03d40272c8Removed old GATKReport code and moved the new stuff in its place.
Eric Banks
2012-05-18 01:44:31 -0400
a26b04ba17Extensive refactoring of the GATKReports. This was a beast.
Eric Banks
2012-05-18 01:11:26 -0400
5189b06468New annotation for indels that describe if they're STR's and their characteristics. If an indel is a STR, 3 fields are added to INFO: STR (boolean), RU = repeat unit (String), RPA = number of repetitions per allele. So, for example, if ATATAT* context gets changed to ATAT and ATATATAT, then RU=AT and RPA=3,2,4. Will be made standard annotation shortly. Added unit tests for new functionality. Pending: refactor VariantContextUtils.isRepeat() to unify code, and fix VariantEval functionality.
Guillermo del Angel
2012-05-17 15:28:19 -0400
9c6bccfd8bbuild system overhaul
David Roazen
2012-05-10 11:31:32 -0400
0f7c917e7aBetter error checking and messages for bad alleles
Eric Banks
2012-05-17 13:36:42 -0400
6967b3de6cDownsampler: checking in the new standalone downsampler implementations without the engine modifications
David Roazen
2012-03-27 10:19:40 -0400
b9a2e41c4bCan't partition these in their current state
Joel Thibault
2012-05-15 13:42:42 -0400
76905e9342Minor cleanup before push
Joel Thibault
2012-05-15 13:34:49 -0400
229d1aa904Bjorn -> Nexus
Joel Thibault
2012-05-14 14:47:35 -0400
ca39387ec7Retrieve from the DB in block mode
Joel Thibault
2012-05-14 16:28:18 -0400
747e3f6c94Modify the DB schema to use block writes
Joel Thibault
2012-05-11 16:59:43 -0400
d44886d9e8Very naughty bug: VE output is not at all gatherable but no one told this to Queue. Fixed.
Eric Banks
2012-05-15 10:29:04 -0400
819c3d0c15Adding to the Hrun docs
Eric Banks
2012-05-15 10:27:52 -0400
b16e169412Variant Call QC was calling melt() without importing the reshape package. It's unclear how this ever worked...
Christopher Hartl
2012-05-15 07:34:36 -0400
2abd1e06ccMore fixes to prevent NPE in pool caller
Guillermo del Angel
2012-05-14 22:02:39 -0400
7b81559a9bOne more pool caller bug fix: don't create output file for noisy simulation in unit test, or else previous results will be deleted
Guillermo del Angel
2012-05-14 16:27:38 -0400
617ac0b88fMore pool caller bug fixes
Guillermo del Angel
2012-05-14 16:15:54 -0400
578092b120Pool caller bug fixes: avoid NPE in null tracker positions, fix so that we can (in theory) use Pool AF with non-pool GL model for testing
Guillermo del Angel
2012-05-14 15:03:53 -0400
5fc3adbb04One more VariantsToTable bug fix
Guillermo del Angel
2012-05-14 14:10:07 -0400
04d691f04aForgot to update MD5's due to new Exact AF model in pool caller (all changes legit, minor QUAL/QD/SB differences). Fixed bug in VariantsToTable from previous commit
Guillermo del Angel
2012-05-14 14:01:29 -0400
ae26f0fe14a) Fully functional and working multiallelic exact model for pools. Needs cleanup/more testing. b) Better unit test for pool genotype likelihoods - it now optionally generates actual noisy pileups that can be used for assessing GL accuracy, c) Totally experimental, hidden option in VariantsToTable to output genotype fields. Specifying -GF will output columns of form Sample.FieldName - needs also more testing
Guillermo del Angel
2012-05-14 10:55:35 -0400
67e5c3ff9fSolved major scalability problem in pool caller - exact model may have been linear but computing pool GL's was O(n^p) where p was max # of alleles (4 in SNP discovery mode). Linearized approach follows exact AF model with queue of AC conformations to add - may refactor code to eliminate duplication later, as linear multiallelic pool AF model will use same approach. TBD: how to print PL's with -Infinity value, right now since we never cap PL printing we end up with big nonsense numbers in those positions and vcf's look ugly. Calling MT in CEU trio with pool size = 100 goes from 2 days to 55 minutes (sic)
Guillermo del Angel
2012-05-11 10:05:09 -0400
9acef4b206Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Guillermo del Angel
2012-05-10 16:00:58 -0400
da6f16986ePreparatory refactorings for pool indel calling and for optimizations: restructure code in PoolSNPGenotypeLikelihoods that will be shared with indels, and make it easier to rewrite when optimized version that's linear in pool size is ready (current version is linear in #of pools but not yet on pool size).
Guillermo del Angel
2012-05-10 16:00:37 -0400
c9dd0f3173Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2012-05-10 13:09:10 -0400
0cdadffe14Committing the best of the frantic pre-CSHL experiments: Better algorithm for partioning reads amongst the alleles they support. Require the read's original alignment to actually overlap the variant. QD uses the non-informative reads when calculating D. More HC-specific annotations for potential use in a statistical filtering strategy. Increasing the minimum kmer length in the assembly graphs. Misc minor bug fixes.
Ryan Poplin
2012-05-10 13:09:03 -0400
89f8a6b2e6Revert bad part of last commit that shouldn't have been pushed
Guillermo del Angel
2012-05-10 10:41:08 -0400
27b1aa5dd3Don't allow N's in insertions when discovering indels. Maybe better solution will be to use them as wildcards and merge them with compatible regular insertion alleles but for now it's easier to ignore them. Minor refactoring of Allele.accepableAlleleBases to support this. Added unit test to test consensus allele counter in presence of N's
Guillermo del Angel
2012-05-10 10:29:19 -0400
4f37d6d399Fixing docs
Eric Banks
2012-05-10 00:56:00 -0400
51936dcef3Update indices to better match queries Only query for the requested samples
Joel Thibault
2012-05-09 14:21:37 -0400
f4ae4a0a70Initial versions of Queue scripts for Mongo testing
Joel Thibault
2012-05-07 10:19:27 -0400
5427f8dffaMongo Long/Integer confusion
Joel Thibault
2012-05-02 15:47:17 -0400
c56370a503Update GATKPerformanceOverTime script for GATK 1.6
David Roazen
2012-05-09 13:47:41 -0400
398dceec56Basic test script to cut up a BAM and run it through cramtools
Mark DePristo
2012-05-08 19:46:22 -0400
c81acfc15dWorking implementation of BCF2
Mark DePristo
2012-05-08 19:41:27 -0400
a5193c2399Mostly complete reference implementation of BCF2
Mark DePristo
2012-05-08 00:17:30 -0400
237a41d3d3Phase II of BCF2 reader / writer
Mark DePristo
2012-05-07 08:38:22 -0400
eb6721bd44Initial test simple BCF2 encoder / decoder
Mark DePristo
2012-05-04 15:42:02 -0400
473d07b0c5fixing up docs from previous Pool Caller commit
Eric Banks
2012-05-08 11:02:55 -0400
b4999d14c1updating docs
Eric Banks
2012-05-08 10:58:46 -0400
33a1dd2048Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Guillermo del Angel
2012-05-08 10:42:12 -0400
7584b1ea17Back off optimization of pool vcf that didn't print genotypes. Many site attributes require GT in genotypes to be computed correctly. Better to change string representation of polyploid genotypes, TBD better solution
Guillermo del Angel
2012-05-08 10:41:39 -0400
5cf4fd63c2Catch malformed base qualities and throw as a User Error
Eric Banks
2012-05-08 09:34:57 -0400
a4f4b5007bMerge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Guillermo del Angel
2012-05-08 09:34:33 -0400
605984353fPool Caller improvements: a) New non-standard private annotation Heteroplasmy which measures mean heteroplasmy (pool AF) across called samples, meant for easier mtDNA calling. Pure homoplasmic variants (pool AF = 1 or 0) would have heteroplasmy=1. b) Don't output pool genotypes by default for large pool sizes because it makes file sizes explode and they're unreadable. c) Refactored classes ExactACCounts and ExactACSet and moved to superclass AlleleFrequencyCalculationModel because both Pool and Exact AF calculation models will use it. d) Initial refactorings and skeleton for linearized multi-allelic exact model (not done yet). e) Unit test for Pool AF calculation model.
Guillermo del Angel
2012-05-08 09:33:38 -0400
c40cda7e3cNope, loads of integration tests had to be changed.
Eric Banks
2012-05-07 14:30:42 -0400
66838a073eVery annoying: we have been emitting an extra TAB in the header of the VCF (which breaks some parsers) for sites-only file. Hopefully not too many integration tests will need to be fixed...
Eric Banks
2012-05-07 12:20:11 -0400
a90482c772Rev. tribble to v101 with another putative open file leak fix
Mark DePristo
2012-05-04 15:38:24 -0400
9424acb3c8BCF2: Fix issue with parsing of filters
David Roazen
2012-05-04 15:08:53 -0400
e506de47b3BCF2: Use the reference's sequence dictionary in BCF2Writer, don't require the VCF header to have contig declarations
David Roazen
2012-05-04 14:54:50 -0400
b28de6674dBCF2: set VC stop position to allow BCF2ToVCF walker to work correctly
David Roazen
2012-05-04 13:21:58 -0400
6b769e91d8BCF2: third checkpoint
David Roazen
2012-05-04 00:00:13 -0400
fa84d50a2bRev. tribble for putative bugfixes for not closing streams
Mark DePristo
2012-05-04 10:20:46 -0400
23e3668e2cAdded JUST_BCF2 to PRS walker based on GVCF tests. Example: -T ProfileRodSystem -mode JUST_BCF2 -R <fasta> -vcf <input> -o out.txt [-performanceTest]
Khalid Shakir
2012-05-03 22:08:18 -0400
7c11dde328Updated DPP test MD5's due to template length (TLEN) changes when Picard was revved.
Khalid Shakir
2012-05-03 14:47:58 -0400
fbb40c3c42BCF2: checkpoint for Mark
David Roazen
2012-05-03 14:09:11 -0400
c9829374d3Oops, was using the wrong variables to print in the HaplotypeResolver. Fixing for Ryan.
Eric Banks
2012-05-03 13:39:49 -0400
f3433201b1Merged bug fix from Stable into Unstable
Eric Banks
2012-05-03 11:11:00 -0400
557da77a1aDon't compute QD if there is no QUAL; added integration test for this
Eric Banks
2012-05-03 11:02:37 -0400
1fc7b5d58bMerged bug fix from Stable into Unstable
Eric Banks
2012-05-03 10:37:58 -0400
567d01cee8- Added option to output the father's allele first in phased child haplotypes - BUG corrected causing wrong phasing of child/father pairs
Laurent Francioli
2012-05-03 15:26:39 +0200
96e5a26223PED support for Inbreeding Coefficient annotation
Laurent Francioli
2012-04-25 16:51:16 +0200
0f4cc1884dRev to tribble 99, optimized AsciiFeatureCodec
Mark DePristo
2012-05-03 07:30:24 -0400
43d97c2e00Rev Tribble to r97, adding binary feature support
Mark DePristo
2012-05-03 07:02:28 -0400
58c470a6c5Rev'ing Tribble from 53 to 94
Mark DePristo
2012-04-28 13:20:16 -0400
e448cfcc59Forgot to update these md5s
Eric Banks
2012-05-02 21:09:50 -0400
b8b7f28aa9Revving Picard to pick up new SamFileHeaderMerger. Updated ReadFilter abstract class to implement (via UnsupportedOperationException) the new SamRecordFilter.filterOut(). In IndelRealignerIntegrationTest updates for Picard fixes to SAMRecord.getInferredInsertSize() in svn r1115 & r1124. - Ran FixMates to create new input BAM since running IR with variable maxReadsInMemory means all reads weren't realigned leading to different outputs. - Updated md5s to match new expectations after looking at TLEN diff engine output.
Khalid Shakir
2012-05-02 16:47:28 -0400
b32f09b949some more updates to the BQSR scala script
Mauricio Carneiro
2012-05-02 16:23:02 -0400
f51a1d0d61Better error message to the BAMScheduler
Mauricio Carneiro
2012-05-02 16:10:00 -0400
a5d17e02c7quick lua script to merge recalibration reports by hand.
Mauricio Carneiro
2012-05-02 15:06:32 -0400
623b36fbc4Add header lines for AC,AF, and AN tags
Eric Banks
2012-05-02 15:33:34 -0400
6fac8f2c70More test coverage on PoolAFCalculationModel: add more tests for multiallelic case with higher ploidy
Guillermo del Angel
2012-05-02 14:12:02 -0400
bb756447e2Move mongodb package to a location where walkers will be visible from the command line
Joel Thibault
2012-05-02 11:39:41 -0400
429800a192Fix corner case rounding issue in MathUtils unit test: 10^logFactorial(4)) was 23.999999... which if cast directly yielded 23 - so, do pre-rounding to ensure correct integer result if caller will cast value.
Guillermo del Angel
2012-05-02 09:57:06 -0400
76a95fdedfFull implementation of multiallelic exact model for pools. Still super-linear so not useable at scale but it should be a gold standard to compare to. Unit tests are not exhaustive yet, will be expanded to provide better test coverage. Small inconsequential optimization in MathUtils: we're already caching log10(factorial(n)) for large n, so might as well use the cached values to compute binomial and multinomial coefficients instead of the log-gamma approximation which is more expensive (doesn't seem to save much time either in PoolCaller nor in UG though).
Guillermo del Angel
2012-05-02 09:24:28 -0400
4d732fa586Move all MongoDB files into private/java/src/org/broadinstitute/sting/mongodb
Joel Thibault
2012-05-01 18:20:18 -0400
bdf6d1f109updates to BQSR queue script
Mauricio Carneiro
2012-05-01 17:36:19 -0400
619a69a5f1As promised in the release notes for 1.6, I am removing the old deprecated genotyping framework revolving around the misordering of alleles and have moved the fixed version in its place in preparation for release 1.7 (or 2.0?).
Eric Banks
2012-05-01 16:18:24 -0400
c255dd5917Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Joel Thibault
2012-05-01 16:10:38 -0400
51af61b5d7Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2012-05-01 16:07:23 -0400
cc646690d6updating HaplotypeCaller integration tests
Ryan Poplin
2012-05-01 16:07:18 -0400
fc55dcec3cUnfortunately the reverse trimming of alleles still doesn't work with mixed records in some corner cases. Turning it off for now.
Ryan Poplin
2012-05-01 16:02:36 -0400
2187d71bb2Adding some quick debugging, custom annotations to the calls coming out of the HaplotypeCaller.
Ryan Poplin
2012-05-01 15:55:14 -0400
20a0078f23Merging active regions across shard boundries if they are contiguous, have the same active status and don't grow too big.
Ryan Poplin
2012-05-01 15:51:36 -0400
0f3af9555bAdding an option to SelectVariants which allows the user to re-genotype through the exact model (if PLs are present) the samples in order to recalculate the QUAL and genotypes. This is really the correct way to select a subset of samples, especially when originally called from low coverage data. Also added integration test to cover this case.
Eric Banks
2012-05-01 14:58:06 -0400
aa4d41cce0Minor cleanup before push
Joel Thibault
2012-05-01 14:15:44 -0400
b101b9c30bAdd Mongo switch
Joel Thibault
2012-04-12 13:35:20 -0400
1b609e9075Move Mongo to server couchdb
Joel Thibault
2012-04-26 15:50:39 -0400
fd57d27f45Move MongoDB connection handling to a separate class
Joel Thibault
2012-04-26 15:48:48 -0400
db3cd1abd5Use 2 MongoDB collections (tables): one for INFO/attributes, one for samples/genotypes.
Joel Thibault
2012-04-23 16:38:41 -0400
04e1be9106Better handling of Mongo errors + exceptions
Joel Thibault
2012-04-13 11:44:08 -0400
ca737479cfQuery for stop locations because we don't have that information in the reference
Joel Thibault
2012-04-12 16:17:42 -0400
1cda87a4adSet ROD priority list to input
Joel Thibault
2012-04-20 14:51:21 -0400
a7fe847fafSet the priority list and don't bother combining if not needed
Joel Thibault
2012-04-20 14:18:19 -0400
f739305f43Combine the variants found at a location
Joel Thibault
2012-04-20 14:04:31 -0400
020f884d5aUse new key of source ROD plus alleles
Joel Thibault
2012-04-19 17:06:37 -0400
221ce9c3d6Add alleles to the primary key
Joel Thibault
2012-04-17 16:21:46 -0400
3198ce5471Can have multiple variants at a location
Joel Thibault
2012-04-17 12:50:36 -0400
Eric Banks
Guillermo del Angel
David Roazen
Joel Thibault
Christopher Hartl
Ryan Poplin
Mark DePristo
Khalid Shakir
Laurent Francioli
Mauricio Carneiro