dfbffc95a3getting rid of the old Indel BQSR
Mauricio Carneiro
2012-03-02 18:54:35 -0500
f879daa7d0Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2012-03-05 08:29:08 -0500
d6871967aeAdding more unit tests and contracts to PairHMM util class. Updating HaplotypeCaller to use the new PairHMM util class. Now that the HMM result isn't dependent on the length of the haplotype there is no reason to ensure all haplotypes have the save length which simplifies the code considerably.
Ryan Poplin
2012-03-05 08:28:42 -0500
3b5a7c34d7Added argument to ValidationAmplicons to only output valid sequences - useful for not having to post-filter or grep resulting files before delivering downstream
Guillermo del Angel
2012-03-04 10:24:29 -0500
69611af7d3Workaround for bug in Picard in ReadGroupProperties
Mark DePristo
2012-03-02 18:53:45 -0500
914c23da51Generic infrastructure for quantizing quality scores
Mark DePristo
2012-03-02 16:09:38 -0500
ba71b0aee4ReadGroupProperties mk3
Mark DePristo
2012-03-02 14:51:23 -0500
fc1c0a9d8fMinor change: switched HSP default fasta from bundle/g1k to Picard since in all oneoff runs of the HSP the BAMs were aligned by Picard to Picard's reference.
Khalid Shakir
2012-03-02 14:15:56 -0500
1e07e97b58Optimization: create allele list just once, not for each genotype
Eric Banks
2012-03-02 13:30:17 -0500
0a7137616cNow converts gatkreports to properly typed R data types in gsa.read.gatkreport
Mark DePristo
2012-03-02 09:11:59 -0500
0ad7d5fbc1Standalone common Pair HMM utility class with associated unit tests.
Ryan Poplin
2012-03-01 22:41:13 -0500
2f334a57c2ReadGroupProperties mk2
Mark DePristo
2012-03-01 18:43:23 -0500
4409293b5dget rid of the sorting parameter
Mauricio Carneiro
2012-03-01 17:31:36 -0500
29f74b658bUnit tests for the context covariate
Mauricio Carneiro
2012-03-01 17:11:05 -0500
aff508e091ReadGroupProperties walker and associated infrastructure
Mark DePristo
2012-03-01 15:01:11 -0500
88e060e1e9Merge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Eric Banks
2012-03-01 10:55:21 -0500
ed70d9b380The reduced reads + calling script I am using; adding now for Khalid's benefit
Eric Banks
2012-03-01 10:55:08 -0500
2af470404cHaplotypeCaller integration test goes back to using flat base insertion and base deletion quality scores while the BQSR is in flux.
Ryan Poplin
2012-03-01 09:05:55 -0500
9e95b10789Context covariate now operates as a highly compressed bitset
Mauricio Carneiro
2012-02-29 18:56:11 -0500
d379c3763aDNA Sequence to BitSet and vice-versa conversion tools
Mauricio Carneiro
2012-02-29 18:04:02 -0500
3ddcd6879fBugfix for fullRefresh mode for gsafolkLogsForTableau
Mark DePristo
2012-02-28 10:36:58 -0500
129b5e7f6bMerge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Eric Banks
2012-02-28 10:09:34 -0500
a4a279ce80Damn you, Mark
Eric Banks
2012-02-28 10:09:09 -0500
0681bea5a5Changed DoC from PartitionType.INTERVAL to PartitionType.NONE since it doesn't have a way to gather scattered outputs. Added MultiallelicSummary to HSP eval.
Khalid Shakir
2012-02-28 09:25:38 -0500
bd398e30fdAnother quick optimization
Eric Banks
2012-02-28 09:25:35 -0500
40bdadbda5Minor optimization as per Mark
Eric Banks
2012-02-28 09:24:07 -0500
d7928ad669Drat, missed one: handle null alleles being passed in.
Eric Banks
2012-02-27 21:31:54 -0500
1245a3c868Tool for diagnosing new technology error modes
Mauricio Carneiro
2012-02-27 19:36:21 -0500
24356f11b7Merged bug fix from Stable into Unstable
Mark DePristo
2012-02-27 17:13:17 -0500
0b29d54937Changed most BAMSchedule ReviewedStingExceptions to UserExceptions
Mark DePristo
2012-02-27 17:08:41 -0500
f9e8e82e33Removed unused class variable from VCFHeaderLineTranslator
Mark DePristo
2012-02-27 17:07:19 -0500
100ddef930Fix typo in VariantContextBuilder
Mark DePristo
2012-02-27 17:06:45 -0500
ca0931c01fAdding test for reading samtools VCF file
Mark DePristo
2012-02-27 17:05:32 -0500
33cf1368baAdded options to add XHMM command-line parameters for discovery and genotyping
Menachem Fromer
2012-02-27 16:03:02 -0500
bd944ab04fAnother test where we no longer print out 'NaN' for the AF.
Eric Banks
2012-02-27 15:19:08 -0500
5f7ccdcc01Avoid calling getBasePileup when there's no pileup in NBaseCount annotation
Mark DePristo
2012-02-27 15:12:25 -0500
52871187d7Adding integration test for file with no GTs. Also updated md5 for one other test (since we no longer print out 'NaN' for the AF).
Eric Banks
2012-02-27 15:09:56 -0500
729bb954e2Throws ReviewedStingException for a bug when parent VariantContext argument is null
Mark DePristo
2012-02-27 15:09:00 -0500
998ed8fff3Bug fix to deal with VCF records that don't have GTs. While in there, optimized a bunch of related functions (including removing a copy of the method calculateChromosomeCounts(); why did we have 2 copies? very dangerous).
Eric Banks
2012-02-27 14:56:10 -0500
4d9582de77More general catching of Exceptions in interval reading to throw MalformedFile exception in all cases
Mark DePristo
2012-02-27 14:02:26 -0500
9712fed7a5Trap SAMFormatException and rethrow as MalformatedBAM exception
Mark DePristo
2012-02-27 13:34:44 -0500
1ea34058c2Updating integration tests now that standard annotations support multiple alleles
Eric Banks
2012-02-27 11:32:26 -0500
64754e7870Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Eric Banks
2012-02-27 11:31:41 -0500
850c5d0db2Enabling Rank Sum Tests for multi-allelics: use ref vs any alt allele.
Eric Banks
2012-02-27 09:59:36 -0500
dfdf4f989bEnabling Fisher Strand for multi-allelics: use the alt allele with max AC. Added minor optimization to the method in the VC.
Eric Banks
2012-02-27 09:50:09 -0500
16122bea8dMerge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Guillermo del Angel
2012-02-25 13:57:54 -0500
dea35943d1a) Bug fix in calling new functions that give indel bases and length from regular pileup in LocusIteratorByState, b) Added unit test to cover these.
Guillermo del Angel
2012-02-25 13:57:28 -0500
c8a06e53c1DoC now properly handles reference N bases + misc. additional cleanups
Mark DePristo
2012-02-25 11:32:50 -0500
50de1a3eabFixing bad VCFIntegration tests
Mark DePristo
2012-02-25 11:26:36 -0500
9bad51877eGeneralized gsafolkLSFLogs.py to gsafolkLogsForTableau.py
Mark DePristo
2012-02-24 15:52:45 -0500
80b5c7ad21Fix gitVersionNumbers script to not print git status messages to our file
Mark DePristo
2012-02-24 15:51:45 -0500
747e1a728fScript to recreate entire GATKLog db from scratch
Mark DePristo
2012-02-24 10:22:38 -0500
e94a534076Added dry run and verbose options to gsafolkLSFLogs
Mark DePristo
2012-02-24 10:00:04 -0500
253bb46bcdAdd support to analyzeRunReports to tag xml logs with git version numbers
Mark DePristo
2012-02-24 09:24:49 -0500
c9a4c74f7aa) Bug fixes for last commit related to PileupElements (unit tests are forthcoming). b) Changes needed to make pool caller work in GENOTYPE_GIVEN_ALLELES mode c) Bug fix (yet again) for UG when GENOTYPE_GIVEN_ALLELES and EMIT_ALL_SITES are on, when there's no coverage at site and when input vcf has genotypes: output vcf would still inherit genotypes from input vcf. Now, we just build vc from scratch instead of initializing from input vc. We just take location and alleles from vc
Guillermo del Angel
2012-02-24 10:27:59 -0500
470375db58added integration test for the ReduceReadsStash bug reported by Adam
Mauricio Carneiro
2012-02-23 18:58:46 -0500
ee9a56ad27Fix subtle bug in the ReduceReads stash reported by Adam
Mauricio Carneiro
2012-02-23 18:25:01 -0500
e0c189909fAdded support for breakpoint alleles
Mark DePristo
2012-02-23 12:14:48 -0500
522ace6d57CNV discovery is also a long-running job (depending on the number of samples)
Menachem Fromer
2012-02-23 11:28:22 -0500
6866a41914Added functionality in pileups to not only determine whether there's an insertion or deletion following the current position, but to also get the indel length and involved bases - definitely needed for extended event removal, and needed for pool caller indel functionality.
Guillermo del Angel
2012-02-23 09:45:47 -0500
d34f07dba0Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Eric Banks
2012-02-22 20:41:03 -0500
2b6c0939abMerge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2012-02-22 19:00:38 -0500
8695738400Bug fix in HaplotypeCaller's GENOTYPE_GIVEN_ALLELES mode for insertions greater than length 1. The allele being genotyped was off by one base pair.
Ryan Poplin
2012-02-22 19:00:04 -0500
2c1b14d35eMostly small changes to my own scala scripts: .vcf.gz compatibility for output files, smarter beagle generation, simple script to scatter-gather combine variants. Whole genome indel calling now uses the gold standard indel set.
Christopher Hartl
2012-02-22 17:20:04 -0500
9b61a398b3Merge branch 'master' of ssh://ni.broadinstitute.org/humgen/gsa-scr1/chartl/dev/unstable
Christopher Hartl
2012-02-22 17:18:10 -0500
ca7b5e068fupdating HaplotypeCaller integration tests after change to separate insertion and deletion GOP.
Ryan Poplin
2012-02-22 15:23:24 -0500
e39638323bMisc cleanup in HaplotypeCaller's HMM code now that we have separate GOP for insertions and deletions
Ryan Poplin
2012-02-22 12:24:43 -0500
a611f86558CalibrateGenotypeLikelihoods now accepts any number of external likelihood VCFs. We decided in the dev group to have the assigned name be a combination of the sample name provided in the VCF and the name provided to the rod binding.
Ryan Poplin
2012-02-22 12:23:45 -0500
685bcaced2Merge branch 'master' of ssh://ni.broadinstitute.org/humgen/gsa-scr1/chartl/dev/unstable
Christopher Hartl
2012-02-21 13:53:37 -0500
0f5674b95eRedid fix for corner case when forming consensus with reads that start/end with insertions and that don't agree with each other in inserted bases: since I can't iterate over the elements of a HashMap because keys might change during iteration, and since I can't use ConcurrentHashMaps, the code now copies structure of (bases, number of times seen) into ArrayList, which can be addressed by element index in order to iterate on it.
Guillermo del Angel
2012-02-20 09:12:51 -0500
fe102a5d47Fix for my renaming of the BQSR walker
Ryan Poplin
2012-02-18 11:13:20 -0500
3d9eee4942Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2012-02-18 10:55:29 -0500
a8be96f63dThis caching in the BQSR seems to be too slow now that there are so many keys
Ryan Poplin
2012-02-18 10:54:39 -0500
78718b8d6aAdding Genotype Given Alleles mode to the HaplotypeCaller. It constructs the possible haplotypes via assembly and then injects the desired allele to be genotyped.
Ryan Poplin
2012-02-18 10:31:26 -0500
e724c63f2bReverting last commit until I learn how to effectively replicate and debug pipeline test failures, and until I also learn how to effectively remove a kep from a HashMap that's being iterated on
Guillermo del Angel
2012-02-17 17:18:43 -0500
f2ef8d1d23Reverting last commit until I learn how to effectively replicate and debug pipeline test failures, and until I also learn how to effectively remove a kep from a HashMap that's being iterated on
Guillermo del Angel
2012-02-17 17:15:53 -0500
3e031a540fSolve merge conflict
Guillermo del Angel
2012-02-17 10:56:03 -0500
cd352f502dCorner case bug fix: if a read starts with an insertion, when computing the consensus allele for calling the insertion was only added to the last element in the consensus key hash map. Now, an insertion that partially overlaps with several candidate alleles will have their respective count increased for all of them
Guillermo del Angel
2012-02-17 10:21:37 -0500
2f33c57060No reason to restrict HaplotypeScore to bi-allelic SNPs when the plumbing for multi-allelic events is already present.
Eric Banks
2012-02-16 13:58:00 -0500
2f08846d82Merged bug fix from Stable into Unstable
Guillermo del Angel
2012-02-14 21:26:25 -0500
7dc6f73399Bug fix for validation site selector: records with AC=0 in them were always being thrown out if input vcf was sites-only, even when -ignorePolymorphicStatus flag was set
Guillermo del Angel
2012-02-14 21:11:24 -0500
30085781cfMerge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2012-02-14 14:01:20 -0500
ae5b42c884Put base insertion and base deletions in the SAMRecord as a string of quality scores instead of an array of bytes. Start of a proper genotype given alleles mode in HaplotypeCaller
Ryan Poplin
2012-02-14 14:01:04 -0500
8f7587048cUpdate the expected novel TiTv in the HybridSelectionPipelineTest
David Roazen
2012-02-13 20:25:52 -0500
dfcdf92afaRevert "Disable HaplotypeCaller integration tests in Stable"
David Roazen
2012-02-13 16:37:31 -0500
85d31f80a2Merged bug fix from Stable into Unstable
David Roazen
2012-02-13 16:37:11 -0500
d5fce22d78Disable HaplotypeCaller integration tests in Stable
David Roazen
2012-02-13 16:28:19 -0500
03e5184741Fix serious engine bug that could cause reads to be dropped under certain circumstances
David Roazen
2012-02-13 13:40:58 -0500
8742f5e36cUpdating BQSR scala script to take any number of known sites files and to use the scatter count input argument.
Ryan Poplin
2012-02-13 15:44:30 -0500
ad90af94edMerge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Eric Banks
2012-02-13 15:10:10 -0500
0920a1921eMinor fixes to splitting multi-allelic records (as regards printing indel alleles correctly); minor code refactoring; adding integration tests to cover +/- splitting multi-allelics.
Eric Banks
2012-02-13 15:09:53 -0500
14981bed10Cleaning up VariantsToTable: added docs for supported fields; removed one-off hidden arguments for multi-allelics; default behavior is now to include multi-allelics in one record; added option to split multi-allelics into separate records.
Eric Banks
2012-02-13 14:32:03 -0500
e9338e2c20Context covariate needs to look in the reverse direction for negative stranded reads.
Ryan Poplin
2012-02-13 13:40:41 -0500
41ffd08d53On the fly base quality score recalibration now happens up front in a SAMIterator on input instead of in a lazy-loading fashion if the BQSR table is provided as an engine argument. On the fly recalibration is now completely hooked up and live.
Ryan Poplin
2012-02-13 12:35:09 -0500
Mauricio Carneiro
Ryan Poplin
Guillermo del Angel
Mark DePristo
Khalid Shakir
Eric Banks
Menachem Fromer
Christopher Hartl
David Roazen