chartl 6dec042288 Re-enabling indel cleaning, explicitly calling fix mates in the case where indel cleaning is not scatter/gathered ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4324 348d0f76-0448-11de-a6fe-93d51630548a		2010-09-21 20:37:49 +00:00
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qscript	Re-enabling indel cleaning, explicitly calling fix mates in the case where indel cleaning is not scatter/gathered	2010-09-21 20:37:49 +00:00
src	Fix for Matt: For Mac OS 10.6 temporary directories replace paths like '/var/folders/Ax/AxRUoz51Fh05fVe-j6C1Wk+++TI/-Tmp-/' with '/tmp/' so that google reflections 0.95RC2 still works on classes in the directory.	2010-09-20 22:02:07 +00:00
test/org/broadinstitute/sting/queue/util	Exposed CommandLineFunction defaults to the Queue.jar command line (see -help).	2010-08-11 21:58:26 +00:00