gatk3的最后一个经典版本3.8

ebanks 940d75171a Big cleaner changes: ... 1. Added a Walker to merge intervals before cleaning 2. (Almost) all Walkers can filter out 454 reads (and do by default) 3. Got rid of -all command and related pieces (time to switch to CleanedReadsInjector) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1090 348d0f76-0448-11de-a6fe-93d51630548a		2009-06-25 14:31:24 +00:00
R	Apprach v2. Added python analysis script, so java no longer must be used to analyses quality score data. About to refactor out lots of unneeded code	2009-06-20 16:00:23 +00:00
c	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
doc	Fairly detailed first pass at a README for the MSA realigner	2009-06-23 01:54:38 +00:00
java	Big cleaner changes:	2009-06-25 14:31:24 +00:00
packages	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
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	Much improved python analysis routines, as well as easier / more correct merging utility. Better R scripts, which now close recalibration data by the confidence of the quality score itself	2009-06-24 01:12:35 +00:00
settings	Bump picard and sam to latest version.	2009-06-18 21:59:40 +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	Apprach v2. Added python analysis script, so java no longer must be used to analyses quality score data. About to refactor out lots of unneeded code	2009-06-20 16:00:23 +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