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57 Commits (ffbd4d85f2e0112b32df0bbba00330b00a0806cf)

Author SHA1 Message Date
Khalid Shakir b8b7f28aa9 Revving Picard to pick up new SamFileHeaderMerger. 
Updated ReadFilter abstract class to implement (via UnsupportedOperationException) the new SamRecordFilter.filterOut().
In IndelRealignerIntegrationTest updates for Picard fixes to SAMRecord.getInferredInsertSize() in svn r1115 & r1124.
- Ran FixMates to create new input BAM since running IR with variable maxReadsInMemory means all reads weren't realigned leading to different outputs.
- Updated md5s to match new expectations after looking at TLEN diff engine output.
 2012-05-02 16:47:28 -04:00
Matt Hanna e923a2e512 Revving Picard to incorporate final version of ReadWalker performance improvements. 2012-01-10 12:12:33 -05:00
Matt Hanna e6e80e8d3f Update Picard to fix a bug Mauricio found in Picard where Picard unnecessarily depends on Snappy during some usages of SortingCollection. 2011-12-29 14:35:02 -05:00
Khalid Shakir b4b7ae1bd9 Revved Picard to incorporate tfennell's AsyncSAMFileWriter. 
Removed DbSnpFileGenerator and related files as they were removed from PPP r2063 by ktibbett.
 2011-12-06 10:37:42 -05:00
Matt Hanna 9afe6fc7ac Picard upgrade to 1.55. 2011-10-24 17:02:27 -04:00
Khalid Shakir 20ac24464d Rev'ved picard to read new analysis_files.txt with a blank line after header and no reference sequence. 
Updated error messages and unit tests.
 2011-08-29 19:33:04 -04:00
Khalid Shakir 9b446020f9 Using picard implementations for accessing aggregation directories. 
Added more utilities to PicardPrivate.
Revved picard.
 2011-07-18 21:49:03 -04:00
Matt Hanna 00b650a35d Get rid of accidental commit of emacs backup '~' file. 2011-07-17 20:52:46 -04:00
Matt Hanna 0a0363aef2 Revving Picard to get a parser that works with the latest metrics file formats 
we're starting to see.
 2011-07-17 20:43:35 -04:00
hanna 14d7ee073b Rev Picard to get new PF_INDEL_RATE metric. Rev preQC generator script 
to incorporate PF_INDEL_RATE.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5998 348d0f76-0448-11de-a6fe-93d51630548a
 2011-06-14 17:43:43 +00:00
hanna 6d5e45b5c6 Revbump Picard dependencies at Tim/Kathleen's request. Exclude anonymous 
classes from PluginManager.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5699 348d0f76-0448-11de-a6fe-93d51630548a
 2011-04-27 20:38:05 +00:00
kshakir 4f8411f4b5 Revved Picard to access new flag to disable mmap for bam indices. Only added a 3% speed boost but the mmap was added to the heap count, making it harder to specify/restrict the total resident memory size in LSF. Specifying -Xmx4g will now stay much closer to 4g resident memory usage versus bumping up to 9g when accessing 900 x ~8Mb bai's. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5549 348d0f76-0448-11de-a6fe-93d51630548a
 2011-04-01 01:40:41 +00:00
hanna 8d2c14b29c Update Picard / sam-jdk at Tim's request. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4925 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-03 02:17:25 +00:00
hanna 70bb480939 The battle is over. Picard is revved. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4200 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-03 05:28:01 +00:00
hanna b6af17b82d Rev Picard with new IndexedFastaSequenceFile patch. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3700 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-01 03:05:43 +00:00
hanna 4840ef6d3e Another rev of picard for /dev/null writing. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3627 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-24 19:22:47 +00:00
hanna c32f9d78ae Rev picard again, this time for error writing to /dev/null. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3626 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-24 04:08:26 +00:00
hanna 26d51bbe14 Another round of optimizations from Alec. Switching the header merger to 
an IdentityHashMap provides another 10x+ performance boost over his previous
optimization for us.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3616 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-23 14:54:58 +00:00
hanna 003dd4de3e Rev Picard with performance enhancements. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3615 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-22 22:54:23 +00:00
hanna db1383d0b2 Rev the latest version of Picard. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3575 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-16 23:55:07 +00:00
hanna c1ecf75dd5 Update to the latest rev of the picard sharding patch. Includes updates reflecting 
the imminent move of IlluminaUtil into picard public.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3493 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-06 20:33:21 +00:00
hanna 76efa757f0 Switched over to reviewed version of Picard patch. In process, did some optimization to the IntervalSharder 
which improved startup time 5-10x when dynamically merging many BAMs.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3331 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-08 14:12:22 +00:00
hanna 4bb8984f80 Updating picard -- switching to Alec's more robust fix for gzip decompression issue 
and updating serialization components.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3154 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-12 19:56:45 +00:00
hanna b60197ae10 Another round of cleanup and simplification in Picard -- Picard's unit tests 
are now passing for my branch.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3100 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-31 01:02:59 +00:00
hanna 400684542c Revisions to take into account finalization of Picard patch: naming changes, better definition 
of public interfaces.  This won't be the last Picard patch, but it should be the last big one.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3096 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-30 19:28:14 +00:00
hanna 85037ab13f Fix for Kiran's sharding issue (Invalid GZIP header). General cleanup of 
Picard patch, including move of some of the Picard private classes we use to Picard public.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3087 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-29 03:21:27 +00:00
hanna 46c14ec63f New, much less memory intensive implementation of BAM file sharding. Streams indices together with the expectation 
that bins will be present in the bin sparse array, which avoids the problem of having to hold the sparse bin array
stored in every BAM file index in memory at the same time.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3075 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-25 17:41:22 +00:00
hanna 1f451e17e5 Changing preloaded index to only "preload" reference sequences on demand. 
Results in drastic lowering of startup cost when multiple BAM files are 
merged.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3066 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-23 22:02:28 +00:00
hanna 884a577013 Phase 2 of Picard patch refactoring: kill off SAMFileReader2/BAMFileReader2, merging the changes back into the base classes. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3065 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-23 16:48:11 +00:00
hanna c0eb5c27ea Lower memory support for merged sharding. Merged sharding is still not available. 
WARNING: If you update frequently, you might have to rm -rf ~/.ant/cache -- this is an unfortunate side effect of the way we
	 distribute picard-private.jar.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3050 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 22:03:47 +00:00
hanna 96662d8d1b Moving from GATK dependencies on isolated classes checked into the GATK 
codebase to a dependency on a jar file compiled from my private picard branch.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3034 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-18 17:43:42 +00:00
alecw 3feead019d New Picard and SAM-JDK with automatic sequence name truncation 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2557 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-11 20:49:13 +00:00
alecw b5e5e27225 New versions of picard-private, sam and picard jars for TileCovariate and regeneration of NM tag 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2456 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-28 22:18:55 +00:00
hanna d1d6b79673 Update picard public and private to match new SAM update. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2438 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-23 22:34:12 +00:00
alecw 159778416c In TableRecalibrationWalker, update UQ tag if it was present in the original SAMRecord. This required a new sam.jar, which caused some other files to need to be changed. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2435 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-23 21:42:36 +00:00
hanna 1fcd28bba9 Update xml descriptor with proper version number. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2090 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-19 17:32:22 +00:00
alecw d1325909f7 Picard-public 1.08 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2084 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-19 17:22:56 +00:00
alecw db793ac870 Picard-public 1.08 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2083 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-19 17:21:00 +00:00
hanna 8145ed4672 Take 2, updating picard with bug fix for bam files containing no reads. 
Just stomped on the existing md5s because that's what Eric told me to do.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2029 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-12 22:52:08 +00:00
hanna 8406325247 New Picard is breaking one of the integration tests. 
Revert until we find out whether the cause is legit.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2017 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-11 03:59:32 +00:00
hanna bae4d3f7ea Updated Picard with fix for Doug Voet. Thanks Alec. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2015 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-11 02:01:08 +00:00
hanna 85a4fbc256 Bumping version of Picard for firehose compatibility. 
Integration tests were validated against svn rev 1861, before the wonder
twins committed their changes.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1864 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-16 19:38:56 +00:00
aaron 48b478f751 epic fail! 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1752 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-30 20:49:42 +00:00
aaron 2e4949c4d6 Rev'ing Picard, which includes the update to get all the reads in the query region (GSA-173). With it come a bunch of fixes, including retiring the FourBaseRecaller code, and updated md5 for some walker tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1751 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-30 20:37:59 +00:00
hanna ddf4003536 Updates to picard public / private and sam. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1123 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-30 14:50:55 +00:00
hanna 9fe330cdf1 Bump picard and sam to latest version. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1051 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-18 21:59:40 +00:00
hanna ad80894afa Bumped picard to latest svn version. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@965 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-10 14:36:34 +00:00
hanna 5e8c08ee63 Update to latest version of picard. Change imports in all classes dependent on picard public from import edu.mit.broad.picard... to import net.sf.picard... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@849 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-28 20:13:01 +00:00
hanna aa17c4a468 Farewell, functionalj. You promised much, but you could not deliver. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@847 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-28 01:35:49 +00:00
hanna 4ab9bfe662 Upped sam-jdk jar to new version in public picard repository. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@739 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-17 15:03:05 +00:00