gatk-3.8

gatk3的最后一个经典版本3.8

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asivache ebec0ec171 A standalone companion to BamToFastqWalker: does the same thing but without calling in gatk's heavy artillery (does not "require" a reference either). Extracts seqs and quals and places them into fastq; along the way it also reverse complements reads that align to the negative strand (so that fastq contains reads as they come from the machine). git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1419 348d0f76-0448-11de-a6fe-93d51630548a		2009-08-12 20:24:37 +00:00
R	Updated python files	2009-07-07 14:15:39 +00:00
c	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
doc	moved to wiki	2009-07-22 16:35:23 +00:00
java	A standalone companion to BamToFastqWalker: does the same thing but without calling in gatk's heavy artillery (does not "require" a reference either). Extracts seqs and quals and places them into fastq; along the way it also reverse complements reads that align to the negative strand (so that fastq contains reads as they come from the machine).	2009-08-12 20:24:37 +00:00
packages	Added indel cleaner and quality scores recalibrator to the GATK package.	2009-07-24 16:20:38 +00:00
perl	A little gadget to select random samples from input stream(s) of unknown length. By default, selects a single line (with probability 1/TOTAL_NUMBER_OF_LINES_READ), with -N option randomly selects specified number of lines. Can read from STDIN or from arbitrary number of input streams (all streams will be merged). Examples:\n cat file1 file2 file3 \| randomSampleFromStream.pl -N 5 \n\n or \n randomSampleFromStream.pl file1 file2 file3	2009-07-31 18:55:14 +00:00
python	I've pulled out the functionality of the analyzer into a single python file which doesn't require all of the irrelevant config parameters (which would cause problems for external users). I'll release this and the simple config file to 1KG for use in analyzing recalibration efforts.	2009-08-11 02:56:43 +00:00
settings	Switched to Reflections (http://code.google.com/p/reflections/) project for	2009-07-21 18:32:22 +00:00
shell	Version 0.2.1 (released) of the TableRecalibrator	2009-06-25 22:50:55 +00:00
testdata	2009_02 release is no longer with us. Update the bam list.	2009-08-11 12:49:23 +00:00
build.xml	Exclude secondary base caller code from playground jar. Still TODO: figure	2009-07-30 21:02:46 +00:00
ivy.xml	Switched to Reflections (http://code.google.com/p/reflections/) project for	2009-07-21 18:32:22 +00:00