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116 Commits (fff63bab53a8570420feb88237e011219b882309)

Author SHA1 Message Date
Ernesto Brau 446b11913b Added FPGA support for PairHMM via GKL, and marked as 'experimental' 2017-06-07 14:39:11 -04:00
Ernesto Brau e8b42c4dfd Use GKL's implementation of Vector Logless Pair HMM 
Fixed MuTect2 tests by removing old -alwaysloadVectorHmm flag; upgraded to GKL 0.5.2; FASTEST_AVAILABLE pairhmm option; improved documenting comments in code

Made FASTEST_AVAIALABLE the default for the pairHMM cmdline argument

Make LOGLESS_CACHING the default pairHMM unified cmdline argument, fix error message if choose an unrecognized pairHMM

Updae MD5s
 2017-06-07 13:33:32 -04:00
Samuel Friedman ed440f1684 respond to review comments 2017-05-05 16:29:01 -04:00
Samuel Friedman a8f70c891f Create GMM from model reports in VQSR 2017-04-26 16:02:06 -04:00
Ron Levine 687dee22ac Fix CombineVariants merge for different types 2017-03-14 16:42:16 -04:00
Ron Levine 1e88d849e3 Fixed ClippingOP.getNewAlignmentStartOffset() to handle N cases properly and added unit test 2017-03-06 15:40:01 -05:00
Ron Levine 61875e4dfa Fix LeftAlignAndTrimVariants -split to not change no-call genotypes to hom-ref 2017-02-22 17:57:59 -05:00
Ron Levine 1d36d9fd69 Move htsjdk to ver 2.9.0 and picard to ver 2.8.3 2017-02-17 07:03:03 -05:00
Geraldine Van der Auwera b42dc1624b Documentation fixes 
- Fix missing closing code block tag
	- SOR fix + minor fix to template
	- Minor typo fixes
	- Make no_cmdline_in_header arg visible in docs
	- Caveats for UG-only args that are difficult to move out of common collection
	- Reference -L and -XL in -gvcf documentation
	- Annotation doc fixes (dsde-docs#1289)
	- Unhide some ContEst args and make Advanced
	- Fix inputPrior error message
	- Update web urls
	- Add JEXL doc link
 2016-12-05 14:09:44 -05:00
Ron Levine 262c08aee3 Make exit system file type message generic 2016-11-23 10:12:21 -05:00
Ron Levine 22d94a7096 Fix adapter bounday for positive strand 2016-11-16 16:41:17 -05:00
Ron Levine 2d06f33227 Set HTSJDK log level 2016-11-15 07:08:19 -05:00
Ron Levine df0ba2ce8d BaseCountsBySample counting bases at a particular position 2016-11-08 13:31:05 -05:00
David Benjamin 029632eb1c backport numerics changes in new qual 2016-11-01 03:16:21 -04:00
Ron Levine d7090ef158 Write saved WARN messages to stderr instead of stdout 2016-10-21 13:01:07 -04:00
Ron Levine cfd3ffa2c0 Replace SAMFileReader with calls to SamReaderFactory 2016-10-14 11:22:54 -04:00
David Benjamin 318bee2269 Backport new AFCalculator 2016-09-21 15:21:56 -04:00
Ron Levine abc4d5b7b3 Bypass spanning deletions in Rank Sum tests 2016-08-17 14:02:22 -04:00
Peter Fan 3510906c7f addresses issue #1280 now interval padding works for exclude intervals 2016-08-10 13:45:45 -04:00
Andrii Nikitiuk a465c87ff8 Added support for directly reading SRA runs 2016-08-02 15:21:14 -04:00
Ron Levine 4f2e312805 Throw an exception for invalid Picard intervals 2016-07-15 11:20:53 -04:00
Ron Levine aace73e884 Enable control of reporting periodicity 2016-07-13 07:24:03 -04:00
Takuto Sato d6d0678b50 Build on Laura's code and finish porting MuTect1 clustered read position filter. 2016-07-11 17:33:08 -04:00
Samuel Lee 9b32cf5291 Fixed merging of GVCF blocks by fixing rounding of GQ values in ReferenceConfidenceModel. 2016-07-06 10:08:08 -04:00
Takuto Sato 2c94f74a95 Merge pull request #1404 from broadinstitute/ldg_M2_addM1filters 
MuTect 2: port strand artifact filter from MuTect 1
 2016-07-05 13:27:35 -04:00
Steve Huang 1ff234e7dd remove alt alleles, when genotype count is explosively large, based on alleles' highest supporting haplotype score; max tolerable genotype count is controlled by a default value overridable by user 
remove alt alleles, when genotype count is explosively large, based on alleles' highest supporting haplotype score; max tolerable genotype count is controlled by a default value overridable by user
 2016-06-30 22:36:49 -04:00
Takuto Sato 63e0865491 Built on Laura's code to port the strand bias filter from M1 and refactored code aroud SomaticGenotypingEngine. Added a new integration test. 2016-06-29 22:46:40 -04:00
meganshand 556cc69185 Fix for int overflow in RankSum calculation 2016-06-29 12:02:13 -04:00
Valentin Ruano Rubio 07052ba8ea Changes to use the median rather than the second best likelihood for the NON_REF allele 
Addresses issue #1378 following the first proposal using the 'median' rather than the 'mean'.
 2016-06-28 13:10:22 -04:00
Ron Levine 3c5eac8c17 Move htsjdk and picard to version 2.5.0 2016-06-28 09:42:32 -04:00
Ron Levine 427645162b SelectVariants works with non-diploids 2016-06-21 12:26:13 -04:00
Yossi Farjoun f0f482c1fe - added an option to merge GenomeLocs that are abutting (contiguous) rather than actually overlapping. (#1399) 
- this should make ValidateVariants much faster.

- fixed NPE that occurs when there is no -L argument
 2016-06-06 11:46:15 -04:00
Geraldine Van der Auwera d87345cd1d GATKDocs overhaul 
- Fixed displaying of default values
    - Removed code cruft
    - Reorganized tooldoc categories and improved names
    - Reorganized tools within categories where applicable
    - Touched up various tool docs
    - Switched default gatkdocs output to html
    - Added parameter in agrregator pom to control output type
    - Set gatkdocs publishing script to output php
    - Deprecated GenotypeAndValidate walker
    - Added back PhoneHome arguments with @Deprecated annotations
 2016-05-29 16:35:08 -04:00
Geraldine Van der Auwera 5b80c92cb7 Improved article linking in error messages 2016-05-27 13:49:31 -04:00
Valentin Ruano Rubio 9d32dec9cd Fix for the sum(AD) > DP bug. 
Closes issue #1340
 2016-05-26 15:04:52 -04:00
Yossi Farjoun 25fa25b618 Added option to validate gvcf (for ValidateVariants) (#1379) 
* with option --gvcf CLP will now put extra checks that a gvcf must adhere to (existance of <NON_REF> allele at every variant, and that the variants in total cover the entire requested intervals, or the whole genome if no intervals have been specified)
* works on gvcf produced by HC when using either GVCF or BP_RESOLUTION mode
* added positive and negative tests
 2016-05-26 06:42:45 -04:00
Mark Fleharty d611c45806 Adding OtherArgumentRequired option to allow an argument to require an additional argument. 2016-05-17 16:31:41 -04:00
David Benjamin aecaa6d38e Allow GenotypeGVCFs to emit ref sites. 2016-04-27 15:53:44 -04:00
meganshand 509400495b Changes edge case calculation for RankSumTest #1341 2016-04-22 14:41:05 -04:00
Ron Levine e2828104b1 SelectVariants and VariantFiltration not updating AC, AN and AF for --setFilteredGtToNocall 2016-04-17 10:24:05 -04:00
Ron Levine 0eba8822e2 Change HashMap to LinkedHashMap for predictable iteration 2016-04-10 20:10:38 -04:00
Ron Levine e4003bc792 Add informative exceptions to getSAMFileSamples() 2016-03-31 13:41:11 -04:00
Ron Levine edc1b20132 Output a summary of WARN messages 2016-03-29 11:39:18 -04:00
Geraldine Van der Auwera 9a306ca221 Update licenses 2016-03-05 01:09:43 -08:00
Ron Levine 5e2ffc188b Merge pull request #1295 from broadinstitute/rhl_sv_error_output_1194 
Correct error messages and error handling in multiple tools
 2016-02-29 17:05:24 -05:00
Ron Levine 40a5adf767 Change error output to use the correct argument 2016-02-29 13:21:03 -05:00
meganshand c7e0f5b225 Removes Dithering from Rank Sum Test 
Fixing empty group case

Fixing MD5s

First comments addressed

Added permutation test

Adding new RankSum to AS_RankSum

Speeding up permutation algorithm and updating MD5s

Missed a few tests

Addressing comments

Changing md5s
 2016-02-29 11:45:27 -05:00
Yossi Farjoun 7896055be3 - Fixed bug in GenomeLoc parser 
- Added a warning when two contigs are too similar that it might cause problems with parsing
- Added tests of modified parser and of warning.
 2016-02-02 06:53:22 -05:00
Takuto Sato 243a0fcb74 Allele-specific insert size ranksum annotation 2016-01-28 16:03:57 -05:00
Laura Gauthier 5592e4ead0 Add new -AS mode to run VQSR (both VariantRecalibrator and ApplyRecalibration) in an allele-specific manner 2016-01-22 13:18:21 -05:00