gatk3的最后一个经典版本3.8

depristo ca8a3bd85e Another temp checking for rearranging things ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1048 348d0f76-0448-11de-a6fe-93d51630548a		2009-06-18 21:04:36 +00:00
R	Added R script and uncommented a line in recal_qual.py	2009-06-03 03:15:45 +00:00
c	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
doc	Preparation for point release of read calibrator: no artificial heap size limit, no duplicate dbsnp records.	2009-06-11 18:39:33 +00:00
java	Another temp checking for rearranging things	2009-06-18 21:04:36 +00:00
packages	Package annotator for Alec.	2009-06-17 22:40:40 +00:00
perl	checking in new folder for perl scripts AND a simple script that takes an input text file and reference dictionary (.fai) and performs stable sort of the input lines according to the contig order specified by the dictionary. Position of the contig filed to sort on in the input lines is specified as --k POS option. Input lines may specify contigs that are not in the dictionary, in this case the additional contigs will be added at the end of the sorted output, after all known contigs. The sorting order between these additional contigs is simply the order in which they first appear in the input	2009-05-27 16:34:55 +00:00
python	Script that aligns paired-end BAMs using BWA.	2009-06-18 18:14:58 +00:00
settings	Bumped picard to latest svn version.	2009-06-10 14:36:34 +00:00
shell	Adding a script for diff'ing the output of samtools and the GATK for the whole genome and each individual chromosome.	2009-06-02 21:19:39 +00:00
testdata	Better interface to the tabular ROD, now makes writing files easier. Also has corresponding test files	2009-05-14 23:20:11 +00:00
build.xml	Cleanup. Move output of packaging to dist directory. Don't always create resources directory. Make jar take on the package name.	2009-06-16 22:47:23 +00:00
ivy.xml	Add bcel and cleanup.	2009-06-17 19:28:04 +00:00