a79144f7db
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-12-09 15:57:24 +01:00
5a06170804
Corrected bug causing getChildrenWithParents() to not take the last family member into consideration.
2011-12-09 14:51:34 +01:00
252e0f3d0a
Merged bug fix from Stable into Unstable
2011-12-08 13:11:39 -05:00
1bfe28067f
Don't try to genotype an indel even bigger than the reference window size, or else we'll be out of bounds. Necessary to handle Phase 1 integrated callset with large deletions. Better error indication when validating a GenomeLoc.
2011-12-08 12:54:08 -05:00
9def841275
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-12-07 13:36:16 -05:00
4055877708
Prints 0.0 TiTv not NaN when there are no variants
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-- Updated md5
2011-12-07 12:07:54 -05:00
15533e08df
Fixed issue with RODWalker parallelization.
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Turns out that someone previously upped the declared size of a ROD shard to 100M bases, making
each ROD shard larger than the size of chr20. Why didn't we see this in Stable? Because the
ShardStrategy/ShardStrategyFactory mechanism was dutifully ignoring the shard size specification.
When I rolled the ShardStrategy/ShardStrategyFactory mechanics back into the DataSources as part
of the async I/O project, I inadvertently reenabled this specifier.
2011-12-07 11:55:42 -05:00
5d2212bc8e
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-12-07 09:03:17 -05:00
6bf18899df
Fix for variant summary -- now treats all 50 bp deletions or insertions as CNVs
2011-12-07 09:02:49 -05:00
c9b2cd8ba5
Fix for chartl's stale null representation issue.
2011-12-06 18:05:17 -05:00
f5b977fc88
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-12-06 10:11:35 -05:00
4001c22a11
Better file count / buffering variation in test suite. Parameterized read shard buffering. Misc cleanup.
2011-12-06 10:10:38 -05:00
677bea0abd
Right aligning GATKReport numeric columns and updated MD5s in tests.
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PreQC parses file with spaces in sample names by using tabs only.
PostQC allows passing the file names for the evals so that flanks can be evaled.
BaseTest's network temp dir now adds the user name to the path so files aren't created in the root.
HybridSelectionPipeline:
- Updated to latest versions of reference data.
- Refactored Picard parsing code replacing YAML.
2011-12-05 23:22:15 -05:00
3060a4a15e
Support for list of known CNVs in VariantEval
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-- VariantSummary now includes novelty of CNVs by reciprocal overlap detection using the standard variant eval -knownCNVs argument
-- Genericizes loading for intervals into interval tree by chromosome
-- GenomeLoc methods for reciprocal overlap detection, with unit tests
2011-11-30 17:05:16 -05:00
b65db6a854
First draft of a test script for I/O performance with the new asynchronous I/O processing.
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Also includes convenience parameters for specifying the IO/CPU threading balance outside of a tag. Will be killed when
Queue gets better support for tagged arguments (hopefully soon).
2011-11-30 13:13:16 -05:00
28b286ad39
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-30 09:11:53 -05:00
20bffe0430
Adapted for the new version of MendelianViolation
2011-11-30 14:46:38 +01:00
1cb5e9e149
Removed outdated (and unused) -familyStr commandline argument
2011-11-30 14:45:04 +01:00
f49dc5c067
Added functionality to get all children that have both parents (useful when trios are needed)
2011-11-30 14:43:37 +01:00
a4606f9cfe
Merge branch 'MendelianViolation'
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Conflicts:
public/java/src/org/broadinstitute/sting/utils/MendelianViolation.java
2011-11-30 11:13:15 +01:00
b279ae4ead
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-30 10:10:21 +01:00
91413cf0d9
Merged bug fix from Stable into Unstable
2011-11-29 14:01:23 -05:00
cb284eebde
Further updating VQSR tutorial wiki docs to reflect the bundle
2011-11-29 14:00:57 -05:00
dcb889665d
Merged bug fix from Stable into Unstable
2011-11-29 09:58:49 -05:00
447e9bff9e
Updating VQSR tutorial wiki docs to reflect the bundle
2011-11-29 09:57:45 -05:00
110298322c
Adding Transmission Disequilibrium Test annotation to VariantAnnotator and integration test to test it.
2011-11-29 09:29:18 -05:00
ab67011791
Corrected bug introduced in the last update and causing no families to be returned by getFamilies in case the samples were not specified
2011-11-29 11:18:15 +01:00
d7d8b8e380
Tribble v42 changes the Codec.canDecode method to take in a String instead of a File; this is something that Jim was adamant about (because Tribble can handle streams other than files). I didn't want the next person who needed to rev Tribble to deal with this change additionally, so I took care of updating the GATK now.
2011-11-28 14:18:28 -05:00
a09c01fcec
Removed walker argument FamilyStructure as this is now supported by the engine (ped file)
2011-11-28 17:18:11 +01:00
795c99d693
Adapted MendelianViolation to the new ped family representation. Adapted all classes using MendelianViolation too.
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MendelianViolationEvaluator was added a number of useful metrics on allele transmission and MVs
2011-11-28 17:13:14 +01:00
e877db8f42
Changed visibility of getSampleDB from protected to public as the sampleDB needs to be accessible from Annotators and Evaluators too.
2011-11-28 17:11:30 +01:00
5c2595701c
Added a function to get families only for a given list of samples.
2011-11-28 17:10:33 +01:00
3c36428a20
Bug fix for TiTv calculation -- shouldn't be rounding
2011-11-28 10:20:34 -05:00
436b4dc855
Updated docs
2011-11-28 08:59:48 -05:00
b1dd632d5d
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
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Conflicts:
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
2011-11-25 16:16:44 +01:00
e319079c32
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-23 13:02:11 -05:00
4107636144
VariantEval updates
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-- Performance optimizations
-- Tables now are cleanly formatted (floats are %.2f printed)
-- VariantSummary is a standard report now
-- Removed CompEvalGenotypes (it didn't do anything)
-- Deleted unused classes in GenotypeConcordance
-- Updates integration tests as appropriate
2011-11-23 13:02:07 -05:00
5a4856b82e
GATKReports now support a format field per column
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-- You can tell the table to format your object with "%.2f" for example.
2011-11-23 11:31:04 -05:00
c8bf7d2099
Check for null comment
2011-11-23 10:47:21 -05:00
6c2555885c
Caching getSimpleName() in VariantEval is a big performance improvement
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-- Removed the SimpleMetricsByAC table, as one should just use the AlleleCount Stratefication and the upcoming VariantSummary table
2011-11-23 08:34:05 -05:00
32adbd614f
Solve merge conflict
2011-11-22 22:48:46 -05:00
941f3784dc
Solve merge conflict
2011-11-22 22:48:03 -05:00
75d93e6335
Another corner condition fix: skip likelihood computation in case we cut so many bases there's no haplotype or read left
2011-11-22 22:46:12 -05:00
a3aef8fa53
Final performance optimization for GenotypesContext
2011-11-22 17:19:30 -05:00
990c02e4de
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-22 17:19:11 -05:00
38a90da92c
Fixed merge conflict to Unstable
2011-11-22 14:39:45 -05:00
32a77a8a56
Prevent out of bound error in case read span > reference context + indel length. Can happen in RNAseq reads with long N CIGAR operators in the middle.
2011-11-22 13:57:24 -05:00
5821c11fad
For BAM and Reviewed errors we now check the error message to see if it's actually a 'too many open files' problem and, if so, we generate a User Error instead.
2011-11-22 10:50:22 -05:00
5443d3634a
Again, fixing the add call when we really mean replace
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-- Updating MD5s for UG to reflect that what was previously called ./.:.:10:0,0,0 is now just ./. Eric will fix long-standing bug in QD observed from this change
-- VFW MD5s restored to their old correct values. There was a bug in my implementation to caused the genotypes to not be parsed from the lazy output even through the header was incorrect.
2011-11-21 19:15:56 -05:00
9ea7b70a02
Added decode method to LazyGenotypesContext
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-- AbstractVCFCodec calls this if the samples are not sorted. Previously called getGenotypes() which didn't actually trigger the decode
2011-11-21 16:21:23 -05:00
Laurent Francioli
Guillermo del Angel
Mark DePristo
Matt Hanna
Khalid Shakir
Ryan Poplin
Eric Banks