92c7cfa1c8
BWA bindings and tests moved to public (was required for ValidationAmplicons)
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Integration tests for ValidationAmplicons. New argument to disable BWA, lowercase letters only for repetitiveness instead.
2011-07-19 20:11:31 -04:00
07e716d23a
PickSequenomProbes2 expanded functionality: lowercasing based on sequence uniqueness, preserving reference base prior to indel (not a part of the VC as I thought it was), masking deletion bases with 'N's, flanking insertion with 'N's, output is a fasta formatted file. Renamed to ValidationAmplicons since this is really not for picking sequenom probes, but for generating amplicon sequence from which other applications (like sequenom) can choose PCR primers. Moved from private to public.
2011-07-19 15:21:47 -04:00
837fb8f689
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-12 15:39:26 -04:00
5077c94d85
Adding MappingQualityUnavailableReadFilter to the SNP and indel CountCovariates
2011-07-12 15:39:07 -04:00
01fd6a6949
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-12 15:20:44 -04:00
ccedd6ff4c
Difference is now the general form -- used to be SummarizedDifference. The old Difference class is now a subclass of Difference that includes pointers to specific the master and test DiffElements.
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Added a size() function that calculates the number of elements tree from a DiffElement.
2011-07-12 15:20:28 -04:00
a2597e7f00
This commit incorporates several different changes that each pretty much break all the VCF-based integration tests, so I bunched them all together. We now officially emit VCF4.1 files (woo hoo), which means that the VCF headers are now all different (header version is 4.1 plus counts for some of the annotations are 'A' or 'G'). Also, I've added a Read Filter for reads with MQ=255 ('unavailable' in the SAM spec) and have applied this to the UG and the RMS MQ annotation.
2011-07-12 14:11:53 -04:00
329c3d8050
Merged bug fix from Stable into Unstable
2011-07-12 13:55:51 -04:00
73735863b0
Fix for the case of requesting genotype for a sample that doesn't exist in a VariantContext
2011-07-12 13:55:21 -04:00
c4c145afb9
Merged bug fix from Stable into Unstable
2011-07-12 13:44:48 -04:00
cfe43e3971
Bug fix for Genotype given alleles: if we are in INDEL mode ignore SNPs and MNPs instead of emitting an empty site with alleles but no annotations
2011-07-12 13:43:46 -04:00
05212aea62
reader now takes an argument for the maximum number of elements to read from the file.
2011-07-12 08:53:19 -04:00
8056a3fe89
getElement() now uses O(1) get from hash instead of linear O(n) search. Enables us to read large files easily.
2011-07-12 08:52:31 -04:00
f313e14e4e
Now deletes the dump directory on ant clean
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Moving diffengine tests from private to public
2011-07-12 08:50:58 -04:00
d7d15019dd
Adding support for other simple header line types (e.g. ALT) and cleaning up the interface a bit.
2011-07-12 01:16:21 -04:00
400b0d4422
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-11 23:38:57 -04:00
d5056ad899
Merge branch 'master' into diffit
2011-07-11 23:16:15 -04:00
893cc2e103
Making the package public, so there's no dependances from public -> private
2011-07-11 23:15:08 -04:00
5e593793af
DiffEngine utility function simpleDiffFiles
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printSummaryReport now uses GATKReport for nice formating
Moved print formatting arguments into inner class provided to printing functions themselves, not the class
BAMDiffableReader only reads 1000 entries to avoid performance issue. Work around for BAM files with non-unique names
Uncommented all of the incorrectly commented out CombineVariants integrationtests
BaseTest now uses DiffEngine to provide inline differences to VCF and BAM files
2011-07-11 23:10:27 -04:00
e3748675db
Support for VCF 4.1 header counts
2011-07-11 17:40:45 -04:00
d6517adb42
Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-11 16:16:37 -04:00
86890c6357
N and K (in binomial probability) got switched in RFA Walker with the last commit. No longer will NaNs be produced.
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Added: TableToVCF. Kind of a longer-term project, but there are lots of variant calls available in a weird tabular format. I used this to convert Ju Et Al small indels to VCF. I'll check against the 1000G ASN superpopulation calls to see if we see a good amount of recapitulation, and if so, i'll put them in unvalidated comparisons. Minor chances to the TableCodec and TableFeatures to allow for this (the codec can sometimes drop a column, and the feature now allows you to grab on to its header).
2011-07-11 16:16:15 -04:00
6e7b5e1e7a
Merged bug fix from Stable into Unstable
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Merge branch 'master' into unstable
2011-07-08 21:19:45 -04:00
7fbc5987d0
Merge branch 'master' of ssh://delangel@nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-07-08 21:17:32 -04:00
bd29236684
Merge branch 'master' into diffengine
2011-07-08 14:08:17 -04:00
224574424e
Bug fix: if we're genotyping a very long indel (>100 bp) fail gracefully instead of with an array out of bounds exception
2011-07-08 12:48:49 -04:00
2a4b3ae4a2
Cleaning up / removing most of the monkeying around with annotation values that happens in VariantDataManager
2011-07-08 12:48:33 -04:00
8add2a3866
Merge branch 'master' into diffengine
2011-07-08 09:15:54 -04:00
cc143493e3
Merged bug fix from Stable into Unstable
2011-07-07 23:01:24 -04:00
4cfe0dd857
Test for bad alleles so that we don't generate IndexOutOfBoundsExceptions
2011-07-07 23:01:03 -04:00
3d4f0e9dd7
Now supports the case where you have multiple AC values in the info field.
2011-07-07 17:21:15 -04:00
212e9a1a0c
Fixing unstable build after stable commit
2011-07-07 15:18:57 -04:00
11d9a0473a
Merged bug fix from Stable into Unstable
2011-07-07 15:03:58 -04:00
50111db2b7
Fixing non-determinism in single-threaded VQSR by moving references to cern.Normal over to the static random generator available in GenomeAnalysisEngine
2011-07-07 15:02:48 -04:00
ccf34f7e45
(1) Added very useful helper class TestDataProvider to BaseTest that making creating data providers for TestNG far easier
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(2) DiffEngine now officially working with with summaries. Extensive UnitTests all around!
2011-07-06 21:57:22 -04:00
52f6f9fdcc
Merged bug fix from Stable into Unstable
2011-07-06 16:05:48 -04:00
54121eb082
Catch malformed bams that cause the writer to run in infinite loops
2011-07-06 16:05:08 -04:00
76a01a7453
Merged bug fix from Stable into Unstable
2011-07-06 12:53:09 -04:00
14fee4ccbd
Patch from Bob to deal with symbolic alleles: these weren't getting padded but they should be.
2011-07-06 12:51:44 -04:00
bdef233d4d
Merged bug fix from Stable into Unstable
2011-07-06 10:05:02 -04:00
e8ed6b7f0f
Adding more comments to main VQSR walker. Fixing copyright lines. Bug fix for default paths to now point to public/R/ instead of R/ Bug fix in VQSR for the path to the R scripts not ending in a slash.
2011-07-06 10:01:14 -04:00
8e8b901d12
Merged bug fix from Stable into Unstable
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Merge branch 'master' into unstable
2011-07-06 09:57:55 -04:00
81a4d18468
Mark several indel-related arguments as @Hidden
2011-07-06 09:56:38 -04:00
fb315b5f8c
Merge branch 'incoming'
2011-07-02 18:10:48 -04:00
41d46059e7
fixing bad format statement
2011-07-02 18:09:17 -04:00
3804afeb8a
Merge branch 'incoming'
2011-07-02 17:55:39 -04:00
781c0c33a4
Use the worst X% of calls in addition to the bad training sites list. Don't include the already added calls in the calculation of X%
2011-07-02 17:55:10 -04:00
6b8af6afd8
Merge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-02 17:15:56 -04:00
fdc2ebb321
Adding ability to specify in VQSR a list of bad sites to use when training the negative model. Just add bad=true to the list of rod tags for your bad sites track.
2011-07-02 17:15:13 -04:00
09af6bbc6c
Ugh - backed out experimental code not for public consumption unintendedly committed
2011-07-02 16:58:57 -04:00
Christopher Hartl
Ryan Poplin
Mark DePristo
Eric Banks
Guillermo del Angel