gatk-3.8

gatk3的最后一个经典版本3.8

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kcibul be2f8478c0 added supression of failure messages git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1164 348d0f76-0448-11de-a6fe-93d51630548a		2009-07-03 15:19:37 +00:00
R	Version 0.2.1 (released) of the TableRecalibrator	2009-06-25 22:50:55 +00:00
c	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
doc	up on the wiki, removing it from the repo. Ignore my last commit	2009-07-01 15:42:02 +00:00
java	added supression of failure messages	2009-07-03 15:19:37 +00:00
packages	Oops. Specified incorrect classname in packgae for depth of coverage walker.	2009-07-02 21:40:40 +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	Lot of code for coverage evaluation tools including first version of python script to evaluate the downsampled SSG callls made and the java code to make all the calls at Hapmap chip sites at various downsampling levels; ListUtils contains functions for randomnly subsetting lists (with replacement) which are useful for subsetting the same elements in both the reads and the offsets lists of a LocusWalker	2009-07-03 08:07:02 +00:00
settings	Updates to picard public / private and sam.	2009-06-30 14:50:55 +00:00
shell	Version 0.2.1 (released) of the TableRecalibrator	2009-06-25 22:50:55 +00:00
testdata	bam and fasta files generated with the artificial tools. These will be included in the GATK distro.	2009-07-01 22:49:31 +00:00
build.xml	Convert the somatic coverage tool to output from the packaging tool rather than from the dist target.	2009-06-18 21:29:30 +00:00
ivy.xml	Add bcel and cleanup.	2009-06-17 19:28:04 +00:00