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
63213e8eb5
Expanding the HaplotypeCaller integration tests to cover a wider range of data
2012-08-22 14:18:44 -04:00
901f47d8af
Final step (for now) in VA refactoring: update MD5's because, a) since it's not guaranteed that we'll iterate through reads/pileups in the same order, the rank sum dithering will change annotations, b) FS uses new generic threshold to distinguish uninformative reads (it used to use ad-hoc thresholds), c) AD definition changed and throws away uninformative reads, d) shortened general ploidy integration tests for quicker debugging. May have missed some MD5's in the update so there may be lingering test failures still
2012-08-22 11:38:51 -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
94e7f677ad
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-08-21 10:21:47 -04:00
418ace463a
More merge conflict resolution
2012-08-21 10:15:52 -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
286b658fab
Re-enabling parallelism in the BaseRecalibrator now that the release is out.
2012-08-20 21:25:14 -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
5db3bd6fd2
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-08-20 15:28:57 -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
154f65e0de
Temporarily disabling multi-threaded usage of BaseRecalibrator for performance reasons.
2012-08-20 12:43:17 -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.
...
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
2df04dc48a
Fix for performance problem in GGA mode related to previous --regenotype commit. Instead of trying to hack around the determination of the calculation model when it's not needed, just simply overload the calculateGenotypes() method to add one that does simple genotyping. Re-enabling the Pool Caller integration tests.
2012-08-16 13:05:17 -04:00
9035b554fb
Adding tests for the --solid_nocall_strategy argument
2012-08-15 23:13:24 -04:00
3556c36668
Disable general ploidy integration tests because they are running forever
2012-08-15 21:13:16 -04:00
243af0adb1
Expanded the BQSR reporting script
...
-- Includes header page
-- Table of arguments (Arguments)
-- Summary of counts (RecalData0)
-- Summary of counts by qual (RecalData1)
-- Fixed bug in output that resulted in covariates list always being null (updated md5s accordingly)
-- BQSR.R loads all relevant libaries now, include gplots, grid, and gsalib to run correctly
2012-08-12 13:45:14 -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
71ee8d87b3
Rename per-sample ML allelic fractions and counts so that they don't have the same name as the per-site INFO fields, and clarify wording in VCF header
2012-08-09 09:58:20 -04:00
250ffd2ad7
Merged bug fix from Stable into Unstable
2012-08-08 15:50:07 -04:00
78c1556186
Fixing ReduceReads downsampling bug -- downsampled reads were not being excluded from the read window, causing them to trail back and get caught by the sliding window exception
2012-08-08 15:49:31 -04:00
1223d77546
Removing argument from HaplotypeCaller that was made unneccesary by recent improvements to triggering around large events
2012-08-08 15:13:20 -04:00
4b2e3cec0b
Quick pass of FindBugs 'inefficient use of keySet iterator instead of entrySet iterator' fixes for core tools.
2012-08-08 14:29:41 -04:00
3e2752667c
Intermediate checkin for ReducedReads with HaplotypeCaller - change min read count over k-mer to average count over k-mer when doing assembly of a reduced read (not optimal, currently trying max and then will decide on best approach), fix merge conflicts
2012-08-08 12:07:33 -04:00
2c76f71a03
Update -maxAlleles argument in integration tests
2012-08-06 22:48:04 -04:00
c66a896b8e
Fix UG integration test broken by new -maxAltAlleles nomenclature
2012-08-06 21:29:21 -04:00
97c5ed4feb
Merge branch 'master' of ssh://gsa4.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-08-06 20:22:31 -04:00
238d55cb61
Fixes for running HaplotypeCaller with reduced reads: a) minor refactoring, pulled out code to compute mean representative count to ReadUtils, b) Don't use min representative count over kmer when constructing de Bruijn graph - this creates many paths with multiplicity=1 and makes us lose a lot of SNP's at edge of capture targets. Use mean instead
2012-08-06 20:22:12 -04:00
d85b38e4da
Updating HaplotypeCaller integration tests
2012-08-06 12:02:19 -04:00
Mark DePristo
Ryan Poplin
Guillermo del Angel
Eric Banks
Mauricio Carneiro