14a77b1e71
Getting rid of redundant methods in MathUtils. Adding unit tests for approximateLog10SumLog10 and normalizeFromLog10. Increasing the precision of the Jacobian approximation used by approximateLog10SumLog which changes the UG+HC integration tests ever so slightly.
2012-03-05 12:28:32 -05:00
f879daa7d0
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-03-05 08:29:08 -05:00
d6871967ae
Adding more unit tests and contracts to PairHMM util class. Updating HaplotypeCaller to use the new PairHMM util class. Now that the HMM result isn't dependent on the length of the haplotype there is no reason to ensure all haplotypes have the save length which simplifies the code considerably.
2012-03-05 08:28:42 -05:00
3b5a7c34d7
Added argument to ValidationAmplicons to only output valid sequences - useful for not having to post-filter or grep resulting files before delivering downstream
2012-03-04 10:24:29 -05:00
69611af7d3
Workaround for bug in Picard in ReadGroupProperties
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-- NPE caused when you call getRunDate on a read group without a date.
2012-03-02 18:53:45 -05:00
ba71b0aee4
ReadGroupProperties mk3
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-- Includes sequencing date
2012-03-02 16:12:42 -05:00
1e07e97b58
Optimization: create allele list just once, not for each genotype
2012-03-02 13:30:17 -05:00
0ad7d5fbc1
Standalone common Pair HMM utility class with associated unit tests.
2012-03-01 22:41:13 -05:00
2f334a57c2
ReadGroupProperties mk2
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-- Includes paired end status (T/F)
-- Includes count of reads used in calculation
-- Includes simple read type (2x76 for example)
-- Better handling of insert size, read length when there's no data, or the data isn't paired end by emitting NA not 0
2012-03-01 18:43:53 -05:00
486712bfc2
ugly RG encoding
2012-03-01 17:56:45 -05:00
29f74b658b
Unit tests for the context covariate
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this is simple, but it's the infra-structure to start messing around with the context.
2012-03-01 17:56:45 -05:00
aff508e091
ReadGroupProperties walker and associated infrastructure
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-- ReadGroupProperties: Emits a GATKReport containing read group, sample, library, platform, center, median insert size and median read length for each read group in every BAM file.
-- Median tool that collects up to a given maximum number of elements and returns the median of the elements.
-- Unit and integration tests for everything.
-- Making name of TestProvider protected so subclasses and override name more easily
2012-03-01 15:01:11 -05:00
9e95b10789
Context covariate now operates as a highly compressed bitset
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* All contexts with 'N' bases are now collapsed as uninformative
* Context size is now represented internally as a BitSet but output as a dna string
* Temporarily disabled sorted outputs because of null objects
2012-02-29 19:25:21 -05:00
d379c3763a
DNA Sequence to BitSet and vice-versa conversion tools
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* Turns DNA sequences (for context covariates) into bit sets for maximum compression
* Allows variable context size representation guaranteeing uniqueness.
* Works with long precision, so it is limited to a context size of 31 bases (can be extended with BigNumber precision if necessary).
* Unit Tests added
2012-02-29 19:25:20 -05:00
129b5e7f6b
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-02-28 10:09:34 -05:00
a4a279ce80
Damn you, Mark
2012-02-28 10:09:09 -05:00
0681bea5a5
Changed DoC from PartitionType.INTERVAL to PartitionType.NONE since it doesn't have a way to gather scattered outputs.
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Added MultiallelicSummary to HSP eval.
2012-02-28 09:27:27 -05:00
bd398e30fd
Another quick optimization
2012-02-28 09:25:35 -05:00
40bdadbda5
Minor optimization as per Mark
2012-02-28 09:24:07 -05:00
d7928ad669
Drat, missed one: handle null alleles being passed in.
2012-02-27 21:31:54 -05:00
24356f11b7
Merged bug fix from Stable into Unstable
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-- Resolved conflict
Conflicts:
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
2012-02-27 17:13:17 -05:00
0b29d54937
Changed most BAMSchedule ReviewedStingExceptions to UserExceptions
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-- As these represent the bulk of the StingExceptions coming from BAMSchedule and are caused by simple problems like the user providing bad input tmp directories, etc.
2012-02-27 17:08:41 -05:00
f9e8e82e33
Removed unused class variable from VCFHeaderLineTranslator
2012-02-27 17:07:19 -05:00
100ddef930
Fix typo in VariantContextBuilder
2012-02-27 17:06:45 -05:00
ca0931c01f
Adding test for reading samtools VCF file
2012-02-27 17:05:50 -05:00
bd944ab04f
Another test where we no longer print out 'NaN' for the AF.
2012-02-27 15:19:08 -05:00
5f7ccdcc01
Avoid calling getBasePileup when there's no pileup in NBaseCount annotation
2012-02-27 15:12:25 -05:00
52871187d7
Adding integration test for file with no GTs. Also updated md5 for one other test (since we no longer print out 'NaN' for the AF).
2012-02-27 15:09:56 -05:00
729bb954e2
Throws ReviewedStingException for a bug when parent VariantContext argument is null
2012-02-27 15:09:00 -05:00
998ed8fff3
Bug fix to deal with VCF records that don't have GTs. While in there, optimized a bunch of related functions (including removing a copy of the method calculateChromosomeCounts(); why did we have 2 copies? very dangerous).
2012-02-27 14:56:10 -05:00
4d9582de77
More general catching of Exceptions in interval reading to throw MalformedFile exception in all cases
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-- Now throws UserException no matter what happens during the reading of the intervals file.
2012-02-27 14:02:26 -05:00
9712fed7a5
Trap SAMFormatException and rethrow as MalformatedBAM exception
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-- Trap errors in header and rethrow
-- Wrap underlying iterator in MalformatedBAMErrorReformattingIterator
2012-02-27 13:52:50 -05:00
1ea34058c2
Updating integration tests now that standard annotations support multiple alleles
2012-02-27 11:32:26 -05:00
64754e7870
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-02-27 11:31:41 -05:00
850c5d0db2
Enabling Rank Sum Tests for multi-allelics: use ref vs any alt allele.
2012-02-27 09:59:36 -05:00
dfdf4f989b
Enabling Fisher Strand for multi-allelics: use the alt allele with max AC. Added minor optimization to the method in the VC.
2012-02-27 09:50:09 -05:00
16122bea8d
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-02-25 13:57:54 -05:00
dea35943d1
a) Bug fix in calling new functions that give indel bases and length from regular pileup in LocusIteratorByState, b) Added unit test to cover these.
2012-02-25 13:57:28 -05:00
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
c9a4c74f7a
a) Bug fixes for last commit related to PileupElements (unit tests are forthcoming). b) Changes needed to make pool caller work in GENOTYPE_GIVEN_ALLELES mode c) Bug fix (yet again) for UG when GENOTYPE_GIVEN_ALLELES and EMIT_ALL_SITES are on, when there's no coverage at site and when input vcf has genotypes: output vcf would still inherit genotypes from input vcf. Now, we just build vc from scratch instead of initializing from input vc. We just take location and alleles from vc
2012-02-24 10:27:59 -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
6866a41914
Added functionality in pileups to not only determine whether there's an insertion or deletion following the current position, but to also get the indel length and involved bases - definitely needed for extended event removal, and needed for pool caller indel functionality.
2012-02-23 09:45:47 -05:00
d34f07dba0
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-02-22 20:41:03 -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
75783af6fc
int <-> BitSet conversion utils for MathUtils
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* added unit tests.
2012-02-21 14:10:36 -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
Ryan Poplin
Guillermo del Angel
Mark DePristo
Eric Banks
Mauricio Carneiro
Khalid Shakir
Christopher Hartl