gatk3的最后一个经典版本3.8

asivache b4136b6d6e a few tweaks to make it more robust: ignore reads with cigars containing anything but I,D,M; don't set up contig ordering manually, rely upon reference sequence and its dictionary; don't die if a record does not have NM tag, but faal back to direct counting instead; now requires reference as a cmdline arg ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@378 348d0f76-0448-11de-a6fe-93d51630548a		2009-04-13 04:49:19 +00:00
c	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
doc	Updated with last week / next week for 6 April.	2009-04-06 14:05:20 +00:00
java	a few tweaks to make it more robust: ignore reads with cigars containing anything but I,D,M; don't set up contig ordering manually, rely upon reference sequence and its dictionary; don't die if a record does not have NM tag, but faal back to direct counting instead; now requires reference as a cmdline arg	2009-04-13 04:49:19 +00:00
python	Helper utility for merging BAM files	2009-04-09 20:10:41 +00:00
settings	Bump sam jdk to svn rev 207.	2009-04-08 22:16:46 +00:00
shell	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
testdata	Skeleton of new directory structure.	2009-03-11 20:05:05 +00:00
build.xml	Added MatchSQTagToStrand jar target.	2009-04-13 00:50:36 +00:00
ivy.xml	Added castor dependency.	2009-04-07 22:27:39 +00:00