hanna 2953c9f069 Efficiency improvement requested by the Picard team in IndexedFastaSequenceFile: improve the memory efficiency ... (and loading time) of long reference sequences by better controlling the input buffer size. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3665 348d0f76-0448-11de-a6fe-93d51630548a		2010-06-29 07:22:07 +00:00
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ArtificialFastaUtils.java	made a fake fasta generator, so we can now generate a complete bam / fasta combo of made up data.	2009-07-01 21:35:34 +00:00
FastaSequenceIndex.java	Adding new support for reference data. ReferenceDataSource is a new class that manages reference data, and allows IndexedFastaSequenceFile to be a simple reader. This checkin also includes FastaSequenceIndexBuilder, which reads a fasta file and creates an index, like samtools faidx. Right now this is not enabled, because we are still working out thread safety. So the only new UI change is that GATK can be run without a fai file. Soon, we will enable 1) GATK to be run without a dict file too, and 2) both dict and fai files will be saved on disk for future program executions. For more info, see ReferenceDataSource.java	2010-06-10 20:10:23 +00:00
FastaSequenceIndexBuilder.java	Updating the way reference data is processed, so GATK creates the .fasta.fai and .dict files automatically. If either (or both) don't exist, GATK will create them in the same folder as the fasta file. If it can't write the file, GATK will fail with a message to create them manually.	2010-06-21 21:42:42 +00:00
IndexedFastaSequenceFile.java	Efficiency improvement requested by the Picard team in IndexedFastaSequenceFile: improve the memory efficiency	2010-06-29 07:22:07 +00:00
package-info.java	Put a major.minor version into the GATK Javadoc for reading. Also,	2010-01-15 21:48:30 +00:00