gatk3的最后一个经典版本3.8

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Phillip Dexheimer a35f5b8685 Moved arguments controlling options in output files into the engine * Arguments involved are --no_cmdline_in_header, --sites_only, and --bcf for VCF files and --bam_compression, --simplifyBAM, --disable_bam_indexing, and --generate_md5 for BAM files * PT 52740563 * Removed ReadUtils.createSAMFileWriterWithCompression(), replaced with ReadUtils.createSAMFileWriter(), which applies all appropriate engine-level arguments * Replaced hard-coded field names in ArgumentDefinitionField (Queue extension generator) with a Reflections-based lookup that will fail noisily during extension generation if there's an error		2014-09-05 21:18:11 -04:00
licensing	deleted old license files	2013-07-02 16:36:47 -04:00
protected	Moved arguments controlling options in output files into the engine	2014-09-05 21:18:11 -04:00
public	Moved arguments controlling options in output files into the engine	2014-09-05 21:18:11 -04:00
settings/helpTemplates	changed the GATKDocs format to PHP	2014-08-18 18:04:07 -04:00
.gitignore	Fixed bug using GraphBased due to infinite likelihoods resulting from the calculation of alignment cost of very long insertion or deletions (done in linear scale)	2014-04-01 16:14:52 -04:00
README.md	Update README file for the 2.6 release	2013-06-20 13:08:29 -04:00
ant-bridge.sh	Refactored maven directories and java packages replacing "sting" with "gatk".	2014-05-19 17:36:39 -04:00
intellij_example.tar.bz2	Removed the intellij files from the root and made an example package for new users. This allows users to start at the same page and then change it as they see fit without interfering with the repo (thanks guillermo!)	2012-09-27 11:04:56 -04:00
pom.xml	Now passing in the path to the GATK directory to tests.	2014-09-02 01:40:59 +08:00

README.md

The Genome Analysis Toolkit

See http://www.broadinstitute.org/gatk/