6e1a86bc3e
Bug fixes to VariantContext and GenotypeCollection
2011-11-15 09:21:30 -05:00
4ff8225d78
GenotypeMap -> GenotypeCollection part 3
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-- Test code actually builds
2011-11-14 17:51:41 -05:00
f0234ab67f
GenotypeMap -> GenotypeCollection part 2
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-- Code actually builds
2011-11-14 17:42:55 -05:00
2e9d5363e7
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-14 15:32:06 -05:00
1fbdcb4f43
GenotypeMap -> GenotypeCollection
2011-11-14 15:32:03 -05:00
4dc9dbe890
One quick fix to previous commit
2011-11-14 14:42:12 -05:00
7b2a7cfbe7
Transfer headers from the resource VCF when possible when using expressions. While there, VA was modified so that it didn't assume that the ID field was present in the VC's info map in preparation for Mark's upcoming changes.
2011-11-14 14:31:27 -05:00
9b5c79b49d
Renamed InferredGeneticContext to CommonInfo
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-- I have no idea why I named this InferredGeneticContext, a totally meaningless term
-- Renamed to CommonInfo.
-- Made package protected, as no one should use this outside of VariantContext and Genotype
-- UGEngine was using IGC constant, but it's now using the public one in VariantContext.
2011-11-14 14:28:52 -05:00
077397cb4b
Deleted MutableVariantContext
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-- All methods that used this capable now use VariantContext directly instead
2011-11-14 14:19:06 -05:00
b11c535527
Deleted MutableGenotype
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-- This class wasn't really used anywhere, and so removed to control code bloat.
2011-11-14 13:16:36 -05:00
79987d685c
GenotypeMap contains a Map, not extends it
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-- On path to replacing it with GenotypeCollection
2011-11-14 12:55:03 -05:00
7aee80cd3b
Fix to deal with reduced reads containing a deletion
2011-11-14 12:23:46 -05:00
3d2970453b
Misc minor cleanup
2011-11-14 09:41:54 -05:00
b7c33116af
Minor docs update
2011-11-12 23:21:07 -05:00
76d357be40
Updating docs example to use -L since that's best practice
2011-11-12 23:20:05 -05:00
fee9b367e4
VariantContext genotypes are now stored as GenotypeMap objects
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-- Enables further sophisticated optimizations, as this class can be smarter about storing the data and will directly support operations like subset to samples
-- All instances in the gatk that used Map<String, Genotype> now use GenotypeMap type.
-- Amazingly, there were many places where HashMap<String, Genotype> is used, so that the order of the genotypes is technically undefined and could be dangerous. Now everything uses GenotypeMap with a specific ordering of samples (by name)
-- Integrationtests updated and all pass
2011-11-11 15:00:35 -05:00
cd3146f4cf
Add hidden option to ValidationAmplicons to output slightly modified format to make file work with downstream SQNM tools more seamlessly at request of GAP: one line per record, keep probe identifier to 20 characters, no * in ref allele.
2011-11-11 14:07:07 -05:00
40fbeafa37
VQSR will now detect if the negative model failed to converge properly because of having too few data points and automatically retry with more appropriate clustering parameters.
2011-11-11 11:52:30 -05:00
4938569b3a
More general handling of parameters for VariantContextBenchmark
2011-11-11 10:22:19 -05:00
ef9f8b5d46
Added subContextOfSamples to VariantContext
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-- This is a more convenient accesssor than subContextOfGenotypes, represents nearly all of the use cases of the former function, and potentially can be implemented more efficiently.
2011-11-11 10:07:11 -05:00
e216e85465
First working version of VariantContextBenchmark
2011-11-11 09:56:00 -05:00
ee40791776
Attributes are now Map<String,Object> not Map<String,?>
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-- Allows us to avoid an unnecessary copy when creating InferredGeneticContext (whose name really needs to change).
2011-11-11 09:55:42 -05:00
dc9b351b5e
Meaningful error message when an IntervalArg file fails to parse correctly
2011-11-10 17:10:26 -05:00
bb7bf74aa8
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-10 16:05:43 -05:00
153e52ffed
VariantEvalIntegrationTest for IntervalStratification
2011-11-10 14:10:39 -05:00
060c7ce8ae
It wouldn't harm integrationtests if we had our logic right... :-)
2011-11-10 14:03:22 -05:00
39678b6a20
Check for reads with missing read groups and throw a UserException when encountered. Mauricio said this wouldn't break integration tests.
2011-11-10 13:34:45 -05:00
dd1810140f
-stratIntervals is optional
2011-11-10 13:27:32 -05:00
67b022c34b
Cleanup for new SampleUtils function
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-- getVCFHeadersFromRods(rods) is now available so that you don't have getVCFHeadersFromRods(rods, null) throughout the codebase
2011-11-10 13:27:13 -05:00
35fe9c8a06
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-10 11:11:33 -05:00
dc4932f93d
VariantEval module to stratify the variants by whether they overlap an interval set
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The primary use of this stratification is to provide a mechanism to divide asssessment of a call set up by whether a variant overlaps an interval or not. I use this to differentiate between variants occurring in CCDS exons vs. those in non-coding regions, in the 1000G call set, using a command line that looks like:
-T VariantEval -R human_g1k_v37.fasta -eval 1000G.vcf -stratIntervals:BED ccds.bed -ST IntervalStratification
Note that the overlap algorithm properly handles symbolic alleles with an INFO field END value. In order to safely use this module you should provide entire contigs worth of variants, and let the interval strat decide overlap, as opposed to using -L which will not properly work with symbolic variants.
Minor improvements to create() interval in GenomeLocParser.
2011-11-10 10:58:40 -05:00
0d8983feee
outputting the RG information
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setReadGroup now sets the read group attribute for the GATKSAMRecord
2011-11-09 23:35:00 -05:00
315ac68b0b
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-09 22:37:36 -05:00
6313aae2c4
Adding checks for hasBasePileup() before calling getBasePileup() as per GS thread
2011-11-09 22:37:26 -05:00
74a18d3de8
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-09 22:29:40 -05:00
24712c0221
Merged bug fix from Stable into Unstable
2011-11-09 22:28:27 -05:00
8942406aa2
Use MathUtils to compare doubles instead of testing for equality
2011-11-09 22:05:21 -05:00
348f2db7fd
Fix for HMM optimization. If the two penalty arrays match exactly the function should return the end of the array instead of 0.
2011-11-09 22:00:52 -05:00
82bf09edf3
Mark Standard Annotations with an asterisk
2011-11-09 20:42:31 -05:00
04b122be29
Fix for bug reported on GetSatisfaction
2011-11-09 20:33:36 -05:00
d00b2c6599
Adding a synthetic read for filtered data
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* Generalized the concept of a synthetic read to cread both running consensus and a synthetic reads of filtered data.
* Synthetic reads can now have deletions (but not insertions)
* New reduced read tag for filtered data synthetic reads *(RF)*
* Sliding window header now keeps information of consensus and filtered data
* Synthetic reads are created simultaneously, new functionality is controlled internally by addToSyntheticReads
2011-11-09 20:16:22 -05:00
21bf43f3bb
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-09 15:34:40 -05:00
02d5e3025e
Added integration test for intervals from bed file
2011-11-09 15:34:19 -05:00
85bffe1dca
Merged bug fix from Stable into Unstable
2011-11-09 15:29:14 -05:00
d828eba7f4
Allow comments in a table-formatted file to precede the header line.
2011-11-09 15:27:38 -05:00
8205efbb29
Merge branch 'master' into intervals
2011-11-09 15:27:15 -05:00
d64f8a89a9
Instead of the SelfScopingFeatureCodec interface, pushed this functionality into Tribble itself. Now we can e.g. determine that a file can be parsed by the BedCodec on the fly.
2011-11-09 15:24:29 -05:00
f080f64f99
Preserve RG information on new GATKSAMRecord from SAMRecord
2011-11-09 14:39:20 -05:00
f9530e0768
Clean unnecessary attributes from the read
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this gives on average 40% file size reduction.
2011-11-09 14:39:20 -05:00
9427ada498
Fixing no cigar bug
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empty GATKSAMRecords will have a null cigar. Treat them accordingly.
2011-11-09 14:39:20 -05:00
Mark DePristo
Eric Banks
Guillermo del Angel
Ryan Poplin
Mauricio Carneiro
Christopher Hartl