gatk3的最后一个经典版本3.8

Mauricio Carneiro d00b2c6599 Adding a synthetic read for filtered data ... * Generalized the concept of a synthetic read to cread both running consensus and a synthetic reads of filtered data. * Synthetic reads can now have deletions (but not insertions) * New reduced read tag for filtered data synthetic reads *(RF)* * Sliding window header now keeps information of consensus and filtered data * Synthetic reads are created simultaneously, new functionality is controlled internally by addToSyntheticReads		2011-11-09 20:16:22 -05:00
public	Adding a synthetic read for filtered data	2011-11-09 20:16:22 -05:00
settings	Instead of the SelfScopingFeatureCodec interface, pushed this functionality into Tribble itself. Now we can e.g. determine that a file can be parsed by the BedCodec on the fly.	2011-11-09 15:24:29 -05:00
.gitignore	Minor additions to the shared .gitignore file, now that Mark has checked one in.	2011-10-26 12:24:28 -04:00
LICENSE	One last test...	2011-06-28 19:18:17 -04:00
build.xml	No more hunting down R "resources". As a tradeoff Rscript cannot be specified on the commandline and will be found in the environment path.	2011-10-27 14:17:07 -04:00
ivy.xml	Fixed Ant / PluginManager issue where reflections was picking up all class files under current working directory due to "." in jar manifest classpaths.	2011-09-27 14:33:57 -04:00