b7b57ef39a
Updating MD5 to reflect canonical ordering of calculation
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-- We should no longer have md5s changing because of hashmaps changing their sort order on us
-- Added GenotypeLikelihoodsUnitTests
-- Refactored ExactAFCaclculation to put the PL -> QUAL calculation in the GenotypeLikelihoods class to avoid the code copy.
2011-11-19 15:57:33 -05:00
73119c8e3c
Merge with master
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-- A few bug fixes
2011-11-19 09:56:06 -05:00
f685fff79b
Killing the final versions of old new VariantContext interface
2011-11-18 21:32:43 -05:00
6cf315e17b
Change interface to getNegLog10PError to getLog10PError
2011-11-18 21:07:30 -05:00
c7f2d5c7c7
Final minor fix to contract
2011-11-18 19:40:05 -05:00
b5de182014
isEmpty now checks if mReadBases is null
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Since newly created reads have mReadBases == null. This is an effort to centralize the place to check for empty GATKSAMRecords.
2011-11-18 18:34:05 -05:00
8ab3ee9c65
Merge remote-tracking branch 'unstable/master' into rr
2011-11-18 16:50:25 -05:00
333e5de812
returning read instead of GATKSAMRecord
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Do not create new GATKSAMRecord when read has been fully clipped, because it is essentially the same as returning the currently fully clipped read.
2011-11-18 16:49:59 -05:00
8bb4d4dca3
First pass of the asynchronous block loader.
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Block loads are only triggered on queue empty at this point. Disabled by
default (enable with nt:io=?).
2011-11-18 15:02:59 -05:00
a2e79fbe8a
Fixes to contracts
2011-11-18 14:18:53 -05:00
660d6009a2
Documentation and contracts for GenotypesContext and VariantContextBuilder
2011-11-18 13:59:30 -05:00
f54afc19b4
VariantContextBuilder
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-- New approach to making VariantContexts modeled on StringBuilder
-- No more modify routines -- use VariantContextBuilder
-- Renamed isPolymorphic to isPolymorphicInSamples. Same for mono
-- getChromosomeCount -> getCalledChrCount
-- Walkers changed to use new VariantContext. Some deprecated new VariantContext calls remain
-- VCFCodec now uses optimized cached information to create GenotypesContext.
2011-11-18 12:39:10 -05:00
6459784351
Merged bug fix from Stable into Unstable
2011-11-18 12:34:57 -05:00
c62082ba1b
Making this class public again as per request from Cancer folks
2011-11-18 12:34:27 -05:00
8710673a97
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-18 12:29:33 -05:00
768b27322b
I figured out why we were getting tons of hom var genotype calls with Mauricio's low quality (synthetic) reduced reads: the RR implementation in the UG was not capping the base quality by the mapping quality, so all the low quality reads were used to generate GLs. Fixed.
2011-11-18 12:29:15 -05:00
7490dbb6eb
First version of VariantContextBuilder
2011-11-18 11:06:15 -05:00
f48d4cfa79
Bug fix: fully clipping GATKSAMRecords and flushing ops
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Reads that are emptied after clipping become new GATKSAMRecords.
When applying ClippingOps, the ops are cleared after the clipping
2011-11-18 00:24:39 -05:00
fa454c88bb
UnitTests for VariantContext for chrCount, getSampleNames, Order function
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-- Major change to how chromosomeCounts is computed. Now NO_CALL alleles are always excluded. So ChromosomeCounts(A/.) is 1, the previous result would have been 2.
-- Naming changes for getSamplesNameInOrder()
2011-11-17 20:37:22 -05:00
02f22cc9f8
No more VC integration tests. All tests are now unit tests
2011-11-17 15:33:09 -05:00
23359d1c6c
Bugfix for pruneVariantContext, which was dropping the ref base for padding
2011-11-17 15:32:52 -05:00
473b860312
Major determinism fix for UG and RankSumTest
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-- Now these routines all iterate in sample name order (genotypes.iterateInSampleNameOrder) so that the results of UG and the annotator do not depend on the particular order of samples we see for the exact model and the RankSumTest
2011-11-17 15:31:45 -05:00
c50274e02e
During flanking interval creation merging overlapping flanks so that on scatter the list doesn't accidentally genotype the same site twice.
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Moved flanking interval utilies to IntervalUtils with UnitTests.
2011-11-17 13:56:42 -05:00
bad19779b9
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-17 13:29:43 -05:00
16a021992b
Updated header description for the INFO and FORMAT DP fields to be more accurate.
2011-11-17 13:17:53 -05:00
e7d41d8d33
Minor cleanup
2011-11-17 12:00:28 -05:00
7e66677769
Expanded UnitTests for VariantContext
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Tests for
-- getGenotype and getGenotypes
-- subContextBySample
-- modify routines
2011-11-16 20:45:15 -05:00
72f00e2883
Merging Roger's Unit tests for Reduce Reads from RR repository
2011-11-16 17:26:49 -05:00
aa0610ea92
GenotypeCollection renamed to GenotypesContext
2011-11-16 16:24:05 -05:00
974daaca4d
V13 version in archive. Can you pulled out wholesale for performance testing
2011-11-16 16:08:46 -05:00
caf6080402
Better algorithm for merging genotypes in CombineVariants
2011-11-16 15:17:33 -05:00
101ffc4dfd
Expanded, contrastive VariantContextBenchmark
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-- Compares performance across a bunch of common operations with GATK 1.3 version of VariantContext and GATK 1.4
-- 1.3 VC and associated utilities copied wholesale into test directory under v13
2011-11-16 13:35:16 -05:00
e56d52006a
Continuing bugfixes to get new VC working
2011-11-16 10:39:17 -05:00
eb8e031f75
Merged bug fix from Stable into Unstable
2011-11-16 09:57:37 -05:00
6a5d5e7ac9
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/stable
2011-11-16 09:57:13 -05:00
7ac5cf8430
Getting rid of unsupported CountReadPairs walker in stable. Removal of
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remainder of pairs processing framework to follow in unstable.
2011-11-16 09:53:59 -05:00
c2ebe58712
Merge remote-tracking branch 'Laurent/master'
2011-11-16 09:34:47 -05:00
7d77fc51f5
Corrected bug causing PhaseByTransmission to crash in case of new Genotype.Type
2011-11-16 03:32:43 -05:00
0d163e3f52
SnpEff 2.0.4 support
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-Modified the SnpEff parser to work with the SnpEff 2.0.4 VCF output format
-Assigning functional classes and effect impacts now handled directly
by SnpEff rather than the GATK
-Removed support for SnpEff 2.0.2, as we no longer trust the output of that
version since it doesn't exclude effects associated with certain nonsensical
transcripts. These effects are excluded as of 2.0.4.
-Updated unit and integration tests
This support is based on a *release-candidate* of SnpEff 2.0.4, and so is subject
to change between now and the next GATK release.
2011-11-15 18:36:22 -05:00
df415da4ab
More bug fixes on the way to passing all tests
2011-11-15 17:38:12 -05:00
0be23aae4e
Bugfixes on way to a working refactored VariantContext
2011-11-15 17:20:14 -05:00
231c47c039
Bugfixes on way to a working refactored VariantContext
2011-11-15 16:42:50 -05:00
fb685f88ec
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-15 16:23:53 -05:00
2b2514dad2
Moved many unused phasing walkers and utilities to archive
2011-11-15 16:14:50 -05:00
460a51f473
ID field now stored in the VariantContext itself, not the attributes
2011-11-15 14:56:33 -05:00
7fada320a9
The right fix for this test is just to delete it.
2011-11-15 14:53:27 -05:00
b45d10e6f1
The DP in the FORMAT field (per sample) must also use the representative count or else it's always 1 for reduced reads.
2011-11-15 10:23:59 -05:00
233e581828
Merging in Master
2011-11-15 09:28:24 -05:00
b66556f4a0
Update error message so that it's clear ReadPair Walkers are exceptions
2011-11-15 09:22:57 -05:00
6e1a86bc3e
Bug fixes to VariantContext and GenotypeCollection
2011-11-15 09:21:30 -05:00
284430d61d
Added more basic UnitTests for ReadClipper
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hardClipByReadCoordinatesWorks
hardClipLowQualTailsWorks
2011-11-15 00:13:52 -05:00
8e91e19229
Merge branch 'master' of ssh://nickel/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-15 00:13:37 -05:00
cde829899d
compress Reduce Read counts bytes by offset
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compressed the representation of the reduce reads counts by offset results in 17% average compression in final BAM file size.
Example compression -->
from : 10, 10, 11, 11, 12, 12, 12, 11, 10
to: 10, 0, 1, 1,2, 2, 2, 1, 0
2011-11-14 18:30:24 -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
ab0ee9b847
Perform only necessary validation in VariantContext modify methods
2011-11-14 16:49:59 -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
1347beef40
Merge branch 'PhaseByTransmission'
2011-11-14 11:31:28 +01:00
6881d4800c
Added Integration tests for Phasing by Transmission
2011-11-14 10:47:51 +01:00
34acf8b978
Added Unit tests for new methods in GenotypeLikelihoods
2011-11-14 10:47:02 +01:00
1202a809cb
Added Basic Unit Tests for ReadClipper
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Tests some but not all functions
Some tests have been disabled because they are not working
2011-11-13 22:27:49 -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
Mark DePristo
Mauricio Carneiro
Matt Hanna
Eric Banks
Roger Zurawicki
Khalid Shakir
Laurent Francioli
David Roazen
Guillermo del Angel
Ryan Poplin