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
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
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
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
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
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
hanna
aaron
jmaguire