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
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main/java/org/mycompany/app	Split all imports of tools|engine from utils, and all tools from engine.	2014-10-24 20:59:46 +08:00
test/java/org/mycompany/app	Added introductory CRAM support.	2015-01-26 14:47:39 -03:00