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6685 Commits (e7b4959ebe48bb4e7f547d01cc1e8a50cbdf77f0)

Author SHA1 Message Date
Kiran V Garimella 6f095a7752 Merge branch 'laptop' 2011-07-21 03:17:14 -04:00
Kiran V Garimella c40b0fe1a3 Only evaluate genotypes that have a PQ field 2011-07-21 03:16:57 -04:00
Kiran V Garimella 11e498979f Merge branch 'laptop' 2011-07-21 03:13:56 -04:00
Kiran V Garimella 593787c1d0 Only evaluate genotypes that have a PQ field 2011-07-21 03:12:50 -04:00
Kiran V Garimella f01fc732f4 Merge branch 'laptop' 2011-07-21 03:04:30 -04:00
Kiran V Garimella 8d7b7e259e Track number of genotypes with PQ field 2011-07-21 03:04:09 -04:00
Kiran V Garimella d8f5bbeefc Merge branch 'laptop' 2011-07-21 03:02:06 -04:00
Kiran V Garimella 67031de95c Formatting changes 2011-07-21 03:01:53 -04:00
Kiran V Garimella c135d8832c Merge branch 'laptop' 2011-07-21 02:59:46 -04:00
Kiran V Garimella bfecc60fd6 Formatting changes 2011-07-21 02:59:32 -04:00
Kiran V Garimella a687f04615 Merge branch 'laptop' 2011-07-21 02:51:37 -04:00
Kiran V Garimella 620a4e5aed Handle missing PQ fields 2011-07-21 02:51:29 -04:00
Kiran V Garimella 82a0e67219 Merge branch 'laptop' 2011-07-21 02:46:59 -04:00
Kiran V Garimella c8d381f51e Formatting fixes for haplotype metrics 2011-07-21 02:46:43 -04:00
Kiran V Garimella 1992973e05 Merge branch 'laptop' 2011-07-21 02:43:19 -04:00
Kiran V Garimella 3cde209632 Print haplotype metrics 2011-07-21 02:42:58 -04:00
Kiran V Garimella de239d8f44 Merge branch 'laptop' 2011-07-21 02:16:14 -04:00
Kiran V Garimella aafe9e6ca7 Try again to suppress hom genotypes 2011-07-21 02:15:44 -04:00
Kiran V Garimella 77e10a3280 Merge branch 'laptop' 2011-07-21 02:11:02 -04:00
Kiran V Garimella e5c50fb3de Suppress matching hom genotypes 2011-07-21 02:10:15 -04:00
Kiran V Garimella 50ab8c513b Merge branch 'laptop' 2011-07-21 02:00:56 -04:00
Kiran V Garimella ba4b1ce171 Even more formatting changes, trying to get the haplotypes to line up nicely 2011-07-21 02:00:34 -04:00
Kiran V Garimella 7770ddf2d6 Merge branch 'laptop' 2011-07-21 01:56:44 -04:00
Kiran V Garimella 5d21f7fa91 Don't show reference allele status 2011-07-21 01:56:39 -04:00
Kiran V Garimella 7695eb753d More formatting 2011-07-21 01:53:36 -04:00
Kiran V Garimella 98444cbebb Merge branch 'laptop' 2011-07-21 01:47:01 -04:00
Kiran V Garimella dcd7d97b60 Formatting. 2011-07-21 01:46:38 -04:00
Kiran V Garimella e2d0a2c459 Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-21 01:42:50 -04:00
Kiran V Garimella 6cf26d8e7f Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/kiran/repositories/Sting-Unstable 2011-07-21 01:40:56 -04:00
Kiran V Garimella e5b61eb9a0 Walker to compare RBP and Beagle haplotypes 2011-07-21 01:40:25 -04:00
Mark DePristo 6fa17d86ae Completely hacked together version of a FreeMarker + javadoc + custom doclet walker documentation generator 2011-07-21 00:18:07 -04:00
Guillermo del Angel 32730b1832 Fixed md5 due to new PL ordering 2011-07-20 22:17:15 -04:00
Mark DePristo 45c73ff0e5 Runs and emits an HTML document 2011-07-20 17:16:33 -04:00
Mark DePristo d31b176e15 Removed GATK use of distributed parallelism framework. 
Moved distributed GATK prototype code into distributedutils, separating from threading package
 2011-07-20 16:26:09 -04:00
Matt Hanna 4b0b7f4b32 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-20 14:49:25 -04:00
Matt Hanna f14f20d718 Fix bug involving reuse of the sample variable. 
Cleaned up some otherwise unused comments and code.
 2011-07-20 14:48:33 -04:00
Guillermo del Angel 0a1d2df8cb Merged bug fix from Stable into Unstable 2011-07-20 13:19:35 -04:00
Guillermo del Angel f15023b7d2 Bad bug fix: output GLs in multiallelic records were in incorred order (misread spec) 2011-07-20 12:10:48 -04:00
Mauricio Carneiro c09f92ccee Fixing the illegal character accidently entered 2011-07-20 11:39:04 -04:00
Mauricio Carneiro 4e00666632 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-20 11:38:16 -04:00
Roger Zurawicki ea90af199c Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-20 11:17:36 -04:00
Roger Zurawicki d3a8363491 Changed MRAV to ADAV 
Updated ReducedBAMEvaluation to allow multiple parameters to be tested
Fixed previous error
 2011-07-20 10:49:50 -04:00
Guillermo del Angel b9c9e0e952 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-20 10:45:16 -04:00
Guillermo del Angel 7140280bf6 Further bug fixes/cleanups for PrintReadsWalker 2011-07-20 10:44:37 -04:00
Guillermo del Angel a2d90a3590 Bug fix: reverted logic so that default behavior skips over sample lookup 2011-07-20 10:23:10 -04:00
Guillermo del Angel e8409c80fa Further protection vs null pointers in PrintReadsWalker 2011-07-19 21:59:24 -04:00
Christopher Hartl 5d706c9e92 Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 
Removing PSP and CSM

Conflicts:

	public/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/CreateSequenomMask.java
	public/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java
 2011-07-19 20:25:33 -04:00
Guillermo del Angel fb2d475c22 Bug fix to prevent null pointer 2011-07-19 20:13:56 -04:00
Christopher Hartl 92c7cfa1c8 BWA bindings and tests moved to public (was required for ValidationAmplicons) 
Integration tests for ValidationAmplicons. New argument to disable BWA, lowercase letters only for repetitiveness instead.
 2011-07-19 20:11:31 -04:00
David Roazen baae381acb Revert "Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable" 
This reverts commit 039a6bb01f345322ce2be50ae3634308bb24e77e, reversing
changes made to b9c9973d1c638dfc9f8c19b5eb845e99844f9d29.
 2011-07-19 18:38:53 -04:00