9a6b1f2681
Fixed bug where exome could not output after contig change
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Check for new contig uses ContigIndex, not the string
2011-09-11 21:56:30 -04:00
30be6d8bd6
Removing the copy of the original assembler since it has been successfully assimilated
2011-09-11 21:00:27 -04:00
9344938360
Uncomment code to add deleted bases covering an indel to per-sample genotype reporting, update integration tests accordingly
2011-09-10 19:41:01 -04:00
b399424a9c
Fix integration test affected by non-calling all-zero PL samples, and add a more complicated multi-sample integration test from a phase 1 case, GBR with mixed technologies and complex input alleles
2011-09-09 20:44:47 -04:00
e95d484757
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-09 18:31:14 -04:00
a807205fc3
a) Minor optimization to softMax() computation to avoid redundant operations, results in about 5-10% increase in speed in indel calling.
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b) Added (but left commented out since it may affect integration tests and to isolate commits) fix to per-sample DP reporting, so that deletions are included in count.
c) Bug fix to avoid having non-reference genotypes assigned to samples with PL=0,0,0. Correct behavior should be to no-call these samples, and to ignore these samples when computing AC distribution since their likelihoods are not informative.
2011-09-09 18:00:23 -04:00
9e650dfc17
Fixing SelectVariants documentation
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getting rid of messages telling users to go for the YAML file. The idea is to not support these anymore.
2011-09-09 16:25:31 -04:00
72536e5d6d
Done
2011-09-09 15:44:47 -04:00
3c8445b934
Performance bugfix for GenomeLoc.hashcode
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-- old version overflowed so most GenomeLocs had 0 hashcode. Now uses or not plus to combine
2011-09-09 14:25:37 -04:00
c6436ee5f0
Whitespace cleanup
2011-09-09 14:24:29 -04:00
87dc5cfb24
Whitespace cleanup
2011-09-09 14:23:42 -04:00
7f9000382e
Making indel calls default in the MDCP
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You can turn off indel calling by using -noIndels.
2011-09-09 14:09:26 -04:00
1953edcd2d
updating Validate Variants deletion integration test
2011-09-09 13:39:08 -04:00
9ada9b3ed4
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-09 13:15:36 -04:00
354529bff3
adding Validate Variants integration test with a deletion
2011-09-09 13:15:24 -04:00
91c949db74
Fixing ValidateVariants so that it validates deletion records. Fixing GATKdocs.
2011-09-09 12:57:14 -04:00
06cb20f2a5
Intermediate commit cleaning up scatter intervals
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-- Adding unit tests to ensure uniformity of intervals
2011-09-09 12:56:45 -04:00
6bd8a53efd
Fix nasty bug involving the build report generation when multiple test targets are specified on the same command line.
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Ant immutable properties: sometimes your friend, often your enemy.
2011-09-09 12:13:10 -04:00
60a3618845
Added "alltests" build targets.
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To run the same set of tests as the bamboo "All Tests" plan (unit tests,
integration tests, and pipeline tests):
ant alltests
To do the same as above on only the public portion of the codebase:
ant alltests.public
2011-09-09 12:13:10 -04:00
51eb95d638
Missed these tests before
2011-09-09 11:46:37 -04:00
b318fcba35
Added ability to profile the VCF output system too. Also, don't make the index test required.
2011-09-09 11:13:11 -04:00
6ad8943ca0
CompOverlap no longer keeps track of the number of comp sites since it wasn't (and cannot) keeping track of them correctly.
2011-09-09 09:45:24 -04:00
510d5e7730
Merged bug fix from Stable into Unstable
2011-09-09 01:34:55 -04:00
367bbee25a
Fixed typo when printing the contents or last N lines of a file. Thanks to larryns.
2011-09-09 01:33:25 -04:00
7fefc224ba
Unify outputs from PostCallingQC script to produce results compatible with
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the QC database building process.
2011-09-08 16:31:04 -04:00
507574b1c8
Merge branch 'cancer'
2011-09-08 16:10:02 -04:00
61bccb71c6
Improvements to AssignSomaticStatus
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-- Added SOMATIC_AC_TAG_NAME, SOMATIC_NONREF_TAG_NAME tags
-- Added minimalVCF option for testing output
2011-09-08 16:09:33 -04:00
388c9a9c55
Enable public-only tests.
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Public-only tests will allow us to check for runtime public -> private
dependencies when bamboo updates the github repository (currently, we
only check for *compile-time* public -> private dependencies).
To compile/run only public tests, append ".public" to the name of an existing
test target:
ant test.public
ant integrationtest.public
ant performancetest.public
ant pipelinetest.public
ant pipelinetestrun.public
2011-09-08 15:58:42 -04:00
48461b34af
Added TYPE argument to print out VariantType
2011-09-08 15:01:13 -04:00
eaaba6eb51
Confirming that when stratifying by sample in VE the monomorphic sites for a given sample are not counted for the relevant metrics. Adding integration test to cover it.
2011-09-08 13:17:34 -04:00
c204a08319
Merge branch 'cancer'
2011-09-08 13:10:37 -04:00
beabb67669
Working version of AssignSomaticStatus
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-- Called 2400 somatic mutations (~ right number) when calling NA12878 vs. her parents.
-- Now ready for testing in the 100 T/N pairs
2011-09-08 13:09:26 -04:00
5edc8f8578
Moved to private package (intended home)
2011-09-08 11:54:55 -04:00
7557f4a03a
AssignSomaticStatus, now with the correct mathematical model
2011-09-08 11:54:14 -04:00
2636d216de
Adding indel vqsr integration test
2011-09-08 10:38:13 -04:00
9cba1019c8
Another fix for genotype given alleles for indels. Expanding the indel integration tests to include multiallelics and indel records that overlap
2011-09-08 09:25:13 -04:00
e0020b2b29
Fixing PrintRODs. Now has input and only prints out one copy of each record
2011-09-08 08:58:37 -04:00
6e6bf796d5
first version of somatic detector
2011-09-08 08:48:02 -04:00
29c968ab60
clean up
2011-09-08 08:42:43 -04:00
59841f8232
Fixing genotype given alleles for indels. Only take the records that start at this locus.
2011-09-08 08:41:16 -04:00
cd2c511c4a
GCF improvements
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-- Support for streaming VCF writing via the VCFWriter interface
-- GCF now has a header and a footer. The header is minimal, and contains a forward pointer to the position of the footer in the file.
-- Readers now read the header, and then jump to the footer to get the rest of the "header" information
-- Version now a field in GCF
2011-09-07 23:28:46 -04:00
fe5724b6ea
Refactored indexing part of StandardVCFWriter into superclass
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-- Now other implementations of the VCFWriter can easily share common functions, such as writing an index on the fly
2011-09-07 23:27:08 -04:00
7f9047aec1
updating parameters in assembler to decrease runtime
2011-09-07 20:35:08 -04:00
7ba6c29d32
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-07 19:18:24 -04:00
0e8536f5f3
Adding the ability to add multiple kmer lengths in the debruijn graph.
2011-09-07 19:17:45 -04:00
01b6177ce1
Renaming GVCF -> GCF
2011-09-07 17:10:56 -04:00
b220ed0d75
Merge branch 'master' into rodrewrite
2011-09-07 17:05:35 -04:00
45d54f6258
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-07 16:49:49 -04:00
9604fb2ba3
Necessary but not sufficient step to fix GenotypeGivenAlleles mode in UG which is now busted
2011-09-07 16:49:16 -04:00
2ded027762
Removed dysfunctional tranches support from VariantEval
2011-09-07 16:09:24 -04:00
Roger Zurawicki
Ryan Poplin
Guillermo del Angel
Mauricio Carneiro
Mark DePristo
David Roazen
Eric Banks
Khalid Shakir
Matt Hanna