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7359 Commits (b399424a9cd4c842e8dac0e2e0f9c17ba4002ff4)

Author SHA1 Message Date
Mauricio Carneiro 47b47078ad Merged bug fix from Stable into Unstable 2011-06-30 15:22:14 -04:00
Mauricio Carneiro 64048a67e8 cleaning up ghost scala scripts. Deleting clearly unused one and moving others to qscripts.archive 2011-06-30 15:20:43 -04:00
Mauricio Carneiro b17ed7e504 Merged bug fix from Stable into Unstable 2011-06-30 15:04:30 -04:00
Mauricio Carneiro 867056af51 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable 2011-06-30 15:03:18 -04:00
Mark A. DePristo 57806d514a Merged bug fix from Stable into Unstable 2011-06-30 15:01:50 -04:00
Mark A. DePristo 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
Mauricio Carneiro 75f93882c7 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable 2011-06-30 14:59:10 -04:00
Ryan Poplin 41c43d6248 Merged bug fix from Stable into Unstable 2011-06-30 14:56:42 -04:00
Mauricio Carneiro 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
Ryan Poplin f4ae6edb92 Moving some of the released R scripts into public from private 2011-06-30 14:55:25 -04:00
Mauricio Carneiro 197b7141c1 Added an optional argument -bt <num_threads> for BWA to run multithreaded. 2011-06-30 14:41:57 -04:00
Mauricio Carneiro 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
Mark A. DePristo 5f83a5cb09 Revert "VCF4 test walker isn't useful anymore" 
This reverts commit 744fcb5c6d0e0993fdfa4b3c70428ef18dff2a21.
 2011-06-30 14:16:36 -04:00
Mauricio Carneiro 5d112219e7 Merged bug fix from Stable into Unstable 2011-06-30 13:50:51 -04:00
Mauricio Carneiro bb6b1d615b Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable 2011-06-30 13:50:16 -04:00
Eric Banks 26c4ef3813 Merged bug fix from Stable into Unstable 2011-06-30 13:18:44 -04:00
Eric Banks 804d5f22d5 Reverting previous change, as promised. 2011-06-30 13:18:30 -04:00
Eric Banks 521a0710e3 Merged bug fix from Stable into Unstable 2011-06-30 13:17:29 -04:00
Eric Banks 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
Mark A. DePristo 18e2e1441a VCF4 test walker isn't useful anymore 2011-06-30 12:49:30 -04:00
Eric Banks 8a5bfb425c Merged bug fix from Stable into Unstable 2011-06-30 11:56:14 -04:00
Eric Banks 352c38fc0b Updated to reflect dbsnp conversion fix 2011-06-30 11:55:56 -04:00
Eric Banks 58720601b4 Merged bug fix from Stable into Unstable 2011-06-30 11:44:33 -04:00
Eric Banks f51478595b I guess I don't want to lose these 2011-06-30 11:43:46 -04:00
Mauricio Carneiro efd99c3c11 new home for the core qscripts 2011-06-30 11:32:06 -04:00
Mauricio Carneiro a26a793532 moving the oneoffs queue scripts to their new home. 2011-06-30 11:29:33 -04:00
Matt Hanna 843f604be2 Bugfixing: better handling of missing Picard directories. Writing dates in 
a format more conducive to R parsing.
 2011-06-30 11:20:50 -04:00
Guillermo del Angel 375dfd4bd4 Merge branch 'master' of ssh://delangel@nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-06-30 08:30:26 -04:00
Guillermo del Angel 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
Mauricio Carneiro 7cfe9d1f94 Merged bug fix from Stable into Unstable 2011-06-30 01:17:32 -04:00
Mauricio Carneiro 36620c62be Saving the walkers I 'care about'. 2011-06-30 00:20:26 -04:00
Guillermo del Angel 50c32ce52e VariantsToTableFix 2011-06-29 21:39:53 -04:00
Guillermo del Angel 9b134f3b96 VariantsToTableFix 2011-06-29 21:33:41 -04:00
Mauricio Carneiro 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. 
Conflicts:
	private/java/src/org/broadinstitute/sting/gatk/walkers/replication_validation/ReplicationValidationWalker.java
 2011-06-29 18:30:46 -04:00
Mauricio Carneiro a3c17a38bb Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable 2011-06-29 18:26:11 -04:00
Mauricio Carneiro 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
Mauricio Carneiro 9e5d0d8155 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-06-29 18:09:58 -04:00
Mauricio Carneiro 231845ab2f Moved around packages and imports for the Replication Validation walker to work with the new private/public framework. 
Pooled caller implemented but is failing tests (always choosing AC=0).
 2011-06-29 18:09:26 -04:00
David Roazen ef51429b66 Merged bug fix from Stable into Unstable 2011-06-29 17:38:00 -04:00
David Roazen f18fffd625 Fixing broken paths to the testdata directory throughout the codebase. 2011-06-29 17:36:47 -04:00
Guillermo del Angel 2b88033ef4 Enable considering 454 reads, just lower GOP by 15 2011-06-29 16:12:55 -04:00
Mauricio Carneiro 18666a2c0b Merged bug fix from Stable into Unstable 2011-06-29 16:10:16 -04:00
Mauricio Carneiro 2ad4d2f0bb Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable 2011-06-29 16:06:14 -04:00
Mauricio Carneiro 1085df8b7b Making the BQSR pipeline publicly available and supported. 
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
Mauricio Carneiro 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
Guillermo del Angel dc4f63a1a8 a) consensus goes to week queue 
b) New experimental TechnologyComposition annotation
c) SelectVariants fixes
 2011-06-29 16:00:23 -04:00
Eric Banks dcd520a42e Merged bug fix from Stable into Unstable 2011-06-29 15:59:27 -04:00
Eric Banks 70ba851478 Might as well check for the illegal state and throw an exception 2011-06-29 15:59:10 -04:00
Eric Banks 0b622e8d67 Merged bug fix from Stable into Unstable 2011-06-29 15:54:38 -04:00
Eric Banks 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