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
b32f09b949
some more updates to the BQSR scala script
2012-05-02 16:23:02 -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
a5d17e02c7
quick lua script to merge recalibration reports by hand.
2012-05-02 16:06:04 -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
6fac8f2c70
More test coverage on PoolAFCalculationModel: add more tests for multiallelic case with higher ploidy
2012-05-02 14:12:02 -04:00
bb756447e2
Move mongodb package to a location where walkers will be visible from the command line
2012-05-02 11:58:06 -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
bdf6d1f109
updates to BQSR queue script
2012-05-01 17:36:33 -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
cc646690d6
updating HaplotypeCaller integration tests
2012-05-01 16:07:18 -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
2187d71bb2
Adding some quick debugging, custom annotations to the calls coming out of the HaplotypeCaller.
2012-05-01 15:55:14 -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
d93a413f2e
Add MongoDB dependency
2012-05-01 13:53:43 -04:00
0cf3603c73
Merged bug fix from Stable into Unstable
2012-05-01 13:39:27 -04:00
c2b74eca64
Remove unnecessary and obscure usage of old R
2012-05-01 13:39:09 -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
fdffe1d61b
Merged bug fix from Stable into Unstable
2012-05-01 11:04:46 -04:00
0c8e801021
Removing public to private dependency
2012-05-01 11:04:11 -04:00
e964d17518
Removing public to private dependency
2012-05-01 11:02:28 -04:00
ef082356e9
Merge remote-tracking branch 'unstable/master'
2012-05-01 08:47:08 -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
825ad30477
Adding readgroup filter option to BQSR queue script
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
Khalid Shakir
Mauricio Carneiro
Eric Banks
Guillermo del Angel
Joel Thibault
Ryan Poplin
Mark DePristo
David Roazen
Christopher Hartl