gatk3的最后一个经典版本3.8

aaron 78b7fb25c7 allow contig names to have spaces in the fai. This is not yet supported by samtools fai generator (which truncates at the first space), but we might as well fix it on our side. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1022 348d0f76-0448-11de-a6fe-93d51630548a		2009-06-16 22:23:12 +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	allow contig names to have spaces in the fai. This is not yet supported by samtools fai generator (which truncates at the first space), but we might as well fix it on our side.	2009-06-16 22:23:12 +00:00
packages	Plumbed packaging support into build.xml and added package for GATK.	2009-06-15 19:41:16 +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	Trivial change	2009-06-12 19:11:28 +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	Plumbed packaging support into build.xml and added package for GATK.	2009-06-15 19:41:16 +00:00
ivy.xml	Update to latest version of picard. Change imports in all classes dependent on picard public from import edu.mit.broad.picard... to import net.sf.picard...	2009-05-28 20:13:01 +00:00