76efa757f0
Switched over to reviewed version of Picard patch. In process, did some optimization to the IntervalSharder
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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
7d2df3f511
example windowed ROD walker for Kristian, and updates to Tribble
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3325 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 17:12:50 +00:00
78409dca0d
turned off the progress output from tribble when making an index, and fixing a case where the index file isn't writable so we instead make the index in memory.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3312 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-06 16:36:58 +00:00
d91b27aca1
updating Tribble with VCF changes from Eric
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3310 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-06 04:03:21 +00:00
7467ec2fd6
updating the reflections library; Matt found a problem where the reflections library doesn't sort out non-java objects from the classpath (affects only OS X so far). I'll push back the changes to
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the reflections library people.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3307 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-06 02:08:41 +00:00
97dd04cbf0
updating Tribble ahead of the big VCF commit
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3297 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 05:17:54 +00:00
447081583a
rev tribble with updated version
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3287 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-03 04:07:28 +00:00
b648e89096
updating Tribble with a bunch of bug and performance fixes found while performance testing GeliText in the GATK
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3267 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-28 18:45:10 +00:00
64c5f287c5
fixes for edge-cases when using reflections to find classes outside of the main jar. Will push as a patch to reflections
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3264 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-27 17:46:46 +00:00
c647153b10
Adding Jama for Ryan.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3262 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-27 14:30:36 +00:00
f6468f9143
a fix for a bug we've worked around in the reflections package: previously it didn't find classes that weren't in the main jar. Fixed in this version.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3261 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-27 04:49:49 +00:00
4bb8984f80
Updating picard -- switching to Alec's more robust fix for gzip decompression issue
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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
b60197ae10
Another round of cleanup and simplification in Picard -- Picard's unit tests
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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
400684542c
Revisions to take into account finalization of Picard patch: naming changes, better definition
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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
85037ab13f
Fix for Kiran's sharding issue (Invalid GZIP header). General cleanup of
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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
46c14ec63f
New, much less memory intensive implementation of BAM file sharding. Streams indices together with the expectation
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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
1f451e17e5
Changing preloaded index to only "preload" reference sequences on demand.
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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
884a577013
Phase 2 of Picard patch refactoring: kill off SAMFileReader2/BAMFileReader2, merging the changes back into the base classes.
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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
169d0c6e8f
Up the svn revision number in an attempt to force an update, again due to an
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artifact of the way we build picard-private-parts.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3051 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-19 22:39:56 +00:00
c0eb5c27ea
Lower memory support for merged sharding. Merged sharding is still not available.
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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
96662d8d1b
Moving from GATK dependencies on isolated classes checked into the GATK
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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
8fd3351971
adding a stripped down Tribble library for the start of integration
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2851 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-17 21:29:25 +00:00
3feead019d
New Picard and SAM-JDK with automatic sequence name truncation
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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
b5e5e27225
New versions of picard-private, sam and picard jars for TileCovariate and regeneration of NM tag
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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
d1d6b79673
Update picard public and private to match new SAM update.
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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
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.
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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
84921b18ed
Push version number of picard-private-parts
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2163 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-25 19:28:57 +00:00
5f2801e015
Push version number of picard-private-parts
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2162 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-25 19:28:42 +00:00
d563f4bd2c
Add IlluminaUtil to picard-private.jar
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2161 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-25 19:25:21 +00:00
1fcd28bba9
Update xml descriptor with proper version number.
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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
4082f4677e
Picard-private with classes for reading Picard dbSNP binary file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2086 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-19 17:24:28 +00:00
7463904428
Picard-private with classes for reading Picard dbSNP binary file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2085 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-19 17:23:37 +00:00
d1325909f7
Picard-public 1.08
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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
db793ac870
Picard-public 1.08
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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
8eff1cc436
Extract and include only the Tim Fennell-approved parts of picard private.
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Hopefully this is a temporary solution and these classes will be migrated
into picard-public.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2041 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-13 19:42:33 +00:00
8145ed4672
Take 2, updating picard with bug fix for bam files containing no reads.
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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
8406325247
New Picard is breaking one of the integration tests.
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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
bae4d3f7ea
Updated Picard with fix for Doug Voet. Thanks Alec.
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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
85a4fbc256
Bumping version of Picard for firehose compatibility.
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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
48b478f751
epic fail!
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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
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.
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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
b43925c01e
Switched to Reflections ( http://code.google.com/p/reflections/ ) project for
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inspecting the source tree and loading walkers, rather than trying to roll
our own by hand.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1286 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-21 18:32:22 +00:00
ddf4003536
Updates to picard public / private and sam.
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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
9fe330cdf1
Bump picard and sam to latest version.
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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
ad80894afa
Bumped picard to latest svn version.
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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
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...
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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
aa17c4a468
Farewell, functionalj. You promised much, but you could not deliver.
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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
4ab9bfe662
Upped sam-jdk jar to new version in public picard repository.
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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
8cce3d908f
Bumped sam to latest.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@690 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-13 19:19:55 +00:00
a573b8ede1
Bumped sam-jdk version to fix bug unzipping bam files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@554 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-28 20:02:05 +00:00
hanna
aaron
alecw