[Debian-med-packaging] Picard tools shell script [PATCH]

[Shaun Jackman]

Hi Tim,

I've packaged Picard Tools for Debian [1], which is composed of two
binary packages: libsam-java and picard-tools. I wrote up a small shell
script, picard-tools, to launch the various utilities of Picard Tools in
a fashion similar to samtools. The script and a terse man page are
attached. Would you be interested in distributing this script with
Picard Tools?

Cheers,
Shaun

[1] http://packages.debian.org/picard-tools
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.TH picard-tools "1" "July 2010" "picard-tools 1.25" "User Commands"
.SH NAME
picard-tools \- manipulate SAM and BAM files
.SH SYNOPSIS
\fBpicard-tools\fR \fICOMMAND\fR [\fIOPTION\fR]...
.SH DESCRIPTION
SAM (Sequence Alignment/Map) format is a generic format for storing
large nucleotide sequence alignments.

Picard Tools includes these utilities to manipulate SAM and BAM files:
 BamToBfq
 BuildBamIndex
 CalculateHsMetrics
 CleanSam
 CollectAlignmentSummaryMetrics
 CollectGcBiasMetrics
 CollectInsertSizeMetrics
 CompareSAMs
 CreateSequenceDictionary
 EstimateLibraryComplexity
 FastqToSam
 FixMateInformation
 MarkDuplicates
 MeanQualityByCycle
 MergeBamAlignment
 MergeSamFiles
 NormalizeFasta
 QualityScoreDistribution
 ReplaceSamHeader
 RevertSam
 SamFormatConverter
 SamToFastq
 SortSam
 ValidateSamFile
 ViewSam
.SH "REPORTING BUGS"
samtools-devel at lists.sourceforge.net
.SH COPYRIGHT
Copyright 2010 The Broad Institute
.SH "SEE ALSO"
http://picard.sourceforge.net/