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depristo 59083a47d5 Initial Analysis toolkit 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-02-26 21:50:29 +00:00
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apps Initial Analysis toolkit 2009-02-26 21:50:29 +00:00
util Initial Analysis toolkit 2009-02-26 21:50:29 +00:00
AlignmentBlock.java Initial Analysis toolkit 2009-02-26 21:50:29 +00:00
BAMFileConstants.java Initial Analysis toolkit 2009-02-26 21:50:29 +00:00
BAMFileIndex.java Initial Analysis toolkit 2009-02-26 21:50:29 +00:00
BAMFileReader.java Initial Analysis toolkit 2009-02-26 21:50:29 +00:00
BAMFileWriter.java Initial Analysis toolkit 2009-02-26 21:50:29 +00:00
BAMRecord.java Initial Analysis toolkit 2009-02-26 21:50:29 +00:00
BAMRecordCodec.java Initial Analysis toolkit 2009-02-26 21:50:29 +00:00
BinaryCigarCodec.java Initial Analysis toolkit 2009-02-26 21:50:29 +00:00
BinaryTagCodec.java Initial Analysis toolkit 2009-02-26 21:50:29 +00:00
Cigar.java Initial Analysis toolkit 2009-02-26 21:50:29 +00:00
CigarElement.java Initial Analysis toolkit 2009-02-26 21:50:29 +00:00
CigarOperator.java Initial Analysis toolkit 2009-02-26 21:50:29 +00:00
NotPrimarySkippingIterator.java Initial Analysis toolkit 2009-02-26 21:50:29 +00:00
SAMFileHeader.java Initial Analysis toolkit 2009-02-26 21:50:29 +00:00
SAMFileReader.java Initial Analysis toolkit 2009-02-26 21:50:29 +00:00
SAMFileWriter.java Initial Analysis toolkit 2009-02-26 21:50:29 +00:00
SAMFileWriterFactory.java Initial Analysis toolkit 2009-02-26 21:50:29 +00:00
SAMFileWriterImpl.java Initial Analysis toolkit 2009-02-26 21:50:29 +00:00
SAMFormatException.java Initial Analysis toolkit 2009-02-26 21:50:29 +00:00
SAMLocusIterator.java Initial Analysis toolkit 2009-02-26 21:50:29 +00:00
SAMProgramRecord.java Initial Analysis toolkit 2009-02-26 21:50:29 +00:00
SAMReadGroupRecord.java Initial Analysis toolkit 2009-02-26 21:50:29 +00:00
SAMRecord.java Initial Analysis toolkit 2009-02-26 21:50:29 +00:00
SAMRecordComparator.java Initial Analysis toolkit 2009-02-26 21:50:29 +00:00
SAMRecordCoordinateComparator.java Initial Analysis toolkit 2009-02-26 21:50:29 +00:00
SAMRecordQueryNameComparator.java Initial Analysis toolkit 2009-02-26 21:50:29 +00:00
SAMRecordSetBuilder.java Initial Analysis toolkit 2009-02-26 21:50:29 +00:00
SAMSequenceRecord.java Initial Analysis toolkit 2009-02-26 21:50:29 +00:00
SAMTag.java Initial Analysis toolkit 2009-02-26 21:50:29 +00:00
SAMTextHeaderCodec.java Initial Analysis toolkit 2009-02-26 21:50:29 +00:00
SAMTextReader.java Initial Analysis toolkit 2009-02-26 21:50:29 +00:00
SAMTextWriter.java Initial Analysis toolkit 2009-02-26 21:50:29 +00:00
SAMTools.java Initial Analysis toolkit 2009-02-26 21:50:29 +00:00
SAMUtils.java Initial Analysis toolkit 2009-02-26 21:50:29 +00:00
TextCigarCodec.java Initial Analysis toolkit 2009-02-26 21:50:29 +00:00
TextTagCodec.java Initial Analysis toolkit 2009-02-26 21:50:29 +00:00