asivache 2f29cf59ba Very early, half-baked version. All it can do right now is to take two SAM files with end1 and end2 individual single-end alignmnets from a pair-end run and spit out a "paired" BAM file that contains ONLY properly paired ends (both ends align uniquely && both ends align to the same chromosome && the ends align in proper orientation). Insert size is currently not used (and not set in the output). Unpaired/unmapped reads are NOT transferred into the output bam. For the pairs that do get written, the output is (should be) standard-conforming: all flags are properly set and mate pair information is correct. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1637 348d0f76-0448-11de-a6fe-93d51630548a		2009-09-16 18:38:18 +00:00
..
bwa	Proof-of-concept perfect read aligner, implemented as described in sec 2.4 of BWA paper. Has successfully aligned a handful of reads. Requires significant cleanup and refactoring.	2009-09-14 21:54:56 +00:00
gatk	By default, VF should ask for deleted bases so that they show up in coverage.	2009-09-16 16:46:09 +00:00
playground	Very early, half-baked version. All it can do right now is to take two SAM files with end1 and end2 individual single-end alignmnets from a pair-end run and spit out a "paired" BAM file that contains ONLY properly paired ends (both ends align uniquely && both ends align to the same chromosome && the ends align in proper orientation). Insert size is currently not used (and not set in the output). Unpaired/unmapped reads are NOT transferred into the output bam. For the pairs that do get written, the output is (should be) standard-conforming: all flags are properly set and mate pair information is correct.	2009-09-16 18:38:18 +00:00
secondarybase	Cleanup...deprecate FastaSequenceFile2 in favor of IndexedFastaSequenceFile or ReferenceSequenceFile from Picard, depending on the application.	2009-07-08 18:49:08 +00:00
utils	-deal with offsets that can be -1	2009-09-16 16:44:57 +00:00