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6947 Commits (cf3e826a6978fcd50dfd3410a22ebf304e511e2f)

Author SHA1 Message Date
Matt Hanna 7054c5342f When using the BWA bindings, you have to explicitly call close() to get the 
bindings to release memory.
It may or may not be possible to implicitly close triggered by the GC; I'll add a JIRA.
 2011-07-21 12:13:29 -04:00
Guillermo del Angel 84c66d4b92 Bug fixes 2011-07-21 11:52:51 -04:00
Guillermo del Angel c4684f4659 A true oneoff: walker that reads in vcf with multiallelic PL's in wrong ordering and flips them around to output in correct order 2011-07-21 11:20:46 -04:00
Kiran V Garimella 623143454b Merge branch 'laptop' 2011-07-21 11:07:02 -04:00
Kiran V Garimella bf6388fa8c Print haplotype start locus 2011-07-21 11:06:45 -04:00
Christopher Hartl 15610ce0c3 Per Matt's request, disabling BWA-based integration tests so he can assess bamboo memory usage. 2011-07-21 11:04:22 -04:00
Kiran V Garimella 1aefc02d2e Merge branch 'laptop' 2011-07-21 10:54:15 -04:00
Kiran V Garimella 45e536dca8 Reenable haplotype printing 2011-07-21 10:40:40 -04:00
Guillermo del Angel 664246937c Try to resolve merge conflict 2011-07-21 10:19:26 -04:00
Kiran V Garimella 1933be36b4 Ignore sites where the alleles don't match between the two files 2011-07-21 03:44:02 -04:00
Kiran V Garimella d9909537ef Merge branch 'laptop' 2011-07-21 03:22:59 -04:00
Kiran V Garimella 58873c391f Don't print the haplotypes anymore - the metrics will do 2011-07-21 03:22:44 -04:00
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