5d112219e7
Merged bug fix from Stable into Unstable
2011-06-30 13:50:51 -04:00
bb6b1d615b
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-06-30 13:50:16 -04:00
26c4ef3813
Merged bug fix from Stable into Unstable
2011-06-30 13:18:44 -04:00
804d5f22d5
Reverting previous change, as promised.
2011-06-30 13:18:30 -04:00
521a0710e3
Merged bug fix from Stable into Unstable
2011-06-30 13:17:29 -04:00
9e234cf5d6
This is a temporary commit for Picard. It will absolutely break integration tests, but I'm going to revert it in 1 minute. Because we don't want them in unstable, I need to push this into stable.
2011-06-30 13:17:14 -04:00
8a5bfb425c
Merged bug fix from Stable into Unstable
2011-06-30 11:56:14 -04:00
352c38fc0b
Updated to reflect dbsnp conversion fix
2011-06-30 11:55:56 -04:00
58720601b4
Merged bug fix from Stable into Unstable
2011-06-30 11:44:33 -04:00
f51478595b
I guess I don't want to lose these
2011-06-30 11:43:46 -04:00
efd99c3c11
new home for the core qscripts
2011-06-30 11:32:06 -04:00
a26a793532
moving the oneoffs queue scripts to their new home.
2011-06-30 11:29:33 -04:00
7cfe9d1f94
Merged bug fix from Stable into Unstable
2011-06-30 01:17:32 -04:00
36620c62be
Saving the walkers I 'care about'.
2011-06-30 00:20:26 -04:00
6382232279
Opting to maintain the Replication/Validation files/package in unstable/private. Resolving the conflict from the stable -> unstable merge so it doesn't affect other mergers in the futures.
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Conflicts:
private/java/src/org/broadinstitute/sting/gatk/walkers/replication_validation/ReplicationValidationWalker.java
2011-06-29 18:30:46 -04:00
a3c17a38bb
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-06-29 18:26:11 -04:00
0d1978756e
Removing the replication/validation files and package from the stable repo. It should only exist in private/unstable.
2011-06-29 18:25:47 -04:00
9e5d0d8155
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-06-29 18:09:58 -04:00
231845ab2f
Moved around packages and imports for the Replication Validation walker to work with the new private/public framework.
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Pooled caller implemented but is failing tests (always choosing AC=0).
2011-06-29 18:09:26 -04:00
ef51429b66
Merged bug fix from Stable into Unstable
2011-06-29 17:38:00 -04:00
f18fffd625
Fixing broken paths to the testdata directory throughout the codebase.
2011-06-29 17:36:47 -04:00
18666a2c0b
Merged bug fix from Stable into Unstable
2011-06-29 16:10:16 -04:00
2ad4d2f0bb
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-06-29 16:06:14 -04:00
1085df8b7b
Making the BQSR pipeline publicly available and supported.
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this is for all the Pacbio validation that is going on right no in the cancer group. They are all using this script, and I'm happy to support it.
2011-06-29 16:05:32 -04:00
ec9d8313ee
Giving the BQSR pipeline script a more appropriate name since more people are using it now.
2011-06-29 16:03:26 -04:00
dcd520a42e
Merged bug fix from Stable into Unstable
2011-06-29 15:59:27 -04:00
70ba851478
Might as well check for the illegal state and throw an exception
2011-06-29 15:59:10 -04:00
0b622e8d67
Merged bug fix from Stable into Unstable
2011-06-29 15:54:38 -04:00
1f19afe1d9
Fixed bug in the IndelRealigner: now that variants are correctly typed in VariantContext, it is possible that a variant can be an indel but neither an insertion or a deletion; added a isComplexIndel() method and now we check for such an event in the realigner (we don't use them to generate alternate consenses). Also, added a isMNP() method while I was there so that it would be consistent with other variant types.
2011-06-29 15:54:09 -04:00
fcd6539a7c
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-06-29 15:40:29 -04:00
ebe6dda0c1
Oops...we were pulling only first of pair alignment summary metrics into QC
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before; now (I think) we're pulling cumulative metrics instead. We should
eventually consider incorporating the 1 of pair, 2 of pair, and unpaired
metrics as well.
2011-06-29 15:39:07 -04:00
0afe487681
Merged bug fix from Stable into Unstable
2011-06-29 14:56:49 -04:00
f018c27050
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-06-29 14:56:22 -04:00
33c67a139c
Wrong package; this should have been moved when VC got moved in from Tribble
2011-06-29 14:56:02 -04:00
47499ebc24
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-06-29 14:53:17 -04:00
9a22d78e48
Fix up gsalib target to work with new public/private directory structure.
2011-06-29 14:48:10 -04:00
b66820da35
Initial phase of PreQC database generation, plus refactoring of pm input
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parser and per sample metrics generator to provide supporting methods for
PreQC database generation.
2011-06-29 14:43:17 -04:00
dee10140dd
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-06-29 13:58:04 -04:00
8586c86bc4
My commit from last week to fix the old dbsnp rod conversion only worked for locus traversals. Updated now to work for all traversals.
2011-06-29 13:56:37 -04:00
f736a1d61b
Updated md5's from previous checkin
2011-06-29 13:37:15 -04:00
5b6d279a2e
Two bug fixes:
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a) Modified the way clipped bases are dealt with in ReadPosRankSumTest when annotating indels. Cigar string cannot be trusted because BWA can clip good high quality bases and some sites get incorrect ReadPos annotations if BWA systematically clips at an indel breakpoint.
b) PL header needs to specify "." as length. Otherwise we fail VCF validation if multiallelic sites are present.
2011-06-29 10:21:27 -04:00
643458d7db
Updated the tribble jar -- this should fix most of the integration test
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failures we've been seeing.
Note that with tribble's new svn repository the revision numbers have reset,
hence "revision 3"
2011-06-29 01:11:03 -04:00
0a96f53772
One last test...
2011-06-28 19:18:17 -04:00
efff6060b7
Revert "Final test commits before going live."
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This reverts commit ba1443e54b829dd97af636415ed0d5cdaf256ad3.
2011-06-28 18:58:55 -04:00
755b80dc74
Final test commits before going live.
2011-06-28 18:56:00 -04:00
7e243fae6e
Bug fixes for build.xml related to the public/private restructuring.
2011-06-28 12:55:18 -04:00
139c6b84a1
Modified build.xml and the help extractor doclet to use the output of "git
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describe" as an absolute version number (if the repository has at least one
tag), using the raw SHA-1 hash value as a fallback version number in the case
where there are no tags.
2011-06-28 08:37:05 -04:00
3c9497788e
Reorganized the codebase beneath top-level public and private directories,
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removing the playground and oneoffprojects directories in the process. Updated
build.xml accordingly.
2011-06-28 06:55:19 -04:00
b46279d62e
required RODs are now checked by annotations.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6080 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-25 06:38:19 +00:00
3879b02cdd
updating a package
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6079 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-24 20:13:28 +00:00
Mauricio Carneiro
Eric Banks
David Roazen
Matt Hanna
Guillermo del Angel
carneiro
ebanks