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13 Commits (8c18ead5e42aaebb9dd6bd9cd2a97be8c3de5567)

Author SHA1 Message Date
Geraldine Van der Auwera 697c4b0cf1 Added else clause to handle symbolic alleles 
Add test for createAlleleMapping
 2015-06-17 10:52:56 -04:00
David Roazen caafe84e74 Rev htsjdk to version 1.132 and picard to version 1.131, and switch to using the versions in maven central 
-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
Ron Levine d5f98e99f0 Bypass reads with a bad CIGAR length 2015-04-21 11:55:56 -04:00
rpoplin b8b23b931e Merge pull request #807 from broadinstitute/rhl_handle_cigar 
Process X and = CIGAR operators
 2015-02-01 11:09:52 -05:00
Phillip Dexheimer 3354c07b1c Added optional element "includeUnmapped" to the PartitionBy annotation 
* The value of this element (default true) determines whether Queue will explicitly run this walker over unmapped reads
 * This patch fixes a runtime error when FindCoveredIntervals was used with Queue
 * PT 81777160
 2015-01-31 15:47:57 -05:00
Ron Levine 9d4b876ccd Process X and = CIGAR operators 
Add simple BaseRecalibrator integration test for CIGAR = and X operators
 2015-01-29 17:00:00 -05:00
Khalid Shakir 1808c90d2a Added introductory CRAM support. 
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
Phillip Dexheimer 6190d660e0 Edits to work with the latest htsjdk release: 
* 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
Ron Levine 069398ad46 Added more tests and documentation 2014-12-19 12:57:43 -05:00
Valentin Ruano-Rubio c5977e5c8f Correct wrong left-alignment of reads in HC bamout 
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
Khalid Shakir 8b81031bf8 Disabling tests for Lsf706 specific functionality. 2014-11-04 01:31:18 +08:00
Khalid Shakir 5c9fe1a06d Split all imports of tools|engine from utils, and all tools from engine. 
Second of two commits, modifying actual files.
 2014-10-24 20:59:46 +08:00
Khalid Shakir bb7151192a Split all imports of tools|engine from utils, and all tools from engine. 
First of two commits, renaming files only.
 2014-10-24 20:59:45 +08:00