gatk-3.8

Commit Graph

Author	SHA1	Message	Date
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
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
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

Author

SHA1

Message

Date

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

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

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

3 Commits (09686f4595b517a29a3feac6a59b9fe1c947ba9d)