c8a06e53c1
DoC now properly handles reference N bases + misc. additional cleanups
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-- DoC now by default ignores bases with reference Ns, so these are not included in the coverage calculations at any stage.
-- Added option --includeRefNSites that will include them in the calculation
-- Added integration tests that ensures the per base tables (and so all subsequent calculations) work with and without reference N bases included
-- Reorganized command line options, tagging advanced options with @Advanced
2012-02-25 11:32:50 -05:00
50de1a3eab
Fixing bad VCFIntegration tests
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-- Left disabled a test that should have been enabled
-- Didn't add the md5 to the test I actually added
-- Now VCFIntegrationTests should be working!
2012-02-25 11:26:36 -05:00
ee9a56ad27
Fix subtle bug in the ReduceReads stash reported by Adam
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* The tailSet generated every time we flush the reads stash is still being affected by subsequent clears because it is just a pointer to the parent element in the original TreeSet. This is dangerous, and there is a weird condition where the clear will affects it.
* Fix by creating a new set, given the tailSet instead of trying to do magic with just the pointer.
2012-02-23 18:35:25 -05:00
e0c189909f
Added support for breakpoint alleles
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-- See https://getsatisfaction.com/gsa/topics/support_vcf_4_1_structural_variation_breakend_alleles?utm_content=topic_link&utm_medium=email&utm_source=new_topic
-- Added integrationtest to ensure that we can parse and write out breakpoint example
2012-02-23 12:14:48 -05:00
2b6c0939ab
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-02-22 19:00:38 -05:00
8695738400
Bug fix in HaplotypeCaller's GENOTYPE_GIVEN_ALLELES mode for insertions greater than length 1. The allele being genotyped was off by one base pair.
2012-02-22 19:00:04 -05:00
2c1b14d35e
Mostly small changes to my own scala scripts: .vcf.gz compatibility for output files, smarter beagle generation, simple script to scatter-gather combine variants. Whole genome indel calling now uses the gold standard indel set.
2012-02-22 17:20:04 -05:00
9b61a398b3
Merge branch 'master' of ssh://ni.broadinstitute.org/humgen/gsa-scr1/chartl/dev/unstable
2012-02-22 17:18:10 -05:00
75783af6fc
int <-> BitSet conversion utils for MathUtils
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* added unit tests.
2012-02-21 14:10:36 -05:00
685bcaced2
Merge branch 'master' of ssh://ni.broadinstitute.org/humgen/gsa-scr1/chartl/dev/unstable
2012-02-21 13:53:37 -05:00
0f5674b95e
Redid fix for corner case when forming consensus with reads that start/end with insertions and that don't agree with each other in inserted bases: since I can't iterate over the elements of a HashMap because keys might change during iteration, and since I can't use ConcurrentHashMaps, the code now copies structure of (bases, number of times seen) into ArrayList, which can be addressed by element index in order to iterate on it.
2012-02-20 09:12:51 -05:00
3d9eee4942
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-02-18 10:55:29 -05:00
a8be96f63d
This caching in the BQSR seems to be too slow now that there are so many keys
2012-02-18 10:54:39 -05:00
78718b8d6a
Adding Genotype Given Alleles mode to the HaplotypeCaller. It constructs the possible haplotypes via assembly and then injects the desired allele to be genotyped.
2012-02-18 10:31:26 -05:00
e724c63f2b
Reverting last commit until I learn how to effectively replicate and debug pipeline test failures, and until I also learn how to effectively remove a kep from a HashMap that's being iterated on
2012-02-17 17:18:43 -05:00
f2ef8d1d23
Reverting last commit until I learn how to effectively replicate and debug pipeline test failures, and until I also learn how to effectively remove a kep from a HashMap that's being iterated on
2012-02-17 17:15:53 -05:00
3e031a540f
Solve merge conflict
2012-02-17 10:56:03 -05:00
cd352f502d
Corner case bug fix: if a read starts with an insertion, when computing the consensus allele for calling the insertion was only added to the last element in the consensus key hash map. Now, an insertion that partially overlaps with several candidate alleles will have their respective count increased for all of them
2012-02-17 10:21:37 -05:00
2f08846d82
Merged bug fix from Stable into Unstable
2012-02-14 21:26:25 -05:00
7dc6f73399
Bug fix for validation site selector: records with AC=0 in them were always being thrown out if input vcf was sites-only, even when -ignorePolymorphicStatus flag was set
2012-02-14 21:11:24 -05:00
30085781cf
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-02-14 14:01:20 -05:00
ae5b42c884
Put base insertion and base deletions in the SAMRecord as a string of quality scores instead of an array of bytes. Start of a proper genotype given alleles mode in HaplotypeCaller
2012-02-14 14:01:04 -05:00
85d31f80a2
Merged bug fix from Stable into Unstable
2012-02-13 16:37:11 -05:00
03e5184741
Fix serious engine bug that could cause reads to be dropped under certain circumstances
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When aggregating raw BAM file spans into shards, the IntervalSharder tries to combine
file spans when it can. Unfortunately, the method that combines two BAM file
spans was seriously flawed, and would produce a truncated union if the file spans
overlapped in certain ways. This could cause entire regions of the BAM file containing
reads within the requested intervals to be dropped.
Modified GATKBAMFileSpan.union() to correct this problem, and added unit tests
to verify that the correct union is produced regardless of how the file spans
happen to overlap.
Thanks to Khalid, who did at least as much work on this bug as I did.
2012-02-13 16:25:21 -05:00
ad90af94ed
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-02-13 15:10:10 -05:00
0920a1921e
Minor fixes to splitting multi-allelic records (as regards printing indel alleles correctly); minor code refactoring; adding integration tests to cover +/- splitting multi-allelics.
2012-02-13 15:09:53 -05:00
14981bed10
Cleaning up VariantsToTable: added docs for supported fields; removed one-off hidden arguments for multi-allelics; default behavior is now to include multi-allelics in one record; added option to split multi-allelics into separate records.
2012-02-13 14:32:03 -05:00
e9338e2c20
Context covariate needs to look in the reverse direction for negative stranded reads.
2012-02-13 13:40:41 -05:00
41ffd08d53
On the fly base quality score recalibration now happens up front in a SAMIterator on input instead of in a lazy-loading fashion if the BQSR table is provided as an engine argument. On the fly recalibration is now completely hooked up and live.
2012-02-13 12:35:09 -05:00
3caa1b83bb
Updating HC integration tests
2012-02-11 11:48:32 -05:00
9b8fd4c2ff
Updating the half of the code that makes use of the recalibration information to work with the new refactoring of the bqsr. Reverting the covariate interface change in the original bqsr because the error model enum was moved to a different class and didn't make sense any more.
2012-02-11 10:57:20 -05:00
f52f1f659f
Multiallelic implementation of the TDT should be a pairwise list of values as per Mark Daly. Integration tests change because the count in the header is now A instead of 1.
2012-02-10 14:15:59 -05:00
1fb19a0f98
Moving the covariates and shared functionality to public
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so Ryan can work on the recalibration on the fly without breaking the build. Supposedly all the secret sauce is in the BQSR walker, which sits in private.
2012-02-10 11:44:01 -05:00
5e18020a5f
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-02-10 11:08:33 -05:00
f53cd3de1b
Based on Ryan's suggestion, there's a new contract for genotyping multiple alleles. Now the requester submits alleles in any arbitrary order - rankings aren't needed. If the Exact model decides that it needs to subset the alleles because too many were requested, it does so based on PL mass (in other words, I moved this code from the SNPGenotypeLikelihoodsCalculationModel to the Exact model). Now subsetting alleles is consistent.
2012-02-10 11:07:32 -05:00
5af373a3a1
BQSR with indels integrated!
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* added support to base before deletion in the pileup
* refactored covariates to operate on mismatches, insertions and deletions at the same time
* all code is in private so original BQSR is still working as usual in public
* outputs a molten CSV with mismatches, insertions and deletions, time to play!
* barely tested, passes my very simple tests... haven't tested edge cases.
2012-02-09 18:46:45 -05:00
7a937dd1eb
Several bug fixes to new genotyping strategy. Update integration tests for multi-allelic indels accordingly.
2012-02-09 16:14:22 -05:00
0f728a0604
The Exact model now subsets the VC to the first N alleles when the VC contains more than the maximum number of alleles (instead of throwing it out completely as it did previously). [Perhaps the culling should be done by the UG engine? But theoretically the Exact model can be called outside of the UG and we'd still want the context subsetted.]
2012-02-09 14:02:34 -05:00
aa097a83d5
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-02-09 11:26:48 -05:00
b57d4250bf
Documentation request by Eric. At each stage of the GATK where filtering occurs, added documentation suggesting the goal of the filtering along with examples of suggested inputs and outputs.
2012-02-09 11:24:52 -05:00
d561914d4f
Revert "First implementation of GATKReportGatherer"
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premature push from my part. Roger is still working on the new format and we need to update the other tools to operate correctly with the new GATKReport.
This reverts commit aea0de314220810c2666055dc75f04f9010436ad.
2012-02-08 23:28:55 -05:00
2f800b078c
Changes to default behavior of UG: multi-allelic mode is always on; max number of alternate alleles to genotype is 3; alleles in the SNP model are ranked by their likelihood sum (Guillermo will do this for indels); SB is computed again.
2012-02-08 15:27:16 -05:00
51ac87b28c
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-02-08 08:43:55 -05:00
5b58fe741a
Retiring Picard customizations for async I/O and cleaning up parts of the code to use common Picard utilities I recently discovered.
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Also embedded bug fix for issues reading sparse shards and did some cleanup based on comments during BAM reading code transition meetings.
2012-02-08 08:34:37 -05:00
cda1e1b207
Minor manual merge update for List class to Seq interface usage.
2012-02-08 02:24:54 -05:00
ef74363b1b
Merged bug fix from Stable into Unstable
2012-02-08 02:14:26 -05:00
23e7f1bed9
When an interval list specifies overlapping intervals merge them before scattering.
2012-02-08 02:12:16 -05:00
337819e791
disabling the test while we fix it
2012-02-07 19:22:32 -05:00
c0c676590b
First implementation of GATKReportGatherer
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- Added the GATKReportGatherer
- Added private methods in GATKReport to combine Tables and Reports
- It is very conservative and it will only gather if the table columns, match.
- At the column level it uses the (redundant) row ids to add new rows. It will throw an exception if it is overwriting data.
Added the gatherer functions to CoverageByRG
Also added the scatterCount parameter in the Interval Coverage script
Made some more GATKReport methods public
The UnitTest included shows that the merging methods work
Added a getter for the PrimaryKeyName
Fixed bugs that prevented the gatherer form working
Working GATKReportGatherer
Has only the functional to addLines
The input file parser assumes that the first column is the primary key
Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
2012-02-07 18:14:47 -05:00
e89887cd8e
laying groundwork to have insertions and deletions going through the system.
2012-02-07 18:11:53 -05:00
Mark DePristo
Mauricio Carneiro
Ryan Poplin
Christopher Hartl
Guillermo del Angel
David Roazen
Eric Banks
Matt Hanna
Khalid Shakir
Roger Zurawicki