gatk-3.8

Author	SHA1	Message	Date
depristo	2b02324587	Support for detecting and automatically excluding reads reading into the adaptor sequence and, if desired, also only showing the first pair when two reads overlap in the fragment. Not enabled, an intermediate check in before updating and verifying the impact on locus walkers everywhere. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3465 348d0f76-0448-11de-a6fe-93d51630548a	2010-05-30 18:00:12 +00:00
hanna	c1e53d407d	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had unicode quote characters embedded in it. These characters were invisible inside IntelliJ but cause compile warnings for Ryan and Aaron, who for whatever reason have a different default charset. Fixed. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3203 348d0f76-0448-11de-a6fe-93d51630548a	2010-04-20 15:26:32 +00:00
hanna	1bc26f69e9	An attempt to cleanup the Utils directory. Email to follow. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3198 348d0f76-0448-11de-a6fe-93d51630548a	2010-04-19 23:00:08 +00:00