2bcded11cb
VariantAnnotator checks alleles when annotationg with external resource
2015-10-08 17:01:30 -04:00
0dacf60012
Changed calls for RGQ=0 from 0/0 to ./. in output of GenotypeGVCFs.
2015-09-23 15:35:09 -04:00
5f76ae6a37
Don't have the Indel Realigner change IUPAC reference bases.
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This change doesn't affect the performance of the Indel Realigner at all (as per tests).
This is just a request from the Picard side (where further testing is happening).
2015-09-04 13:42:23 -04:00
2afe3f7a21
Make GenotypeGVCFs subset Strand Allele Counts intelligently
2015-08-22 08:33:09 -04:00
158477ea6c
Re-ran the updateAllLicenses.sh script
2015-08-21 11:32:51 -04:00
beec624a63
Move htsjdk & picard to rev 1.138
2015-08-20 10:42:25 -04:00
19bbe45cbc
Updated licenses for 2015
2015-08-06 15:23:11 -04:00
697c4b0cf1
Added else clause to handle symbolic alleles
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Add test for createAlleleMapping
2015-06-17 10:52:56 -04:00
caafe84e74
Rev htsjdk to version 1.132 and picard to version 1.131, and switch to using the versions in maven central
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-We now pull htsjdk and picard from maven central.
-Updated the GATK codebase as necessary to adapt to changes in the Feature
interface.
-Since VCFHeader now requires that all header lines have unique keys, uniquified
the keys of GVCFBlock header lines by including the min/max GQ in the key.
Updated MD5s accordingly.
-Other MD5s changed as a result of an htsjdk fix to eliminate "-0" in VCF output.
2015-05-14 15:26:23 -04:00
d5f98e99f0
Bypass reads with a bad CIGAR length
2015-04-21 11:55:56 -04:00
b8b23b931e
Merge pull request #807 from broadinstitute/rhl_handle_cigar
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Process X and = CIGAR operators
2015-02-01 11:09:52 -05:00
9d4b876ccd
Process X and = CIGAR operators
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Add simple BaseRecalibrator integration test for CIGAR = and X operators
2015-01-29 17:00:00 -05:00
1808c90d2a
Added introductory CRAM support.
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Replaced usage of GATKSamRecordFactory with calls to wrapper GATKSAMRecord extending SAMRecord.
Minor other updates for test changes.
Added exampleCRAM.cram generated by GATK, with .bai and .crai indexes generated by CRAMTools.
CRAM-to-CRAM test disabled due to https://github.com/samtools/htsjdk/issues/148
Using exampleBAM.bam input, outputs of GATK's generated CRAM match CRAMTools generated CRAM, but not samtools/PrintReads SAM output, as things like insert sizes are different.
If required for other tools, CRAM indexes must be generated via CRAMTools until we can generate them via CRAMFileWriter.
Generation of exampleCRAM.cram:
* java -jar target/executable/GenomeAnalysisTK.jar -T PrintReads -R public/gatk-utils/src/test/resources/exampleFASTA.fasta -I public/gatk-utils/src/test/resources/exampleBAM.bam -o public/gatk-utils/src/test/resources/exampleCRAM.cram
* java -jar cramtools-2.1.jar index -I public/gatk-utils/src/test/resources/exampleCRAM.cram
* java -jar cramtools-2.1.jar index -I public/gatk-utils/src/test/resources/exampleCRAM.cram --bam-style-index
CRAM generation by existing tools:
* samtools view -C -T public/gatk-utils/src/test/resources/exampleFASTA.fasta -o testSamtools.cram public/gatk-utils/src/test/resources/exampleBAM.bam
* java -jar cramtools-2.1.jar cram --ignore-md5-mismatch --capture-all-tags -Q -n -R public/gatk-utils/src/test/resources/exampleFASTA.fasta -I public/gatk-utils/src/test/resources/exampleBAM.bam -O testCRAMTools.cram
* java -jar target/executable/GenomeAnalysisTK.jar -T PrintReads -R public/gatk-utils/src/test/resources/exampleFASTA.fasta -I public/gatk-utils/src/test/resources/exampleBAM.bam -o testGATK.cram
CRAMTools view of the above:
* java -jar cramtools-2.1.jar bam --skip-md5-check -R public/gatk-utils/src/test/resources/exampleFASTA.fasta -I public/gatk-utils/src/test/resources/exampleCRAM.cram | tail -n 1
* java -jar cramtools-2.1.jar bam --skip-md5-check -R public/gatk-utils/src/test/resources/exampleFASTA.fasta -I testSamtools.cram | tail -n 1
* java -jar cramtools-2.1.jar bam --skip-md5-check -R public/gatk-utils/src/test/resources/exampleFASTA.fasta -I testCRAMTools.cram | tail -n 1
* java -jar cramtools-2.1.jar bam --skip-md5-check -R public/gatk-utils/src/test/resources/exampleFASTA.fasta -I testGATK.cram | tail -n 1
2015-01-26 14:47:39 -03:00
6190d660e0
Edits to work with the latest htsjdk release:
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* TextCigarCodec.decode() is now static, and the getSingleton() method is gone
* MergingSamRecordIterator now wants a Collection<SamReader> rather than Collection<SAMFileReader> in the constructor
* SeekableBufferedStream now correctly reads the requested number of bytes, removed workaround in GATKBAMIndex
2015-01-13 21:32:10 -05:00
069398ad46
Added more tests and documentation
2014-12-19 12:57:43 -05:00
c5977e5c8f
Correct wrong left-alignment of reads in HC bamout
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Story:
-----
https://www.pivotaltracker.com/story/show/80684230
Changes:
-------
- Corrected the bug: AlignmentUtils#createReadAlignedToRef was
not realigning against the reference but the best haplotype for
the read.
Test:
----
- Added integration test in HaplotypeCallerIntegrationTest to check
that the bug has been fixed.
- Fixed md5s modified by this change; these are cause due to small
changes in the state of the random-number generator and read vs
variant site overlapping.
2014-11-10 10:09:58 -05:00
8b81031bf8
Disabling tests for Lsf706 specific functionality.
2014-11-04 01:31:18 +08:00
5c9fe1a06d
Split all imports of tools|engine from utils, and all tools from engine.
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Second of two commits, modifying actual files.
2014-10-24 20:59:46 +08:00
bb7151192a
Split all imports of tools|engine from utils, and all tools from engine.
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First of two commits, renaming files only.
2014-10-24 20:59:45 +08:00
Ron Levine
Samuel Lee
Eric Banks
Bertrand Haas
Geraldine Van der Auwera
David Roazen
rpoplin
Khalid Shakir
Phillip Dexheimer
Valentin Ruano-Rubio