gatk3的最后一个经典版本3.8

Christopher Hartl 339ef92eac Goodbye SW by default. Now aligned reads that overlap intron-exon junctions are scored where they are by default, but warns the user (and flags the record in the VCF) if there's evidence to suggest that there is an indel throwing off the scoring (e.g. if the best score of a realigned unmapped read is >5 log orders better than the best score of a scored mapped read). Unmapped reads are still SW-aligned to the junction-junction sequence. This should result in a rather massive speedup, so far untested. ... UGBoundAF has to go in at some point. In the process of rewriting the math for bounding the allele frequency (it was assuming uniform tails, which is silly since i derived the posterior distribution in closed form sometime back, just need to find it)		2011-12-19 12:18:18 -05:00
public	Goodbye SW by default. Now aligned reads that overlap intron-exon junctions are scored where they are by default, but warns the user (and flags the record in the VCF) if there's evidence to suggest that there is an indel throwing off the scoring (e.g. if the best score of a realigned unmapped read is >5 log orders better than the best score of a scored mapped read). Unmapped reads are still SW-aligned to the junction-junction sequence. This should result in a rather massive speedup, so far untested.	2011-12-19 12:18:18 -05:00
settings	Revved Picard to incorporate tfennell's AsyncSAMFileWriter.	2011-12-06 10:37:42 -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	One last test...	2011-06-28 19:18:17 -04:00
build.xml	Extensive unit test for GenotypeContextUnitTest	2011-11-20 18:28:01 -05:00
ivy.xml	Updating the HybridSelectionPipeline for SnpEff 2.0.4 RC3	2011-11-17 14:46:12 -05:00