ee31a54a03
Merged bug fix from Stable into Unstable
2012-09-19 16:09:45 -04:00
7cf9911924
Fixed ReduceReads bug where variant regions were missing.
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This affected variant regions with more than 100 reads and less than 250 reads. Only bams reduced with GATK v2 and 2.1 were affected.
2012-09-19 16:09:08 -04:00
7a7103a757
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-09-19 10:39:18 -04:00
bebd5c14b8
Update general ploidy md5's due to bad merge of md5's in previous commit, and new shortened interval definition for EMIT_ALL_CONFIDENT_SITES was buggy
2012-09-18 20:12:15 -04:00
6b37350bc0
Two hairy bugs in pool caller: a) Site error model wasn't counting errors in insertions correctly - Alleles passed in had padded ref byte, but event base in PileupElement doesn't have it. As a result, mismatch rate was grossly overestimated with insertions and we missed several calls we should have made. Integration test reflects changes. b) Adding a ref GL to the exact model is correct mathematically but AFResult wasn't filled properly. As a result, QUAL was junk in pure ref sites, and in all other sites the last ref GL introduced wasn't properly updating Pr(AF>0). c) Added integration test that covers -out_mode EMIT_ALL_CONFIDENT_SITES. Not fully sure if the math is 100% correct (for both diploid and generalized case) but at least now diploid and non-diploid cases behave similarly. md5 of this new test will fail since it's taking me a long time to run so I'll update from Bamboo output shortly
2012-09-14 13:13:22 -04:00
35d15278af
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-09-11 14:34:17 -04:00
13831106d5
Fix GSA-535: storing likelihoods in allele map was busted when running HaplotypeCaller, only the last likelihood of a haplotype was being stored, as opposed to the max likelihood of all haplotypes mapping to an allele
2012-09-11 11:01:26 -04:00
aa9829b55c
fixing typo
2012-09-10 13:36:37 -04:00
10c720cbba
Merge branch 'master' of ssh://gsa4/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-09-10 09:56:47 -04:00
2d4b00833b
Bug fix for logging likelihoods in new read allele map: reads which were filtered out were being excluded from map, but they should be included in annotations
2012-09-09 20:35:45 -04:00
36913706c0
Bug fix in HC GenotypingEngine to ensure that all the merged complex events get properly added to the priority list used by VariantContextUtils when combining multiallelic events.
2012-09-09 13:47:54 -04:00
688fc9fb56
Bug fix in HC GenotypingEngine to ensure that all the merged complex events get properly added to the priority list used by VariantContextUtils when combining multiallelic events.
2012-09-09 10:36:09 -04:00
cb84a6473f
Downsampling: experimental engine integration
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-Off by default; engine fork isolates new code paths from old code paths,
so no integration tests change yet
-Experimental implementation is currently BROKEN due to a serious issue
involving file spans. No one can/should use the experimental features
until I've patched this issue.
-There are temporarily two independent versions of LocusIteratorByState.
Anyone changing one version should port the change to the other (if possible),
and anyone adding unit tests for one version should add the same unit tests
for the other (again, if possible). This situation will hopefully be extremely
temporary, and last only until the experimental implementation is proven.
2012-09-06 15:03:27 -04:00
d6884e705a
Revert "fixed a typo in StringText.properties"
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This reverts commit b74c1c17e748f75e59d23545084b983e2a8d2fa6.
2012-09-05 15:21:00 -04:00
f4b39a7545
Merge branch 'master' of ssh://gsa4/humgen/gsa-scr1/gsa-engineering/git/unstable
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merging trivially after a commit
2012-09-05 14:33:39 -04:00
6e517df5d9
fixed a typo in StringText.properties
2012-09-05 14:33:08 -04:00
9cc1a9931b
Resolving merge conflicts.
2012-09-04 10:47:38 -04:00
c9944d81ef
Skip array needs to also be used in the updateDataForRead function of the delocalized BQSR.
2012-09-04 10:33:37 -04:00
817ece37a2
General infrastructure for ReadTransformers
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-- These are like read filters but can be applied either on input, on output, of handled by the walker
-- Previous example of BAQ now uses the general framework
-- Resulted in massive conceptual cleanup of SAMDataSource and ReadProperties! Yeah!
-- BQSR now uses this framework. We can now do BQSR on input, on output, or within a walker
-- PrintReads now handles all read transformers in the walker in map, enabling us to parallelize PrintReads with BAQ and BQSR
-- Currently BQSR is excepting in parallel, which subsequent commit with fix
-- Removed global variable setting in GenomeAnalysisEngine for BAQ, as command line parameters are cleanly handled by ReadTransformer infrastructure
-- In principle ReadFilters are just a special kind of ReadTransformer, but this refactoring is larger than I can do. It's a JIRA entry
-- Many files touched simply due to the refactoring and renaming of classes
2012-08-31 13:42:41 -04:00
1200848bbf
Part II of GSA-462: Consistent RODBinding access across Ref and Read trackers
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-- Deleted ReadMetaDataTracker
-- Added function to ReadShard to give us the span from the left most position of the reads in the shard to the right most, which is needed for the new view
2012-08-30 10:15:10 -04:00
e12ae65d33
Changing the commenting style in the BQSR
2012-08-29 11:27:45 -04:00
18eca3544e
Initial commit of the delocalized BQSR written as a read walker.
2012-08-28 15:24:20 -04:00
b3fd74f0c4
HaplotypeCaller forbids BAQ
2012-08-24 13:25:05 -04:00
fe3069b278
Merged bug fix from Stable into Unstable
2012-08-22 14:40:34 -04:00
e5cfdb4811
Bug fix for popular _Duplicate allele added to VariantContext_ error reported on the forum. It seems to be due to lower case bases in the reference being treated as reference mismatches. We would try to turn these mismatches into SNP events, for example c/C. We now uppercase the result from IndexedFastaSequenceFile.getSubsequenceAt()
2012-08-22 14:39:35 -04:00
6a8cf1c84a
Enable and adapt HaplotypeScore and MappingQualityZero as active region annotations now that we have per-read likelihoods passed in to annotations
2012-08-21 14:35:40 -04:00
d0644b3565
Merge branch 'master' of ssh://gsa4.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-08-21 10:35:23 -04:00
10961db3ce
Another round of FindBugs fixes. Object returns its internal reference to an externally mutable array. Very dangerous.
2012-08-21 09:35:55 -04:00
605acaae9c
Another round of FindBugs fixes. Object internally stores a reference to an externally mutable array. Very dangerous.
2012-08-21 09:33:58 -04:00
55b7949d68
Another round of FindBugs fixes. Comparator doesn't implement Serializable.
2012-08-21 09:20:55 -04:00
7bbd2a7a20
Fixing merge conflicts
2012-08-20 20:38:25 -04:00
77fbaec044
Another round of FindBugs fixes. Class implements its own compareTo() but uses base Object.equals() which can lead to unpredictable behavior.
2012-08-20 16:55:00 -04:00
a9472c1980
Another round of FindBugs fixes. Inefficient use of keySet iterator instead of entrySet iterator.
2012-08-20 16:11:45 -04:00
464d49509a
Pulling out common caller arguments into its own StandardCallerArgumentCollection base class so that every caller isn't exposed to the unused arguments from every other caller.
2012-08-20 15:28:39 -04:00
c67d708c51
Bug fix in HaplotypeCaller for non-regular bases in the reference or reads. Those events don't get created any more. Bug fix for advanced GenotypeFullActiveRegion mode: custom variant annotations created by the HC don't make sense when in this mode so don't try to calculate them.
2012-08-20 13:41:08 -04:00
963ad03f8b
Second step of interface cleanup for variant annotator: several bug fixes, don't hash pileup elements to Maps because the hashCode() for a pileup element is not implemented and strange things can happen. Still several things to do, not done yet
2012-08-19 21:18:18 -04:00
b61ecc7c19
Fix merge conflicts
2012-08-16 20:45:52 -04:00
d26183e0ec
First preliminary big refactoring of UG annotation engine. Goals: a) Remove gigantic hack that cached per-read haplotype likelihoods in a static array so that annotations would go back and retrieve them, b) unify interface for annotations between HaplotypeCaller and UnifiedGenotyper, c) as a consequence, removed and cleaned duplicated code. As a bonus, annotations have now more relevant info to help them compute values.
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Major idea is that per-read haplotype likelihoods are now stored in a single unified object of class PerReadAlleleLikelihoodMap. Class implementation in theory hides internal storage details from outside work (still may need work cleaning up interface), and this object(or rather, a Map from Sample->perReadAlleleLikelihoodMap) is produced by UGCalcLikelihoods. The genotype calculation is also able to potentially use this info if needed. All InfoFieldAnnotations now get an extra argument with this map. Currently, this map is only produced for indels in UG, or for all variants within HaplotypeCaller. If this map is absent (SNPs in UG), the old Pileup interface is used, but it's avoided whenever possible. FORMAT annotations are not yet changed but will be focus of second step. Major benefit will be that annotations will be able to very easily discard non-informative reads for certain events. HaplotypeCaller also uses this new class, and no longer hard-codes the mapping of allele ->list(reads) but instead uses the same objects and interfaces as the rest of the modules. Code still needs further testing/cleaning/reviewing/debugging
2012-08-16 20:36:53 -04:00
05cbf1c8c0
FindBugs 'Efficiency' fixes
2012-08-16 15:40:52 -04:00
dac3958461
Killing off some FindBugs 'Usability' issues
2012-08-16 13:32:44 -04:00
eca9613356
Adding support of X and = CIGAR operators to the GATK
2012-08-10 14:54:07 -04:00
2a113977a9
Resolving merge conflicts with the new MD5s
2012-08-10 11:47:00 -04:00
5f82ffd5d8
Adding LowQual filter to the output of the HaplotypeCaller.
2012-08-10 11:25:14 -04:00
9887bc4410
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-08-09 16:31:06 -04:00
abb168e1ba
Merged bug fix from Stable into Unstable
2012-08-09 16:09:58 -04:00
67d4148b32
Fixing but reported by Thomas in the forum where reads were soft-clipped beyond the limits of the contig and ReduceReads was failing with a NoSuchElement exception. Now we hard clip anything that goes beyond the boundaries of the contig.
2012-08-09 15:58:18 -04:00
58420098ac
Merged bug fix from Stable into Unstable
2012-08-09 13:02:23 -04:00
c6132ebe26
Fixed divide by zero bug when downsampler goes over regions where reads are all filtered out. Added Guillermo's bug report as an integration test
2012-08-09 13:02:11 -04:00
e48727dae3
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-08-09 10:31:10 -04:00
5be7e0621d
Merge branch 'master' of ssh://gsa4.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-08-09 09:58:34 -04:00
Mauricio Carneiro
Ryan Poplin
Guillermo del Angel
David Roazen
Yossi Farjoun
Mark DePristo
Eric Banks