gatk3的最后一个经典版本3.8

Go to file

David Roazen 51ec5404d4 SAMDataSource: always consolidate cigar strings into canonical form -Collapses zero-length and repeated cigar elements, neither of which can necessarily be handled correctly by downstream code (like LIBS). -Consolidation is done before read filters, because not all read filters behave correctly with non-consoliated cigars. -Examined other uses of consolidateCigar() throughout the GATK, and found them to not be redundant with the new engine-level consolidation (they're all on artificially-created cigars in the HaplotypeCaller and SmithWaterman classes) -Improved comments in SAMDataSource.applyDecoratingIterators() -Updated MD5s; differences were examined and found to be innocuous -Two tests: -Unit test for ReadFormattingIterator -Integration test for correct handling of zero-length cigar elements by the GATK engine as a whole		2013-06-19 13:29:01 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	Swapping in logless Pair HMM for default usage with UG:	2013-06-18 10:06:27 -04:00
public	SAMDataSource: always consolidate cigar strings into canonical form	2013-06-19 13:29:01 -04:00
settings	Rev picard, sam-jdk, tribble, and variant to version 1.91.1453	2013-05-07 14:21:15 -04:00
.gitignore	Detect stuck lock-acquisition calls, and disable file locking for tests	2013-04-24 22:49:02 -04:00
README.md	Create README.md	2013-06-17 16:03:45 -03:00
build.xml	Restore scala compilation by default in build.xml	2013-05-31 11:28:29 -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
ivy.xml	Brought all of ReduceReads to fastutils	2013-02-23 22:53:23 -05:00

README.md

gsa-unstable

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