e448cfcc59
Forgot to update these md5s
2012-05-02 21:09:50 -04:00
b8b7f28aa9
Revving Picard to pick up new SamFileHeaderMerger.
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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.
2012-05-02 16:47:28 -04:00
f51a1d0d61
Better error message to the BAMScheduler
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In the case where the BAM file was aligned using a reference but analysis is being attempted with a different reference.
2012-05-02 16:10:00 -04:00
940029fa5d
Fixing on-the-fly recalibration (caught by Ryan)
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low quality bases in the tails were being turned to N's in the final read.
2012-05-02 16:06:04 -04:00
623b36fbc4
Add header lines for AC,AF, and AN tags
2012-05-02 15:33:34 -04:00
429800a192
Fix 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.
2012-05-02 09:57:06 -04:00
76a95fdedf
Full 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).
2012-05-02 09:24:28 -04:00
4d732fa586
Move all MongoDB files into private/java/src/org/broadinstitute/sting/mongodb
2012-05-01 18:23:51 -04:00
619a69a5f1
As 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?).
2012-05-01 16:18:24 -04:00
c255dd5917
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-05-01 16:10:38 -04:00
51af61b5d7
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-05-01 16:07:23 -04:00
fc55dcec3c
Unfortunately the reverse trimming of alleles still doesn't work with mixed records in some corner cases. Turning it off for now.
2012-05-01 16:02:36 -04:00
20a0078f23
Merging active regions across shard boundries if they are contiguous, have the same active status and don't grow too big.
2012-05-01 15:51:36 -04:00
0f3af9555b
Adding 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.
2012-05-01 14:58:06 -04:00
aa4d41cce0
Minor cleanup before push
2012-05-01 14:16:44 -04:00
b101b9c30b
Add Mongo switch
2012-05-01 14:00:48 -04:00
1b609e9075
Move Mongo to server couchdb
2012-05-01 13:59:47 -04:00
fd57d27f45
Move MongoDB connection handling to a separate class
2012-05-01 13:59:37 -04:00
db3cd1abd5
Use 2 MongoDB collections (tables): one for INFO/attributes, one for samples/genotypes.
2012-05-01 13:57:23 -04:00
04e1be9106
Better handling of Mongo errors + exceptions
2012-05-01 13:57:23 -04:00
ca737479cf
Query for stop locations because we don't have that information in the reference
2012-05-01 13:57:23 -04:00
1cda87a4ad
Set ROD priority list to input
2012-05-01 13:57:23 -04:00
a7fe847faf
Set the priority list and don't bother combining if not needed
2012-05-01 13:57:23 -04:00
f739305f43
Combine the variants found at a location
2012-05-01 13:57:23 -04:00
020f884d5a
Use new key of source ROD plus alleles
2012-05-01 13:57:23 -04:00
221ce9c3d6
Add alleles to the primary key
2012-05-01 13:57:23 -04:00
3198ce5471
Can have multiple variants at a location
2012-05-01 13:57:22 -04:00
11ed8e61c9
Add referenceBaseForIndel to the Mongo VariantContext objects
2012-05-01 13:53:44 -04:00
7ed0ee7ed0
Skip locations with no genotypes instead of throwing a NPE
2012-05-01 13:53:44 -04:00
4bdfeacdaa
Handle multiple samples/genotypes per location
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TODO: sample selection
2012-05-01 13:53:43 -04:00
1f7c628796
Insert the ROD filename into MongoDB as part of the primary key
2012-05-01 13:53:43 -04:00
bb8a6e9b0a
Initial test of write and read from MongoDB
2012-05-01 13:53:43 -04:00
c0084c741b
Pilot BCF2 Implementation: Checkpointing the code
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* Not working yet, still very much a work-in-progress with lots of placeholders
* Needed to check this in to enable possible collaboration, since it's
going slower than anticipated and the conference deadline looms.
2012-05-01 12:23:10 -04:00
e964d17518
Removing public to private dependency
2012-05-01 11:02:28 -04:00
462450c3e3
disabling all BQSR unit tests
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with the changes to the cycle covariate, some tests need updates, others need to be completely re-written.
2012-04-30 14:39:55 -04:00
e185632013
Exhaustive unit tests for Pool SNP genotype likelihoods:
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a) Add ability for ErrorModel to be specified by external log-probability vector for testing.
b) For a given depth and ploidy(=2*samples/pool), create artificial high quality pileup testing from AC=0 to AC=ploidy, and test that pool GL's have expected content.Misc. refactorings and cleanups
c) Misc. cleanups and beautification.
2012-04-30 14:29:46 -04:00
7d029b9a28
Merge branch 'master' of ssh://ni.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-04-30 12:16:30 -04:00
944a7d815e
Bringing VQSRV3 up to date. Lots of new features (un-classifying the worst-performing training sites, treating the x% best/worst sites as postive/negative points, ability to pass in a monomorphic track to see ROC curves output). Minor changes to AlleleBalance: weighted average was incorrectly specified (using logscale actually biased the average towards the AB of low-quality genotypes), and breaking out AB by het, hom, and diploid to bring it in line with some (private) changes to the indel likelihood model that (correctly) computes these values for indels.
2012-04-28 11:31:03 -04:00
54a9bc2da2
Bug fix in reverse trim alleles for the case of mixed records that become non-mixed after subsetting the alleles.
2012-04-28 09:12:26 -04:00
e332aeaf70
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-04-27 16:21:21 -04:00
2b5dd28550
Bug fix in reverse trim alleles for the case of mixed records.
2012-04-27 16:21:02 -04:00
1db2d1ba82
Do not add the first and last 4 cycles to the recalibration tables.
2012-04-27 15:18:07 -04:00
08dbd756f3
Quick QC walkers to look at the error profile of indels in the read
2012-04-27 15:18:07 -04:00
730208133b
Several fixes and improvements to Pool caller with ancillary test functions (not done yet):
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a) Utility class called Probability Vector that holds a log-probability vector and has the ability to clip ends that deviate largely from max value.
b) Used this class to hold site error model, since likelihoods of error model away from peak are so far down that it's not worth computing with them and just wastes time.
c) Expand unit tests and add an exhaustive test for ErrorModel class.
d) Corrected major math bug in ErrorModel uncovered by exhaustive test: log(e^x) is NOT x if log's base = 10.
e) Refactored utility functions that created artificial pileups for testing into separate class ArtificialPileupTestProvider. Right now functionality is limited (one artificial contig of 10 bp), can only specify pileups in one position with a given number of matches and mismatches to ref) but functionality will be expanded in future to cover more test cases.
f) Use this utility class for IndelGenotypeLikelihoods unit test and for PoolGenotypeLikelihoods unit test (the latter testing functionality still not done).
g) Linearized implementation of biallelic exact model (very simple approach, similar to diploid exact model, just abort if we're past the max value of AC distribution and below a threshold). Still need to add unit tests for this and to expand to multiallelic model.
h) Update integration test md5's due to minor differences stemming from linearized exact model and better error model math
2012-04-27 14:41:17 -04:00
0439047269
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-04-27 10:49:45 -04:00
05b44dd017
The genotypeCounts array wasn't always being initialized before it was accessed, leading to a NPE (which got caught and thrown as a JEXL expression when used in selection). Added unit test to cover all genotype count methods.
2012-04-27 10:49:36 -04:00
9801dd114f
Bug fix for: https://getsatisfaction.com/gsa/topics/problem_with_indelrealigner_and_l_unmapped
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The GATK -L unmapped is for GenomeLocs with SAMRecord.NO_ALIGNMENT_REFERENCE_NAME, not SAMRecord.getReadUnmappedFlag()
Previously unmapped flag reads in the last bin were being printed while also seeking for the reads without a reference contig.
2012-04-27 09:58:38 -04:00
2f86ccb086
Correct md5's for previous code change
2012-04-26 16:20:41 -04:00
972d6531b6
Corner case fix for indel GL computation: sometimes (depending on surrounding context) reads which are not informative of two candidate haplotypes end up having marginally higher likelihoods with one haplotype as opposed to another, depending on uncertainty on alignments in surrounding regions. So, a sample whose GL is -0.0001,-0.0005,-0.001 may have its genotype set to 1/1 due to this statistical noise. We already have a tolerance comparing max(gl)-min(gl) to avoid genotyping, so this tolerance is now increased from 0.001 to 0.1 (equivalent to 1 PL unit) to avoid genotyping a sample if all PLs are within this threshold. Changed 2 integration test md5s that hit this case.
2012-04-26 10:15:26 -04:00
ab2a952ad1
PED support for Inbreeding Coefficient annotation
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Signed-off-by: Eric Banks <ebanks@broadinstitute.org>
2012-04-25 12:56:47 -04:00
Eric Banks
Khalid Shakir
Mauricio Carneiro
Guillermo del Angel
Joel Thibault
Ryan Poplin
David Roazen
Christopher Hartl
Laurent Francioli