ebanks ab6a815184 As per the comments in the commit itself: when reads get mapped to the junction of two chromosomes (e.g. MT since it is actually circular DNA), their unmapped bit is set, but they are given legitimate coordinates. The Picard code will come in and move the read all the way back to its mate - which can be arbitrarily far away and cause records to be written out of order. Very evil. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5484 348d0f76-0448-11de-a6fe-93d51630548a		2011-03-21 20:30:24 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src	As per the comments in the commit itself: when reads get mapped to the junction of two chromosomes (e.g. MT since it is actually circular DNA), their unmapped bit is set, but they are given legitimate coordinates. The Picard code will come in and move the read all the way back to its mate - which can be arbitrarily far away and cause records to be written out of order. Very evil.	2011-03-21 20:30:24 +00:00
test	Finally found the bug that everyone is reporting on GS. Iterators on PriorityQueues aren't guaranteed to return elements in sorted order (a pretty stupid contract) - so we were passing items to the constrained writer out of order. Just do a Collections.sort instead (1 line of code). Happy father's day!	2011-03-18 21:28:19 +00:00