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6527 Commits (f01fc732f4d4af77a3719d8d13761b6577dd2e48)

Author SHA1 Message Date
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
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
David Roazen eb63b48414 Revert "Resolving conflict" 
This reverts commit 87f0d4a8b0627b3be86acdfef5a9f2fc6ea923ee.
 2011-07-19 18:36:53 -04:00
Roger Zurawicki a3cecf0668 Resolving conflict 2011-07-19 17:20:27 -04:00
Roger Zurawicki 3d72b98a35 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable 
Conflicts:
	private/java/test/org/broadinstitute/sting/gatk/walkers/reducereads/ReduceReadsIntegrationTest.java
 2011-07-19 17:16:20 -04:00
Roger Zurawicki d92d00a85d Changed MRAV to ADAV to reflect real implementation (Max reads to Average Depth at Variant Sites). 
Optimized Mapping Quality calculation.
 Correctly filtered reads below minimum Mapping Quality threshold
 2011-07-19 16:59:06 -04:00
Mauricio Carneiro 8a7e698883 better debug output for plotting. 2011-07-19 15:28:54 -04:00
Christopher Hartl 07e716d23a PickSequenomProbes2 expanded functionality: lowercasing based on sequence uniqueness, preserving reference base prior to indel (not a part of the VC as I thought it was), masking deletion bases with 'N's, flanking insertion with 'N's, output is a fasta formatted file. Renamed to ValidationAmplicons since this is really not for picking sequenom probes, but for generating amplicon sequence from which other applications (like sequenom) can choose PCR primers. Moved from private to public. 2011-07-19 15:21:47 -04:00
Guillermo del Angel 6181d1e4cb Fixed integration test for VariantsToTable: now the * in REF column is not output 2011-07-19 14:42:11 -04:00
Guillermo del Angel e6d306458c Merge bug fixes 2011-07-19 14:36:20 -04:00