Eric Banks 666862af19 Added @Hidden option for GSA production use to cap the max alleles for indels at a lower number than for SNPs		2012-05-21 16:03:29 -04:00
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alignment	At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings.	2012-01-17 14:47:53 -05:00
analyzecovariates	Active Region Traversal should use GATKSAMRecords everywhere instead of SAMRecords. misc cleanup.	2012-02-03 17:13:52 -05:00
commandline	Rev Tribble to r97, adding binary feature support	2012-05-03 07:31:48 -04:00
gatk	Added @Hidden option for GSA production use to cap the max alleles for indels at a lower number than for SNPs	2012-05-21 16:03:29 -04:00
jna	Device files like /dev/null are now tracked as special by Queue and are not used to generate .out file paths, scattered into a temporary directory, gathered, deleted, etc.	2012-01-23 16:17:04 -05:00
queue	Refactoring/fixing up UG HMM code: a) Make code use PairHMM class instead of having duplicated code. That way UG and HaplotypeCaller now use same core code. Changes to be able to do this: 1. Compute context-dependent GOP as a function of read, not of haplotype, b) Extracted code to initialize HMM arrays into separate method, c) Move PairHMM class and unit test to public, d) Reenable banded code in PairHMM, inverted sense of flag (true=enable feature) but leave off in HaplotypeCaller.	2012-04-17 14:22:48 -04:00
utils	Removed old GATKReport code and moved the new stuff in its place.	2012-05-18 01:44:31 -04:00