gatk3的最后一个经典版本3.8

ebanks 009e71fcd9 We need to sort cleaned reads ourselves (instead of letting SAMFileWriter ... do it) because the SAM headers are often screwed up and claim to be "unsorted". While here, I broke off the module from the SortSamIterator in case someone else wants to use it. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@654 348d0f76-0448-11de-a6fe-93d51630548a		2009-05-11 15:43:42 +00:00
c	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
doc	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
java	We need to sort cleaned reads ourselves (instead of letting SAMFileWriter	2009-05-11 15:43:42 +00:00
python	Reference-ordered data relies on bugs in the old command-line argument system to work. Update the ROD system to from -B track1 type1 file1 track2 type2 file2 to -B track1,type1,file1 -B track2,type2,file2.	2009-05-08 15:28:19 +00:00
settings	Bumped sam-jdk version to fix bug unzipping bam files.	2009-04-28 20:02:05 +00:00
shell	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
testdata	Better validation scripts and data	2009-04-29 17:40:07 +00:00
build.xml	Added BCEL and some basic instrumenation code to the test library.	2009-05-06 17:18:23 +00:00
ivy.xml	Change the sample XML marshalling code over to simple XML, and take out the castor lines in the ivy.xml	2009-05-08 00:08:25 +00:00