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
60fe2e06d1
Revert accidental checkin of hacked picard build.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@543 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-27 09:47:10 +00:00
dd408a2a9a
First draft of actual pooled EM caller.
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Produces sane looking output on region of 1kG pilot1:
CALL NA12813.SRP000031.2009_02.bam CC 0.609084 0.609084
CALL NA12003.SRP000031.2009_02.bam CC 2.114234 2.114234 CCCCC
CALL NA06994.SRP000031.2009_02.bam CC 0.910114 0.910114 C
CALL NA18940.SRP000031.2009_02.bam CT 2.589749 0.910114 T
CALL NA18555.SRP000031.2009_02.bam CC 0.609084 0.609084
Next up, eval vs. Baseline pilot1 calls and pilot3 deep-coverage truth.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@525 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 13:42:15 +00:00
feebd8cd55
Latest version of sam.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@436 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 21:02:25 +00:00
8efedacabf
Bump sam jdk to svn rev 207.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@340 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-08 22:16:46 +00:00
067ae09cd0
Bump picard and samtools to latest.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@207 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-27 02:26:28 +00:00
1fcf4c0cbf
Update picard to work with new samtools.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@123 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-20 21:51:26 +00:00
6e2d939905
Added subversion rev 180 of the sam library.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@120 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-20 20:17:51 +00:00
1096bbd4d9
Moved build.xml, ivy.xml and settings to root of Sting repository.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@88 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-18 19:13:19 +00:00
alecw
hanna
aaron
jmaguire