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  • 11abb4f9d1 Better error message. Christopher Hartl 2011-11-09 11:25:28 -0500
  • d3a533b82e Revert "a" Christopher Hartl 2011-11-09 11:22:26 -0500
  • 5eaf800281 a Christopher Hartl 2011-11-09 11:22:20 -0500
  • 5451fbc2b2 Merged bug fix from Stable into Unstable Christopher Hartl 2011-11-09 11:06:15 -0500
  • 091229e4db MVLikelihoodRatio now checks if the family string is provided before attempting to instantiate. Also check that variant contexts have both genotypes and genotype likelihoods. Table codec now yells at users for not providing a HEADER with the table - parsing tables without a header line was causing the first line of the file to be eaten. Table feature now has a toString method. Christopher Hartl 2011-11-09 11:03:29 -0500
  • e1b4c3968f Fixing GATKSAMRecord bug Mauricio Carneiro 2011-11-08 16:50:03 -0500
  • 8e519e7d5d Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2011-11-08 16:07:12 -0500
  • c49efcf631 Two small improvements to ValidationSiteSelector: a) add argument to ignore genotypes, and make sure selection works in sites-only VCF (in which case we can't select for polymorphism in samples), b) add ability to include filtered sites if requested Guillermo del Angel 2011-11-08 16:06:18 -0500
  • e973ca2010 fixing merge conflict. Ryan Poplin 2011-11-08 14:55:05 -0500
  • b0e6afec48 Bug fix for HMM optimization. Need to also check the gap continuation penalty array for the index with the first discrepancy. Ryan Poplin 2011-11-08 14:51:25 -0500
  • 571c724cfd Added reporting of the number of genotypes updated. Laurent Francioli 2011-11-08 15:15:51 +0100
  • 94dc447a70 Merged bug fix from Stable into Unstable Ryan Poplin 2011-11-07 15:26:35 -0500
  • 0b181be61f Bug fix in SelectVariants when using a discordance track but no sample specifications. Added integration test to test this. Ryan Poplin 2011-11-07 15:25:16 -0500
  • 66ad2b941c Merged bug fix from Stable into Unstable Eric Banks 2011-11-07 15:08:30 -0500
  • 6297561326 Adding the new jar Eric Banks 2011-11-07 15:08:19 -0500
  • 41f296ee6d Merged bug fix from Stable into Unstable Eric Banks 2011-11-07 15:00:25 -0500
  • 86312a956a Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable Eric Banks 2011-11-07 14:59:49 -0500
  • 0534149708 Merged bug fix from Stable into Unstable Ryan Poplin 2011-11-07 14:07:08 -0500
  • 2d1e385ca4 Adding note to VQSR docs about Rscript being needed in the environment PATH. Ryan Poplin 2011-11-07 14:04:13 -0500
  • bb448b27d2 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-11-07 13:26:37 -0500
  • 63eeb5a56c MultiSampleCalling script update Mark DePristo 2011-11-07 13:23:34 -0500
  • 759f4fe6b8 Moving unclaimed walker with bad integration test to archive Eric Banks 2011-11-07 13:16:38 -0500
  • aa0c8c3600 Revving Tribble jar to v40. Our last jar was busted. Eric Banks 2011-11-07 11:30:08 -0500
  • c1986b6335 Add notes to the GATKdocs as to when a particular annotation can/cannot be calculated. Eric Banks 2011-11-07 11:06:19 -0500
  • 724e3f3b0d Merged bug fix from Stable into Unstable Eric Banks 2011-11-06 22:23:22 -0500
  • cdd40d1222 Removing contracts for the SimpleTimer Eric Banks 2011-11-06 22:22:49 -0500
  • 2f2c81dccb Adding argument to control scatter count Ryan Poplin 2011-11-06 12:56:22 -0500
  • 4a1e8ecbb7 Updating HaplotypeCaller qscript to work with most recent Queue Ryan Poplin 2011-11-06 12:53:54 -0500
  • 5c565d28b9 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2011-11-06 10:26:19 -0500
  • ebdced412c misc cleanup Ryan Poplin 2011-11-06 10:26:07 -0500
  • 3517489a22 Better --sample selection integration test for VE. The previous one would return true even if --sample was not working at all. Eric Banks 2011-11-06 01:07:49 -0400
  • 1c4e429a1c Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-11-06 00:05:56 -0400
  • a12bc63e5c Get rid of support for bams without sample information in the read groups. This hidden option wasn't being used anyways because it wasn't hooked up properly in the AlignmentContext. Eric Banks 2011-11-05 23:54:28 -0400
  • ad57bcd693 Adding integration test to cover using expressions with IDs (-E foo.ID) Eric Banks 2011-11-05 23:53:15 -0400
  • e89fe7770e Merged bug fix from Stable into Unstable Eric Banks 2011-11-05 22:41:21 -0400
  • 90a053ea93 Don't change the mapping quality of MQ=255 reads in IR Eric Banks 2011-11-05 22:40:45 -0400
  • 611a395783 Now properly extending candidate haplotypes with bases from the reference context instead of filling with padding bases. Functionality in the private Haplotype class is no longer necessary so removing it. No need to have four different Haplotype classes in the GATK. Ryan Poplin 2011-11-05 12:18:56 -0400
  • fd09d92801 Added contracts to SyntheticRead class Mauricio Carneiro 2011-11-04 16:26:23 -0400
  • 839cab7427 Generalizing RunningConsensus to SyntheticRead Mauricio Carneiro 2011-11-04 16:07:51 -0400
  • 56674e3518 Removing SlidingReads Mauricio Carneiro 2011-11-04 15:13:33 -0400
  • 18837e3e32 Moving SlidingRead functionality into SlidingWindow Mauricio Carneiro 2011-11-04 15:10:21 -0400
  • bf822172c7 Renaming the compressor classes Mauricio Carneiro 2011-11-04 14:55:54 -0400
  • 56a6bb6e98 Fixing BAMRecord illegal access Mauricio Carneiro 2011-11-04 14:32:32 -0400
  • de07e06cbc Merge remote-tracking branch 'unstable/master' Eric Banks 2011-11-04 15:57:13 -0400
  • 888d3b4fdc Initial graph pruning algorithm for the assembler. Ryan Poplin 2011-11-04 14:02:50 -0400
  • e99871f587 Bug fix for decode loc Mark DePristo 2011-11-04 13:20:54 -0400
  • a340a1aeac Bug fix. decodeLoc() should update lineNo so you get meaningful line no when indexing Mark DePristo 2011-11-04 11:44:24 -0400
  • 849c0757f2 Bug fix for LocusScatterFunction when no intervals are provided Mark DePristo 2011-11-04 10:55:09 -0400
  • 9f260c0dc1 Zero byte index bug fix for RandomlySplitVariants + cleanup Mark DePristo 2011-11-04 09:45:20 -0400
  • 5a47c3c8a0 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-11-04 09:36:42 -0400
  • 020b8b88ef GATKSAMRecord refactor in the tools Mauricio Carneiro 2011-11-03 17:33:42 -0400
  • e89ff063fc GATKSAMRecord refactor Mauricio Carneiro 2011-11-03 15:12:55 -0400
  • f1df6c0c81 Misc cleanup in haplotype caller after incorporating Mark's FragmentCollection to merge overlapping read pairs. Ryan Poplin 2011-11-03 13:51:19 -0400
  • 748f8f1edc Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-11-03 10:06:48 -0400
  • 385a6abec1 Fixed a bug that wrongly swapped the mother and father genotypes in case the child genotype missing. Laurent Francioli 2011-11-03 13:04:53 +0100
  • 893787de53 Functions getAsMap and getNegLog10GQ now handle missing genotype case. Laurent Francioli 2011-11-03 13:04:11 +0100
  • c7f51e92a0 Mostly working version of multi-sample analysis qscript Mark DePristo 2011-11-02 23:00:17 -0400
  • e8bceb1eaa Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2011-11-02 21:13:54 -0400
  • 78a00d2ddc Updating UG integration tests (needed updating only because the -mbq default is different from the old -mmq one). Eric Banks 2011-11-02 21:13:44 -0400
  • 52b16bf739 Must check whether there's a normal vs. extended pileup before asking for it. Eric Banks 2011-11-02 20:45:24 -0400
  • e1edd6bd12 Removing the min mapping quality argument since it wasn't being used in the normal processing of the pileups in UG - only for indel pileups. Instead, we apply the min base quality to the reads in the pileup for indels and define it to be the min 'confidence' of the base. Docs are updated but I didn't rename the argument as I don't want people to complain. Eric Banks 2011-11-02 20:32:58 -0400
  • c22a14ee3b Merged bug fix from Stable into Unstable Mauricio Carneiro 2011-11-02 17:53:56 -0400
  • e4a583a53f Fixing docs: No -I in this walker Mauricio Carneiro 2011-11-02 17:53:10 -0400
  • e94fcf537b Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2011-11-02 16:29:19 -0400
  • 4d35272916 Bug fixes with Mauricio to functions in ReadUtils used by reduced reads and the haplotype caller. Ryan Poplin 2011-11-02 16:29:10 -0400
  • 8a2929c1dd Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable Mark DePristo 2011-11-02 16:21:00 -0400
  • e2f40da27f Scala script to run multi-sample analysis Mark DePristo 2011-11-02 16:20:57 -0400
  • bd977c2d92 Bug fix to avoid infinite loop in GATKScatterFunction Mark DePristo 2011-11-02 16:20:42 -0400
  • 19ad5b635a - Calculation of parent/child pairs corrected - Separated the reporting of single and double mendelian violations in trios Laurent Francioli 2011-11-02 18:35:31 +0100
  • 967ff647b8 Reduced reads shouldn't contribute to Fisher Strand calculations Eric Banks 2011-11-02 13:07:20 -0400
  • cf0e699226 QualByDepth was inefficiently iterating over the pileup 2 times for some reason. Removed non-useful annotation classes. Eric Banks 2011-11-02 12:58:38 -0400
  • 4501dce58d Fixing merge conflict Eric Banks 2011-11-02 12:50:32 -0400
  • 54331b44e9 New way of looking at the size of a pileup: there's a physical number of elements in the data structure and there's a representative depth of coverage (since a reduced read represents depth >= 1). The size() method has been removed because its meaning is ambiguous. Updated several annotations and the UG engine to make use of the representative depths. Eric Banks 2011-11-02 12:47:30 -0400
  • c1da8cd5e7 Final version of bp-resolved locus scatter/gather Mark DePristo 2011-11-02 11:26:34 -0400
  • 392e0aeace Moved unit tests into master IntervalUtilsUnitTest Mark DePristo 2011-11-02 10:52:00 -0400
  • c2b97030a4 IntervalUtils for completely balanced locus-based scatter/gather Mark DePristo 2011-11-02 10:49:40 -0400
  • 119ca7d742 Fixed a bug in parent/child pairs reporting causing a crash in case the -mvf option was used and mother was not provided Laurent Francioli 2011-11-02 08:22:33 +0100
  • b91a9c4711 - Fixed parent/child pairs handling (was crashing before) - Added parent/child pair reporting Laurent Francioli 2011-11-02 08:04:01 +0100
  • 5fc613f972 Better default partition types for walkers Mark DePristo 2011-11-01 19:47:10 -0400
  • 53c9f49050 Fixing contracts! Mauricio Carneiro 2011-11-01 18:09:29 -0400
  • 7d194afda8 Revert "Using isReduceRead from GATKSAMRecord" Mauricio Carneiro 2011-11-01 17:54:30 -0400
  • 36600fd8e9 added MQ of low MQ/BQ to consensus RMS Mauricio Carneiro 2011-11-01 17:46:12 -0400
  • 18f4c63d44 Using isReduceRead from GATKSAMRecord Mauricio Carneiro 2011-11-01 17:15:58 -0400
  • b004489c6d Moving ReduceRead TAG to GATKSAMRecord Mauricio Carneiro 2011-11-01 17:11:47 -0400
  • 2b200c34a6 Removing testEqualBases Mauricio Carneiro 2011-11-01 17:05:27 -0400
  • 17cc484dbd Revert "ReduceReads ref bases are now output as '=' Mauricio Carneiro 2011-11-01 16:35:07 -0400
  • 76c32f5409 Revert "Compressed read group information" Mauricio Carneiro 2011-11-01 16:33:21 -0400
  • 0839c75c8d More minor fixes to docs Eric Banks 2011-10-31 21:49:27 -0400
  • 74b018a1f3 Minor fixes to docs Eric Banks 2011-10-31 21:41:43 -0400
  • b51c36abb3 TEST: equal '=' base test implementation Mauricio Carneiro 2011-10-31 18:01:04 -0400
  • 31ee5432c5 Merged bug fix from Stable into Unstable Eric Banks 2011-10-31 14:56:59 -0400
  • cdde32acbd Merged bug fix from Stable into Unstable David Roazen 2011-10-31 14:21:15 -0400
  • f62af0291b Check for invalid VCF records (not enough tokens) instead of assuming they are there. Eric Banks 2011-10-31 14:09:51 -0400
  • bed0acaed4 nWayOut now adds PG tag to the header as it should. Also, additional hidden option added: keepPGTags. If invoked, IndelRealigner PG tags from previous runs (if any) are kept in the header and the new PG tag is simply added, instead of overriding them Andrey Sivachenko 2011-10-31 12:28:28 -0400
  • 7a8e49154d Fixing contracts Mauricio Carneiro 2011-10-31 09:17:34 -0400
  • ab4f58a5e9 A base for a test walker for reduce reads Mauricio Carneiro 2011-10-30 22:26:16 -0400
  • e220507ff9 Compressed read group information Mauricio Carneiro 2011-10-30 21:09:06 -0400
  • 389380a590 ReduceReads ref bases are now output as '=' to save space Mauricio Carneiro 2011-10-30 11:57:52 -0400
  • dbd8c25787 No more R resources in the DPP Mauricio Carneiro 2011-10-28 16:57:01 -0400
  • e25d40882a Swapping Thread.sleep(0) with Object.wait(0) caused Queue to lock up. Thanks to rpoplin for pointing it out. Khalid Shakir 2011-10-28 15:49:12 -0400