depristo c1abcfb014 Fixed problem where we were considering reads out of order because their stop positions where out of order, but with equal starts. This involved a change in the ordering feature of GenomeLoc, which now no longer sorts by both start and stop. So as long as the start positions are equal, things are considered "in order". Perhaps this isn't a good idea to change... ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@291 348d0f76-0448-11de-a6fe-93d51630548a		2009-04-03 19:53:33 +00:00
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src/org/broadinstitute/sting	Fixed problem where we were considering reads out of order because their stop positions where out of order, but with equal starts. This involved a change in the ordering feature of GenomeLoc, which now no longer sorts by both start and stop. So as long as the start positions are equal, things are considered "in order". Perhaps this isn't a good idea to change...	2009-04-03 19:53:33 +00:00
test/org/broadinstitute/sting/utils/cmdLine	Fix argument parser test case.	2009-03-27 16:05:18 +00:00