NOTE!!

The modifications listed here are obsolete. Most things have already been fixed in a newer Picard version (2.20 when writing this) or can be worked around in ways that are better than using a modified version. For more information see ​http://baseplugins.thep.lu.se/ticket/1160

Picard modifications

We have made some changes to Picard, ​http://broadinstitute.github.io/picard/, that we feel are useful for a wider audience. The changes can be found and tracked on a ​GitHub fork of the main Picard and HTSJDK projects:

• ​https://github.com/nnordborg/picard/tree/lorry
• ​https://github.com/nnordborg/htsjdk/tree/lorry

Documentation

Documentation for Picard can be found at ​http://broadinstitute.github.io/picard/

Downloads

Binary releases of the modified Picard.

Fork version	Date	Binary	Picard version
1.128-5	October 14, 2015	picard-tools-1.128-5.zip​	1.128
1.128-4	March 6, 2015	picard-tools-1.128-4.zip​	1.128
1.128-3	January 20, 2015	picard-tools-1.128-3.zip​	1.128	Notes
1.120-2	September 26, 2014	picard-tools-1.120-2.zip​	1.120
1.115-1	August 19, 2014	picard-tools-1.115-1.zip​	1.115

Documentation of changes

Fork release version 5

1. [Picard AddOrReplaceReadGroups]: ​Add Read Group Library tag to SAM records

Fork release version 4

1. [Picard IlluminaBasecallsToFastq and IlluminaBasecallsToSam]: ​Allow barcode files with 0 length

Fork release version 3

1. [Picard - IlluminaBasecallsToFastq and IlluminaBasecallsToSam]: ​Do not write FASTQ/BAM/SAM files for unmapped barcode if no 'N' in mapping file
2. [HTSJDK]: ​Add support for setting compression level when opening GZIP files for writing
3. [Picard]: ​Set compression level to value of COMPRESSION_LEVEL command line parameter

Fork release version 2

1. [Picard - CheckIlluminaDirectory]: ​Use TileMetrics.bin instead of TileMetricsOut.bin if it is larger
2. [Picard - CheckIlluminaDirectory]: ​Log failures with ERROR level instead of INFO level

Fork release version 1

1. [HTSJDK]: ​Print regular log messages to stdout and error messages to stderr
2. [Picard]: ​Use nnordborg/htsjdk/lorry branch instead of samtools/htsjdk/master
3. [Picard]: ​Print information messages to stdout instead of stderr
4. [Picard - ExtractIlluminaBarcodes]: ​Added support for FIRST_TILE and TILE_LIMIT parameters
5. [Picard - IlluminaBaseCallsToFastq]: ​Closing 'underlyingIterator' when the 'CountLimitedIterator' is closed (to get rid of the 'Too many open files' problem)