47b47078ad
Merged bug fix from Stable into Unstable
2011-06-30 15:22:14 -04:00
64048a67e8
cleaning up ghost scala scripts. Deleting clearly unused one and moving others to qscripts.archive
2011-06-30 15:20:43 -04:00
b17ed7e504
Merged bug fix from Stable into Unstable
2011-06-30 15:04:30 -04:00
867056af51
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-06-30 15:03:18 -04:00
57806d514a
Merged bug fix from Stable into Unstable
2011-06-30 15:01:50 -04:00
defa3cfe85
Moved around private walkers into appropriate directories in private gatk.walkers. Moved a few public walkers into private qc package, and some private qc walkers into the public directory. Removed several obviously broken and/or unused walkers.
2011-06-30 14:59:58 -04:00
75f93882c7
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-06-30 14:59:10 -04:00
41c43d6248
Merged bug fix from Stable into Unstable
2011-06-30 14:56:42 -04:00
2cb1376ed0
VCFStreaming was failing integration tests because now select variants outputs the samples in alphabetical order, instead of random as before. Fixed the MD5.
2011-06-30 14:55:39 -04:00
f4ae6edb92
Moving some of the released R scripts into public from private
2011-06-30 14:55:25 -04:00
197b7141c1
Added an optional argument -bt <num_threads> for BWA to run multithreaded.
2011-06-30 14:41:57 -04:00
f4463d38ca
BWA requires pair ended reads to be sorted by read names when operating over BAM files, but Picard sorts by coordinate, so in case we use BWA in pair ended reads, the pipeline now resorts the BAM in read name order, realigns it then sorts it in coordinate order.
2011-06-30 14:29:21 -04:00
5f83a5cb09
Revert "VCF4 test walker isn't useful anymore"
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This reverts commit 744fcb5c6d0e0993fdfa4b3c70428ef18dff2a21.
2011-06-30 14:16:36 -04:00
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
18e2e1441a
VCF4 test walker isn't useful anymore
2011-06-30 12:49:30 -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
843f604be2
Bugfixing: better handling of missing Picard directories. Writing dates in
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a format more conducive to R parsing.
2011-06-30 11:20:50 -04:00
331b47afbd
Merge branch 'master' of ssh://delangel@nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-06-30 08:29:11 -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
2b88033ef4
Enable considering 454 reads, just lower GOP by 15
2011-06-29 16:12:55 -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
dc4f63a1a8
a) consensus goes to week queue
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b) New experimental TechnologyComposition annotation
c) SelectVariants fixes
2011-06-29 16:00:23 -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
e91ae6b265
AF matching when selecting random variants
2011-06-29 15:00:26 -04:00
Mauricio Carneiro
Mark A. DePristo
Ryan Poplin
Eric Banks
Matt Hanna
Guillermo del Angel
David Roazen