/BAM Hybrid Selection Metrics" id="PicardHsMetrics" version="1.56.0">
+  <description>for targeted resequencing data</description>
+  <command interpreter="python">
+
+    picard_wrapper.py -i "${input_file}" -d "${html_file.files_path}" -t "${html_file}" --datatype "${input_file.ext}"
+    --baitbed "${bait_bed}" --targetbed "${target_bed}" -n "${out_prefix}" --tmpdir "${__new_file_path__}"
+    -j "\$JAVA_JAR_PATH/CalculateHsMetrics.jar"
+
+  </command>
+  <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
+  <inputs>
+    <param format="sam,bam" name="input_file" type="data" label="SAM/BAM dataset to generate statistics for" />
+    <param name="out_prefix" value="Picard HS Metrics" type="text" label="Title for the output file" help="Use to remind you what the job was for." size="80" />
+    <param name="bait_bed" type="data" format="bed,interval" label="Bait intervals: Sequences for bait in the design" help="Note specific format requirements below!" size="80" />
+    <param name="target_bed" type="data" format="bed,interval" label="Target intervals: Sequences for targets in the design" help="Note specific format requirements below!" size="80" />
+    <!--
+    
+    Users can be enabled to set Java heap size by uncommenting this option and adding '-x "$maxheap"' to the <command> tag.
+    If commented out the heapsize defaults to the value specified within picard_wrapper.py
+    
+    <param name="maxheap" type="select" 
+       help="If in doubt, try the default. If it fails with a complaint about java heap size, try increasing it please - larger jobs will require your own hardware."
+     label="Java heap size">
+    <option value="4G" selected = "true">4GB default </option>
+    <option value="8G" >8GB use if 4GB fails</option>
+    <option value="16G">16GB - try this if 8GB fails</option>
+    </param>
+    
+    -->
+  </inputs>
+  <outputs>
+    <data format="html" name="html_file" label="${out_prefix}.html" />
+  </outputs>
+  <tests>
+    <test>
+      <!-- Uncomment this if maxheap parameter is enabled
+      <param name="maxheap" value="8G"  />
+      -->
+      <param name="out_prefix" value="HSMetrics" />
+      <param name="input_file" value="picard_input_summary_alignment_stats.sam" ftype="sam" />
+      <param name="bait_bed" value="picard_input_bait.bed" />
+      <param name="target_bed" value="picard_input_bait.bed"  />
+      <output name="html_file" file="picard_output_hs_transposed_summary_alignment_stats.html" ftype="html" lines_diff="212"/>
+    </test>
+  </tests>
+  <help>
+
+.. class:: infomark
+
+**Summary**
+
+Calculates a set of Hybrid Selection specific metrics from an aligned SAM or BAM file.
+
+.. class:: warnmark
+
+**WARNING about bait and target files**
+
+Picard is very fussy about the bait and target file format. If these are not exactly right, it will fail with an error something like:
+
+Exception in thread "main" net.sf.picard.PicardException: Invalid interval record contains 6 fields: chr1       45787123        45787316      CASO_22G_25063  1000    +
+
+If you see an error like that from this tool, please do NOT report it to any of the Galaxy mailing lists as it is not a bug! 
+It means you must reformat your bait and target files. Galaxy cannot do that for you automatically unfortunately.
+
+The required definition is described in the documentation at http://www.broadinstitute.org/gsa/wiki/index.php/Built-in_command-line_arguments
+and the sample provided looks like this:
+
+chr1    1104841 1104940 +       target_1
+chr1    1105283 1105599 +       target_2
+chr1    1105712 1105860 +       target_3
+chr1    1105960 1106119 +       target_4
+
+So your bait and target files MUST have 5 columns with chr, start, end, strand and name tab delimited and in exactly that order.
+Note that the Picard mandated sam header described in the documentation linked above is automagically added by the tool in Galaxy.
+
+.. class:: infomark
+
+**Picard documentation**
+
+This is a Galaxy wrapper for CalculateHsMetrics.jar, a part of the external package Picard-tools_.
+
+ .. _Picard-tools: http://www.google.com/search?q=picard+samtools
+
+-----
+
+.. class:: infomark
+
+**Inputs, outputs, and parameters**
+
+Picard documentation says (reformatted for Galaxy):
+
+Calculates a set of Hybrid Selection specific metrics from an aligned SAM or BAM file.
+
+.. csv-table::
+   :header-rows: 1
+
+   "Option", "Description"
+   "BAIT_INTERVALS=File","An interval list file that contains the locations of the baits used. Required."
+   "TARGET_INTERVALS=File","An interval list file that contains the locations of the targets. Required."
+   "INPUT=File","An aligned SAM or BAM file. Required."
+   "OUTPUT=File","The output file to write the metrics to. Required. Cannot be used in conjuction with option(s) METRICS_FILE (M)"
+   "METRICS_FILE=File","Legacy synonym for OUTPUT, should not be used. Required. Cannot be used in conjuction with option(s) OUTPUT (O)"
+   "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created. Default value: false"
+
+HsMetrics
+
+ The set of metrics captured that are specific to a hybrid selection analysis.
+
+Output Column Definitions::
+
+  1. BAIT_SET: The name of the bait set used in the hybrid selection.
+  2. GENOME_SIZE: The number of bases in the reference genome used for alignment.
+  3. BAIT_TERRITORY: The number of bases which have one or more baits on top of them.
+  4. TARGET_TERRITORY: The unique number of target bases in the experiment where target is usually exons etc.
+  5. BAIT_DESIGN_EFFICIENCY: Target terrirtoy / bait territory. 1 == perfectly efficient, 0.5 = half of baited bases are not target.
+  6. TOTAL_READS: The total number of reads in the SAM or BAM file examine.
+  7. PF_READS: The number of reads that pass the vendor's filter.
+  8. PF_UNIQUE_READS: The number of PF reads that are not marked as duplicates.
+  9. PCT_PF_READS: PF reads / total reads. The percent of reads passing filter.
+ 10. PCT_PF_UQ_READS: PF Unique Reads / Total Reads.
+ 11. PF_UQ_READS_ALIGNED: The number of PF unique reads that are aligned with mapping score > 0 to the reference genome.
+ 12. PCT_PF_UQ_READS_ALIGNED: PF Reads Aligned / PF Reads.
+ 13. PF_UQ_BASES_ALIGNED: The number of bases in the PF aligned reads that are mapped to a reference base. Accounts for clipping and gaps.
+ 14. ON_BAIT_BASES: The number of PF aligned bases that mapped to a baited region of the genome.
+ 15. NEAR_BAIT_BASES: The number of PF aligned bases that mapped to within a fixed interval of a baited region, but not on a baited region.
+ 16. OFF_BAIT_BASES: The number of PF aligned bases that mapped to neither on or near a bait.
+ 17. ON_TARGET_BASES: The number of PF aligned bases that mapped to a targetted region of the genome.
+ 18. PCT_SELECTED_BASES: On+Near Bait Bases / PF Bases Aligned.
+ 19. PCT_OFF_BAIT: The percentage of aligned PF bases that mapped neither on or near a bait.
+ 20. ON_BAIT_VS_SELECTED: The percentage of on+near bait bases that are on as opposed to near.
+ 21. MEAN_BAIT_COVERAGE: The mean coverage of all baits in the experiment.
+ 22. MEAN_TARGET_COVERAGE: The mean coverage of targets that recieved at least coverage depth = 2 at one base.
+ 23. PCT_USABLE_BASES_ON_BAIT: The number of aligned, de-duped, on-bait bases out of the PF bases available.
+ 24. PCT_USABLE_BASES_ON_TARGET: The number of aligned, de-duped, on-target bases out of the PF bases available.
+ 25. FOLD_ENRICHMENT: The fold by which the baited region has been amplified above genomic background.
+ 26. ZERO_CVG_TARGETS_PCT: The number of targets that did not reach coverage=2 over any base.
+ 27. FOLD_80_BASE_PENALTY: The fold over-coverage necessary to raise 80% of bases in "non-zero-cvg" targets to the mean coverage level in those targets.
+ 28. PCT_TARGET_BASES_2X: The percentage of ALL target bases acheiving 2X or greater coverage.
+ 29. PCT_TARGET_BASES_10X: The percentage of ALL target bases acheiving 10X or greater coverage.
+ 30. PCT_TARGET_BASES_20X: The percentage of ALL target bases acheiving 20X or greater coverage.
+ 31. PCT_TARGET_BASES_30X: The percentage of ALL target bases acheiving 30X or greater coverage.
+ 32. HS_LIBRARY_SIZE: The estimated number of unique molecules in the selected part of the library.
+ 33. HS_PENALTY_10X: The "hybrid selection penalty" incurred to get 80% of target bases to 10X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 10X coverage I need to sequence until PF_ALIGNED_BASES = 10^6 * 10 * HS_PENALTY_10X.
+ 34. HS_PENALTY_20X: The "hybrid selection penalty" incurred to get 80% of target bases to 20X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 20X coverage I need to sequence until PF_ALIGNED_BASES = 10^6 * 20 * HS_PENALTY_20X.
+ 35. HS_PENALTY_30X: The "hybrid selection penalty" incurred to get 80% of target bases to 10X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 30X coverage I need to sequence until PF_ALIGNED_BASES = 10^6 * 30 * HS_PENALTY_30X.
+
+.. class:: warningmark
+
+**Warning on SAM/BAM quality**
+
+Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT**
+flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears to be the only way to deal with SAM/BAM that cannot be parsed.
+
+
+  </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rgPicardInsertSize.xml	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,97 @@
+<tool name="Insertion size metrics" id="PicardInsertSize" version="1.56.0">
+  <description>for PAIRED data</description>
+  <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
+  <command interpreter="python">
+   picard_wrapper.py -i "${input_file}" -n "${out_prefix}" --tmpdir "${__new_file_path__}" --deviations "${deviations}"
+   --histwidth "${histWidth}" --minpct "${minPct}" --malevel "${malevel}"
+   -j "\$JAVA_JAR_PATH/CollectInsertSizeMetrics.jar" -d "${html_file.files_path}" -t "${html_file}"
+  </command>
+  <inputs>
+    <param format="bam,sam" name="input_file" type="data" label="SAM/BAM dataset to generate statistics for"
+      help="If empty, upload or import a SAM/BAM dataset."/>
+    <param name="out_prefix" value="Insertion size metrics" type="text"
+      label="Title for the output file" help="Use this remind you what the job was for" size="120" />
+    <param name="deviations" value="10.0" type="float"
+      label="Deviations" size="5" 
+      help="See Picard documentation: Generate mean, sd and plots by trimming the data down to MEDIAN + DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION" />
+     <param name="histWidth" value="0" type="integer"
+      label="Histogram width" size="5" 
+      help="Explicitly sets the histogram width option - leave 0 to ignore" />
+     <param name="minPct" value="0.05" type="float"
+      label="Minimum percentage" size="5" 
+      help="Discard any data categories (out of FR, TANDEM, RF) that have fewer than this percentage of overall reads" />
+     <param name="malevel" value="0" type="select" multiple="true"  label="Metric Accumulation Level"
+      help="Level(s) at which metrics will be accumulated">
+      <option value="ALL_READS" selected="true">All reads (default)</option>
+      <option value="SAMPLE" default="true">Sample</option>
+      <option value="LIBRARY" default="true">Library</option>
+      <option value="READ_GROUP" default="true">Read group</option>
+     </param>
+  </inputs>
+  <outputs>
+    <data format="html" name="html_file" label="InsertSize_${out_prefix}.html"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input_file" value="picard_input_tiny.sam" />
+      <param name="out_prefix" value="Insertion size metrics" />
+      <param name="deviations" value="10.0" />
+      <param name="histWidth" value="0" />
+      <param name="minPct" value="0.01" />
+      <param name="malevel" value="ALL_READS" />
+      <output name="html_file" file="picard_output_insertsize_tinysam.html" ftype="html" compare="contains" lines_diff="40" />
+    </test>
+  </tests>
+  <help>
+
+
+.. class:: infomark
+
+**Purpose**
+
+Reads a SAM or BAM file and describes the distribution 
+of insert size (excluding duplicates) with metrics and a histogram plot.
+
+**Picard documentation**
+
+This is a Galaxy wrapper for CollectInsertSizeMetrics, a part of the external package Picard-tools_.
+
+ .. _Picard-tools: http://www.google.com/search?q=picard+samtools
+
+.. class:: warningmark
+
+**Useful for paired data only**
+
+This tool works for paired data only and can be expected to fail for single end data.
+
+-----
+
+.. class:: infomark
+
+**Inputs, outputs, and parameters**
+
+Picard documentation says (reformatted for Galaxy):
+
+.. csv-table::
+   :header-rows: 1
+
+    Option,Description
+    "INPUT=File","SAM or BAM file Required."
+    "OUTPUT=File","File to write insert size metrics to Required."
+    "HISTOGRAM_FILE=File","File to write insert size histogram chart to Required."
+    "TAIL_LIMIT=Integer","When calculating mean and stdev stop when the bins in the tail of the distribution contain fewer than mode/TAIL_LIMIT items. This also limits how much data goes into each data category of the histogram."
+    "HISTOGRAM_WIDTH=Integer","Explicitly sets the histogram width, overriding the TAIL_LIMIT option. Also, when calculating mean and stdev, only bins LE HISTOGRAM_WIDTH will be included. "
+    "MINIMUM_PCT=Float","When generating the histogram, discard any data categories (out of FR, TANDEM, RF) that have fewer than this percentage of overall reads. (Range: 0 to 1) Default value: 0.01."
+    "STOP_AFTER=Integer","Stop after processing N reads, mainly for debugging. Default value: 0."
+    "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created. Default value: false."
+
+.. class:: warningmark
+
+**Warning on SAM/BAM quality**
+
+Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT**
+flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears
+to be the only way to deal with SAM/BAM that cannot be parsed.
+
+  </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rgPicardLibComplexity.xml	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,123 @@
+<tool name="Estimate Library Complexity" id="rgEstLibComp" version="1.56.0">
+  <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
+  <command interpreter="python">
+   picard_wrapper.py -i "${input_file}" -n "${out_prefix}" --tmpdir "${__new_file_path__}" --minid "${minIDbases}"
+   --maxdiff "${maxDiff}" --minmeanq "${minMeanQ}" --readregex "${readRegex}" --optdupdist "${optDupeDist}"
+   -j "\$JAVA_JAR_PATH/EstimateLibraryComplexity.jar" -d "${html_file.files_path}" -t "${html_file}"
+  </command>
+  <inputs>
+    <param format="bam,sam" name="input_file" type="data" label="SAM/BAM dataset"
+      help="If empty, upload or import a SAM/BAM dataset."/>
+    <param name="out_prefix" value="Library Complexity" type="text"
+      label="Title for the output file" help="Use this remind you what the job was for." size="80" />
+    <param name="minIDbases" value="5" type="integer"  label="Minimum identical bases at starts of reads for grouping" size="5" 
+      help="Total_reads / 4^max_id_bases reads will be compared at a time. Lower numbers = more accurate results and exponentially more time/memory." />
+     <param name="maxDiff" value="0.03" type="float"
+      label="Maximum difference rate for identical reads" size="5" 
+      help="The maximum rate of differences between two reads to call them identical" />
+     <param name="minMeanQ" value="20" type="integer"
+      label="Minimum percentage" size="5" 
+      help="The minimum mean quality of bases in a read pair. Lower average quality reads filtered out from all calculations" />
+     <param name="readRegex" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*" type="text" size="120"
+      label="Regular expression that can be used to parse read names in the incoming SAM file" 
+      help="Names are parsed to extract: tile/region, x coordinate and y coordinate, to estimate optical duplication rate" >
+      <sanitizer>
+        <valid initial="string.printable">
+         <remove value="&apos;"/>
+        </valid>
+        <mapping initial="none">
+          <add source="&apos;" target="__sq__"/>
+        </mapping>
+      </sanitizer>
+     </param>
+     <param name="optDupeDist" value="100" type="text"
+      label="The maximum offset between two duplicte clusters in order to consider them optical duplicates." size="5" 
+      help="e.g. 5-10 pixels. Later Illumina software versions multiply pixel values by 10, in which case 50-100" />
+
+  </inputs>
+  <outputs>
+    <data format="html" name="html_file" label="${out_prefix}_lib_complexity.html"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input_file" value="picard_input_tiny.sam" />
+      <param name="out_prefix" value="Library Complexity" />
+      <param name="minIDbases" value="5" />
+      <param name="maxDiff" value="0.03" />
+      <param name="minMeanQ" value="20" />
+      <param name="readRegex" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*" />
+      <param name="optDupeDist" value="100" />      
+      <output name="html_file" file="picard_output_estlibcomplexity_tinysam.html" ftype="html" lines_diff="30" />
+    </test>
+  </tests>
+  <help>
+
+.. class:: infomark
+
+**Purpose**
+
+Attempts to estimate library complexity from sequence alone. 
+Does so by sorting all reads by the first N bases (5 by default) of each read and then 
+comparing reads with the first N bases identical to each other for duplicates. Reads are considered to be 
+duplicates if they match each other with no gaps and an overall mismatch rate less than or equal to MAX_DIFF_RATE (0.03 by default).
+
+Reads of poor quality are filtered out so as to provide a more accurate estimate. 
+The filtering removes reads with any no-calls in the first N bases or with a mean base quality lower than 
+MIN_MEAN_QUALITY across either the first or second read.
+
+The algorithm attempts to detect optical duplicates separately from PCR duplicates and excludes these in the 
+calculation of library size. Also, since there is no alignment to screen out technical reads one 
+further filter is applied on the data. After examining all reads a histogram is built of 
+[#reads in duplicate set -> #of duplicate sets]; all bins that contain exactly one duplicate set are
+then removed from the histogram as outliers before library size is estimated.
+
+**Picard documentation**
+
+This is a Galaxy wrapper for EstimateLibraryComplexity, a part of the external package Picard-tools_.
+
+ .. _Picard-tools: http://www.google.com/search?q=picard+samtools
+
+-----
+
+.. class:: infomark
+
+**Inputs, outputs, and parameters**
+
+Picard documentation says (reformatted for Galaxy):
+
+.. csv-table::
+   :header-rows: 1
+
+    Option	Description
+    "INPUT=File","One or more files to combine and estimate library complexity from. Reads can be mapped or unmapped. This option may be specified 0 or more times."
+    "OUTPUT=File","Output file to writes per-library metrics to. Required."
+    "MIN_IDENTICAL_BASES=Integer","The minimum number of bases at the starts of reads that must be identical for reads to be grouped together for duplicate detection. In effect total_reads / 4^max_id_bases reads will be compared at a time, so lower numbers will produce more accurate results but consume exponentially more memory and CPU. Default value: 5."
+    "MAX_DIFF_RATE=Double","The maximum rate of differences between two reads to call them identical. Default value: 0.03. "
+    "MIN_MEAN_QUALITY=Integer","The minimum mean quality of the bases in a read pair for the read to be analyzed. Reads with lower average quality are filtered out and not considered in any calculations. Default value: 20."
+    "READ_NAME_REGEX=String","Regular expression that can be used to parse read names in the incoming SAM file. Read names are parsed to extract three variables: tile/region, x coordinate and y coordinate. These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. The regular expression should contain three capture groups for the three variables, in order. Default value: [a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*. This option can be set to 'null' to clear the default value."
+    "OPTICAL_DUPLICATE_PIXEL_DISTANCE=Integer","The maximum offset between two duplicte clusters in order to consider them optical duplicates. This should usually be set to some fairly small number (e.g. 5-10 pixels) unless using later versions of the Illumina pipeline that multiply pixel values by 10, in which case 50-100 is more normal. Default value: 100"
+    "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created. Default value: false. This option can be set to 'null' to clear the default value. "
+
+.. class:: warningmark
+
+**Warning on SAM/BAM quality**
+
+Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT**
+flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears
+to be the only way to deal with SAM/BAM that cannot be parsed.
+
+.. class:: infomark
+
+**Note on the Regular Expression**
+
+(from the Picard docs)
+This tool requires a valid regular expression to parse out the read names in the incoming SAM or BAM file. 
+These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. 
+The regular expression should contain three capture groups for the three variables, in order. 
+Default value: [a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.
+
+
+  </help>
+</tool>
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rgPicardMarkDups.xml	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,130 @@
+<tool name="Mark Duplicate reads" id="rgPicardMarkDups" version="1.56.0">
+  <command interpreter="python">
+   picard_wrapper.py -i "${input_file}" -n "${out_prefix}" --tmpdir "${__new_file_path__}" -o "${out_file}"
+   --remdups "${remDups}" --assumesorted "${assumeSorted}" --readregex "${readRegex}" --optdupdist "${optDupeDist}"
+   -j "\$JAVA_JAR_PATH/MarkDuplicates.jar" -d "${html_file.files_path}" -t "${html_file}" -e "${input_file.ext}"
+  </command>
+  <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
+  <inputs>
+    <param format="bam,sam" name="input_file" type="data" label="SAM/BAM dataset to mark duplicates in"
+      help="If empty, upload or import a SAM/BAM dataset."/>
+    <param name="out_prefix" value="Dupes Marked" type="text"
+      label="Title for the output file" help="Use this remind you what the job was for" size="80" />
+    <param name="remDups" value="false" type="boolean"  label="Remove duplicates from output file"
+      truevalue="true" falsevalue="false" checked="yes" 
+      help="If true do not write duplicates to the output file instead of writing them with appropriate flags set." />
+    <param name="assumeSorted" value="true" type="boolean"  label="Assume reads are already ordered"
+      truevalue="true" falsevalue="false" checked="yes" 
+      help="If true assume input data are already sorted (most Galaxy SAM/BAM should be)." />
+     <param name="readRegex" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*" type="text" size="80"
+      label="Regular expression that can be used to parse read names in the incoming SAM file" 
+      help="Names are parsed to extract: tile/region, x coordinate and y coordinate, to estimate optical duplication rate" >
+      <sanitizer>
+        <valid initial="string.printable">
+         <remove value="&apos;"/>
+        </valid>
+        <mapping initial="none">
+          <add source="&apos;" target="__sq__"/>
+        </mapping>
+      </sanitizer>
+     </param>
+     <param name="optDupeDist" value="100" type="integer"
+      label="The maximum offset between two duplicate clusters in order to consider them optical duplicates." size="5" 
+      help="e.g. 5-10 pixels. Later Illumina software versions multiply pixel values by 10, in which case 50-100." >
+      <validator type="in_range" message="Minimum optical dupe distance must be positive" min="0" />    
+     </param>
+
+  </inputs>
+  <outputs>
+    <data format="bam" name="out_file" label="MarkDups_${out_prefix}.bam"/>
+    <data format="html" name="html_file" label="MarkDups_${out_prefix}.html"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input_file" value="picard_input_tiny_coord.bam" ftype="bam" />
+      <param name="out_prefix" value="Dupes Marked" />
+      <param name="remDups" value="false" />
+      <param name="assumeSorted" value="true" />
+      <param name="readRegex" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*" />
+      <param name="optDupeDist" value="100" />      
+      <output name="out_file" file="picard_output_markdups_sortedpairsam.bam" ftype="bam" compare="diff" />
+      <output name="html_file" file="picard_output_markdups_sortedpairsam.html" ftype="html" lines_diff="75" />
+    </test>
+    <test>
+      <param name="input_file" value="picard_input_tiny_coord.sam" ftype="sam" />
+      <param name="out_prefix" value="Dupes Marked" />
+      <param name="remDups" value="true" />
+      <param name="assumeSorted" value="true" />
+      <param name="readRegex" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*" />
+      <param name="optDupeDist" value="100" />
+      <output name="out_file" file="picard_output_markdups_remdupes.bam" ftype="bam" compare="diff" />
+      <output name="html_file" file="picard_output_markdups_sortedpairsam.html" ftype="html" lines_diff="75" />
+    </test>
+  </tests>
+  
+  <help>
+
+.. class:: infomark
+
+**Purpose**
+
+Marks all duplicate reads in a provided SAM or BAM file and either removes them or flags them.
+
+**Picard documentation**
+
+This is a Galaxy wrapper for MarkDuplicates, a part of the external package Picard-tools_.
+
+ .. _Picard-tools: http://www.google.com/search?q=picard+samtools
+
+-----
+
+.. class:: infomark
+
+**Inputs, outputs, and parameters**
+
+Picard documentation says (reformatted for Galaxy):
+
+.. csv-table:: Mark Duplicates docs
+   :header-rows: 1
+
+    Option,Description
+    "INPUT=File","The input SAM or BAM file to analyze. Must be coordinate sorted. Required."
+    "OUTPUT=File","The output file to right marked records to Required."
+    "METRICS_FILE=File","File to write duplication metrics to Required."
+    "REMOVE_DUPLICATES=Boolean","If true do not write duplicates to the output file instead of writing them with appropriate flags set. Default value: false."
+    "ASSUME_SORTED=Boolean","If true, assume that the input file is coordinate sorted, even if the header says otherwise. Default value: false."
+    "MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=Integer","This option is obsolete. ReadEnds will always be spilled to disk. Default value: 50000."
+    "MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=Integer","Maximum number of file handles to keep open when spilling read ends to disk."
+    "READ_NAME_REGEX=String","Regular expression that can be used to parse read names in the incoming SAM file. Read names are parsed to extract three variables: tile/region, x coordinate and y coordinate. "
+    "OPTICAL_DUPLICATE_PIXEL_DISTANCE=Integer","The maximum offset between two duplicte clusters in order to consider them optical duplicates. This should usually be set to some fairly small number (e.g. 5-10 pixels) unless using later versions of the Illumina pipeline that multiply pixel values by 10, in which case 50-100 is more normal. Default value: 100"
+
+.. class:: warningmark
+
+**Warning on SAM/BAM quality**
+
+Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT**
+flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears
+to be the only way to deal with SAM/BAM that cannot be parsed.
+.. class:: infomark
+
+**Note on the Regular Expression**
+
+(from the Picard docs)
+This tool requires a valid regular expression to parse out the read names in the incoming SAM or BAM file. These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. The regular expression should contain three capture groups for the three variables, in order. Default value: [a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).
+
+Examines aligned records in the supplied SAM or BAM file to locate duplicate molecules. All records are then written to the output file with the duplicate records flagged unless the remove duplicates option is selected. In some cases you may want to do this, but please only do this if you really understand what you are doing.
+
+  </help>
+</tool>
+
+
+
+
+
+
+
+
+
+
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bfast_out1.sam	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,23 @@
+@HD	VN:0.1.2	SO:unsorted	GO:none
+@SQ	SN:phiX174	LN:5386
+@PG	ID:bfast	VN:0.6.4d
+random_phiX_region_0	0	phiX174	553	255	50M	*	0	0	TTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTT	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~	PG:Z:bfast	AS:i:2500	NM:i:0	NH:i:1	IH:i:1	HI:i:1	MD:Z:50	XA:i:0
+random_phiX_region_1	0	phiX174	3693	255	50M	*	0	0	GTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTA	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~	PG:Z:bfast	AS:i:2500	NM:i:0	NH:i:1	IH:i:1	HI:i:1	MD:Z:50	XA:i:0
+random_phiX_region_2	0	phiX174	375	255	50M	*	0	0	AATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCA	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~	PG:Z:bfast	AS:i:2500	NM:i:0	NH:i:1	IH:i:1	HI:i:1	MD:Z:50	XA:i:0
+random_phiX_region_3	0	phiX174	3168	255	50M	*	0	0	GGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTC	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~	PG:Z:bfast	AS:i:2500	NM:i:0	NH:i:1	IH:i:1	HI:i:1	MD:Z:50	XA:i:0
+random_phiX_region_4	0	phiX174	5254	255	50M	*	0	0	ACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGAC	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~	PG:Z:bfast	AS:i:2500	NM:i:0	NH:i:1	IH:i:1	HI:i:1	MD:Z:50	XA:i:0
+random_phiX_region_5	0	phiX174	5066	255	50M	*	0	0	AGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCA	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~	PG:Z:bfast	AS:i:2500	NM:i:0	NH:i:1	IH:i:1	HI:i:1	MD:Z:50	XA:i:0
+random_phiX_region_6	0	phiX174	1226	255	50M	*	0	0	CACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGC	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~	PG:Z:bfast	AS:i:2500	NM:i:0	NH:i:1	IH:i:1	HI:i:1	MD:Z:50	XA:i:0
+random_phiX_region_7	0	phiX174	1096	255	50M	*	0	0	AACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCG	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~	PG:Z:bfast	AS:i:2500	NM:i:0	NH:i:1	IH:i:1	HI:i:1	MD:Z:50	XA:i:0
+random_phiX_region_8	0	phiX174	535	255	50M	*	0	0	CTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTT	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~	PG:Z:bfast	AS:i:2500	NM:i:0	NH:i:1	IH:i:1	HI:i:1	MD:Z:50	XA:i:0
+random_phiX_region_9	0	phiX174	3669	255	50M	*	0	0	CAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCA	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~	PG:Z:bfast	AS:i:2500	NM:i:0	NH:i:1	IH:i:1	HI:i:1	MD:Z:50	XA:i:0
+random_phiX_region_10	0	phiX174	4887	255	50M	*	0	0	TACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTC	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~	PG:Z:bfast	AS:i:2500	NM:i:0	NH:i:1	IH:i:1	HI:i:1	MD:Z:50	XA:i:0
+random_phiX_region_11	0	phiX174	1849	255	50M	*	0	0	TATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGA	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~	PG:Z:bfast	AS:i:2500	NM:i:0	NH:i:1	IH:i:1	HI:i:1	MD:Z:50	XA:i:0
+random_phiX_region_12	0	phiX174	4145	255	50M	*	0	0	AGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATA	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~	PG:Z:bfast	AS:i:2500	NM:i:0	NH:i:1	IH:i:1	HI:i:1	MD:Z:50	XA:i:0
+random_phiX_region_13	0	phiX174	1853	255	50M	*	0	0	TTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCA	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~	PG:Z:bfast	AS:i:2500	NM:i:0	NH:i:1	IH:i:1	HI:i:1	MD:Z:50	XA:i:0
+random_phiX_region_14	0	phiX174	2800	255	50M	*	0	0	CCGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGC	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~	PG:Z:bfast	AS:i:2300	NM:i:1	NH:i:1	IH:i:1	HI:i:1	MD:Z:11T38	XA:i:0
+random_phiX_region_15	0	phiX174	1910	255	50M	*	0	0	AACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTT	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~	PG:Z:bfast	AS:i:2500	NM:i:0	NH:i:1	IH:i:1	HI:i:1	MD:Z:50	XA:i:0
+random_phiX_region_16	0	phiX174	3366	255	50M	*	0	0	GCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCA	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~	PG:Z:bfast	AS:i:2500	NM:i:0	NH:i:1	IH:i:1	HI:i:1	MD:Z:50	XA:i:0
+random_phiX_region_17	0	phiX174	2165	255	50M	*	0	0	CATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAG	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~	PG:Z:bfast	AS:i:2500	NM:i:0	NH:i:1	IH:i:1	HI:i:1	MD:Z:50	XA:i:0
+random_phiX_region_18	0	phiX174	2051	255	50M	*	0	0	TGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~	PG:Z:bfast	AS:i:2500	NM:i:0	NH:i:1	IH:i:1	HI:i:1	MD:Z:50	XA:i:0
+random_phiX_region_19	0	phiX174	5099	255	50M	*	0	0	GCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACT	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~	PG:Z:bfast	AS:i:2500	NM:i:0	NH:i:1	IH:i:1	HI:i:1	MD:Z:50	XA:i:0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bwa_wrapper_in2.fastqsanger	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,120 @@
+@seq1/1
+GGACTCAGATAGTAATCC
++
+II#IIIIIII$5+.(9II
+@seq2/1
+ATTCGACCTATCCTTGCG
++
+IIIIIIIIIIIIIIIIII
+@seq3/1
+GTAACAAAGTTTGGATTG
++
+IIIIIIIIIIIIIIIIII
+@seq4/1
+AGCCGCTCGTCTTTTATG
++
+IIIIIIIIIIIIIIIIII
+@seq5/1
+CAGTTATATGGCTTTTGG
++
+IIIIIIIIIIIIIIIIII
+@seq6/1
+AGGCGCTCGTCTTGGTAT
++
+IIIIIIIIIIIIIIIIII
+@seq7/1
+TGTAGGTGGTCAACCAAT
++
+IIIIIIIIIIIIIIIIII
+@seq8/1
+ACACCCGTCCTTTACGTC
++
+IIIIIIIIIIIIIIIIII
+@seq9/1
+GCCGCTATTCAGGTTGTT
++
+IIIIIIIIIIIIIIIIII
+@seq10/1
+ATTCTTTCTTTTCGTATC
++
+IIIIIIIIIIIIIIIIII
+@seq11/1
+GCATTTCTACTCCTTCTC
++
+II#IIIIIII$5+.(9II
+@seq12/1
+CGCGCTTCGATAAAAATG
++
+IIIIIIIIIIIIIIIIII
+@seq13/1
+ATTTCTACTCTTTCTCAT
++
+IIIIIIIIIIIIIIIIII
+@seq14/1
+CCCTTTTGAATGTCACGC
++
+IIIIIIIIIIIIIIIIII
+@seq15/1
+CCAACTTACCAAGGTGGG
++
+IIIIIIIIIIIIIIIIII
+@seq16/1
+TCAGGGTATTAAAAGAGA
++
+IIIIIIIIIIIIIIIIII
+@seq17/1
+GTGATGTGCTTGCTACCG
++
+IIIIIIIIIIIIIIIIII
+@seq18/1
+TCAATCCCCCATGCTTGG
++
+IIIIIIIIIIIIIIIIII
+@seq19/1
+TTCCTGCGCTTAATGCTT
++
+IIIIIIIIIIIIIIIIII
+@seq20/1
+CTTATTACCATTTCAACT
++
+IIIIIIIIIIIIIIIIII
+@seq21/1
+CTGATACCAATAAAACCC
++
+II#IIIIIII$5+.(9II
+@seq22/1
+AATCAAACTTACCAAGGG
++
+IIIIIIIIIIIIIIIIII
+@seq23/1
+TGTGCTTCCCCAACTTGA
++
+IIIIIIIIIIIIIIIIII
+@seq24/1
+TTTCTCAATCCCCAATGC
++
+IIIIIIIIIIIIIIIIII
+@seq25/1
+TTGCTACTGACCGCTCTT
++
+IIIIIIIIIIIIIIIIII
+@seq26/1
+CCGCGTGAAATTTCTATG
++
+IIIIIIIIIIIIIIIIII
+@seq27/1
+CGCTAATCAAGTTGTTTC
++
+IIIIIIIIIIIIIIIIII
+@seq28/1
+AAAGAGATTATTTGTCGG
++
+IIIIIIIIIIIIIIIIII
+@seq29/1
+CAAATTAATGCGCGCTTC
++
+IIIIIIIIIIIIIIIIII
+@seq30/1
+ATCCCCTATGCTTGGCTT
++
+IIIIIIIIIIIIIIIIII
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bwa_wrapper_in3.fastqsanger	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,120 @@
+@seq1/2
+ACGCTCCTTTAAAATATC
++
+IIIII$%*$G$A31I&&B
+@seq2/2
+CAGCTCGAGAAGCTCTTA
++
+IIIIIIIIIIIIIIIIII
+@seq3/2
+CTACTGACCGCTCTCGTG
++
+IIIIIIIIIIIIIIIIII
+@seq4/2
+TAGGTGGTCAACCATTTT
++
+IIIIIIIIIIIIIIIIII
+@seq5/2
+TTTCTATGTGGCTTAATA
++
+IIIIIIIIIIIIIIIIII
+@seq6/2
+GTAGGTGGTCAACAATTT
++
+IIIIIIIIIIIIIIIIII
+@seq7/2
+TTTAATTGCAGGGGCTTC
++
+IIIIIIIIIIIIIIIIII
+@seq8/2
+ATGCGCTCTATTCTCTGG
++
+IIIIIIIIIIIIIIIIII
+@seq9/2
+TTCTGTTGGTGCTGATAT
++
+IIIIIIIIIIIIIIIIII
+@seq10/2
+AGGGCGTTGAGTTCGATA
++
+IIIIIIIIIIIIIIIIII
+@seq11/2
+ATCCCCAATGCTTGGCTT
++
+IIIII$%*$G$A31I&&B
+@seq12/2
+GGATTGGCGTTTCCAACC
++
+IIIIIIIIIIIIIIIIII
+@seq13/2
+CCCCAATCCTTGCCTTCC
++
+IIIAAIIIIIIIIIIIII
+@seq14/2
+TGATATTTTGACTTTGAG
++
+IIIIIIIIIIIIIIIIII
+@seq15/2
+TTACGAAACGCGACGCCG
++
+IIIIIIIIIIIIIIIIII
+@seq16/2
+TTATTTTTCTCCAGCCAC
++
+IIIIIIIIIIIIIIIIII
+@seq17/2
+AAACAATACTTTAGGCAT
++
+IIIIIIIIIIIIIIIIII
+@seq18/2
+CCGTTCCATAAGCAGATG
++
+IIIIIIIIIIIIIIIIII
+@seq19/2
+GAGCGTCCTGGTGCTGAT
++
+IIIIIIIIIIIIIIIIII
+@seq20/2
+ACTCCGGTTATCGCTGGC
++
+IIIIIIIIIIIIIIIIII
+@seq21/2
+TAAGCATTTGGTTCAGGG
++
+IIIII$%*$G$A31I&&B
+@seq22/2
+GTTACGACGCGACGCCGT
++
+IIIIIIIIIIIIIIIIII
+@seq23/2
+TTTAATAACCCTATAGAC
++
+IIIIIIIIIIIIIIIIII
+@seq24/2
+CTTGGCTTCCCTAAGCAG
++
+IIIIIIIIIIIIIIIIII
+@seq25/2
+CGTGCTCGTTGCTGCGTT
++
+IIIIIIIIIIIIIIIIII
+@seq26/2
+AAGGATGTTTTCCGTTCT
++
+IIIIIIIIIIIIIIIIII
+@seq27/2
+TGTTTGGTGCTGATATTG
++
+IIIIIIIIIIIIIIIIII
+@seq28/2
+TCCAGCCACTAAAGTGAG
++
+IIIIIIIIIIIIIIIIII
+@seq29/2
+GATAATGATTGGGGTATC
++
+IIIIIIIIIIIIIIIIII
+@seq30/2
+ACCATAAGCAGATGGATA
++
+IIIIIIIIIIIIIIIIII
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bwa_wrapper_out3.sam	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,63 @@
+@SQ	SN:phiX174	LN:5386
+@RG	ID:abcdefg	LB:lib-mom-A	PL:ILLUMINA	SM:mom	DS:descrip	DT:2010-11-01	PI:400
+@PG	ID:bwa	PN:bwa	VN:0.5.9-r16
+seq1	113	phiX174	340	37	18M	=	322	-18	GGATTACTATCTGAGTCC	II9(.+5$IIIIIII#II	RG:Z:abcdefg	XT:A:U	NM:i:0	SM:i:37	AM:i:25	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:18
+seq1	177	phiX174	322	25	18M	=	340	18	GATATTTTAAAGGAGCGT	B&&I13A$G$*%$IIIII	RG:Z:abcdefg	XT:A:U	NM:i:2	SM:i:25	AM:i:25	X0:i:1	X1:i:0	XM:i:2	XO:i:0	XG:i:0	MD:Z:2C8A6
+seq2	65	phiX174	141	37	18M	=	159	18	ATTCGACCTATCCTTGCG	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:0	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:18
+seq2	129	phiX174	159	37	18M	=	141	-18	CAGCTCGAGAAGCTCTTA	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:0	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:18
+seq3	65	phiX174	505	37	18M	=	523	18	GTAACAAAGTTTGGATTG	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:0	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:18
+seq3	129	phiX174	523	37	18M	=	505	-18	CTACTGACCGCTCTCGTG	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:0	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:18
+seq4	69	phiX174	945	0	*	=	945	0	AGCCGCTCGTCTTTTATG	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg
+seq4	137	phiX174	945	23	18M	=	945	0	TAGGTGGTCAACCATTTT	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:1	SM:i:23	AM:i:0	X0:i:1	X1:i:1	XM:i:1	XO:i:0	XG:i:0	MD:Z:12A5	XA:Z:phiX174,+945,17M1S,2;
+seq5	65	phiX174	4985	37	18M	=	5003	18	CAGTTATATGGCTTTTGG	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:1	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:1	XO:i:0	XG:i:0	MD:Z:13G4
+seq5	129	phiX174	5003	37	18M	=	4985	-18	TTTCTATGTGGCTTAATA	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:1	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:1	XO:i:0	XG:i:0	MD:Z:13A4
+seq6	65	phiX174	925	37	11M1D7M	=	944	19	AGGCGCTCGTCTTGGTAT	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:1	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:11^T7
+seq6	129	phiX174	944	37	18M	=	925	-19	GTAGGTGGTCAACAATTT	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:0	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:18
+seq7	65	phiX174	943	25	18M	=	960	17	TGTAGGTGGTCAACCAAT	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:2	SM:i:25	AM:i:25	X0:i:1	X1:i:1	XM:i:2	XO:i:0	XG:i:0	MD:Z:14A1T1	XA:Z:phiX174,+943,13M1I4M,2;
+seq7	129	phiX174	960	37	18M	=	943	-17	TTTAATTGCAGGGGCTTC	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:0	SM:i:37	AM:i:25	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:18
+seq8	69	phiX174	1715	0	*	=	1715	0	ACACCCGTCCTTTACGTC	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg
+seq8	137	phiX174	1715	37	18M	=	1715	0	ATGCGCTCTATTCTCTGG	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:1	SM:i:37	AM:i:0	X0:i:1	X1:i:0	XM:i:1	XO:i:0	XG:i:0	MD:Z:10A7
+seq9	65	phiX174	2596	37	18M	=	2613	17	GCCGCTATTCAGGTTGTT	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:1	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:1	XO:i:0	XG:i:0	MD:Z:7A10
+seq9	129	phiX174	2613	37	18M	=	2596	-17	TTCTGTTGGTGCTGATAT	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:0	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:18
+seq10	65	phiX174	4149	25	18M	=	4168	19	ATTCTTTCTTTTCGTATC	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:2	SM:i:25	AM:i:25	X0:i:1	X1:i:0	XM:i:2	XO:i:0	XG:i:0	MD:Z:5G11G0
+seq10	129	phiX174	4168	37	18M	=	4149	-19	AGGGCGTTGAGTTCGATA	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:0	SM:i:37	AM:i:25	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:18
+seq11	65	phiX174	4072	37	18M	=	4091	19	GCATTTCTACTCCTTCTC	II#IIIIIII$5+.(9II	RG:Z:abcdefg	XT:A:U	NM:i:1	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:1	XO:i:0	XG:i:0	MD:Z:12T5
+seq11	129	phiX174	4091	37	18M	=	4072	-19	ATCCCCAATGCTTGGCTT	IIIII$%*$G$A31I&&B	RG:Z:abcdefg	XT:A:U	NM:i:0	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:18
+seq12	65	phiX174	5349	37	18M	=	5365	16	CGCGCTTCGATAAAAATG	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:0	SM:i:37	AM:i:25	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:18
+seq12	129	phiX174	5365	25	18M	=	5349	-16	GGATTGGCGTTTCCAACC	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:2	SM:i:25	AM:i:25	X0:i:1	X1:i:0	XM:i:2	XO:i:0	XG:i:0	MD:Z:0T9A7
+seq13	65	phiX174	4074	37	18M	=	4093	19	ATTTCTACTCTTTCTCAT	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:1	SM:i:37	AM:i:25	X0:i:1	X1:i:0	XM:i:1	XO:i:0	XG:i:0	MD:Z:17A0
+seq13	129	phiX174	4093	25	18M	=	4074	-19	CCCCAATCCTTGCCTTCC	IIIAAIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:2	SM:i:25	AM:i:25	X0:i:1	X1:i:0	XM:i:2	XO:i:0	XG:i:0	MD:Z:7G4G5
+seq14	65	phiX174	3998	37	18M	=	4016	18	CCCTTTTGAATGTCACGC	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:1	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:1	XO:i:0	XG:i:0	MD:Z:5C12
+seq14	129	phiX174	4016	37	3M1D15M	=	3998	-18	TGATATTTTGACTTTGAG	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:1	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:3^T15
+seq15	65	phiX174	5198	37	18M	=	5216	18	CCAACTTACCAAGGTGGG	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:1	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:1	XO:i:0	XG:i:0	MD:Z:13C4
+seq15	129	phiX174	5216	37	5M2I11M	=	5198	-18	TTACGAAACGCGACGCCG	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:2	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:2	MD:Z:16
+seq16	65	phiX174	2880	37	10M1I7M	=	2897	17	TCAGGGTATTAAAAGAGA	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:2	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:1	XO:i:1	XG:i:1	MD:Z:5T11
+seq16	129	phiX174	2897	37	18M	=	2880	-17	TTATTTTTCTCCAGCCAC	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:1	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:1	XO:i:0	XG:i:0	MD:Z:6G11
+seq17	65	phiX174	3034	37	18M	=	3053	19	GTGATGTGCTTGCTACCG	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:0	SM:i:37	AM:i:25	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:18
+seq17	129	phiX174	3053	25	18M	=	3034	-19	AAACAATACTTTAGGCAT	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:2	SM:i:25	AM:i:25	X0:i:1	X1:i:0	XM:i:2	XO:i:0	XG:i:0	MD:Z:0T9G7
+seq18	73	phiX174	4088	37	18M	=	4088	0	TCAATCCCCCATGCTTGG	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:1	SM:i:37	AM:i:0	X0:i:1	X1:i:0	XM:i:1	XO:i:0	XG:i:0	MD:Z:9A8
+seq18	133	phiX174	4088	0	*	=	4088	0	CCGTTCCATAAGCAGATG	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg
+seq19	65	phiX174	3304	37	18M	=	3324	20	TTCCTGCGCTTAATGCTT	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:1	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:1	XO:i:0	XG:i:0	MD:Z:6A11
+seq19	129	phiX174	3324	37	18M	=	3304	-20	GAGCGTCCTGGTGCTGAT	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:1	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:1	XO:i:0	XG:i:0	MD:Z:6G11
+seq20	65	phiX174	1082	37	18M	=	1100	18	CTTATTACCATTTCAACT	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:0	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:18
+seq20	129	phiX174	1100	37	18M	=	1082	-18	ACTCCGGTTATCGCTGGC	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:0	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:18
+seq21	65	phiX174	1344	23	18M	=	1363	19	CTGATACCAATAAAACCC	II#IIIIIII$5+.(9II	RG:Z:abcdefg	XT:A:U	NM:i:1	SM:i:23	AM:i:23	X0:i:1	X1:i:1	XM:i:1	XO:i:0	XG:i:0	MD:Z:15T2	XA:Z:phiX174,+1344,15M1D3M,2;
+seq21	129	phiX174	1363	37	18M	=	1344	-19	TAAGCATTTGGTTCAGGG	IIIII$%*$G$A31I&&B	RG:Z:abcdefg	XT:A:U	NM:i:1	SM:i:37	AM:i:23	X0:i:1	X1:i:0	XM:i:1	XO:i:0	XG:i:0	MD:Z:10T7
+seq22	69	phiX174	5215	0	*	=	5215	0	AATCAAACTTACCAAGGG	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg
+seq22	137	phiX174	5215	37	18M	=	5215	0	GTTACGACGCGACGCCGT	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:0	SM:i:37	AM:i:0	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:18
+seq23	65	phiX174	4289	37	18M	=	4308	19	TGTGCTTCCCCAACTTGA	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:1	SM:i:37	AM:i:25	X0:i:1	X1:i:0	XM:i:1	XO:i:0	XG:i:0	MD:Z:6C11
+seq23	129	phiX174	4308	25	18M	=	4289	-19	TTTAATAACCCTATAGAC	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:2	SM:i:25	AM:i:25	X0:i:1	X1:i:0	XM:i:2	XO:i:0	XG:i:0	MD:Z:0A8A8
+seq24	65	phiX174	4084	37	18M	=	4101	17	TTTCTCAATCCCCAATGC	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:0	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:18
+seq24	129	phiX174	4101	37	18M	=	4084	-17	CTTGGCTTCCCTAAGCAG	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:1	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:1	XO:i:0	XG:i:0	MD:Z:10A7
+seq25	65	phiX174	520	37	18M	=	537	17	TTGCTACTGACCGCTCTT	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:1	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:1	XO:i:0	XG:i:0	MD:Z:17C0
+seq25	129	phiX174	537	37	18M	=	520	-17	CGTGCTCGTTGCTGCGTT	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:1	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:1	XO:i:0	XG:i:0	MD:Z:9C8
+seq26	65	phiX174	1976	37	18M	=	1994	18	CCGCGTGAAATTTCTATG	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:0	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:18
+seq26	129	phiX174	1994	37	18M	=	1976	-18	AAGGATGTTTTCCGTTCT	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:0	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:18
+seq27	65	phiX174	2598	37	18M	=	2614	16	CGCTAATCAAGTTGTTTC	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:1	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:1	XO:i:0	XG:i:0	MD:Z:9G8
+seq27	129	phiX174	2614	37	3M1D15M	=	2598	-16	TGTTTGGTGCTGATATTG	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:2	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:1C1^G15
+seq28	65	phiX174	2890	25	18M	=	2906	16	AAAGAGATTATTTGTCGG	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:2	SM:i:25	AM:i:25	X0:i:1	X1:i:0	XM:i:2	XO:i:0	XG:i:0	MD:Z:16T0C0
+seq28	129	phiX174	2906	37	18M	=	2890	-16	TCCAGCCACTAAAGTGAG	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:1	SM:i:37	AM:i:25	X0:i:1	X1:i:0	XM:i:1	XO:i:0	XG:i:0	MD:Z:10T7
+seq29	73	phiX174	5339	37	18M	=	5339	0	CAAATTAATGCGCGCTTC	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:1	SM:i:37	AM:i:0	X0:i:1	X1:i:0	XM:i:1	XO:i:0	XG:i:0	MD:Z:6T11
+seq29	133	phiX174	5339	0	*	=	5339	0	GATAATGATTGGGGTATC	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg
+seq30	65	phiX174	4091	37	18M	=	4108	17	ATCCCCTATGCTTGGCTT	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:1	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:1	XO:i:0	XG:i:0	MD:Z:6A11
+seq30	129	phiX174	4108	37	18M	=	4091	-17	ACCATAAGCAGATGGATA	IIIIIIIIIIIIIIIIII	RG:Z:abcdefg	XT:A:U	NM:i:1	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:1	XO:i:0	XG:i:0	MD:Z:0T17
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/phiX.fasta	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,79 @@
+>phiX174
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT
+GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA
+ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG
+TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA
+GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC
+TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT
+TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT
+CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT
+TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG
+TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC
+GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA
+CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG
+TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT
+AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC
+CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA
+TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC
+TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA
+CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA
+GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT
+GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA
+ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC
+TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT
+TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC
+ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC
+CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT
+GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC
+CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC
+TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG
+TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT
+TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA
+AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT
+TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT
+ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC
+GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC
+TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT
+TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA
+TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG
+TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC
+CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG
+AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC
+CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT
+TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG
+CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA
+AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT
+GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG
+GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA
+TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT
+CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG
+TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA
+GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC
+CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA
+TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA
+AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC
+TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT
+CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA
+TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG
+TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT
+CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT
+TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC
+ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG
+TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA
+ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG
+GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC
+CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT
+GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG
+GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT
+ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG
+CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC
+CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC
+GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT
+CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG
+CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA
+TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT
+TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG
+TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC
+AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC
+TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
+
Binary file test-data/picard_ARRG_input1.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_ARRG_input1.sam	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,25 @@
+@HD	VN:1.0	SO:coordinate
+@SQ	SN:chr1	LN:10001
+@SQ	SN:chr2	LN:100001
+@SQ	SN:chr3	LN:10001
+@SQ	SN:chr4	LN:1001
+@RG	ID:rg1	SM:s1
+@RG	ID:rg2	SM:s3
+bar:record:4	77	chr1	1	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:rg1
+bar:record:6	77	chr1	1	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:rg2
+bar:record:1	77	chr1	10	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:rg1
+bar:record:3	77	chr1	10	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:rg2
+bar:record:1	141	chr1	20	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:rg1
+bar:record:7	77	chr1	20	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:rg2
+bar:record:8	77	chr1	30	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:rg2
+bar:record:4	141	chr1	40	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:rg1
+bar:record:5	77	chr1	40	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:rg2
+bar:record:6	141	chr1	50	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:rg2
+bar:record:2	77	chr2	10	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:rg1
+bar:record:2	141	chr2	30	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:rg2
+bar:record:3	141	chr3	20	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:rg1
+bar:record:8	141	chr3	20	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:rg1
+bar:record:5	141	chr3	40	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:rg1
+bar:record:9	77	chr4	10	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:rg1
+bar:record:7	141	chr4	20	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:rg1
+bar:record:9	141	chr4	60	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:rg1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_ARRG_input2.sam	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,23 @@
+@HD	VN:1.0	SO:coordinate
+@SQ	SN:chr1	LN:10001
+@SQ	SN:chr2	LN:100001
+@SQ	SN:chr3	LN:10001
+@SQ	SN:chr4	LN:1001
+bar:record:4	77	chr1	1	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111
+bar:record:6	77	chr1	1	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111
+bar:record:1	77	chr1	10	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111
+bar:record:3	77	chr1	10	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111
+bar:record:1	141	chr1	20	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222
+bar:record:7	77	chr1	20	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111
+bar:record:8	77	chr1	30	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111
+bar:record:4	141	chr1	40	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222
+bar:record:5	77	chr1	40	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111
+bar:record:6	141	chr1	50	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222
+bar:record:2	77	chr2	10	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111
+bar:record:2	141	chr2	30	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222
+bar:record:3	141	chr3	20	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222
+bar:record:8	141	chr3	20	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222
+bar:record:5	141	chr3	40	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222
+bar:record:9	77	chr4	10	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111
+bar:record:7	141	chr4	20	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222
+bar:record:9	141	chr4	60	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_ARRG_output1.sam	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,24 @@
+@HD	VN:1.0	SO:coordinate
+@SQ	SN:chr1	LN:10001
+@SQ	SN:chr2	LN:100001
+@SQ	SN:chr3	LN:10001
+@SQ	SN:chr4	LN:1001
+@RG	ID:one	PL:illumina	PU:peaewe	LB:lib	SM:sam1
+bar:record:4	77	chr1	1	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:one
+bar:record:6	77	chr1	1	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:one
+bar:record:1	77	chr1	10	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:one
+bar:record:3	77	chr1	10	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:one
+bar:record:1	141	chr1	20	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:one
+bar:record:7	77	chr1	20	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:one
+bar:record:8	77	chr1	30	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:one
+bar:record:4	141	chr1	40	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:one
+bar:record:5	77	chr1	40	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:one
+bar:record:6	141	chr1	50	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:one
+bar:record:2	77	chr2	10	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:one
+bar:record:2	141	chr2	30	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:one
+bar:record:3	141	chr3	20	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:one
+bar:record:8	141	chr3	20	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:one
+bar:record:5	141	chr3	40	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:one
+bar:record:9	77	chr4	10	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:one
+bar:record:7	141	chr4	20	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:one
+bar:record:9	141	chr4	60	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:one
Binary file test-data/picard_ARRG_output2.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_ARRG_output2.sam	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,24 @@
+@HD	VN:1.0	SO:coordinate
+@SQ	SN:chr1	LN:10001
+@SQ	SN:chr2	LN:100001
+@SQ	SN:chr3	LN:10001
+@SQ	SN:chr4	LN:1001
+@RG	ID:M5	PL:IL	PU:PLAT	LB:LIB	DS:description with spaces	SM:smp	CN:FamousCenter
+bar:record:4	77	chr1	1	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:M5
+bar:record:6	77	chr1	1	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:M5
+bar:record:1	77	chr1	10	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:M5
+bar:record:3	77	chr1	10	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:M5
+bar:record:1	141	chr1	20	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:M5
+bar:record:7	77	chr1	20	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:M5
+bar:record:8	77	chr1	30	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:M5
+bar:record:4	141	chr1	40	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:M5
+bar:record:5	77	chr1	40	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:M5
+bar:record:6	141	chr1	50	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:M5
+bar:record:2	77	chr2	10	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:M5
+bar:record:2	141	chr2	30	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:M5
+bar:record:3	141	chr3	20	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:M5
+bar:record:8	141	chr3	20	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:M5
+bar:record:5	141	chr3	40	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:M5
+bar:record:9	77	chr4	10	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:M5
+bar:record:7	141	chr4	20	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:M5
+bar:record:9	141	chr4	60	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:M5
Binary file test-data/picard_ARRG_output3.bam has changed
Binary file test-data/picard_ARRG_output3.bam.bai has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_ARRG_output3.sam	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,24 @@
+@HD	VN:1.0	SO:coordinate
+@SQ	SN:chr1	LN:10001
+@SQ	SN:chr2	LN:100001
+@SQ	SN:chr3	LN:10001
+@SQ	SN:chr4	LN:1001
+@RG	ID:M6	PL:IL	PU:PLAT	LB:LIB	SM:smp1
+bar:record:4	77	chr1	1	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:M6
+bar:record:6	77	chr1	1	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:M6
+bar:record:1	77	chr1	10	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:M6
+bar:record:3	77	chr1	10	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:M6
+bar:record:1	141	chr1	20	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:M6
+bar:record:7	77	chr1	20	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:M6
+bar:record:8	77	chr1	30	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:M6
+bar:record:4	141	chr1	40	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:M6
+bar:record:5	77	chr1	40	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:M6
+bar:record:6	141	chr1	50	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:M6
+bar:record:2	77	chr2	10	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:M6
+bar:record:2	141	chr2	30	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:M6
+bar:record:3	141	chr3	20	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:M6
+bar:record:8	141	chr3	20	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:M6
+bar:record:5	141	chr3	40	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:M6
+bar:record:9	77	chr4	10	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:M6
+bar:record:7	141	chr4	20	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:M6
+bar:record:9	141	chr4	60	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:M6
Binary file test-data/picard_BIS_input1.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_BIS_input1.sam	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,18 @@
+@HD	VN:1.0	SO:coordinate
+@SQ	SN:chr1	LN:101
+@SQ	SN:chr7	LN:404
+@SQ	SN:chr8	LN:202
+@SQ	SN:chr10	LN:303
+@SQ	SN:chr14	LN:505
+@RG	ID:0	SM:Hi,Mom!
+@RG	ID:1	SM:samplesample	DS:ClearDescription
+@PG	ID:1	PN:Hey!	VN:2.0
+@CO	Just a generic comment to make the header longer
+both_reads_align_clip_marked	83	chr7	1	255	101M	=	302	201	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
+both_reads_present_only_first_aligns	89	chr7	1	255	101M	*	0	0	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
+read_2_too_many_gaps	83	chr7	1	255	101M	=	302	201	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
+both_reads_align_clip_adapter	147	chr7	16	255	101M	=	21	-96	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
+both_reads_align_clip_adapter	99	chr7	21	255	101M	=	16	96	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
+both_reads_align_clip_marked	163	chr7	302	255	101M	=	1	-201	NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA	&/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1	RG:Z:0
+read_2_too_many_gaps	163	chr7	302	255	10M1D10M5I76M	=	1	-201	NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA	&/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1	RG:Z:0
+both_reads_present_only_first_aligns	165	*	0	0	*	chr7	1	0	NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA	&/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1	RG:Z:0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_BIS_output1.txt	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,39 @@
+<style type="text/css">
+        tr.d0 td {background-color: oldlace; color: black;}
+        tr.d1 td {background-color: aliceblue; color: black;}
+        </style><?xml version="1.0" encoding="utf-8" ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<meta name="generator" content="Galaxy picard_wrapper tool output - see http://getgalaxy.org/" />
+<title></title>
+<link rel="stylesheet" href="/static/style/base.css" type="text/css" />
+</head>
+<body>
+<div class="document">
+Galaxy tool BamIndexStats run at 12/05/2011 14:18:06</b><br/><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table>
+<tr><td><a href="BamIndexStats.log">BamIndexStats.log</a></td></tr>
+<tr><td><a href="BamIndexStats.metrics.txt">BamIndexStats.metrics.txt</a></td></tr>
+</table><p/>
+<b>Picard on line resources</b><ul>
+<li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li>
+<li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/>
+<b>Picard output</b><hr/>
+<table cellpadding="3" >
+<tr class="d0"><td colspan="2">chr1 length=	101	Aligned= 0	Unaligned= 0</td></tr>
+<tr class="d1"><td colspan="2">chr7 length=	404	Aligned= 7	Unaligned= 0</td></tr>
+<tr class="d0"><td colspan="2">chr8 length=	202	Aligned= 0	Unaligned= 0</td></tr>
+<tr class="d1"><td colspan="2">NoCoordinateCount= 1</td></tr>
+</table>
+<b>Picard Tool Run Log</b><hr/>
+<pre>Thu, 12 May 2011 14:18:06 INFO
+ ## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/shared/jars/BamIndexStats.jar VALIDATION_STRINGENCY=LENIENT INPUT=/udd/rerla/galaxy-central/database/job_working_directory/955/dataset_1015_files/tmp45bd_D.bam returned status 0 and stderr: 
+[Thu May 12 14:18:06 EDT 2011] net.sf.picard.sam.BamIndexStats INPUT=/udd/rerla/galaxy-central/database/job_working_directory/955/dataset_1015_files/tmp45bd_D.bam VALIDATION_STRINGENCY=LENIENT    TMP_DIR=/tmp/rerla VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
+[Thu May 12 14:18:06 EDT 2011] net.sf.picard.sam.BamIndexStats done.
+Runtime.totalMemory()=9109504
+
+
+</pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> 
+generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_BIS_output2.txt	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,41 @@
+<style type="text/css">
+        tr.d0 td {background-color: oldlace; color: black;}
+        tr.d1 td {background-color: aliceblue; color: black;}
+        </style><?xml version="1.0" encoding="utf-8" ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<meta name="generator" content="Galaxy picard_wrapper tool output - see http://getgalaxy.org/" />
+<title></title>
+<link rel="stylesheet" href="/static/style/base.css" type="text/css" />
+</head>
+<body>
+<div class="document">
+Galaxy tool BamIndexStats run at 12/05/2011 14:18:22</b><br/><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table>
+<tr><td><a href="BamIndexStats.log">BamIndexStats.log</a></td></tr>
+<tr><td><a href="BamIndexStats.metrics.txt">BamIndexStats.metrics.txt</a></td></tr>
+</table><p/>
+<b>Picard on line resources</b><ul>
+<li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li>
+<li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/>
+<b>Picard output</b><hr/>
+<table cellpadding="3" >
+<tr class="d0"><td colspan="2">chr1 length=	101	Aligned= 0	Unaligned= 0</td></tr>
+<tr class="d1"><td colspan="2">chr7 length=	404	Aligned= 7	Unaligned= 0</td></tr>
+<tr class="d0"><td colspan="2">chr8 length=	202	Aligned= 0	Unaligned= 0</td></tr>
+<tr class="d1"><td colspan="2">chr10 length=	303	Aligned= 0	Unaligned= 0</td></tr>
+<tr class="d0"><td colspan="2">chr14 length=	505	Aligned= 0	Unaligned= 0</td></tr>
+<tr class="d1"><td colspan="2">NoCoordinateCount= 1</td></tr>
+</table>
+<b>Picard Tool Run Log</b><hr/>
+<pre>Thu, 12 May 2011 14:18:22 INFO
+ ## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/shared/jars/BamIndexStats.jar VALIDATION_STRINGENCY=LENIENT INPUT=/udd/rerla/galaxy-central/database/job_working_directory/957/dataset_1017_files/tmpqXGksN.bam returned status 0 and stderr: 
+[Thu May 12 14:18:21 EDT 2011] net.sf.picard.sam.BamIndexStats INPUT=/udd/rerla/galaxy-central/database/job_working_directory/957/dataset_1017_files/tmpqXGksN.bam VALIDATION_STRINGENCY=LENIENT    TMP_DIR=/tmp/rerla VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
+[Thu May 12 14:18:22 EDT 2011] net.sf.picard.sam.BamIndexStats done.
+Runtime.totalMemory()=9109504
+
+
+</pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> 
+generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_MD_output1.txt	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,112 @@
+## net.sf.picard.metrics.StringHeader
+# net.sf.picard.sam.MarkDuplicates INPUT=picard_input_tiny_coord.bam OUTPUT=picard_MD_output2.bam METRICS_FILE=picard_MD_output1.txt REMOVE_DUPLICATES=false ASSUME_SORTED=true READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VALIDATION_STRINGENCY=LENIENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 TMP_DIR=/tmp/kpvincent VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
+## net.sf.picard.metrics.StringHeader
+# Started on: Tue Apr 19 15:28:21 EDT 2011
+
+## METRICS CLASS	net.sf.picard.sam.DuplicationMetrics
+LIBRARY	UNPAIRED_READS_EXAMINED	READ_PAIRS_EXAMINED	UNMAPPED_READS	UNPAIRED_READ_DUPLICATES	READ_PAIR_DUPLICATES	READ_PAIR_OPTICAL_DUPLICATES	PERCENT_DUPLICATION	ESTIMATED_LIBRARY_SIZE
+	1	3	1	1	1	0	0.428571	3
+
+## HISTOGRAM	java.lang.Double
+BIN	VALUE
+1.0	0.948181
+2.0	1.296997
+3.0	1.425319
+4.0	1.472527
+5.0	1.489893
+6.0	1.496282
+7.0	1.498632
+8.0	1.499497
+9.0	1.499815
+10.0	1.499932
+11.0	1.499975
+12.0	1.499991
+13.0	1.499997
+14.0	1.499999
+15.0	1.5
+16.0	1.5
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+96.0	1.5
+97.0	1.5
+98.0	1.5
+99.0	1.5
+100.0	1.5
+
Binary file test-data/picard_MD_output2.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_MD_output3.txt	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,112 @@
+## net.sf.picard.metrics.StringHeader
+# net.sf.picard.sam.MarkDuplicates INPUT=picard_input_tiny_coord.sam OUTPUT=picard_MD_output4_.sam METRICS_FILE=picard_MD_output3_.txt REMOVE_DUPLICATES=true ASSUME_SORTED=false READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VALIDATION_STRINGENCY=LENIENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 TMP_DIR=/tmp/kpvincent VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
+## net.sf.picard.metrics.StringHeader
+# Started on: Tue Apr 19 15:32:38 EDT 2011
+
+## METRICS CLASS	net.sf.picard.sam.DuplicationMetrics
+LIBRARY	UNPAIRED_READS_EXAMINED	READ_PAIRS_EXAMINED	UNMAPPED_READS	UNPAIRED_READ_DUPLICATES	READ_PAIR_DUPLICATES	READ_PAIR_OPTICAL_DUPLICATES	PERCENT_DUPLICATION	ESTIMATED_LIBRARY_SIZE
+	1	3	1	1	1	0	0.428571	3
+
+## HISTOGRAM	java.lang.Double
+BIN	VALUE
+1.0	0.948181
+2.0	1.296997
+3.0	1.425319
+4.0	1.472527
+5.0	1.489893
+6.0	1.496282
+7.0	1.498632
+8.0	1.499497
+9.0	1.499815
+10.0	1.499932
+11.0	1.499975
+12.0	1.499991
+13.0	1.499997
+14.0	1.499999
+15.0	1.5
+16.0	1.5
+17.0	1.5
+18.0	1.5
+19.0	1.5
+20.0	1.5
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+98.0	1.5
+99.0	1.5
+100.0	1.5
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_MD_output4.sam	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,11 @@
+@HD	VN:1.0	SO:coordinate
+@SQ	SN:chr1	LN:101
+@SQ	SN:chr7	LN:404
+@SQ	SN:chr8	LN:202
+@RG	ID:0	SM:Hi,Mom!
+@PG	ID:1	PN:Hey!	VN:2.0
+both_reads_align_clip_marked	83	chr7	1	255	101M	=	302	201	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
+both_reads_align_clip_adapter	147	chr7	16	255	101M	=	21	-96	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
+both_reads_align_clip_adapter	99	chr7	21	255	101M	=	16	96	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
+both_reads_align_clip_marked	163	chr7	302	255	101M	=	1	-201	NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA	&/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1	RG:Z:0
+both_reads_present_only_first_aligns	165	*	0	0	*	chr7	1	0	NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA	&/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1	RG:Z:0
Binary file test-data/picard_RSH_input1.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_RSH_input1.sam	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,14 @@
+@HD	VN:1.0	SO:coordinate
+@SQ	SN:chr1	LN:101
+@SQ	SN:chr7	LN:404
+@SQ	SN:chr8	LN:202
+@RG	ID:0	SM:What_is_that_sound?
+@PG	ID:1	PN:Greetings!	VN:2.0
+both_reads_align_clip_marked	83	chr7	1	255	101M	=	302	201	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
+both_reads_present_only_first_aligns	89	chr7	1	255	101M	*	0	0	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
+read_2_too_many_gaps	83	chr7	1	255	101M	=	302	201	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
+both_reads_align_clip_adapter	147	chr7	16	255	101M	=	21	-96	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
+both_reads_align_clip_adapter	99	chr7	21	255	101M	=	16	96	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
+both_reads_align_clip_marked	163	chr7	302	255	101M	=	1	-201	NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA	&/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1	RG:Z:0
+read_2_too_many_gaps	163	chr7	302	255	10M1D10M5I76M	=	1	-201	NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA	&/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1	RG:Z:0
+both_reads_present_only_first_aligns	165	*	0	0	*	chr7	1	0	NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA	&/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1	RG:Z:0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_RSH_output1.sam	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,14 @@
+@HD	VN:1.0	SO:coordinate
+@SQ	SN:chr1	LN:101
+@SQ	SN:chr7	LN:404
+@SQ	SN:chr8	LN:202
+@RG	ID:0	SM:What_is_that_sound?
+@PG	ID:1	PN:Greetings!	VN:2.0
+both_reads_align_clip_marked	83	chr7	1	255	101M	=	302	201	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
+both_reads_present_only_first_aligns	89	chr7	1	255	101M	*	0	0	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
+read_2_too_many_gaps	83	chr7	1	255	101M	=	302	201	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
+both_reads_align_clip_adapter	147	chr7	16	255	101M	=	21	-96	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
+both_reads_align_clip_adapter	99	chr7	21	255	101M	=	16	96	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
+both_reads_align_clip_marked	163	chr7	302	255	101M	=	1	-201	NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA	&/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1	RG:Z:0
+read_2_too_many_gaps	163	chr7	302	255	10M1D10M5I76M	=	1	-201	NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA	&/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1	RG:Z:0
+both_reads_present_only_first_aligns	165	*	0	0	*	chr7	1	0	NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA	&/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1	RG:Z:0
Binary file test-data/picard_RSH_output2.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_RSH_output2.sam	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,14 @@
+@HD	VN:1.0	SO:coordinate
+@SQ	SN:chr1	LN:101
+@SQ	SN:chr7	LN:404
+@SQ	SN:chr8	LN:202
+@RG	ID:0	SM:What_is_that_sound?
+@PG	ID:1	PN:Greetings!	VN:2.0
+both_reads_align_clip_marked	83	chr7	1	255	101M	=	302	201	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
+both_reads_present_only_first_aligns	89	chr7	1	255	101M	*	0	0	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
+read_2_too_many_gaps	83	chr7	1	255	101M	=	302	201	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
+both_reads_align_clip_adapter	147	chr7	16	255	101M	=	21	-96	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
+both_reads_align_clip_adapter	99	chr7	21	255	101M	=	16	96	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
+both_reads_align_clip_marked	163	chr7	302	255	101M	=	1	-201	NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA	&/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1	RG:Z:0
+read_2_too_many_gaps	163	chr7	302	255	10M1D10M5I76M	=	1	-201	NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA	&/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1	RG:Z:0
+both_reads_present_only_first_aligns	165	*	0	0	*	chr7	1	0	NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA	&/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1	RG:Z:0
Binary file test-data/picard_RS_input1.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_RS_input2.sam	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,22 @@
+@HD	VN:1.0	SO:unsorted
+@SQ	SN:phiX174	LN:5386
+@PG	ID:Bowtie	VN:0.12.7	CL:"bowtie -q -p 4 -S --phred33-quals /genome/phiX/bowtie_index/phiX dataset_437.dat"
+HWI-EAS91_1_30788AAXX:1:1:1761:343/1	0	phiX174	5	255	50M	*	0	0	TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA	IIIIIII""IIIIIIIIIII?I0IIIIHIIIGIIIII0II?I""IIIIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1647:512/1	0	phiX174	401	255	50M	*	0	0	TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1578:331/1	0	phiX174	209	255	50M	*	0	0	TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1746:351/1	0	phiX174	1218	255	50M	*	0	0	CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1582:633/1	0	phiX174	1517	255	50M	*	0	0	CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1599:330/1	0	phiX174	803	255	50M	*	0	0	AGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAGTGATGTAATGTC	IIIIIII""IIIIIIIIIIIIIIIIIII<III@II"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1598:534/1	0	phiX174	1717	255	50M	*	0	0	GCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1749:466/1	0	phiX174	2201	255	50M	*	0	0	TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1570:620/1	4	*	0	0	*	*	0	0	GAGTAACAAAGTAAAGTTTGGACCGTTTTTGTCTCGTGCTCGTCGCTGCG	IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII"IIIIIII000IIII	XM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1629:446/1	0	phiX174	2301	255	50M	*	0	0	AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1763:587/1	0	phiX174	2501	255	50M	*	0	0	AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1616:363/1	0	phiX174	2718	255	50M	*	0	0	TGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1572:270/1	0	phiX174	3518	255	50M	*	0	0	TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTA	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1768:715/1	0	phiX174	3118	255	50M	*	0	0	ACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCT	IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1785:1272/1	0	phiX174	3818	255	50M	*	0	0	TATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCT	III""""""IIIIIIIII""FI"IIII""II+ICI"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1673:514/1	0	phiX174	4018	255	50M	*	0	0	ATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1652:270/1	4	*	0	0	*	*	0	0	AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGACTTTGCATTGTTTAATTG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II"IIIIIII000IIII	XM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1572:324/1	4	*	0	0	*	*	0	0	AAGGTGCTTAAATTCGTGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC	IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I"IIIIIII000IIII	XM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1634:330/1	0	phiX174	4418	255	50M	*	0	0	GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
Binary file test-data/picard_RS_input3.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_RS_input3.sam	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,26 @@
+@HD	VN:1.0	SO:unsorted
+@SQ	SN:phiX1	LN:1120
+@SQ	SN:phiX2	LN:1190
+@SQ	SN:phiX3	LN:1330
+@SQ	SN:phiX4	LN:910
+@SQ	SN:phiX5	LN:828
+@PG	ID:Bowtie	VN:0.12.7	CL:"bowtie -q -p 4 -S --phred33-quals /tmp/tmp1E6jpl/tmpDg42o9 dataset_437.dat"
+HWI-EAS91_1_30788AAXX:1:1:1578:331/1	0	phiX1	209	255	50M	*	0	0	TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1761:343/1	0	phiX1	5	255	50M	*	0	0	TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA	IIIIIII""IIIIIIIIIII?I0IIIIHIIIGIIIII0II?I""IIIIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1647:512/1	0	phiX1	401	255	50M	*	0	0	TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1746:351/1	0	phiX2	98	255	50M	*	0	0	CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1582:633/1	0	phiX2	397	255	50M	*	0	0	CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1570:620/1	4	*	0	0	*	*	0	0	GAGTAACAAAGTAAAGTTTGGACCGTTTTTGTCTCGTGCTCGTCGCTGCG	IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII"IIIIIII000IIII	XM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1598:534/1	0	phiX2	597	255	50M	*	0	0	GCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1599:330/1	0	phiX1	803	255	50M	*	0	0	AGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAGTGATGTAATGTC	IIIIIII""IIIIIIIIIIIIIIIIIII<III@II"IIIIIII000IIII	XA:i:0	MD:Z:30G19	NM:i:1
+HWI-EAS91_1_30788AAXX:1:1:1749:466/1	0	phiX2	1081	255	50M	*	0	0	TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1572:324/1	4	*	0	0	*	*	0	0	AAGGTGCTTAAATTCGTGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC	IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I"IIIIIII000IIII	XM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1763:587/1	0	phiX3	191	255	50M	*	0	0	AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1616:363/1	0	phiX3	408	255	50M	*	0	0	TGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1652:270/1	4	*	0	0	*	*	0	0	AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGACTTTGCATTGTTTAATTG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II"IIIIIII000IIII	XM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1768:715/1	0	phiX3	808	255	50M	*	0	0	ACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCT	IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1572:270/1	0	phiX3	1208	255	50M	*	0	0	TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTA	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1629:446/1	4	*	0	0	*	*	0	0	AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1673:514/1	0	phiX4	378	255	50M	*	0	0	ATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1785:1272/1	0	phiX4	178	255	50M	*	0	0	TATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCT	III""""""IIIIIIIII""FI"IIII""II+ICI"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1634:330/1	0	phiX4	778	255	50M	*	0	0	GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_RS_input4.fasta	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,82 @@
+>phiX1 length=1120
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT
+GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA
+ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG
+TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA
+GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC
+TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT
+TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT
+CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT
+TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG
+TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC
+GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA
+CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCGGAAGGAG
+TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT
+AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC
+CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA
+TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC
+>phiX2 length=1190
+TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA
+CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA
+GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT
+GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA
+ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC
+TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT
+TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC
+ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAAC
+CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT
+GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC
+CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC
+TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG
+TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT
+TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA
+AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT
+TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT
+ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC
+>phiX3 length=1330
+GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC
+TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT
+TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA
+TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG
+TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC
+CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG
+AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC
+CGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT
+TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG
+CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA
+AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT
+GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG
+GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA
+TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT
+CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG
+TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA
+GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC
+CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA
+TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA
+>phiX4 length=910
+AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC
+TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT
+CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA
+TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG
+TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT
+CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT
+TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC
+ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG
+TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA
+ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG
+GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC
+CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT
+GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGATGAATGCAATGCGACAG
+>phiX5 length=828
+GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT
+ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG
+CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC
+CGTCTTCATTTCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC
+GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT
+CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG
+CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA
+TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT
+TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG
+TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC
+AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC
+TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCC
Binary file test-data/picard_RS_output1.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_RS_output2.sam	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,22 @@
+@HD	VN:1.0	SO:unsorted
+@SQ	SN:phiX174	LN:5386	UR:file:/afs/bx.psu.edu/user/kpvincent/working/phiX.fa	M5:f479307bca04825e98008f37e4f6251a
+@PG	ID:Bowtie	VN:0.12.7	CL:"bowtie -q -p 4 -S --phred33-quals /genome/phiX/bowtie_index/phiX dataset_437.dat"
+HWI-EAS91_1_30788AAXX:1:1:1761:343/1	0	phiX174	5	255	50M	*	0	0	TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA	IIIIIII""IIIIIIIIIII?I0IIIIHIIIGIIIII0II?I""IIIIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1647:512/1	0	phiX174	401	255	50M	*	0	0	TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1578:331/1	0	phiX174	209	255	50M	*	0	0	TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1746:351/1	0	phiX174	1218	255	50M	*	0	0	CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1582:633/1	0	phiX174	1517	255	50M	*	0	0	CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1599:330/1	0	phiX174	803	255	50M	*	0	0	AGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAGTGATGTAATGTC	IIIIIII""IIIIIIIIIIIIIIIIIII<III@II"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1598:534/1	0	phiX174	1717	255	50M	*	0	0	GCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1749:466/1	0	phiX174	2201	255	50M	*	0	0	TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1570:620/1	4	*	0	0	*	*	0	0	GAGTAACAAAGTAAAGTTTGGACCGTTTTTGTCTCGTGCTCGTCGCTGCG	IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII"IIIIIII000IIII	XM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1629:446/1	0	phiX174	2301	255	50M	*	0	0	AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1763:587/1	0	phiX174	2501	255	50M	*	0	0	AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1616:363/1	0	phiX174	2718	255	50M	*	0	0	TGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1572:270/1	0	phiX174	3518	255	50M	*	0	0	TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTA	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1768:715/1	0	phiX174	3118	255	50M	*	0	0	ACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCT	IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1785:1272/1	0	phiX174	3818	255	50M	*	0	0	TATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCT	III""""""IIIIIIIII""FI"IIII""II+ICI"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1673:514/1	0	phiX174	4018	255	50M	*	0	0	ATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1652:270/1	4	*	0	0	*	*	0	0	AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGACTTTGCATTGTTTAATTG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II"IIIIIII000IIII	XM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1572:324/1	4	*	0	0	*	*	0	0	AAGGTGCTTAAATTCGTGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC	IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I"IIIIIII000IIII	XM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1634:330/1	0	phiX174	4418	255	50M	*	0	0	GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_RS_output3.sam	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,26 @@
+@HD	VN:1.0	SO:unsorted
+@SQ	SN:phiX1	LN:1120	UR:picard_RS_input4.fasta	AS:phiX_buildBlah1.1	M5:40156fecb557ec9a4e0e7d0d5379d346	SP:phiX174
+@SQ	SN:phiX2	LN:1190	UR:picard_RS_input4.fasta	AS:phiX_buildBlah1.1	M5:3ecdb3921cbd184296cefdc675595fc1	SP:phiX174
+@SQ	SN:phiX3	LN:1330	UR:picard_RS_input4.fasta	AS:phiX_buildBlah1.1	M5:60435b7625ee8862e4af3e839b195198	SP:phiX174
+@SQ	SN:phiX4	LN:910	UR:picard_RS_input4.fasta	AS:phiX_buildBlah1.1	M5:ae8509d7b91ed64a44dd718513b1fd06	SP:phiX174
+@SQ	SN:phiX5	LN:828	UR:picard_RS_input4.fasta	AS:phiX_buildBlah1.1	M5:459c70115963cbce5021cac2bc9dfbd1	SP:phiX174
+@PG	ID:Bowtie	VN:0.12.7	CL:"bowtie -q -p 4 -S --phred33-quals /tmp/tmp1E6jpl/tmpDg42o9 dataset_437.dat"
+HWI-EAS91_1_30788AAXX:1:1:1570:620/1	4	*	0	0	*	*	0	0	GAGTAACAAAGTAAAGTTTGGACCGTTTTTGTCTCGTGCTCGTCGCTGCG	IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII"IIIIIII000IIII	XM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1572:270/1	0	phiX3	1208	255	50M	*	0	0	TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTA	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1572:324/1	4	*	0	0	*	*	0	0	AAGGTGCTTAAATTCGTGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC	IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I"IIIIIII000IIII	XM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1578:331/1	0	phiX1	209	255	50M	*	0	0	TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1582:633/1	0	phiX2	397	255	50M	*	0	0	CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1598:534/1	0	phiX2	597	255	50M	*	0	0	GCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1599:330/1	0	phiX1	803	255	50M	*	0	0	AGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAGTGATGTAATGTC	IIIIIII""IIIIIIIIIIIIIIIIIII<III@II"IIIIIII000IIII	XA:i:0	MD:Z:30G19	NM:i:1
+HWI-EAS91_1_30788AAXX:1:1:1616:363/1	0	phiX3	408	255	50M	*	0	0	TGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1629:446/1	4	*	0	0	*	*	0	0	AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1634:330/1	0	phiX4	778	255	50M	*	0	0	GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1647:512/1	0	phiX1	401	255	50M	*	0	0	TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1652:270/1	4	*	0	0	*	*	0	0	AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGACTTTGCATTGTTTAATTG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II"IIIIIII000IIII	XM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1673:514/1	0	phiX4	378	255	50M	*	0	0	ATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1746:351/1	0	phiX2	98	255	50M	*	0	0	CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1749:466/1	0	phiX2	1081	255	50M	*	0	0	TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1761:343/1	0	phiX1	5	255	50M	*	0	0	TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA	IIIIIII""IIIIIIIIIII?I0IIIIHIIIGIIIII0II?I""IIIIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1763:587/1	0	phiX3	191	255	50M	*	0	0	AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1768:715/1	0	phiX3	808	255	50M	*	0	0	ACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCT	IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1785:1272/1	0	phiX4	178	255	50M	*	0	0	TATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCT	III""""""IIIIIIIII""FI"IIII""II+ICI"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
Binary file test-data/picard_fastq_to_sam_out1.bam has changed
Binary file test-data/picard_fastq_to_sam_out1.bam.bai has changed
Binary file test-data/picard_fastq_to_sam_out2.bam has changed
Binary file test-data/picard_fastq_to_sam_out2.bam.bai has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_input_bait.bed	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,8 @@
+chr1	1	300	-	CCDS635.1_cds_0_0_chr1_67052401_r
+chr2	1	300	-	CCDS635.1_cds_1_0_chr1_67060632_r
+chr3	1	300	-	CCDS635.1_cds_2_0_chr1_67065091_r
+chr4	1	300	-	CCDS635.1_cds_3_0_chr1_67066083_r
+chr5	1	300	-	CCDS635.1_cds_4_0_chr1_67071856_r
+chr6	1	300	-	CCDS635.1_cds_5_0_chr1_67072262_r
+chr7	1	300	-	CCDS635.1_cds_6_0_chr1_67073897_r
+chr8	1	300	-	CCDS635.1_cds_7_0_chr1_67075981_r
Binary file test-data/picard_input_coordinate_sorted.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_input_hg18.trimmed.fasta	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,302 @@
+>chrM
+GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTT
+CGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTC
+GCAGTATCTGTCTTTGATTCCTGCCTCATTCTATTATTTATCGCACCTACGTTCAATATT
+ACAGGCGAACATACCTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATA
+ACAATTGAATGTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAAAATTTCCACCA
+AACCCCCCCCTCCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAA
+AAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTAGGCGGTATGC
+ACTTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTA
+ATCTCATCAATACAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCA
+TACCCCGAACCAACCAAACCCCAAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCA
+AAGCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATAAACAAATAGGTTTGG
+TCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAAGCATCCCCGTTCCAGTGA
+GTTCACCCTCTAAATCACCACGATCAAAAGGGACAAGCATCAAGCACGCAGCAATGCAGC
+TCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAAT
+>chr1
+AAACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACC
+GCGGTCACACGATTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCC
+CCTCCCCAATAAAGCTAAAACTCACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAG
+ACTACGAAAGTGGCTTTAACATATCTGAACACACAATAGCTAAGACCCAAACTGGGATTA
+GATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATCAACAAAACTGCTCGCCAG
+AACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATCCCTCTAGA
+GGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATA
+TACCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAA
+AGACGTTAGGTCAAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCC
+AGAAAACTACGATAGCCCTTATGAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTG
+AGAGTAGAGTGCTTAGTTGAACAGGGCCCTGAAGCGCGTACACACCGCCCGTCACCCTCC
+>chr2
+TCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCATTTATATAGAGGAGACAA
+GTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTAGCTTAACA
+CAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACC
+TAGCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAAT
+AAAGTATAGGCGATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGA
+TGAAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCTATACCTTCTGCATAATG
+AATTAACTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAAGACCCCCGAAACCAGACGAG
+CTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCAAAATAGTGGGAAGATTTA
+TAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGATAGAATCTT
+>chr3
+AGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAG
+TCCAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATT
+TAACACCCATAGTAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACC
+CACTACCTAAAAAATCCCAAACATATAACTGAACTCCTCACACCCAATTGGACCAATCTA
+TCACCCTATAGAAGAACTAATGTTAGTATAAGTAACATGAAAACATTCTCCTCCGCATAA
+GCCTGCGTCAGATCAAAACACTGAACTGACAATTAACAGCCCAATATCTACAATCAACCA
+ACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGAAAGGTTAA
+AAAAAGTAAAAGGAACTCGGCAAACCTTACCCCGCCTGTTTACCAAAAACATCACCTCTA
+GCATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACC
+CTAACCGTGCAaaggtagcataatcacttgttccttaaatagggacctgtatgaatggct
+ccacgagggttcagctgtctcttacttttaaccagtgaaattgacctgcccgtgaagagg
+cgggcatgacacagcaagacgagaagaccctatggagctttaatttaTTAATGCAAACAG
+TACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATTAAAAATTTCGGTTGGGGC
+GACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAGTCAAAGCG
+AACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAA
+CAGCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGAT
+CAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCT
+ACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTTCTATCTACTTCAAATTCCTC
+CCTGTACGAAAGGACAAGAGAAATAAGGCCTACTTCACAAAGCGCCTTCCCCCGTAAATG
+ATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGAACAGGGTTTgttaagatgg
+cagagcccggtaatcgcataaaacttaaaactttacagtcagaggttcaattcctcttct
+taacaacaTACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGC
+ATTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAA
+CGTTGTAGGCCCCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAA
+AGAGCCCCTAAAACCCGCCACATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGC
+TCTCACCATCGCTCTTCTACTATGAACCCCCCTCCCCATACCCAACCCCCTGGTCAACCT
+CAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAGCCGTTTACTCAATCCTCTG
+>chr4
+ATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGCAGTAGCCCA
+AACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGG
+CTCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCATC
+ATGACCCTTGGCCATAATATGATTTATCTCCACACTAGCAGAGACCAACCGAACCCCCTT
+CGACCTTGCCGAAGGGGAGTCCGAACTAGTCTCAGGCTTCAACATCGAATACGCCGCAGG
+CCCCTTCGCCCTATTCTTCATAGCCGAATACACAAACATTATTATAATAAACACCCTCAC
+CACTACAATCTTCCTAGGAACAACATATGACGCACTCTCCCCTGAACTCTACACAACATA
+TTTTGTCACCAAGACCCTACTTCTAACCTCCCTGTTCTTATGAATTCGAACAGCATACCC
+CCGATTCCGCTACGACCAACTCATACACCTCCTATGAAAAAACTTCCTACCACTCACCCT
+AGCATTACTTATATGATATGTCTCCATACCCATTACAATCTCCAGCATTCCCCCTCAAAC
+CTAAGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAACC
+CCCTTATTTctaggactatgagaatcgaacccatccctgagaatccaaaattctccgtgc
+cacctatcacaccccatcctaAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCC
+GAAAATGTTGGTTATACCCTTCCCGTACTAATTAATCCCCTGGCCCAACCCGTCATCTAC
+TCTACCATCTTTGCAGGCACACTCATCACAGCGCTAAGCTCGCACTGATTTTTTACCTGA
+GTAGGCCTAGAAATAAACATGCTAGCTTTTATTCCAGTTCTAACCAAAAAAATAAACCCT
+CGTTCCACAGAAGCTGCCATCAAGTATTTCCTCACGCAAGCAACCGCATCCATAATCCTT
+CTAATAGCTATCCTCTTCAACAATATACTCTCCGGACAATGAACCATAACCAATACTACC
+AATCAATACTCATCATTAATAATCATAATGGCTATAGCAATAAAACTAGGAATAGCCCCC
+TTTCACTTCTGAGTCCCAGAGGTTACCCAAGGCACCCCTCTGACATCCGGCCTGCTTCTT
+CTCACATGACAAAAACTAGCCCCCATCTCAATCATATACCAAATCTCTCCCTCACTAAAC
+GTAAGCCTTCTCCTCACTCTCTCAATCTTATCCATCATAGCAGGCAGTTGAGGTGGATTA
+AACCAAACCCAGCTACGCAAAATCTTAGCATACTCCTCAATTACCCACATAGGATGAATA
+ATAGCAGTTCTACCGTACAACCCTAACATAACCATTCTTAATTTAACTATTTATATTATC
+CTAACTACTACCGCATTCCTACTACTCAACTTAAACTCCAGCACCACGACCCTACTACTA
+TCTCGCACCTGAAACAAGCTAACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCC
+CTAGGAGGCCTGCCCCCGCTAACCGGCTTTTTGCCCAAATGGGCCATTATCGAAGAATTC
+ACAAAAAACAATAGCCTCATCATCCCCACCATCATAGCCACCATCACCCTCCTTAACCTC
+TACTTCTACCTACGCCTAATCTACTCCACCTCAATCACACTACTCCCCATATCTAACAAC
+>chr5
+GTAAAAATAAAATGACAGTTTGAACATACAAAACCCACCCCATTCCTCCCCACACTCATC
+GCCCTTACCACGCTACTCCTACCTATCTCCCCTTTTATACTAATAATCTTATAGAAATTT
+AGGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCTG
+CAACAGCTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTA
+ATTAAGCTAAGCCCTTACTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAGC
+TAAGCACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCCGCCGGGAAAAAAGGCGGGA
+GAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAATCACCT
+CGGAGCTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCACTC
+AGCCATTTTACCTCACCCCCACTGATGTTCGCCGACCGTTGACTATTCTCTACAAACCAC
+AAAGACATTGGAACACTATACCTATTATTCGGCGCATGAGCTGGAGTCCTAGGCACAGCT
+CTAAGCCTCCTTATTCGAGCCGAGCTGGGCCAGCCAGGCAACCTTCTAGGTAACGACCAC
+ATCTACAACGTTATCGTCACAGCCCATGCATTTGTAATAATCTTCTTCATAGTAATACCC
+ATCATAATCGGAGGCTTTGGCAACTGACTAGTTCCCCTAATAATCGGTGCCCCCGATATG
+GCGTTTCCCCGCATAAACAACATAAGCTTCTGACTCTTACCTCCCTCTCTCCTACTCCTG
+CTCGCATCTGCTATAGTGGAGGCCGGAGCAGGAACAGGTTGAACAGTCTACCCTCCCTTA
+GCAGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTCCTTACACCTA
+GCAGGTGTCTCCTCTATCTTAGGGGCCATCAATTTCATCACAACAATTATCAATATAAAA
+CCCCCTGCCATAACCCAATACCAAACGCCCCTCTTCGTCTGATCCGTCCTAATCACAGCA
+GTCCTACTTCTCCTATCTCTCCCAGTCCTAGCTGCTGGCATCACTATACTACTAACAGAC
+CGCAACCTCAACACCACCTTCTTCGACCCCGCCGGAGGAGGAGACCCCATTCTATACCAA
+CACCTATTCTGATTTTTCGGTCACCCTGAAGTTTATATTCTTATCCTACCAGGCTTCGGA
+ATAATCTCCCATATTGTAACTTACTACTCCGGAAAAAAAGAACCATTTGGATACATAGGT
+ATGGTCTGAGCTATGATATCAATTGGCTTCCTAGGGTTTATCGTGTGAGCACACCATATA
+>chr6
+TTTACAGTAGGAATAGACGTAGACACACGAGCATATTTCACCTCCGCTACCATAATCATC
+GCTATCCCCACCGGCGTCAAAGTATTTAGCTGACTCGCCACACTCCACGGAAGCAATATG
+AAATGATCTGCTGCAGTGCTCTGAGCCCTAGGATTCATCTTTCTTTTCACCGTAGGTGGC
+CTGACTGGCATTGTATTAGCAAACTCATCACTAGACATCGTACTACACGACACGTACTAC
+GTTGTAGCTCACTTCCACTATGTCCTATCAATAGGAGCTGTATTTGCCATCATAGGAGGC
+TTCATTCACTGATTTCCCCTATTCTCAGGCTACACCCTAGACCAAACCTACGCCAAAATC
+CATTTCACTATCATATTCATCGGCGTAAATCTAACTTTCTTCCCACAACACTTTCTCGGC
+CTATCCGGAATGCCCCGACGTTACTCGGACTACCCCGATGCATACACCACATGAAACATC
+CTATCATCTGTAGGCTCATTCATTTCTCTAACAGCAGTAATATTAATAATTTTCATGATT
+TGAGAAGCCTTCGCTTCGAAGCGAAAAGTCCTAATAGTAGAAGAACCCTCCATAAACCTG
+GAGTGACTATATGGATGCCCCCCACCCTACCACACATTCGAAGAACCCGTATACATAAAA
+TCTAGACAaaaaaggaaggaatcgaaccccccaaagctggtttcaagccaaccccatggc
+ctccatgactttttcAAAAAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAAA
+TTATAGGCTAAATCCTATATATCTTAATGGCACATGCAGCGCAAGTAGGTCTACAAGACG
+CTACTTCCCCTATCATAGAAGAGCTTATCACCTTTCATGATCACGCCCTCATAATCATTT
+TCCTTATCTGCTTCCTAGTCCTGTATGCCCTTTTCCTAACACTCACAACAAAACTAACTA
+ATACTAACATCTCAGACGCTCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATCA
+TCCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTACATAACAGACGAGGTCAACG
+ATCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTACTGAACCTACGAGTACACCG
+ACTACGGCGGACTAATCTTCAACTCCTACATACTTCCCCCATTATTCCTAGAACCAGGCG
+>chr7
+ACCTGCGACTCCTTGACGTTGACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGTA
+TAATAATTACATCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTAAAAA
+CAGATGCAATTCCCGGACGTCTAAACCAAACCACTTTCACCGCTACACGACCGGGGGTAT
+ACTACGGTCAATGCTCTGAAATCTGTGGAGCAAACCACAGTTTCATGCCCATCGTCCTAG
+AATTAATTCCCCTAAAAATCTTTGAAATAGGGCCCGTATTTACCCTATAGCACCCCCTCT
+ACCCCCTCTAGAGCCCACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTAA
+GAGAACCAACACCTCTTTACAGTGAAATGCCCCAACTAAATACTACCGTATGGCCCACCA
+TAATTACCCCCATACTCCTTACACTATTCCTCATCACCCAACTAAAAATATTAAACACAA
+ACTACCACCTACCTCCCTCACCAAAGCCCATAAAAATAAAAAATTATAACAAACCCTGAG
+AACCAAAATGAACGAAAATCTGTTCGCTTCATTCATTGCCCCCACAATCCTAGGCCTACC
+CGCCGCAGTACTGATCATTCTATTTCCCCCTCTATTGATCCCCACCTCCAAATATCTCAT
+>chr8
+CAACAACCGACTAATCACCACCCAACAATGACTAATCAAACTAACCTCAAAACAAATGAT
+AGCCATACACAACACTAAAGGACGAACCTGATCTCTTATACTAGTATCCTTAATCATTTT
+TATTGCCACAACTAACCTCCTCGGACTCCTGCCTCACTCATTTACACCAACCACCCAACT
+ATCTATAAACCTAGCCATGGCCATCCCCTTATGAGCGGGCGCAGTGATTATAGGCTTTCG
+CTCTAAGATTAAAAATGCCCTAGCCCACTTCTTACCACAAGGCACACCTACACCCCTTAT
+CCCCATACTAGTTATTATCGAAACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGT
+ACGCCTAACCGCTAACATTACTGCAGGCCACCTACTCATGCACCTAATTGGAAGCGCCAC
+CCTAGCAATATCAACCATTAACCTTCCCTCTACACTTATCATCTTCACAATTCTAATTCT
+ACTGACTATCCTAGAAATCGCTGTCGCCTTAATCCAAGCCTACGTTTTCACACTTCTAGT
+AAGCCTCTACCTGCACGACAACACATAATGACCCACCAATCACATGCCTATCATATAGTA
+AAACCCAGCCCATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCTA
+GCCATGTGATTTCACTTCCACTCCATAACGCTCCTCATACTAGGCCTACTAACCAACACA
+CTAACCATATACCAATGGTGGCGCGATGTAACACGAGAAAGCACATACCAAGGCCACCAC
+ACACCACCTGTCCAAAAAGGCCTTCGATACGGGATAATCCTATTTATTACCTCAGAAGTT
+TTTTTCTTCGCAGGATTTTTCTGAGCCTTTTACCACTCCAGCCTAGCCCCTACCCCCCAA
+CTAGGAGGGCACTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAAGTCCCACTC
+CTAAACACATCCGTATTACTCGCATCAGGAGTATCAATCACCTGAGCTCACCATAGTCTA
+ATAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTATTACAATTTTACTGGGTCTC
+TATTTTACCCTCCTACAAGCCTCAGAGTACTTCGAGTCTCCCTTCACCATTTCCGACGGC
+>chr9
+ATCTACGGCTCAACATTTTTTGTAGCCACAGGCTTCCACGGACTTCACGTCATTATTGGC
+TCAACTTTCCTCACTATCTGCTTCATCCGCCAACTAATATTTCACTTTACATCCAAACAT
+CACTTTGGCTTCGAAGCCGCCGCCTGATACTGGCATTTTGTAGATGTGGTTTGACTATTT
+CTGTATGTCTCCATCTATTGATGAGGGTCTTACTCTTTTAGTATAAATAGTACCGTTAAC
+TTCCAATTAACTAGTTTTGACAACATTCAAAAAAGAGTAATAAACTTCGCCTTAATTTTA
+ATAATCAACACCCTCCTAGCCTTACTACTAATAATTATTACATTTTGACTACCACAACTC
+AACGGCTACATAGAAAAATCCACCCCTTACGAGTGCGGCTTCGACCCTATATCCCCCGCC
+CGCGTCCCTTTCTCCATAAAATTCTTCTTAGTAGCTATTACCTTCTTATTATTTGATCTA
+GAAATTGCCCTCCTTTTACCCCTACCATGAGCCCTACAAACAACTAACCTGCCACTAATA
+GTTATGTCATCCCTCTTATTAATCATCATCCTAGCCCTAAGTCTGGCCTATGAGTGACTA
+CAAAAAGGATTAGACTGAGCCGAATTGGTATATAGTTTAAACAAAACGAATGATTTCGAC
+TCATTAAATTATGATAATCATATTTACCAAATGCCCCTCATTTACATAAATATTATACTA
+GCATTTACCATCTCACTTCTAGGAATACTAGTATATCGCTCACACCTCATATCCTCCCTA
+CTATGCCTAGAAGGAATAATACTATCGCTGTTCATTATAGCTACTCTCATAACCCTCAAC
+ACCCACTCCCTCTTAGCCAATATTGTGCCTATTGCCATACTAGTCTTTGCCGCCTGCGAA
+GCAGCGGTGGGCCTAGCCCTACTAGTCTCAATCTCCAACACATATGGCCTAGACTACGTA
+CATAACCTAAACCTACTCCAATGCTAAAACTAATCGTCCCAACAATTATATTACTACCAC
+TGACATGACTTTCCAAAAAGCACATAATTTGAATCAACACAACCACCCACAGCCTAATTA
+>chr10
+TTAGCATCATCCCCCTACTATTTTTTAACCAAATCAACAACAACCTATTTAGCTGTTCCC
+CAACCTTTTCCTCCGACCCCCTAACAACCCCCCTCCTAATACTAACTACCTGACTCCTAC
+CCCTCACAATCATGGCAAGCCAACGCCACTTATCCAGCGAACCACTATCACGAAAAAAAC
+TCTACCTCTCTATACTAATCTCCCTACAAATCTCCTTAATTATAACATTCACAGCCACAG
+AACTAATCATATTTTATATCTTCTTCGAAACCACACTTATCCCCACCTTGGCTATCATCA
+CCCGATGAGGCAACCAGCCAGAACGCCTGAACGCAGGCACATACTTCCTATTCTACACCC
+TAGTAGGCTCCCTTCCCCTACTCATCGCACTAATTTACACTCACAACACCCTAGGCTCAC
+TAAACATTCTACTACTCACTCTCACTGCCCAAGAACTATCAAACTCCTGAGCCAACAACT
+TAATATGACTAGCTTACACAATAGCTTTTATAGTAAAGATACCTCTTTACGGACTCCACT
+TATGACTCCCTAAAGCCCATGTCGAAGCCCCCATCGCTGGGTCAATAGTACTTGCCGCAG
+TACTCTTAAAACTAGGCGGCTATGGTATAATACGCCTCACACTCATTCTCAACCCCCTGA
+CAAAACACATAGCCTACCCCTTCCTTGTACTATCCCTATGAGGCATAATTATAACAAGCT
+CCATCTGCCTACGACAAACAGACCTAAAATCGCTCATTGCATACTCTTCAATCAGCCACA
+TAGCCCTCGTAGTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCGGCGCAGTCA
+TTCTCATAATCGCCCACGGACTCACATCCTCATTACTATTCTGCCTAGCAAACTCAAACT
+ACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCAC
+TAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTA
+ACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCC
+TACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAA
+CACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAAA
+ACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACCCCGACATCA
+TTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACA
+ACAGAGGCTTACGACCCCTTATTTACCGAGAAAGCTCACAAGAACTGCTAACTCATGCCC
+CCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTA
+GGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAAC
+CACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACAA
+AAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTCT
+CTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTG
+AGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTTCAAACTAGACTACTTCTCCATAAT
+ATTCATCCCTGTAGCATTGTTCGTTACATGGTCCATCATAGAATTCTCACTGTGATATAT
+AAACTCAGACCCAAACATTAATCAGTTCTTCAAATATCTACTCATTTTCCTAATTACCAT
+>chr11
+ACTAATCTTAGTTACCGCTAACAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGG
+AATTATATCCTTCTTGCTCATCAGTTGATGATACGCCCGAGCAGATGCCAACACAGCAGC
+CATTCAAGCAGTCCTATACAACCGTATCGGCGATATCGGTTTCATCCTCGCCTTAGCATG
+ATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAACGCTAATCC
+AAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGG
+TCTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCA
+CTCAAGCACTATAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGA
+AAATAGCCCACTAATCCAAACTCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGC
+AGCAGTCTGCGCCCTTACACAAAATGACATCAAAAAAATCGTAGCCTTCTCCACTTCAAG
+TCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAACCACACCTAGCATTCCTGCA
+CATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTCCATCATCCA
+CAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCT
+CACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGG
+TTTCTACTCCAAAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAGC
+CCTATCTATTACTCTCATCGCTACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTCT
+TCTCACCCTAACAGGTCAACCTCGCTTCCCCACCCTTACTAACATTAACGAAAATAACCC
+CACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCCTATTCGCAGGATTTCTCAT
+TACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTACCTAAAACT
+>chr12
+CACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAAC
+CAACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATT
+CTACCCTAGCATCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCT
+GCCCCTACTCCTCCTAGACCTAACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACA
+GCACCAAATCTCCACCTCCATCATCACCTCAACCCAAAAAGGCATAATTAAACTTTACTT
+CCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAATCACATAACCTATTCCCCC
+GAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAACCACTACTA
+ATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCTG
+ACCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCA
+CCCCATCATACTCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAA
+CACTCACCAAGACCTCAACCCCTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATCG
+CTGTAGTATATCCAAAGACAACCATCATTCCCCCTAAATAAATTAAAAAAACTATTAAAC
+CCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCGACCACACCGCTAACAATCA
+GTACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACCCCATTACTA
+AACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGA
+CCAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATAC
+GCAAAATTAACCCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCAT
+CCAACATCTCCGCATGATGAAACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAAA
+TCACCACAGGACTATTCCTAGCCATACACTACTCACCAGACGCCTCAACCGCCTTTTCAT
+CAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATCATCCGCTACCTTCACGCCA
+ATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCCTATATTACG
+GATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATAG
+CAACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACAG
+TAATTACAAACTTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCT
+GAGGAGGCTACTCAGTAGACAGTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCT
+TACCCTTCATTATTGCAGCCCTAGCAGCACTCCACCTCCTATTCTTGCACGAAACGGGAT
+CAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATCACCTTCCACCCTTACTACA
+CAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACATTAACACTAT
+TCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCC
+CTCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCC
+CTAACAAACTAGGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATCC
+CCATCCTCCATATATCCAAACAACAAAGCATAATATTTCGCCCACTAAGCCAATCACTTT
+ATTGACTCCTAGCCGCAGACCTCCTCATTCTAACCTGAATCGGAGGACAACCAGTAAGCT
+>chr13
+ACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATACTTCACAACAATCCTAATCC
+TAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTCCTTGTAGTA
+TAAACTAATACACCAGTCTTGTAAACCGGAGACGAAAACCTTTTTCCAAGGACAAATCAG
+AGAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTC
+TCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAAC
+AACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAA
+TACTTGACCACCTGTAGTACATAAAAACCCAACCCACATCAAACCCCCCCCCCCCATGCT
+TACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA
+CCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAA
+GTCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCC
+CCTCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTG
+CTACTCTCCTCGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGAC
+ATCTGGTTCCTACTTCAGGGCCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAG
+ACATCACGATG
+>chr20
+NNNNNNNNNNNNNNNNNNNNGATCCAgaggtggaagaggaaggaagcttggaaccctata
+gagttgctgagtgccaggaccagatcctggccctaaacaggtggtaaggaaggagagagt
+gaaggaactgccaggtgacacactcccaccatggacctctgggatcctagctttaagaga
+tcccatcacccacatgaacgtttgaattgacagggggagctgcctggagagtaggcagat
+gcagagctcaagcctgtgcagagcccaggttttgtgagtgggacagttgcagcaaaacac
+aaccataggtgcccatccaccaaggcaggctctccatcttgctcagagtggctctagccc
+ttgctgactgctgggcagggagagagcagagctaacttcctcatgggacctgggtgtgtc
+tgatctgtgcacaccactatccaaccgatcccgaggctccaccctggccactcttgtgtg
+cacacagcacagcctctactgctacacctgagtactttgccagtggcctggaagcacttt
+gtcccccctggcacaaatggtgctggaccacgaggggccagagaacaaagccttgggcgt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_input_sorted_pair.bam	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,10 @@
+bar:record:1	77	chr1	10	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:rg1
+bar:record:1	141	chr1	20	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:rg1
+bar:record:2	77	chr2	10	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:rg1
+bar:record:2	141	chr2	30	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:rg1
+bar:record:3	77	chr1	10	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:rg1
+bar:record:3	141	chr3	20	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:rg1
+bar:record:4	77	chr1	1	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:rg1
+bar:record:4	141	chr1	40	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:rg1
+bar:record:5	77	chr1	40	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:rg1
+bar:record:5	141	chr3	40	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:rg1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_input_sorted_pair.sam	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,15 @@
+@HD	VN:1.0	SO:coordinate
+@SQ	SN:chr1	LN:10001
+@SQ	SN:chr2	LN:10001
+@SQ	SN:chr3	LN:10001
+@RG	ID:rg1	SM:Z
+bar:record:1	77	chr1	10	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:rg1
+bar:record:1	141	chr1	20	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:rg1
+bar:record:2	77	chr1	40	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:rg1
+bar:record:2	141	chr1	50	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:rg1
+bar:record:3	77	chr2	10	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:rg1
+bar:record:3	141	chr2	20	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:rg1
+bar:record:4	77	chr2	50	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:rg1
+bar:record:4	141	chr2	60	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:rg1
+bar:record:5	77	chr3	40	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:rg1
+bar:record:5	141	chr3	50	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:rg1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_input_summary_alignment_stats.sam	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,28 @@
+@HD	VN:1.0	SO:coordinate
+@SQ	SN:chr1	LN:255
+@SQ	SN:chr2	LN:255
+@SQ	SN:chr3	LN:255
+@SQ	SN:chr4	LN:255
+@SQ	SN:chr5	LN:255
+@SQ	SN:chr6	LN:255
+@SQ	SN:chr7	LN:255
+@SQ	SN:chr8	LN:255
+@RG	ID:0	SM:Hi,Mom!
+SL-XAV:1:1:0:764#0/1	89	chr1	1	255	101M	*	0	0	TTCATGCTGANGCNCTCTTACGATCGTACAGATGCAAATATTAACANNCNTTNAAGNNCANNNNNNNNNCAATACAATANTAGAGTACGTNAACACTCCAN	&/,&-.1/6/&&)&).)/,&0768)&/.,/874,&.4137572)&/&&,&1-&.0/&&*,&&&&&&&&&&18775799,&16:8775-56256/69::;0&	RG:Z:0	XN:i:1
+SL-XAV:1:1:0:1668#0/2	153	chr2	1	255	101M	*	0	0	CATCTCTACANGCGCGTCCTACCAGACGCGCTTCCGATCTGAGAGCATACTTTTCATTGGATTCCAGCACAACTCCATTTTTGATCCACTNGACACCTTTN	(/,'-/'0////(1'&&1&&&&'2''-6/,/3-33653.6:1'.86/-++32.-4864653/5/583/346423203+28888644446688456/4880&	RG:Z:0	XN:i:1
+SL-XAV:1:1:0:1914#0/2	153	chr3	1	255	101M	*	0	0	CGTATGCGCTNTTTATGTCGCCCACAGTGCCTAGTATAGCCCCTGCTAATAAAAAGAGATGAATACGTTTACTTAAAAAACTGAAACTAGNAATGTGCAAN	(0,7&&*/*0*,)10/).-*&.&*/6669.&-337599;3,&,6/.,5::999987893+387020775777547999::668997448:::9;999::0&	RG:Z:0
+SL-XAV:1:1:0:1639#0/2	153	chr4	1	255	101M	*	0	0	CGTGATACCANCTCATGTTCACAGCCAAAGCCTGAAGCTGTCTATTATATTTCTCAACCATAAACTTTTGCCTCAGGCATCCGCAGAATGNTTTGCAGCCN	'.&.&&'.0+01'2(1'(''-)','+0041/.+032;:867115/5267-.0/)-5.&-26200224,,0+0/0275/5605688::646875568882*&	RG:Z:0
+SL-XAV:1:1:0:68#0/2	137	chr5	1	255	101M	*	0	0	NTCTCATTTANAAATGGTTATAAAAACATTTATGCTGAAAAGGTGAAGTTCATTAATGAACAGGCTGACTGTCTCACTATCGCGTTCGCANGACGTTATCT	&1<<999;;;;<<<87579:556972789977444.'.023.&,7621/54.49.)/53055-22--''+(.'-))6-168/(3&&0(<).))*&&&&&'0	RG:Z:0
+SL-XAV:1:1:0:700#0/2	137	chr6	1	255	101M	*	0	0	NAATTGTTCTNAGTTTCTCGGTTTATGTGCTCTTCCAGGTGGGTAACACAATAATGGCCTTCCAGATCGTAAGAGCGACGTGTGTTGCACNAGTGTCGATC	&0::887::::6/646::838388811/679:87640&./2+/-4/28:3,536/4''&&.78/(/554/./02*)*',-(57()&.6(6:(0601'/(,*	RG:Z:0
+SL-XAV:1:1:0:1721#0/1	83	chr7	1	255	101M	=	102	40	CAACAGAAGGNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCGAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
+SL-XAV:1:1:0:1721#0/2	163	chr7	102	255	101M	=	1	-40	NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTCACTATGGTACATCTTGTCGTGCGGCNAGAGCATACA	&/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1	RG:Z:0
+SL-XAV:1:1:0:105#0/2	147	chr8	1	255	101M	=	102	79	CACATCGTGANTCTTACAATCTGCGGTTTCAGATGTGGAGCGATGTGTGAGAGATTGAGCAACTGATCTGAAAAGCAGACACAGCTATTCNTAAGATGACN	/))3--/&*()&)&&+'++.'-&,(.))'4,)&'&&,')8,&&*'.&*0'225/&)3-8//)*,5-*).7851453583.3568526:863688:::85.&	RG:Z:0
+SL-XAV:1:1:0:105#0/1	99	chr8	102	255	101M	=	1	-79	NCAGGTTCAANTGTGCAGCCCNTTTTGAGAGATNNNNNNNNTGNNCTGNAANANNGACACAGCTATTCCTAAGATGACAAGATCAGANAANAAGTCAAGCA	&06665578::41.*/7577/&/77403-324.&&&&&&&&/.&&..&&.0&&&&',:9:/-/(55002020+3'12+2/&.2-&//&),&*&&&&&&&51	RG:Z:0
+SL-XAV:1:1:0:1300#0/1	77	*	0	0	*	*	0	0	NAAACACAAGNNANAGTCTTANCNGCTATTCCNNNNNNNNNCTNNNCTNAGNANNACATACAACAGTATCCACACAAGTGTACTCGTNCANACATGTGAAC	&*5535)*-,,&.&.*-1)*,&'&)&1&&.,)&&&&&&&&&)0&&&0'&&&&.&&*2'/4''0/**&)&,'-&*,&,&&&.0.&)&&&**&,.&&&')&&)	RG:Z:0
+SL-XAV:1:1:0:1300#0/2	141	*	0	0	*	*	0	0	NGATCATGGANGACTCTCCCCATCCCCCGCTCCAGCGCTCAGTTATATGCCTAGCCTCGGACACGTCACCAACATCTCACGCACTCTGCANAGTCTCTCAC	&&'+''3*&-/)/1'26/*-2-/542-*&-&/'/*/&-'&)-')&.'-/&&2+122*'&+,(/-&)((,/-,,.'2(2'+)/&/&-66-&&/16&)&*&'3	RG:Z:0
+SL-XAV:1:1:0:1639#0/1	101	*	0	0	*	chr1	1	0	NCCCTCTCAGNNTNTCTGCCANANCCTTAAGCNNNNNNNNNTANNNCTNAANCNNAAACTTTTGCCTCAGGCATCCGCAGAATGTTTNTCNGCCTATATCG	&1::::::64/&/&0:3.280&/&087881,/&&&&&&&&&..&&&..&,,&-&&,265341-)/5680&-.5552-25/322/42/&)&&).421&-&-/	RG:Z:0
+SL-XAV:1:1:0:1668#0/1	101	*	0	0	*	chr2	1	0	NATAGCATACNNTNCATTGGANTNCAGCACAANNNNNNNNNTGNNNCANTNNANNCCTTTGAGATCGGAAGAGCGGTTCAGCAGGAANNCNCAGACCGATC	&1988998890&0&.8863//&.&.0-2875.&&&&&&&&&.)&&&..&.&&.&&.5782-2+262)&-0-0510*.332-2.-,0*&&*&'.&-2-)0.,	RG:Z:0
+SL-XAV:1:1:0:1914#0/1	101	*	0	0	*	chr3	1	0	NTTTTTCTCCNNCNGTGCCTANTNTAGCCCCTNNNNNNNNNAANNNATNANNANNTTTACTTAAAAAACTGAAACTAGTAATGTGCANNANATCGNAAGAG	&0::::<<;90&/&.244760&,&.414798/&&&&&&&&&00&&&0.&/&&-&&.4475687363504.&.557/.*)65.&/*./&&.&.+*)&..).&	RG:Z:0
+SL-XAV:1:1:0:68#0/1	581	*	0	0	*	chr4	1	0	NAATATTCATNNGNTCAGCCTNTNCATTAATTNNNNNNNNNTTNNNATNATNANNTTTTTTATAACCATTTATAAATGAGAGAGATCNTANCACAATATCA	&0<<:::::</&&&.73'290&.&0;:::90&&&&&&&&&&..&&&0)&0-&0&&&.743799995253348597921.,.'050.*&.0&)*)&&&&*).	RG:Z:0
+SL-XAV:1:1:0:700#0/1	581	*	0	0	*	chr5	1	0	NGAAGCCCATNNTNGTGTTACNCNCCTGGAAGNNNNNNNNNACNNNGANACNTNNAACAATTCAGATCGGAAGAGCGGTTCAGCAGANNTNCCGAGACCGA	&.88888:88/&0&,03189.&/&.8/))12/&&&&&&&&&./&&&&.&1.&)&&/35962/6432-3&),0&/2+0,),61&-6,&&&'&/,.0&...)0	RG:Z:0
+SL-XAV:1:1:0:764#0/2	165	*	0	0	*	chr6	1	0	NACAGATGCANATATTAACAGGCTTTAAAGGACAGATGGACTGCAATACAATAATAGAGTACGTCAACACTCCACAGATCGCTAGAGCATNACATCGGTGT	&/:5358::9999::99998255::7275,,/5567-'+387537857:54-4.51'31059547320;73/720+22.4(6.;((.;(;8()(''&&2&&	RG:Z:0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_input_tiny.sam	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,14 @@
+@HD	VN:1.0	SO:queryname
+@SQ	SN:chr1	LN:101
+@SQ	SN:chr7	LN:404
+@SQ	SN:chr8	LN:202
+@RG	ID:0	SM:Hi,Mom!
+@PG	ID:1	PN:Hey!	VN:2.0
+both_reads_align_clip_adapter	99	chr7	21	255	101M	=	16	96	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
+both_reads_align_clip_adapter	147	chr7	16	255	101M	=	21	-96	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
+both_reads_align_clip_marked	83	chr7	1	255	101M	=	302	201	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
+both_reads_align_clip_marked	163	chr7	302	255	101M	=	1	-201	NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA	&/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1	RG:Z:0
+both_reads_present_only_first_aligns	89	chr7	1	255	101M	*	0	0	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
+both_reads_present_only_first_aligns	165	*	0	0	*	chr7	1	0	NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA	&/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1	RG:Z:0
+read_2_too_many_gaps	83	chr7	1	255	101M	=	302	201	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
+read_2_too_many_gaps	163	chr7	302	255	10M1D10M5I76M	=	1	-201	NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA	&/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1	RG:Z:0
Binary file test-data/picard_input_tiny_coord.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_input_tiny_coord.sam	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,14 @@
+@HD	VN:1.0	SO:coordinate
+@SQ	SN:chr1	LN:101
+@SQ	SN:chr7	LN:404
+@SQ	SN:chr8	LN:202
+@RG	ID:0	SM:Hi,Mom!
+@PG	ID:1	PN:Hey!	VN:2.0
+both_reads_align_clip_marked	83	chr7	1	255	101M	=	302	201	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
+both_reads_present_only_first_aligns	89	chr7	1	255	101M	*	0	0	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
+read_2_too_many_gaps	83	chr7	1	255	101M	=	302	201	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
+both_reads_align_clip_adapter	147	chr7	16	255	101M	=	21	-96	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
+both_reads_align_clip_adapter	99	chr7	21	255	101M	=	16	96	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
+both_reads_align_clip_marked	163	chr7	302	255	101M	=	1	-201	NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA	&/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1	RG:Z:0
+read_2_too_many_gaps	163	chr7	302	255	10M1D10M5I76M	=	1	-201	NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA	&/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1	RG:Z:0
+both_reads_present_only_first_aligns	165	*	0	0	*	chr7	1	0	NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA	&/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1	RG:Z:0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_output_AsMetrics_indexed_hg18_sorted_pair.html	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,57 @@
+<style type="text/css">
+        tr.d0 td {background-color: oldlace; color: black;}
+        tr.d1 td {background-color: aliceblue; color: black;}
+        </style><?xml version="1.0" encoding="utf-8" ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<meta name="generator" content="Galaxy picard_wrapper tool output - see http://getgalaxy.org/" />
+<title></title>
+<link rel="stylesheet" href="/static/style/base.css" type="text/css" />
+</head>
+<body>
+<div class="document">
+Galaxy tool CollectAlignmentSummaryMetrics run at 11/11/2011 08:07:27</b><br/><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table>
+<tr><td><a href="CollectAlignmentSummaryMetrics.log">CollectAlignmentSummaryMetrics.log</a></td></tr>
+<tr><td><a href="CollectAlignmentSummaryMetrics.metrics.txt">CollectAlignmentSummaryMetrics.metrics.txt</a></td></tr>
+</table><p/>
+<b>Picard on line resources</b><ul>
+<li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li>
+<li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/>
+<b>Picard output (transposed to make it easier to see)</b><hr/>
+<table cellpadding="3" >
+<tr class="d0"><td colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/data/tmp/tmpLLcl1w/database/files/000/dataset_4.dat OUTPUT=/data/home/rlazarus/galaxy/database/job_working_directory/5/dataset_5_files/CollectAlignmentSummaryMetrics.metrics.txt REFERENCE_SEQUENCE=/data/home/rlazarus/galaxy/database/job_working_directory/5/dataset_5_files/hg19.fa_fake.fasta ASSUME_SORTED=true TMP_DIR=[/tmp] VALIDATION_STRINGENCY=LENIENT    METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false</td></tr><tr class="d0"><td colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># Started on: Fri Nov 11 08:07:22 EST 2011</td></tr><tr class="d0"><td colspan="2">## METRICS CLASS	net.sf.picard.analysis.AlignmentSummaryMetrics</td></tr><tr class="d0"><td>CATEGORY</td><td>FIRST_OF_PAIR&nbsp;</td></tr>
+<tr class="d1"><td>TOTAL_READS</td><td>5&nbsp;</td></tr>
+<tr class="d0"><td>PF_READS</td><td>5&nbsp;</td></tr>
+<tr class="d1"><td>PCT_PF_READS</td><td>1&nbsp;</td></tr>
+<tr class="d0"><td>PF_NOISE_READS</td><td>0&nbsp;</td></tr>
+<tr class="d1"><td>PF_READS_ALIGNED</td><td>0&nbsp;</td></tr>
+<tr class="d0"><td>PCT_PF_READS_ALIGNED</td><td>0&nbsp;</td></tr>
+<tr class="d1"><td>PF_ALIGNED_BASES</td><td>0&nbsp;</td></tr>
+<tr class="d0"><td>PF_HQ_ALIGNED_READS</td><td>0&nbsp;</td></tr>
+<tr class="d1"><td>PF_HQ_ALIGNED_BASES</td><td>0&nbsp;</td></tr>
+<tr class="d0"><td>PF_HQ_ALIGNED_Q20_BASES</td><td>0&nbsp;</td></tr>
+<tr class="d1"><td>PF_HQ_MEDIAN_MISMATCHES</td><td>0&nbsp;</td></tr>
+<tr class="d0"><td>PF_MISMATCH_RATE</td><td>0&nbsp;</td></tr>
+<tr class="d1"><td>PF_HQ_ERROR_RATE</td><td>0&nbsp;</td></tr>
+<tr class="d0"><td>PF_INDEL_RATE</td><td>0&nbsp;</td></tr>
+<tr class="d1"><td>MEAN_READ_LENGTH</td><td>13&nbsp;</td></tr>
+<tr class="d0"><td>READS_ALIGNED_IN_PAIRS</td><td>0&nbsp;</td></tr>
+<tr class="d1"><td>PCT_READS_ALIGNED_IN_PAIRS</td><td>0&nbsp;</td></tr>
+<tr class="d0"><td>BAD_CYCLES</td><td>0&nbsp;</td></tr>
+<tr class="d1"><td>STRAND_BALANCE</td><td>0&nbsp;</td></tr>
+<tr class="d0"><td>PCT_CHIMERAS</td><td>0&nbsp;</td></tr>
+<tr class="d1"><td>PCT_ADAPTER</td><td>0&nbsp;</td></tr>
+<tr class="d0"><td>SAMPLE</td><td>&nbsp;</td></tr>
+<tr class="d1"><td>LIBRARY</td><td>&nbsp;</td></tr>
+<tr class="d0"><td>READ_GROUP
+</td><td>
+&nbsp;</td></tr>
+</table>
+<b>Picard Tool Run Log</b><hr/>
+<pre>INFO:root:## executing java -Xmx4g -jar /data/home/rlazarus/galaxy/tool-data/shared/jars/picard/CollectAlignmentSummaryMetrics.jar VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true  ADAPTER_SEQUENCE= IS_BISULFITE_SEQUENCED=false MAX_INSERT_SIZE=100000 OUTPUT=/data/home/rlazarus/galaxy/database/job_working_directory/5/dataset_5_files/CollectAlignmentSummaryMetrics.metrics.txt R=/data/home/rlazarus/galaxy/database/job_working_directory/5/dataset_5_files/hg19.fa_fake.fasta TMP_DIR=/tmp INPUT=/data/tmp/tmpLLcl1w/database/files/000/dataset_4.dat returned status 0 and nothing on stderr
+
+</pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> 
+generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_output_GcBias_uploaded_hg18_summary_alignment_stats.html	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,28 @@
+@HD	VN:1.0	SO:coordinate
+@SQ	SN:chr1	LN:255
+@SQ	SN:chr2	LN:255
+@SQ	SN:chr3	LN:255
+@SQ	SN:chr4	LN:255
+@SQ	SN:chr5	LN:255
+@SQ	SN:chr6	LN:255
+@SQ	SN:chr7	LN:255
+@SQ	SN:chr8	LN:255
+@RG	ID:0	SM:Hi,Mom!
+SL-XAV:1:1:0:764#0/1	89	chr1	1	255	101M	*	0	0	TTCATGCTGANGCNCTCTTACGATCGTACAGATGCAAATATTAACANNCNTTNAAGNNCANNNNNNNNNCAATACAATANTAGAGTACGTNAACACTCCAN	&/,&-.1/6/&&)&).)/,&0768)&/.,/874,&.4137572)&/&&,&1-&.0/&&*,&&&&&&&&&&18775799,&16:8775-56256/69::;0&	RG:Z:0	XN:i:1
+SL-XAV:1:1:0:1668#0/2	153	chr2	1	255	101M	*	0	0	CATCTCTACANGCGCGTCCTACCAGACGCGCTTCCGATCTGAGAGCATACTTTTCATTGGATTCCAGCACAACTCCATTTTTGATCCACTNGACACCTTTN	(/,'-/'0////(1'&&1&&&&'2''-6/,/3-33653.6:1'.86/-++32.-4864653/5/583/346423203+28888644446688456/4880&	RG:Z:0	XN:i:1
+SL-XAV:1:1:0:1914#0/2	153	chr3	1	255	101M	*	0	0	CGTATGCGCTNTTTATGTCGCCCACAGTGCCTAGTATAGCCCCTGCTAATAAAAAGAGATGAATACGTTTACTTAAAAAACTGAAACTAGNAATGTGCAAN	(0,7&&*/*0*,)10/).-*&.&*/6669.&-337599;3,&,6/.,5::999987893+387020775777547999::668997448:::9;999::0&	RG:Z:0
+SL-XAV:1:1:0:1639#0/2	153	chr4	1	255	101M	*	0	0	CGTGATACCANCTCATGTTCACAGCCAAAGCCTGAAGCTGTCTATTATATTTCTCAACCATAAACTTTTGCCTCAGGCATCCGCAGAATGNTTTGCAGCCN	'.&.&&'.0+01'2(1'(''-)','+0041/.+032;:867115/5267-.0/)-5.&-26200224,,0+0/0275/5605688::646875568882*&	RG:Z:0
+SL-XAV:1:1:0:68#0/2	137	chr5	1	255	101M	*	0	0	NTCTCATTTANAAATGGTTATAAAAACATTTATGCTGAAAAGGTGAAGTTCATTAATGAACAGGCTGACTGTCTCACTATCGCGTTCGCANGACGTTATCT	&1<<999;;;;<<<87579:556972789977444.'.023.&,7621/54.49.)/53055-22--''+(.'-))6-168/(3&&0(<).))*&&&&&'0	RG:Z:0
+SL-XAV:1:1:0:700#0/2	137	chr6	1	255	101M	*	0	0	NAATTGTTCTNAGTTTCTCGGTTTATGTGCTCTTCCAGGTGGGTAACACAATAATGGCCTTCCAGATCGTAAGAGCGACGTGTGTTGCACNAGTGTCGATC	&0::887::::6/646::838388811/679:87640&./2+/-4/28:3,536/4''&&.78/(/554/./02*)*',-(57()&.6(6:(0601'/(,*	RG:Z:0
+SL-XAV:1:1:0:1721#0/1	83	chr7	1	255	101M	=	102	40	CAACAGAAGGNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCGAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
+SL-XAV:1:1:0:1721#0/2	163	chr7	102	255	101M	=	1	-40	NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTCACTATGGTACATCTTGTCGTGCGGCNAGAGCATACA	&/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1	RG:Z:0
+SL-XAV:1:1:0:105#0/2	147	chr8	1	255	101M	=	102	79	CACATCGTGANTCTTACAATCTGCGGTTTCAGATGTGGAGCGATGTGTGAGAGATTGAGCAACTGATCTGAAAAGCAGACACAGCTATTCNTAAGATGACN	/))3--/&*()&)&&+'++.'-&,(.))'4,)&'&&,')8,&&*'.&*0'225/&)3-8//)*,5-*).7851453583.3568526:863688:::85.&	RG:Z:0
+SL-XAV:1:1:0:105#0/1	99	chr8	102	255	101M	=	1	-79	NCAGGTTCAANTGTGCAGCCCNTTTTGAGAGATNNNNNNNNTGNNCTGNAANANNGACACAGCTATTCCTAAGATGACAAGATCAGANAANAAGTCAAGCA	&06665578::41.*/7577/&/77403-324.&&&&&&&&/.&&..&&.0&&&&',:9:/-/(55002020+3'12+2/&.2-&//&),&*&&&&&&&51	RG:Z:0
+SL-XAV:1:1:0:1300#0/1	77	*	0	0	*	*	0	0	NAAACACAAGNNANAGTCTTANCNGCTATTCCNNNNNNNNNCTNNNCTNAGNANNACATACAACAGTATCCACACAAGTGTACTCGTNCANACATGTGAAC	&*5535)*-,,&.&.*-1)*,&'&)&1&&.,)&&&&&&&&&)0&&&0'&&&&.&&*2'/4''0/**&)&,'-&*,&,&&&.0.&)&&&**&,.&&&')&&)	RG:Z:0
+SL-XAV:1:1:0:1300#0/2	141	*	0	0	*	*	0	0	NGATCATGGANGACTCTCCCCATCCCCCGCTCCAGCGCTCAGTTATATGCCTAGCCTCGGACACGTCACCAACATCTCACGCACTCTGCANAGTCTCTCAC	&&'+''3*&-/)/1'26/*-2-/542-*&-&/'/*/&-'&)-')&.'-/&&2+122*'&+,(/-&)((,/-,,.'2(2'+)/&/&-66-&&/16&)&*&'3	RG:Z:0
+SL-XAV:1:1:0:1639#0/1	101	*	0	0	*	chr1	1	0	NCCCTCTCAGNNTNTCTGCCANANCCTTAAGCNNNNNNNNNTANNNCTNAANCNNAAACTTTTGCCTCAGGCATCCGCAGAATGTTTNTCNGCCTATATCG	&1::::::64/&/&0:3.280&/&087881,/&&&&&&&&&..&&&..&,,&-&&,265341-)/5680&-.5552-25/322/42/&)&&).421&-&-/	RG:Z:0
+SL-XAV:1:1:0:1668#0/1	101	*	0	0	*	chr2	1	0	NATAGCATACNNTNCATTGGANTNCAGCACAANNNNNNNNNTGNNNCANTNNANNCCTTTGAGATCGGAAGAGCGGTTCAGCAGGAANNCNCAGACCGATC	&1988998890&0&.8863//&.&.0-2875.&&&&&&&&&.)&&&..&.&&.&&.5782-2+262)&-0-0510*.332-2.-,0*&&*&'.&-2-)0.,	RG:Z:0
+SL-XAV:1:1:0:1914#0/1	101	*	0	0	*	chr3	1	0	NTTTTTCTCCNNCNGTGCCTANTNTAGCCCCTNNNNNNNNNAANNNATNANNANNTTTACTTAAAAAACTGAAACTAGTAATGTGCANNANATCGNAAGAG	&0::::<<;90&/&.244760&,&.414798/&&&&&&&&&00&&&0.&/&&-&&.4475687363504.&.557/.*)65.&/*./&&.&.+*)&..).&	RG:Z:0
+SL-XAV:1:1:0:68#0/1	581	*	0	0	*	chr4	1	0	NAATATTCATNNGNTCAGCCTNTNCATTAATTNNNNNNNNNTTNNNATNATNANNTTTTTTATAACCATTTATAAATGAGAGAGATCNTANCACAATATCA	&0<<:::::</&&&.73'290&.&0;:::90&&&&&&&&&&..&&&0)&0-&0&&&.743799995253348597921.,.'050.*&.0&)*)&&&&*).	RG:Z:0
+SL-XAV:1:1:0:700#0/1	581	*	0	0	*	chr5	1	0	NGAAGCCCATNNTNGTGTTACNCNCCTGGAAGNNNNNNNNNACNNNGANACNTNNAACAATTCAGATCGGAAGAGCGGTTCAGCAGANNTNCCGAGACCGA	&.88888:88/&0&,03189.&/&.8/))12/&&&&&&&&&./&&&&.&1.&)&&/35962/6432-3&),0&/2+0,),61&-6,&&&'&/,.0&...)0	RG:Z:0
+SL-XAV:1:1:0:764#0/2	165	*	0	0	*	chr6	1	0	NACAGATGCANATATTAACAGGCTTTAAAGGACAGATGGACTGCAATACAATAATAGAGTACGTCAACACTCCACAGATCGCTAGAGCATNACATCGGTGT	&/:5358::9999::99998255::7275,,/5567-'+387537857:54-4.51'31059547320;73/720+22.4(6.;((.;(;8()(''&&2&&	RG:Z:0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_output_alignment_summary_metrics.html	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,59 @@
+<style type="text/css">
+        tr.d0 td {background-color: oldlace; color: black;}
+        tr.d1 td {background-color: aliceblue; color: black;}
+        </style><?xml version="1.0" encoding="utf-8" ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<meta name="generator" content="Galaxy picard_wrapper tool output - see http://getgalaxy.org/" />
+<title></title>
+<link rel="stylesheet" href="/static/style/base.css" type="text/css" />
+</head>
+<body>
+<div class="document">
+Galaxy tool CollectAlignmentSummaryMetrics run at 11/11/2011 08:07:10</b><br/><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table>
+<tr><td><a href="CollectAlignmentSummaryMetrics.log">CollectAlignmentSummaryMetrics.log</a></td></tr>
+<tr><td><a href="CollectAlignmentSummaryMetrics.metrics.txt">CollectAlignmentSummaryMetrics.metrics.txt</a></td></tr>
+</table><p/>
+<b>Picard on line resources</b><ul>
+<li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li>
+<li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/>
+<b>Picard output (transposed to make it easier to see)</b><hr/>
+<table cellpadding="3" >
+<tr class="d0"><td colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/data/tmp/tmpLLcl1w/database/files/000/dataset_2.dat OUTPUT=/data/home/rlazarus/galaxy/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetrics.metrics.txt REFERENCE_SEQUENCE=/data/home/rlazarus/galaxy/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetricsfq2hit.fasta_fake.fasta ASSUME_SORTED=true TMP_DIR=[/tmp] VALIDATION_STRINGENCY=LENIENT    METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false</td></tr><tr class="d0"><td colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># Started on: Fri Nov 11 08:07:10 EST 2011</td></tr><tr class="d0"><td colspan="2">## METRICS CLASS	net.sf.picard.analysis.AlignmentSummaryMetrics</td></tr><tr class="d0"><td>CATEGORY</td><td>FIRST_OF_PAIR&nbsp;</td></tr>
+<tr class="d1"><td>TOTAL_READS</td><td>4&nbsp;</td></tr>
+<tr class="d0"><td>PF_READS</td><td>4&nbsp;</td></tr>
+<tr class="d1"><td>PCT_PF_READS</td><td>1&nbsp;</td></tr>
+<tr class="d0"><td>PF_NOISE_READS</td><td>0&nbsp;</td></tr>
+<tr class="d1"><td>PF_READS_ALIGNED</td><td>4&nbsp;</td></tr>
+<tr class="d0"><td>PCT_PF_READS_ALIGNED</td><td>1&nbsp;</td></tr>
+<tr class="d1"><td>PF_ALIGNED_BASES</td><td>404&nbsp;</td></tr>
+<tr class="d0"><td>PF_HQ_ALIGNED_READS</td><td>4&nbsp;</td></tr>
+<tr class="d1"><td>PF_HQ_ALIGNED_BASES</td><td>404&nbsp;</td></tr>
+<tr class="d0"><td>PF_HQ_ALIGNED_Q20_BASES</td><td>28&nbsp;</td></tr>
+<tr class="d1"><td>PF_HQ_MEDIAN_MISMATCHES</td><td>78&nbsp;</td></tr>
+<tr class="d0"><td>PF_MISMATCH_RATE</td><td>0.777228&nbsp;</td></tr>
+<tr class="d1"><td>PF_HQ_ERROR_RATE</td><td>0.777228&nbsp;</td></tr>
+<tr class="d0"><td>PF_INDEL_RATE</td><td>0&nbsp;</td></tr>
+<tr class="d1"><td>MEAN_READ_LENGTH</td><td>101&nbsp;</td></tr>
+<tr class="d0"><td>READS_ALIGNED_IN_PAIRS</td><td>3&nbsp;</td></tr>
+<tr class="d1"><td>PCT_READS_ALIGNED_IN_PAIRS</td><td>0.75&nbsp;</td></tr>
+<tr class="d0"><td>BAD_CYCLES</td><td>63&nbsp;</td></tr>
+<tr class="d1"><td>STRAND_BALANCE</td><td>0.25&nbsp;</td></tr>
+<tr class="d0"><td>PCT_CHIMERAS</td><td>0&nbsp;</td></tr>
+<tr class="d1"><td>PCT_ADAPTER</td><td>0&nbsp;</td></tr>
+<tr class="d0"><td>SAMPLE</td><td>&nbsp;</td></tr>
+<tr class="d1"><td>LIBRARY</td><td>&nbsp;</td></tr>
+<tr class="d0"><td>READ_GROUP
+</td><td>
+&nbsp;</td></tr>
+</table>
+<b>Picard Tool Run Log</b><hr/>
+<pre>INFO:root:## executing java -Xmx4g -jar /data/home/rlazarus/galaxy/tool-data/shared/jars/picard/CreateSequenceDictionary.jar REFERENCE=/tmp/CollectAlignmentSummaryMetricsfq2hit.fasta OUTPUT=/tmp/CollectAlignmentSummaryMetricsfq2hit.dict URI=dataset_1.dat TRUNCATE_NAMES_AT_WHITESPACE=None returned status 0 and nothing on stderr
+
+INFO:root:## executing java -Xmx4g -jar /data/home/rlazarus/galaxy/tool-data/shared/jars/picard/CollectAlignmentSummaryMetrics.jar VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true  ADAPTER_SEQUENCE= IS_BISULFITE_SEQUENCED=false MAX_INSERT_SIZE=100000 OUTPUT=/data/home/rlazarus/galaxy/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetrics.metrics.txt R=/data/home/rlazarus/galaxy/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetricsfq2hit.fasta_fake.fasta TMP_DIR=/tmp INPUT=/data/tmp/tmpLLcl1w/database/files/000/dataset_2.dat returned status 0 and nothing on stderr
+
+</pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> 
+generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_output_collect_AS_sorted_pair.txt	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,12 @@
+## net.sf.picard.metrics.StringHeader
+# net.sf.picard.analysis.CollectAlignmentSummaryMetrics INPUT=testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam OUTPUT=output_test_as/test_as_sorted-pair.txt REFERENCE_SEQUENCE=testdata/picard/reference/Homo_sapiens_assembly18.trimmed.fasta    ASSUME_SORTED=true MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] IS_BISULFITE_SEQUENCED=false TMP_DIR=/tmp/raphael VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
+## net.sf.picard.metrics.StringHeader
+# Started on: Tue Oct 26 14:06:32 EDT 2010
+
+## METRICS CLASS	net.sf.picard.analysis.AlignmentSummaryMetrics
+CATEGORY	TOTAL_READS	PF_READS	PCT_PF_READS	PF_NOISE_READS	PF_READS_ALIGNED	PCT_PF_READS_ALIGNED	PF_HQ_ALIGNED_READS	PF_HQ_ALIGNED_BASES	PF_HQ_ALIGNED_Q20_BASES	PF_HQ_MEDIAN_MISMATCHES	PF_HQ_ERROR_RATE	MEAN_READ_LENGTH	READS_ALIGNED_IN_PAIRS	PCT_READS_ALIGNED_IN_PAIRS	BAD_CYCLES	STRAND_BALANCE	PCT_CHIMERAS	PCT_ADAPTER
+FIRST_OF_PAIR	5	5	1	0	0	0	0	0	0	0	?	13	0	?	0	?	?	0
+SECOND_OF_PAIR	5	5	1	0	0	0	0	0	0	0	?	13	0	?	0	?	?	0
+PAIR	10	10	1	0	0	0	0	0	0	0	?	13	0	?	0	?	?	0
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_output_estlibcomplexity_tinysam.html	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,38 @@
+<style type="text/css">
+        tr.d0 td {background-color: oldlace; color: black;}
+        tr.d1 td {background-color: aliceblue; color: black;}
+        </style><?xml version="1.0" encoding="utf-8" ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<meta name="generator" content="Galaxy rgEstLibComplexity.py tool output - see http://g2.trac.bx.psu.edu/" />
+<title></title>
+<link rel="stylesheet" href="/static/style/base.css" type="text/css" />
+</head>
+<body>
+<div class="document">
+<b><a href="http://rgenetics.org">Galaxy Rgenetics</a> tool output rgEstLibComplexity.py run at 10/04/2011 14:52:24</b><b>Your job produced the following output files.</b><hr/>
+<table>
+<tr><td><a href="estlibcompout.txt">estlibcompout.txt</a></td></tr>
+</table><p/>
+<b>Picard on line resources</b><ul>
+<li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li>
+<li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/>
+<b>Picard output (transposed to make it easier to see)</b><hr/>
+<table cellpadding="3" >
+<tr class="d0"><td>## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td># net.sf.picard.sam.EstimateLibraryComplexity INPUT=[/export/tmp/tmpBfU1Um/database/files/000/dataset_111.dat] OUTPUT=estlibcompout.txt MIN_IDENTICAL_BASES=5 MAX_DIFF_RATE=0.03 MIN_MEAN_QUALITY=20 READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VALIDATION_STRINGENCY=LENIENT    TMP_DIR=/tmp/rerla VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false</td></tr><tr class="d0"><td>## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td># Started on: Sun Apr 10 14:52:24 EDT 2011</td></tr></table>
+<b>Picard log</b><hr/>
+<pre>## executing java -Xmx2g  -jar /udd/rerla/rgalaxy/tool-data/shared/jars/EstimateLibraryComplexity.jar MIN_IDENTICAL_BASES=5 O=estlibcompout.txt VALIDATION_STRINGENCY=LENIENT MIN_MEAN_QUALITY=20 READ_NAME_REGEX="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*" OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 I=/export/tmp/tmpBfU1Um/database/files/000/dataset_111.dat MAX_DIFF_RATE=0.03 returned status 0 and log (stdout/stderr) records: 
+[Sun Apr 10 14:52:24 EDT 2011] net.sf.picard.sam.EstimateLibraryComplexity INPUT=[/export/tmp/tmpBfU1Um/database/files/000/dataset_111.dat] OUTPUT=estlibcompout.txt MIN_IDENTICAL_BASES=5 MAX_DIFF_RATE=0.03 MIN_MEAN_QUALITY=20 READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VALIDATION_STRINGENCY=LENIENT    TMP_DIR=/tmp/rerla VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
+INFO	2011-04-10 14:52:24	EstimateLibraryComplexity	Will store 3098916 read pairs in memory before sorting.
+INFO	2011-04-10 14:52:24	EstimateLibraryComplexity	Finished reading - moving on to scanning for duplicates.
+[Sun Apr 10 14:52:24 EDT 2011] net.sf.picard.sam.EstimateLibraryComplexity done.
+Runtime.totalMemory()=33947648
+
+
+</pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> 
+generated all outputs reported here, using this command line:<br/>
+<pre>java -Xmx2g  -jar /udd/rerla/rgalaxy/tool-data/shared/jars/EstimateLibraryComplexity.jar MIN_IDENTICAL_BASES=5 O=estlibcompout.txt VALIDATION_STRINGENCY=LENIENT MIN_MEAN_QUALITY=20 READ_NAME_REGEX="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*" OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 I=/export/tmp/tmpBfU1Um/database/files/000/dataset_111.dat MAX_DIFF_RATE=0.03</pre>
+</div></body></html>
+
Binary file test-data/picard_output_fixmate_sorted_pair.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_output_fixmate_sorted_pair.sam	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,15 @@
+@HD	VN:1.0	SO:coordinate
+@SQ	SN:chr1	LN:10001
+@SQ	SN:chr2	LN:10001
+@SQ	SN:chr3	LN:10001
+@RG	ID:rg1	SM:Z
+bar:record:1	77	*	0	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:rg1
+bar:record:1	141	*	0	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:rg1
+bar:record:2	77	*	0	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:rg1
+bar:record:2	141	*	0	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:rg1
+bar:record:3	77	*	0	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:rg1
+bar:record:3	141	*	0	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:rg1
+bar:record:4	77	*	0	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:rg1
+bar:record:4	141	*	0	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:rg1
+bar:record:5	77	*	0	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:rg1
+bar:record:5	141	*	0	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:rg1
Binary file test-data/picard_output_fixmate_tiny.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_output_gc_summary_alignment_stats.pdf	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,829 @@
+%PDF-1.4
+%âãÏÓ\r
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_output_gc_summary_alignment_stats.txt	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,102 @@
+## net.sf.picard.metrics.StringHeader
+# net.sf.picard.analysis.CollectGcBiasMetrics REFERENCE_SEQUENCE=testdata/picard/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta INPUT=testdata/picard/sam/summary_alignment_stats_test.sam OUTPUT=output_test_gc_nodict/test_nodic_ref_gc_summary_alignment_stats_test.txt CHART_OUTPUT=output_test_gc_nodict/test_nodic_ref_gc_summary_alignment_stats_test.pdf    WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=1.0E-5 TMP_DIR=/tmp/raphael VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
+## net.sf.picard.metrics.StringHeader
+# Started on: Tue Oct 26 13:54:53 EDT 2010
+
+## METRICS CLASS	net.sf.picard.analysis.GcBiasDetailMetrics
+GC	WINDOWS	READ_STARTS	MEAN_BASE_QUALITY	NORMALIZED_COVERAGE	ERROR_BAR_WIDTH
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+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_output_hs_transposed_summary_alignment_stats.html	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,167 @@
+<style type="text/css">
+        tr.d0 td {background-color: oldlace; color: black;}
+        tr.d1 td {background-color: aliceblue; color: black;}
+        </style><?xml version="1.0" encoding="utf-8" ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<meta name="generator" content="Galaxy picard_wrapper tool output - see http://getgalaxy.org/" />
+<title></title>
+<link rel="stylesheet" href="/static/style/base.css" type="text/css" />
+</head>
+<body>
+<div class="document">
+Galaxy tool wrapper run picard_wrapper at 07/05/2011 00:15:30</b><br/><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table>
+<tr><td><a href="tempSamHead.txt">tempSamHead.txt</a></td></tr>
+<tr><td><a href="rgPicardHsMetrics.bait">rgPicardHsMetrics.bait</a></td></tr>
+<tr><td><a href="CalculateHsMetrics.metrics.txt">CalculateHsMetrics.metrics.txt</a></td></tr>
+</table><p/>
+<b>Picard on line resources - maxrows=100</b><ul>
+<li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li>
+<li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/>
+<b>Picard output (transposed to make it easier to see)</b><hr/>
+<table cellpadding="3" >
+<tr class="d0"><td>## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td># net.sf.picard.analysis.directed.CalculateHsMetrics BAIT_INTERVALS=/udd/rerla/rgalaxy/database/job_working_directory/95/dataset_97_files/rgPicardHsMetrics.bait TARGET_INTERVALS=/udd/rerla/rgalaxy/database/job_working_directory/95/dataset_97_files/rgPicardHsMetrics.bait INPUT=/tmp/6728811.1.all.q/tmpCsP1vm/database/files/000/dataset_95.dat OUTPUT=/udd/rerla/rgalaxy/database/job_working_directory/95/dataset_97_files/CalculateHsMetrics.metrics.txt TMP_DIR=/tmp/6728811.1.all.q/tmpCsP1vm/database/tmp VALIDATION_STRINGENCY=LENIENT    VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false</td></tr><tr class="d0"><td>## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td># Started on: Sat May 07 00:15:15 EDT 2011</td></tr><tr class="d0"><td>## METRICS CLASS	net.sf.picard.analysis.directed.HsMetrics</td></tr><tr class="d0"><td>BAIT_SET</td><td>rgPicardHsMetrics</td></tr>
+<tr class="d1"><td>GENOME_SIZE</td><td>2040</td></tr>
+<tr class="d0"><td>BAIT_TERRITORY</td><td>14601938</td></tr>
+<tr class="d1"><td>TARGET_TERRITORY</td><td>14601938</td></tr>
+<tr class="d0"><td>BAIT_DESIGN_EFFICIENCY</td><td>1</td></tr>
+<tr class="d1"><td>TOTAL_READS</td><td>18</td></tr>
+<tr class="d0"><td>PF_READS</td><td>16</td></tr>
+<tr class="d1"><td>PF_UNIQUE_READS</td><td>16</td></tr>
+<tr class="d0"><td>PCT_PF_READS</td><td>0.888889</td></tr>
+<tr class="d1"><td>PCT_PF_UQ_READS</td><td>0.888889</td></tr>
+<tr class="d0"><td>PF_UQ_READS_ALIGNED</td><td>10</td></tr>
+<tr class="d1"><td>PCT_PF_UQ_READS_ALIGNED</td><td>0.625</td></tr>
+<tr class="d0"><td>PF_UQ_BASES_ALIGNED</td><td>1010</td></tr>
+<tr class="d1"><td>ON_BAIT_BASES</td><td>0</td></tr>
+<tr class="d0"><td>NEAR_BAIT_BASES</td><td>0</td></tr>
+<tr class="d1"><td>OFF_BAIT_BASES</td><td>1010</td></tr>
+<tr class="d0"><td>ON_TARGET_BASES</td><td>0</td></tr>
+<tr class="d1"><td>PCT_SELECTED_BASES</td><td>0</td></tr>
+<tr class="d0"><td>PCT_OFF_BAIT</td><td>1</td></tr>
+<tr class="d1"><td>ON_BAIT_VS_SELECTED</td><td>?</td></tr>
+<tr class="d0"><td>MEAN_BAIT_COVERAGE</td><td>0</td></tr>
+<tr class="d1"><td>MEAN_TARGET_COVERAGE</td><td>?</td></tr>
+<tr class="d0"><td>PCT_USABLE_BASES_ON_BAIT</td><td>0</td></tr>
+<tr class="d1"><td>PCT_USABLE_BASES_ON_TARGET</td><td>0</td></tr>
+<tr class="d0"><td>FOLD_ENRICHMENT</td><td>0</td></tr>
+<tr class="d1"><td>ZERO_CVG_TARGETS_PCT</td><td>0.841776</td></tr>
+<tr class="d0"><td>FOLD_80_BASE_PENALTY</td><td>?</td></tr>
+<tr class="d1"><td>PCT_TARGET_BASES_2X</td><td>0</td></tr>
+<tr class="d0"><td>PCT_TARGET_BASES_10X</td><td>0</td></tr>
+<tr class="d1"><td>PCT_TARGET_BASES_20X</td><td>0</td></tr>
+<tr class="d0"><td>PCT_TARGET_BASES_30X</td><td>0</td></tr>
+<tr class="d1"><td>HS_LIBRARY_SIZE</td><td></td></tr>
+<tr class="d0"><td>HS_PENALTY_10X</td><td>0</td></tr>
+<tr class="d1"><td>HS_PENALTY_20X</td><td>0</td></tr>
+<tr class="d0"><td>HS_PENALTY_30X
+</td><td>0
+</td></tr>
+</table>
+<b>Picard log</b><hr/>
+<pre>## got 10 rows of header
+## executing java -Xmx8G -jar /udd/rerla/rgalaxy/tool-data/shared/jars/CalculateHsMetrics.jar VALIDATION_STRINGENCY=LENIENT BAIT_INTERVALS=/udd/rerla/rgalaxy/database/job_working_directory/95/dataset_97_files/rgPicardHsMetrics.bait TARGET_INTERVALS=/udd/rerla/rgalaxy/database/job_working_directory/95/dataset_97_files/rgPicardHsMetrics.bait INPUT=/tmp/6728811.1.all.q/tmpCsP1vm/database/files/000/dataset_95.dat OUTPUT=/udd/rerla/rgalaxy/database/job_working_directory/95/dataset_97_files/CalculateHsMetrics.metrics.txt TMP_DIR=/tmp/6728811.1.all.q/tmpCsP1vm/database/tmp returned status 0 and stderr: 
+[Sat May 07 00:15:15 EDT 2011] net.sf.picard.analysis.directed.CalculateHsMetrics BAIT_INTERVALS=/udd/rerla/rgalaxy/database/job_working_directory/95/dataset_97_files/rgPicardHsMetrics.bait TARGET_INTERVALS=/udd/rerla/rgalaxy/database/job_working_directory/95/dataset_97_files/rgPicardHsMetrics.bait INPUT=/tmp/6728811.1.all.q/tmpCsP1vm/database/files/000/dataset_95.dat OUTPUT=/udd/rerla/rgalaxy/database/job_working_directory/95/dataset_97_files/CalculateHsMetrics.metrics.txt TMP_DIR=/tmp/6728811.1.all.q/tmpCsP1vm/database/tmp VALIDATION_STRINGENCY=LENIENT    VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8307873-8307942
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8309830-8309966
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8321581-8321736
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8328921-8329047
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8330342-8330469
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8331089-8331268
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8331692-8331978
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8365935-8366090
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8366606-8366726
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8379231-8379407
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8394536-8394660
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8426591-8426689
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8439724-8439837
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8450410-8450571
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8455465-8455675
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8460994-8461085
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8474118-8474378
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8475226-8475324
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8475761-8476349
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8482861-8482979
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8487241-8487268
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8489646-8489840
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8490753-8491059
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8494260-8494405
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8497300-8497434
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8507847-8508429
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8511276-8511546
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8513512-8513524
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8514924-8515035
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8516626-8516644
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8517344-8517353
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8518590-8518779
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8623316-8623458
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8626698-8626844
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8723779-8723843
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8307873-8307942
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8309830-8309966
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8321581-8321736
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8328921-8329047
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8330342-8330469
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8331089-8331268
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8331692-8331978
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8365935-8366090
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8366606-8366726
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8379231-8379407
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8394536-8394660
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8426591-8426689
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8439724-8439837
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8450410-8450571
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8455465-8455675
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8460994-8461085
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8474118-8474378
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8475226-8475324
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8475761-8476349
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8482861-8482979
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8487241-8487268
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8489646-8489840
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8490753-8491059
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8494260-8494405
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8497300-8497434
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8507847-8508429
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8511276-8511546
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8514924-8515035
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8518590-8518779
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8623316-8623458
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8626698-8626844
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:8723779-8723843
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:16408986-16409647
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:16425552-16427522
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:16542527-16542763
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:16572980-16573083
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:16717794-16717995
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:16728357-16728483
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:16860643-16860646
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:125814448-125814568
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:125816060-125816263
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:125817221-125817625
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:125823198-125823404
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:125834519-125834807
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:2019022-2019247
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:2022951-2023081
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:2029465-2029900
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:2037228-2037484
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:2044596-2044723
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:2046671-2046845
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:2048290-2048464
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:2050815-2050986
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:2060417-2060471
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:2063211-2063342
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:2063565-2063623
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:2066228-2066329
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:2067628-2067776
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:2071831-2071995
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:2073346-2073413
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:2074085-2074196
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:2076828-2077071
+WARNING	2011-05-07 00:15:16	IntervalList	Ignoring interval for unknown reference: chr9:2078499-2078613
+
+<b>## WARNING - 434559 log lines truncated - CalculateHsMetrics.log contains entire output</pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> 
+generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_output_insertsize_tinysam.html	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,53 @@
+<style type="text/css">
+        tr.d0 td {background-color: oldlace; color: black;}
+        tr.d1 td {background-color: aliceblue; color: black;}
+        </style><?xml version="1.0" encoding="utf-8" ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<meta name="generator" content="Galaxy picard_wrapper tool output - see http://getgalaxy.org/" />
+<title></title>
+<link rel="stylesheet" href="/static/style/base.css" type="text/css" />
+</head>
+<body>
+<div class="document">
+Galaxy tool CollectInsertSizeMetrics run at 13/05/2011 15:20:46</b><br/><table cellpadding="10"><tr><td>
+<a href="InsertSizeHist.pdf"><img src="InsertSizeHist.jpg" title="Click image preview for a print quality PDF version" hspace="10" align="middle"></a>
+</tr></td></table>
+<b>The following output files were created (click the filename to view/download a copy):</b><hr/><table>
+<tr><td><a href="CollectInsertSizeMetrics.metrics.txt">CollectInsertSizeMetrics.metrics.txt</a></td></tr>
+<tr><td><a href="CollectInsertSizeMetrics.log">CollectInsertSizeMetrics.log</a></td></tr>
+<tr><td><a href="InsertSizeHist.pdf">InsertSizeHist.pdf</a></td></tr>
+<tr><td><a href="InsertSizeHist.jpg">InsertSizeHist.jpg</a></td></tr>
+</table><p/>
+<b>Picard on line resources</b><ul>
+<li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li>
+<li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/>
+<b>Picard output (transposed to make it easier to see)</b><hr/>
+<table cellpadding="3" >
+<tr class="d0"><td colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># net.sf.picard.analysis.CollectInsertSizeMetrics HISTOGRAM_FILE=InsertSizeHist.pdf TAIL_LIMIT=10000 MINIMUM_PCT=0.01 INPUT=/dev/shm/tmpHpwBHW/database/files/000/dataset_1.dat OUTPUT=/udd/rerla/rgalaxy/database/job_working_directory/2/dataset_2_files/CollectInsertSizeMetrics.metrics.txt VALIDATION_STRINGENCY=LENIENT    ASSUME_SORTED=true STOP_AFTER=0 TMP_DIR=/tmp/rerla VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false</td></tr><tr class="d0"><td colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># Started on: Fri May 13 15:20:45 EDT 2011</td></tr><tr class="d0"><td colspan="2">## METRICS CLASS	net.sf.picard.analysis.InsertSizeMetrics</td></tr><tr class="d1"><td colspan="2">## HISTOGRAM	java.lang.Integer</td></tr><tr class="d0"><td colspan="2">MEDIAN_INSERT_SIZE	MIN_INSERT_SIZE	MAX_INSERT_SIZE	MEAN_INSERT_SIZE	STANDARD_DEVIATION	READ_PAIRS	PAIR_ORIENTATION	WIDTH_OF_10_PERCENT	WIDTH_OF_20_PERCENT	WIDTH_OF_30_PERCENT	WIDTH_OF_40_PERCENT	WIDTH_OF_50_PERCENT	WIDTH_OF_60_PERCENT	WIDTH_OF_70_PERCENT	WIDTH_OF_80_PERCENT	WIDTH_OF_90_PERCENT	WIDTH_OF_99_PERCENT</td></tr>
+<tr class="d1"><td colspan="2">96	96	96	96	?	1	FR	1	1	1	1	1	1	1	1	1	1</td></tr>
+<tr class="d0"><td colspan="2">201	201	201	201	?	1	RF	1	1	1	1	1	1	1	1	1	1</td></tr>
+<tr class="d1"><td colspan="2">insert_size	fr_count	rf_count</td></tr>
+<tr class="d0"><td colspan="2">96	1	0</td></tr>
+<tr class="d1"><td colspan="2">201	0	1</td></tr>
+</table>
+<b>Picard Tool Run Log</b><hr/>
+<pre>INFO:root:## executing java -Xmx2g -jar /udd/rerla/rgalaxy/tool-data/shared/jars/CollectInsertSizeMetrics.jar VALIDATION_STRINGENCY=LENIENT I=/dev/shm/tmpHpwBHW/database/files/000/dataset_1.dat O=/udd/rerla/rgalaxy/database/job_working_directory/2/dataset_2_files/CollectInsertSizeMetrics.metrics.txt HISTOGRAM_FILE=InsertSizeHist.pdf TAIL_LIMIT=10000 MINIMUM_PCT=0.01 returned status 0 and stderr: 
+[Fri May 13 15:20:45 EDT 2011] net.sf.picard.analysis.CollectInsertSizeMetrics HISTOGRAM_FILE=InsertSizeHist.pdf TAIL_LIMIT=10000 MINIMUM_PCT=0.01 INPUT=/dev/shm/tmpHpwBHW/database/files/000/dataset_1.dat OUTPUT=/udd/rerla/rgalaxy/database/job_working_directory/2/dataset_2_files/CollectInsertSizeMetrics.metrics.txt VALIDATION_STRINGENCY=LENIENT    ASSUME_SORTED=true STOP_AFTER=0 TMP_DIR=/tmp/rerla VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
+WARNING	2011-05-13 15:20:45	SinglePassSamProgram	File reports sort order 'queryname', assuming it's coordinate sorted anyway.
+INFO	2011-05-13 15:20:46	ProcessExecutor	[1] "FR = red"  "RF = blue"
+INFO	2011-05-13 15:20:46	ProcessExecutor	null device 
+INFO	2011-05-13 15:20:46	ProcessExecutor	          1 
+[Fri May 13 15:20:46 EDT 2011] net.sf.picard.analysis.CollectInsertSizeMetrics done.
+Runtime.totalMemory()=9109504
+
+
+INFO:root:## executing mogrify -format jpg -resize x400 /udd/rerla/rgalaxy/database/job_working_directory/2/dataset_2_files/InsertSizeHist.pdf returned status 0 and nothing on stderr
+
+INFO:root:## executing mogrify -format jpg -resize x400 /udd/rerla/rgalaxy/database/job_working_directory/2/dataset_2_files/InsertSizeHist.pdf returned status 0 and nothing on stderr
+
+</pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> 
+generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html>
+
Binary file test-data/picard_output_markdups_remdupes.bam has changed
Binary file test-data/picard_output_markdups_sortedpairsam.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_output_markdups_sortedpairsam.html	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,160 @@
+<style type="text/css">
+        tr.d0 td {background-color: oldlace; color: black;}
+        tr.d1 td {background-color: aliceblue; color: black;}
+        </style><?xml version="1.0" encoding="utf-8" ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<meta name="generator" content="Galaxy picard_wrapper tool output - see http://getgalaxy.org/" />
+<title></title>
+<link rel="stylesheet" href="/static/style/base.css" type="text/css" />
+</head>
+<body>
+<div class="document">
+Galaxy tool MarkDuplicates run at 12/05/2011 14:34:29</b><br/><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table>
+<tr><td><a href="MarkDuplicates.log">MarkDuplicates.log</a></td></tr>
+<tr><td><a href="MarkDuplicates.metrics.txt">MarkDuplicates.metrics.txt</a></td></tr>
+</table><p/>
+<b>Picard on line resources</b><ul>
+<li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li>
+<li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/>
+<b>Picard output (transposed to make it easier to see)</b><hr/>
+<table cellpadding="3" >
+<tr class="d0"><td colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># net.sf.picard.sam.MarkDuplicates INPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1097.dat OUTPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1098.dat METRICS_FILE=/udd/rerla/galaxy-central/database/job_working_directory/1032/dataset_1099_files/MarkDuplicates.metrics.txt REMOVE_DUPLICATES=true ASSUME_SORTED=true READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VALIDATION_STRINGENCY=LENIENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 TMP_DIR=/tmp/rerla VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false</td></tr><tr class="d0"><td colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># Started on: Thu May 12 14:34:28 EDT 2011</td></tr><tr class="d0"><td colspan="2">## METRICS CLASS	net.sf.picard.sam.DuplicationMetrics</td></tr><tr class="d0"><td>LIBRARY</td><td>&nbsp;</td></tr>
+<tr class="d1"><td>UNPAIRED_READS_EXAMINED</td><td>1&nbsp;</td></tr>
+<tr class="d0"><td>READ_PAIRS_EXAMINED</td><td>3&nbsp;</td></tr>
+<tr class="d1"><td>UNMAPPED_READS</td><td>1&nbsp;</td></tr>
+<tr class="d0"><td>UNPAIRED_READ_DUPLICATES</td><td>1&nbsp;</td></tr>
+<tr class="d1"><td>READ_PAIR_DUPLICATES</td><td>1&nbsp;</td></tr>
+<tr class="d0"><td>READ_PAIR_OPTICAL_DUPLICATES</td><td>0&nbsp;</td></tr>
+<tr class="d1"><td>PERCENT_DUPLICATION</td><td>0.428571&nbsp;</td></tr>
+<tr class="d0"><td>ESTIMATED_LIBRARY_SIZE
+</td><td>3
+&nbsp;</td></tr>
+<tr class="d0"><td colspan="2">## HISTOGRAM	java.lang.Double</td></tr><tr class="d0"><td colspan="2">BIN	VALUE</td></tr>
+<tr class="d1"><td colspan="2">1.0	0.948181</td></tr>
+<tr class="d0"><td colspan="2">2.0	1.296997</td></tr>
+<tr class="d1"><td colspan="2">3.0	1.425319</td></tr>
+<tr class="d0"><td colspan="2">4.0	1.472527</td></tr>
+<tr class="d1"><td colspan="2">5.0	1.489893</td></tr>
+<tr class="d0"><td colspan="2">6.0	1.496282</td></tr>
+<tr class="d1"><td colspan="2">7.0	1.498632</td></tr>
+<tr class="d0"><td colspan="2">8.0	1.499497</td></tr>
+<tr class="d1"><td colspan="2">9.0	1.499815</td></tr>
+<tr class="d0"><td colspan="2">10.0	1.499932</td></tr>
+<tr class="d1"><td colspan="2">11.0	1.499975</td></tr>
+<tr class="d0"><td colspan="2">12.0	1.499991</td></tr>
+<tr class="d1"><td colspan="2">13.0	1.499997</td></tr>
+<tr class="d0"><td colspan="2">14.0	1.499999</td></tr>
+<tr class="d1"><td colspan="2">15.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">16.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">17.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">18.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">19.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">20.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">21.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">22.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">23.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">24.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">25.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">26.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">27.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">28.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">29.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">30.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">31.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">32.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">33.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">34.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">35.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">36.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">37.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">38.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">39.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">40.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">41.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">42.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">43.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">44.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">45.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">46.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">47.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">48.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">49.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">50.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">51.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">52.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">53.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">54.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">55.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">56.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">57.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">58.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">59.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">60.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">61.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">62.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">63.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">64.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">65.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">66.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">67.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">68.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">69.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">70.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">71.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">72.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">73.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">74.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">75.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">76.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">77.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">78.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">79.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">80.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">81.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">82.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">83.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">84.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">85.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">86.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">87.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">88.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">89.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">90.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">91.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">92.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">93.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">94.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">95.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">96.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">97.0	1.5</td></tr>
+<tr class="d0"><td colspan="2">98.0	1.5</td></tr>
+<tr class="d1"><td colspan="2">99.0	1.5</td></tr>
+</table>
+<b>Picard Tool Run Log</b><hr/>
+<pre>Thu, 12 May 2011 14:34:29 INFO
+ ## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/shared/jars/MarkDuplicates.jar VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true INPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1097.dat OUTPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1098.dat METRICS_FILE=/udd/rerla/galaxy-central/database/job_working_directory/1032/dataset_1099_files/MarkDuplicates.metrics.txt REMOVE_DUPLICATES=true READ_NAME_REGEX="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*" OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 returned status 0 and stderr: 
+[Thu May 12 14:34:28 EDT 2011] net.sf.picard.sam.MarkDuplicates INPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1097.dat OUTPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1098.dat METRICS_FILE=/udd/rerla/galaxy-central/database/job_working_directory/1032/dataset_1099_files/MarkDuplicates.metrics.txt REMOVE_DUPLICATES=true ASSUME_SORTED=true READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VALIDATION_STRINGENCY=LENIENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 TMP_DIR=/tmp/rerla VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
+INFO	2011-05-12 14:34:28	MarkDuplicates	Start of doWork freeMemory: 8644632; totalMemory: 9109504; maxMemory: 1908932608
+INFO	2011-05-12 14:34:28	MarkDuplicates	Reading input file and constructing read end information.
+INFO	2011-05-12 14:34:28	MarkDuplicates	Will retain up to 7575129 data points before spilling to disk.
+INFO	2011-05-12 14:34:28	MarkDuplicates	Read 7 records. 0 pairs never matched.
+INFO	2011-05-12 14:34:29	MarkDuplicates	After buildSortedReadEndLists freeMemory: 8316168; totalMemory: 130351104; maxMemory: 1908932608
+INFO	2011-05-12 14:34:29	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
+INFO	2011-05-12 14:34:29	MarkDuplicates	Traversing read pair information and detecting duplicates.
+INFO	2011-05-12 14:34:29	MarkDuplicates	Traversing fragment information and detecting duplicates.
+INFO	2011-05-12 14:34:29	MarkDuplicates	Sorting list of duplicate records.
+INFO	2011-05-12 14:34:29	MarkDuplicates	After generateDuplicateIndexes freeMemory: 129615120; totalMemory: 607649792; maxMemory: 1908932608
+INFO	2011-05-12 14:34:29	MarkDuplicates	Marking 3 records as duplicates.
+INFO	2011-05-12 14:34:29	MarkDuplicates	Found 0 optical duplicate clusters.
+INFO	2011-05-12 14:34:29	MarkDuplicates	Before output close freeMemory: 128997520; totalMemory: 607649792; maxMemory: 1908932608
+INFO	2011-05-12 14:34:29	MarkDuplicates	After output close freeMemory: 128997280; totalMemory: 607649792; maxMemory: 1908932608
+[Thu May 12 14:34:29 EDT 2011] net.sf.picard.sam.MarkDuplicates done.
+Runtime.totalMemory()=607649792
+
+
+</pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> 
+generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_output_markdups_sortedpairsam.sam	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,63 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    <meta name="generator" content="Galaxy rgPicardMarkDups.py tool output - see http://g2.trac.bx.psu.edu/" />
+    <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
+  </head>
+  <body>
+    <div class="document">
+      <h3><a href="http://rgenetics.org">Rgenetics</a> tool rgPicardMarkDups.py run at 19/11/2010 18:25:23</h3>
+      <b>Your job produced the following outputs - check here for a record of what was done and any unexpected events</b>
+      <hr />
+      <div>
+	<b>Output files.</b>
+	<table>
+	  <tr><td><a href="rgPicardMarkDups.txt">rgPicardMarkDups.txt  (1.8 KB)</a></td></tr>
+	</table>
+      </div>
+      <hr />
+      <div>
+	<b>Log of activity</b>
+	<hr/>
+	## executing java -Xmx2g -jar /share/shared/relul.galaxy/tool-data/shared/jars/MarkDuplicates.jar I= /share/shared/relul.galaxy/database/files/000/dataset_57.dat O= /share/shared/relul.galaxy/database/files/000/dataset_99.dat M= rgPicardMarkDupsMetrics.txt READ_NAME_REGEX="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*" OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 returned status 1 and log (stdout/stderr) records: 
+<BR />
+[Fri Nov 19 18:25:23 EST 2010] net.sf.picard.sam.MarkDuplicates INPUT=/share/shared/relul.galaxy/database/files/000/dataset_57.dat OUTPUT=/share/shared/relul.galaxy/database/files/000/dataset_99.dat METRICS_FILE=rgPicardMarkDupsMetrics.txt READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100    REMOVE_DUPLICATES=false ASSUME_SORTED=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 TMP_DIR=/tmp/relul VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
+<BR />
+INFO	2010-11-19 18:25:23	MarkDuplicates	Start of doWork freeMemory: 8645600; totalMemory: 9109504; maxMemory: 1908932608
+<BR />
+INFO	2010-11-19 18:25:23	MarkDuplicates	Reading input file and constructing read end information.
+<BR />
+INFO	2010-11-19 18:25:23	MarkDuplicates	Will retain up to 7575129 data points before spilling to disk.
+<BR />
+[Fri Nov 19 18:25:23 EST 2010] net.sf.picard.sam.MarkDuplicates done.
+<BR />
+Runtime.totalMemory()=130351104
+<BR />
+Exception in thread "main" net.sf.picard.PicardException: /share/shared/relul.galaxy/database/files/000/dataset_57.dat is not coordinate sorted.
+<BR />
+	at net.sf.picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:248)
+<BR />
+	at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:109)
+<BR />
+	at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:165)
+<BR />
+	at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:93)
+<BR />
+
+<BR />
+
+      </div>
+
+      <div>
+	<p>Note: The freely available 
+	  <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a>
+	  generated all outputs reported here. These third party tools were orchestrated by the Galaxy 
+	  rgPicardMarkDups.py wrapper and this command line from the Galaxy form:
+	</p>
+	<hr />
+	<div>/share/shared/relul.galaxy/tools/development/rgPicardMarkDups.py -i /share/shared/relul.galaxy/database/files/000/dataset_57.dat -n Dupes Marked --tmp_dir /export/tmp/relul -o /share/shared/relul.galaxy/database/files/000/dataset_99.dat --remdups false --assumesorted true --readregex [a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* --optdupedist 100 -j /share/shared/relul.galaxy/tool-data/shared/jars/MarkDuplicates.jar -d /share/shared/relul.galaxy/database/job_working_directory/81/dataset_98_files -t /share/shared/relul.galaxy/database/files/000/dataset_98.dat</div>
+      </div>
+  </body>
+</html>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_output_validate_tiny_sam.html	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,46 @@
+<style type="text/css">
+        tr.d0 td {background-color: oldlace; color: black;}
+        tr.d1 td {background-color: aliceblue; color: black;}
+        </style><?xml version="1.0" encoding="utf-8" ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<meta name="generator" content="Galaxy rgPicardValidate.py tool output - see http://g2.trac.bx.psu.edu/" />
+<title></title>
+<link rel="stylesheet" href="/static/style/base.css" type="text/css" />
+</head>
+<body>
+<div class="document">
+<b><a href="http://rgenetics.org">Galaxy Rgenetics</a> tool output rgPicardValidate.py run at 19/04/2011 11:19:17</b><br/><b>Running this Galaxy tool produced the following output files (click the filename to view/download a copy).</b><hr/><table>
+<tr><td><a href="rgPicardValidate.out">rgPicardValidate.out</a></td></tr>
+</table><p/>
+<b>Picard on line resources</b><ul>
+<li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li>
+<li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/>
+<b>Picard output</b><hr/>
+<table cellpadding="3" >
+<tr class="d0"><td>['WARNING: Record 1, Read name both_reads_align_clip_marked, NM tag (nucleotide differences) is missing\n']</td></tr>
+<tr class="d1"><td>['WARNING: Record 2, Read name both_reads_present_only_first_aligns, NM tag (nucleotide differences) is missing\n']</td></tr>
+<tr class="d0"><td>['WARNING: Record 3, Read name read_2_too_many_gaps, NM tag (nucleotide differences) is missing\n']</td></tr>
+<tr class="d1"><td>['ERROR: Record 4, Read name both_reads_align_clip_adapter, The record is out of [queryname] order, prior read name [read_2_too_many_gaps], prior coodinates [1:1]\n']</td></tr>
+<tr class="d0"><td>['WARNING: Record 4, Read name both_reads_align_clip_adapter, NM tag (nucleotide differences) is missing\n']</td></tr>
+<tr class="d1"><td>['WARNING: Record 5, Read name both_reads_align_clip_adapter, NM tag (nucleotide differences) is missing\n']</td></tr>
+<tr class="d0"><td>['WARNING: Record 6, Read name both_reads_align_clip_marked, NM tag (nucleotide differences) is missing\n']</td></tr>
+<tr class="d1"><td>['WARNING: Record 7, Read name read_2_too_many_gaps, NM tag (nucleotide differences) is missing\n']</td></tr>
+<tr class="d0"><td>['ERROR: Record 8, Read name both_reads_present_only_first_aligns, The record is out of [queryname] order, prior read name [read_2_too_many_gaps], prior coodinates [1:302]\n']</td></tr>
+</table>
+<b>Picard log</b><hr/>
+<pre>## executing samtools sort /udd/rerla/rgalaxy/database/job_working_directory/98/dataset_100_files/tmpELItj4rgSortBamTemp.bam /udd/rerla/rgalaxy/database/job_working_directory/98/dataset_100_files/rgcleansam.sorted returned status 0. Nothing appeared on stderr/stdout
+
+rectory/98/dataset_100_files/rgPicardValidate.out IGNORE=INVALID_TAG_NM  MAX_OUTPUT=100 TMP_DIR=/tmp returned status 1 and log (stdout/stderr) records: 
+[Tue Apr 19 11:19:17 EDT 2011] net.sf.picard.sam.ValidateSamFile INPUT=/udd/rerla/rgalaxy/database/job_working_directory/98/dataset_100_files/rgcleansam.sorted.bam OUTPUT=/udd/rerla/rgalaxy/database/job_working_directory/98/dataset_100_files/rgPicardValidate.out IGNORE=[INVALID_TAG_NM] MAX_OUTPUT=100 REFERENCE_SEQUENCE=/share/shared/data/hg18/hg18.fasta TMP_DIR=/tmp    MODE=VERBOSE IGNORE_WARNINGS=false VALIDATE_INDEX=true IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
+[Tue Apr 19 11:19:17 EDT 2011] net.sf.picard.sam.ValidateSamFile done.
+Runtime.totalMemory()=9109504
+
+
+</pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> 
+generated all outputs reported here, using this command line:<br/>
+<pre>java -Xmx8g  -jar /udd/rerla/rgalaxy/tool-data/shared/jars/ValidateSamFile.jar I=/udd/rerla/rgalaxy/database/job_working_directory/98/dataset_100_files/rgcleansam.sorted.bam R=/share/shared/data/hg18/hg18.fasta O=/udd/rerla/rgalaxy/database/job_working_directory/98/dataset_100_files/rgPicardValidate.out IGNORE=INVALID_TAG_NM  MAX_OUTPUT=100 TMP_DIR=/tmp</pre>
+</div></body></html>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_summary_alignment_stats.sam	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,28 @@
+@HD	VN:1.0	SO:coordinate
+@SQ	SN:chr1	LN:101
+@SQ	SN:chr2	LN:101
+@SQ	SN:chr3	LN:101
+@SQ	SN:chr4	LN:101
+@SQ	SN:chr5	LN:101
+@SQ	SN:chr6	LN:101
+@SQ	SN:chr7	LN:202
+@SQ	SN:chr8	LN:202
+@RG	ID:0	SM:Hi,Mom!
+SL-XAV:1:1:0:764#0/1	89	chr1	1	255	101M	*	0	0	TTCATGCTGANGCNCTCTTACGATCGTACAGATGCAAATATTAACANNCNTTNAAGNNCANNNNNNNNNCAATACAATANTAGAGTACGTNAACACTCCAN	&/,&-.1/6/&&)&).)/,&0768)&/.,/874,&.4137572)&/&&,&1-&.0/&&*,&&&&&&&&&&18775799,&16:8775-56256/69::;0&	RG:Z:0	XN:i:1
+SL-XAV:1:1:0:1668#0/2	153	chr2	1	255	101M	*	0	0	CATCTCTACANGCGCGTCCTACCAGACGCGCTTCCGATCTGAGAGCATACTTTTCATTGGATTCCAGCACAACTCCATTTTTGATCCACTNGACACCTTTN	(/,'-/'0////(1'&&1&&&&'2''-6/,/3-33653.6:1'.86/-++32.-4864653/5/583/346423203+28888644446688456/4880&	RG:Z:0	XN:i:1
+SL-XAV:1:1:0:1914#0/2	153	chr3	1	255	101M	*	0	0	CGTATGCGCTNTTTATGTCGCCCACAGTGCCTAGTATAGCCCCTGCTAATAAAAAGAGATGAATACGTTTACTTAAAAAACTGAAACTAGNAATGTGCAAN	(0,7&&*/*0*,)10/).-*&.&*/6669.&-337599;3,&,6/.,5::999987893+387020775777547999::668997448:::9;999::0&	RG:Z:0
+SL-XAV:1:1:0:1639#0/2	153	chr4	1	255	101M	*	0	0	CGTGATACCANCTCATGTTCACAGCCAAAGCCTGAAGCTGTCTATTATATTTCTCAACCATAAACTTTTGCCTCAGGCATCCGCAGAATGNTTTGCAGCCN	'.&.&&'.0+01'2(1'(''-)','+0041/.+032;:867115/5267-.0/)-5.&-26200224,,0+0/0275/5605688::646875568882*&	RG:Z:0
+SL-XAV:1:1:0:68#0/2	137	chr5	1	255	101M	*	0	0	NTCTCATTTANAAATGGTTATAAAAACATTTATGCTGAAAAGGTGAAGTTCATTAATGAACAGGCTGACTGTCTCACTATCGCGTTCGCANGACGTTATCT	&1<<999;;;;<<<87579:556972789977444.'.023.&,7621/54.49.)/53055-22--''+(.'-))6-168/(3&&0(<).))*&&&&&'0	RG:Z:0
+SL-XAV:1:1:0:700#0/2	137	chr6	1	255	101M	*	0	0	NAATTGTTCTNAGTTTCTCGGTTTATGTGCTCTTCCAGGTGGGTAACACAATAATGGCCTTCCAGATCGTAAGAGCGACGTGTGTTGCACNAGTGTCGATC	&0::887::::6/646::838388811/679:87640&./2+/-4/28:3,536/4''&&.78/(/554/./02*)*',-(57()&.6(6:(0601'/(,*	RG:Z:0
+SL-XAV:1:1:0:1721#0/1	83	chr7	1	255	101M	=	102	40	CAACAGAAGGNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCGAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
+SL-XAV:1:1:0:1721#0/2	163	chr7	102	255	101M	=	1	-40	NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTCACTATGGTACATCTTGTCGTGCGGCNAGAGCATACA	&/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1	RG:Z:0
+SL-XAV:1:1:0:105#0/2	147	chr8	1	255	101M	=	102	79	CACATCGTGANTCTTACAATCTGCGGTTTCAGATGTGGAGCGATGTGTGAGAGATTGAGCAACTGATCTGAAAAGCAGACACAGCTATTCNTAAGATGACN	/))3--/&*()&)&&+'++.'-&,(.))'4,)&'&&,')8,&&*'.&*0'225/&)3-8//)*,5-*).7851453583.3568526:863688:::85.&	RG:Z:0
+SL-XAV:1:1:0:105#0/1	99	chr8	102	255	101M	=	1	-79	NCAGGTTCAANTGTGCAGCCCNTTTTGAGAGATNNNNNNNNTGNNCTGNAANANNGACACAGCTATTCCTAAGATGACAAGATCAGANAANAAGTCAAGCA	&06665578::41.*/7577/&/77403-324.&&&&&&&&/.&&..&&.0&&&&',:9:/-/(55002020+3'12+2/&.2-&//&),&*&&&&&&&51	RG:Z:0
+SL-XAV:1:1:0:1300#0/1	77	*	0	0	*	*	0	0	NAAACACAAGNNANAGTCTTANCNGCTATTCCNNNNNNNNNCTNNNCTNAGNANNACATACAACAGTATCCACACAAGTGTACTCGTNCANACATGTGAAC	&*5535)*-,,&.&.*-1)*,&'&)&1&&.,)&&&&&&&&&)0&&&0'&&&&.&&*2'/4''0/**&)&,'-&*,&,&&&.0.&)&&&**&,.&&&')&&)	RG:Z:0
+SL-XAV:1:1:0:1300#0/2	141	*	0	0	*	*	0	0	NGATCATGGANGACTCTCCCCATCCCCCGCTCCAGCGCTCAGTTATATGCCTAGCCTCGGACACGTCACCAACATCTCACGCACTCTGCANAGTCTCTCAC	&&'+''3*&-/)/1'26/*-2-/542-*&-&/'/*/&-'&)-')&.'-/&&2+122*'&+,(/-&)((,/-,,.'2(2'+)/&/&-66-&&/16&)&*&'3	RG:Z:0
+SL-XAV:1:1:0:1639#0/1	101	*	0	0	*	chr1	1	0	NCCCTCTCAGNNTNTCTGCCANANCCTTAAGCNNNNNNNNNTANNNCTNAANCNNAAACTTTTGCCTCAGGCATCCGCAGAATGTTTNTCNGCCTATATCG	&1::::::64/&/&0:3.280&/&087881,/&&&&&&&&&..&&&..&,,&-&&,265341-)/5680&-.5552-25/322/42/&)&&).421&-&-/	RG:Z:0
+SL-XAV:1:1:0:1668#0/1	101	*	0	0	*	chr2	1	0	NATAGCATACNNTNCATTGGANTNCAGCACAANNNNNNNNNTGNNNCANTNNANNCCTTTGAGATCGGAAGAGCGGTTCAGCAGGAANNCNCAGACCGATC	&1988998890&0&.8863//&.&.0-2875.&&&&&&&&&.)&&&..&.&&.&&.5782-2+262)&-0-0510*.332-2.-,0*&&*&'.&-2-)0.,	RG:Z:0
+SL-XAV:1:1:0:1914#0/1	101	*	0	0	*	chr3	1	0	NTTTTTCTCCNNCNGTGCCTANTNTAGCCCCTNNNNNNNNNAANNNATNANNANNTTTACTTAAAAAACTGAAACTAGTAATGTGCANNANATCGNAAGAG	&0::::<<;90&/&.244760&,&.414798/&&&&&&&&&00&&&0.&/&&-&&.4475687363504.&.557/.*)65.&/*./&&.&.+*)&..).&	RG:Z:0
+SL-XAV:1:1:0:68#0/1	581	*	0	0	*	chr4	1	0	NAATATTCATNNGNTCAGCCTNTNCATTAATTNNNNNNNNNTTNNNATNATNANNTTTTTTATAACCATTTATAAATGAGAGAGATCNTANCACAATATCA	&0<<:::::</&&&.73'290&.&0;:::90&&&&&&&&&&..&&&0)&0-&0&&&.743799995253348597921.,.'050.*&.0&)*)&&&&*).	RG:Z:0
+SL-XAV:1:1:0:700#0/1	581	*	0	0	*	chr5	1	0	NGAAGCCCATNNTNGTGTTACNCNCCTGGAAGNNNNNNNNNACNNNGANACNTNNAACAATTCAGATCGGAAGAGCGGTTCAGCAGANNTNCCGAGACCGA	&.88888:88/&0&,03189.&/&.8/))12/&&&&&&&&&./&&&&.&1.&)&&/35962/6432-3&),0&/2+0,),61&-6,&&&'&/,.0&...)0	RG:Z:0
+SL-XAV:1:1:0:764#0/2	165	*	0	0	*	chr6	1	0	NACAGATGCANATATTAACAGGCTTTAAAGGACAGATGGACTGCAATACAATAATAGAGTACGTCAACACTCCACAGATCGCTAGAGCATNACATCGGTGT	&/:5358::9999::99998255::7275,,/5567-'+387537857:54-4.51'31059547320;73/720+22.4(6.;((.;(;8()(''&&2&&	RG:Z:0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/random_phiX_1.fastqsanger	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,80 @@
+@random_phiX_region_0
+TTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTT
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_1
+GTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_2
+AATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_3
+GGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_4
+ACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGAC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_5
+AGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_6
+CACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_7
+AACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_8
+CTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTT
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_9
+CAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_10
+TACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_11
+TATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_12
+AGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_13
+TTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_14
+CCGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_15
+AACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTT
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_16
+GCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_17
+CATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_18
+TGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_19
+GCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACT
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/picard_index.loc.sample	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,26 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Picard dict and associated files. You will need
+#to create these data files and then create a picard_index.loc file 
+#similar to this one (store it in this directory) that points to 
+#the directories in which those files are stored. The picard_index.loc 
+#file has this format (longer white space is the TAB character):
+#
+#<unique_build_id>		<dbkey>		<display_name>		<fasta_file_path>
+#
+#So, for example, if you had hg18 indexed and stored in 
+#/depot/data2/galaxy/srma/hg18/, 
+#then the srma_index.loc entry would look like this:
+#
+#hg18	hg18	hg18 Pretty		/depot/data2/galaxy/picard/hg18/hg18.fa
+#
+#and your /depot/data2/galaxy/srma/hg18/ directory
+#would contain the following three files:
+#hg18.fa
+#hg18.dict
+#hg18.fa.fai
+#
+#The dictionary file for each reference (ex. hg18.dict) must be 
+#created via Picard (http://picard.sourceforge.net). Note that
+#the dict file does not have the .fa extension although the
+#path list in the loc file does include it.
+#
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,8 @@
+<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
+<tables>
+    <!-- Location of Picard dict file and other files -->
+    <table name="picard_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/picard_index.loc" />
+    </table>
+</tables>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Aug 13 12:09:14 2013 -0400
@@ -0,0 +1,19 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="picard" version="1.56.0">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://downloads.sourceforge.net/project/picard/picard-tools/1.56/picard-tools-1.56.zip</action>
+                <action type="move_directory_files">
+                    <source_directory>picard-tools-1.56</source_directory>
+                    <destination_directory>$INSTALL_DIR/jars</destination_directory>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/jars</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+        </readme>
+    </package>
+</tool_dependency>