gatk3的最后一个经典版本3.8

Ryan Poplin dda2173c66 Moved the Smith-Watermaning of haplotypes to earlier in the process so that alleles sent to genotyping would have the exact genomic sequence of the active region they represent. As a side effect cleaned up some edge case problems with variants, both real and false, which show up on the edges of active regions. Removed code that was replicated between the Haplotype class and ReadUtils. Finally figured out how to ensure that the indel calls coming out of the HC were left aligned.		2012-04-04 16:04:29 -04:00
public	Moved the Smith-Watermaning of haplotypes to earlier in the process so that alleles sent to genotyping would have the exact genomic sequence of the active region they represent. As a side effect cleaned up some edge case problems with variants, both real and false, which show up on the edges of active regions. Removed code that was replicated between the Haplotype class and ReadUtils. Finally figured out how to ensure that the indel calls coming out of the HC were left aligned.	2012-04-04 16:04:29 -04:00
settings	Rev. tribble to fix BED codec bug in tribble 51	2012-01-17 16:40:26 -05:00
.gitignore	Minor additions to the shared .gitignore file, now that Mark has checked one in.	2011-10-26 12:24:28 -04:00
LICENSE	Updated license year	2012-03-27 14:32:02 -04:00
build.xml	Bug fix to previous UnifiedGenotyperEngine refactoring, removed debug code	2012-03-25 10:20:21 -04:00
ivy.xml	S3 upload now directly creates the XML report in memory and puts that in S3	2012-01-29 15:14:58 -05:00