gatk-3.8

gatk3的最后一个经典版本3.8

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Mark DePristo dc292c0317 FisherStrand now includes all reads and bases, regardless of mapping quality and base quality, just like other annotations -- This actually proved to be a problem with Ion Torrent data where the base quality can be quite low, and so we need to include Q15 bases for calling effectively.		2012-07-18 16:07:46 -04:00
licensing	Remove old licensing	2012-04-25 12:23:08 -04:00
protected/java	Enabled a whole other bunch of integration tests for BQSRv2. While I was there I also changed the default context size for indels to 3 (from 8) since that's what works best in the current implementation (as suggested by Ryan). At this point, all of the new core tools (ReduceReads, BQSRv2, HaplotypeCaller, UG extensions) have been moved over to protected and should be stable. Looks like we are pretty much ready for GATK 2.0!	2012-07-17 23:36:43 -04:00
public	FisherStrand now includes all reads and bases, regardless of mapping quality and base quality, just like other annotations	2012-07-18 16:07:46 -04:00
settings	Rev tribble to 110. Log is:	2012-06-26 15:28:32 -04:00
.gitignore	Minor additions to the shared .gitignore file, now that Mark has checked one in.	2011-10-26 12:24:28 -04:00
build.xml	Change committest target to allow inheritance of properties	2012-07-18 12:45:51 -04:00
ivy.xml	Navel -> GXDB	2012-06-28 13:38:00 -04:00