gatk3的最后一个经典版本3.8

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Khalid Shakir 9bee183f6c Switched to using CRAM's SamReader.Indexing implementation. CRAM now requires .bai index, just like BAM. Test updates: - Updated existing MD5s, as TLEN has changed. - Tests multiple contigs. - Tests several intervals per contig. - Tests when `.cram.bai` is missing, even when `.cram.crai` is present. Updated gatk docs for CRAM support, including: - Arguments that work for both BAM and CRAM listed as such. - Arguments that don't work for CRAM either explicitly say "BAM" or "doesn't work for CRAM". - Instructions on how to recreate a `.cram.bai` using cramtools. Cleaned up IntelliJ IDEA warnings regarding `Arrays.asList()` -> `Collections.singletonList()`.		2015-08-11 17:52:49 -03:00
licensing	Updated licenses for 2015	2015-08-06 15:23:11 -04:00
protected	Updated licenses for 2015	2015-08-06 15:23:11 -04:00
public	Switched to using CRAM's SamReader.Indexing implementation.	2015-08-11 17:52:49 -03:00
settings/helpTemplates	Numerous doc fixes; mostly formatting and clarifications	2015-05-03 00:28:46 +02:00
.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	Added faster built executable, non-packaged jars.	2014-11-05 00:30:46 +08:00
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	Update pom versions to mark the start of GATK 3.5 development	2015-05-15 00:44:54 -04:00

README.md

The Genome Analysis Toolkit

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