depristo 52ad08298a New FastaSequenceFile with support for poor-man's seek and querying the next contig name without loading the whole next contig into memory. Vastly speeds up the performance of jumping to distant parts of the genome with the location operator. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@137 348d0f76-0448-11de-a6fe-93d51630548a		2009-03-22 19:43:56 +00:00
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gatk	Now works on single samples and computes metrics.	2009-03-22 15:45:12 +00:00
illumina	Added a directory to house some Illumina output parsers. Hopefully this will be merged back into Picard at some point.	2009-03-21 17:55:56 +00:00
indels	Henious bug fixed: only rookies forget that external conditions need to be re-checked after loop ends on some other condition, duh! In addition, msa piles are now seeded with a single read sequence each (if there are less then 4 reads it might be hard to seed with two pairs)	2009-03-21 18:32:18 +00:00
projects/fourbasecaller	Java version of basecaller that estimates probability distribution over four-base hypothesis space via an internal-control-initialized Gaussian mixture model over base channel intensities.	2009-03-21 17:58:50 +00:00
utils	New FastaSequenceFile with support for poor-man's seek and querying the next contig name without loading the whole next contig into memory. Vastly speeds up the performance of jumping to distant parts of the genome with the location operator.	2009-03-22 19:43:56 +00:00
ValidateSAM.java	optionally check that the records are sorted.	2009-03-22 15:36:24 +00:00