4748ae0a14
Bugfix: Softclips before Hardclips weren't being accounted for
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caught a bug in the hard clipper where it does not account for hard clipping softclipped bases in the resulting cigar string, if there is already a hard clipped base immediately after it.
* updated unit test for hardClipSoftClippedBases with corresponding test-case.
2011-12-15 12:17:25 -05:00
62a2e335bc
Changing HardClipper contract to allow UNMAPPED reads
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shifted the contract to functions that operate on reference based coordinates. The clipper should do the right thing with unmapped reads, but it needs more testing (Ryan is using it at the moment and says it works). Will write some unit tests.
2011-12-15 11:08:19 -05:00
9333b678b5
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-12-14 18:05:44 -05:00
6fb4be1a09
Cache header merger.
2011-12-14 18:05:31 -05:00
128bdf9c09
Create artificial reads with "default" parameters
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* added functions to create synthetic reads for unit testing with reasonable default parameters
* added more functions to create synthetic reads based on cigar string + bases and quals.
2011-12-14 16:58:14 -05:00
c85100ce9c
Fix ClippingOp bug when performing multiple hardclip ops
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bug: When performing multiple hard clip operations in a read that has indels, if the N+1 hardclip requests to clip inside an indel that has been removed by one of the (1..N) previous hardclips, the hard clipper would go out of bounds.
fix: dynamically adjust the boundaries according to the new hardclipped read length. (this maintains the current contract that hardclipping will never return a read starting or ending in indels).
2011-12-14 16:57:47 -05:00
de5928ac5a
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-12-14 16:24:56 -05:00
4fddac9f22
Updating busted integration tests
2011-12-14 16:24:43 -05:00
01e547eed3
Parallel SAMDataSource initialization
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-- Uses 8 threads to load BAM files and indices in parallel, decreasing costs to read thousands of BAM files by a significant amount
-- Added logger.info message noting progress and cost of reading low-level BAM data.
2011-12-14 16:14:26 -05:00
71b4bb12b7
Bug fix for incorrect logic in subsetSamples
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-- Now properly handles the case where a sample isn't present (no longer adds a null to the genotypes list)
-- Fix for logic failure where if the number of requested samples equals the number of known genotypes then all of the records were returned, which isn't correct when there are missing samples.
-- Unit tests added to handle these cases
2011-12-14 16:14:26 -05:00
35fc2e13c3
Using the new PL cache, fix a bug: when only a subset of the genotyped alleles are used for assigning genotypes (because the exact model determined that they weren't all real) the PLs need to be adjusted to reflect this. While fixing this I discovered that the integration tests are busted because ref calls (ALT=.) were getting annotated with PLs, which makes no sense at all.
2011-12-14 15:31:09 -05:00
1e90d602a4
Optimization: cache up front the PL index to the pair of alleles it represents for all possible numbers of alternate alleles.
2011-12-14 13:38:20 -05:00
988d60091f
Forgot to add in the new result class
2011-12-14 13:37:15 -05:00
106bf13056
Use a thread local result object to collect the results of the exact calculation instead of passing in multiple pre-allocated arrays.
2011-12-14 12:05:50 -05:00
7648521718
Add check for mixed genotype so that we don't exception out for a valid record
2011-12-14 11:26:43 -05:00
9497e9492c
Bug fix for complex records: do not ever reverse clip out a complete allele.
2011-12-14 11:21:28 -05:00
09a5a9eac0
Don't update lineNo for decodeLoc - only for decode (otherwise they get double-counted). Even still, because of the way the GATK currently utilizes Tribble we can parse the same line multiple times, which knocks the line counter out of sync. For now, I've added a TODO in the code to remind us and the error messages note that it's an approximate line number.
2011-12-14 10:43:52 -05:00
d3f4a5a901
Fail gracefully when encountering malformed VCFs without enough data columns
2011-12-14 10:37:38 -05:00
079932ba2a
The log10cache needs to be larger if we want to handle 10K samples in the UG.
2011-12-13 23:36:10 -05:00
7fa1ab1bae
Fix to allow haplotype caller to call indels after UG engine entry points were unified. Adding Haplotype Caller integration test
2011-12-13 17:19:40 -05:00
e47a113c9f
Enabled multi-allelic SNP discovery in the UG. Needs loads of testing so do not use yet. While working in the UG engine, I removed the extraneous and unnecessary MultiallelicGenotypeLikelihoods class: now a VariantContext with PL-annotated Genotypes is passed around instead. Integration tests pass so it must all work, right?
2011-12-12 23:02:45 -05:00
5cc1e72fdb
Parallelized SelectVariants
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* can now use -nt with SelectVariants for significant speedup in large files
* added parallelization integration tests for SelectVariants
2011-12-12 18:41:14 -05:00
a70a0f25fb
Better debug output for SAMDataSource
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output the name and number of the files being loaded by the GATK instead of "coordinate sorted".
2011-12-12 17:57:29 -05:00
d03425df2f
TODO optimization targets
2011-12-12 17:39:51 -05:00
025bdfe2cc
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-12-12 12:19:44 +01:00
7b6338c742
Merge branch 'master' into trialleles
2011-12-11 00:28:46 -05:00
7c4b9338ad
The old bi-allelic implementation of the Exact model has been completely deprecated - you can only use the multi-allelic implementation now.
2011-12-11 00:23:33 -05:00
044f211a30
Don't collapse likelihoods over all alt alleles - that's just not right. For now, the QUAL is calculated for just the most likely of the alt alleles; I need to think about the right way to handle this properly.
2011-12-10 23:57:14 -05:00
364f1a030b
Plumbing added so that the UG engine can handle multiple alleles and they can successfully be genotyped. Alleles that aren't likely are not allowed to be used when assigning genotypes, but otherwise the greedy PL-based approach is what is used. Moved assign genotypes code to UG engine since it has nothing to do with the Exact model. Still have some TODOs in here before I can push this out to everyone.
2011-12-09 14:25:28 -05:00
64dad13e2d
Don't carry around an extra copy of the code for the Haplotype Caller
2011-12-09 11:09:40 -05:00
442ceb6ad9
The Exact model now computes both the likelihoods and posteriors (in separate arrays); likelihoods are used for assigning genotypes, not the posteriors.
2011-12-09 10:16:44 -05:00
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
aa4a8c5303
No dynamic programming solution for assignning genotypes; just done greedily now. Fixed QualByDepth to skip no-call genotypes. No-calls are no longer given annotations (attributes).
2011-12-09 02:25:06 -05:00
8777288a9f
Don't throw a UserException if too many alt alleles are trying to be genotyped. Instead, I've added an argument that allows the user to set the max number of alt alleles to genotype and the UG warns and skips any sites with more than that number.
2011-12-09 00:00:20 -05:00
3e7714629f
Scrapped the whole idea of an int/long as an index into the ACset: with lots of alternate alleles we run into overflow issues. Instead, simply use the ACcounts array as the hash key since it is unique for each AC conformation. To do this, it needed to be wrapped inside an object so hashcode() would work.
2011-12-08 23:50:54 -05:00
4aebe99445
Need to use longs for the set index (because we can run out of ints when there are too many alternate alleles). Integration tests now use the multiallelic implementation.
2011-12-08 15:31:02 -05:00
7750bafb12
Fixed bug where last dependent set index wasn't properly being transferred for sites with many alleles. Adding debugging output.
2011-12-08 13:50:50 -05:00
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
79d18dc078
Fixing indexing bug on the ACsets. Added unit tests for the Exact model code.
2011-12-06 16:17:18 -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
Mauricio Carneiro
Matt Hanna
Eric Banks
Mark DePristo
Ryan Poplin
Laurent Francioli
Guillermo del Angel
Khalid Shakir