Eric Banks dadcfe296d Reworking of the dangling tails merging code. ... We now run Smith-Waterman on the dangling tail against the corresponding reference tail. If we can generate a reasonable, low entropy alignment then we trigger the merge to the reference path; otherwise we abort. Also, we put in a check for low-complexity of graphs and don't let those pass through. Added tests for this implementation that checks exact SW results and correct edges added.		2013-06-11 12:53:04 -04:00
..
net/sf/samtools	Delete unused FastaSequenceIndexBuilder class and accompanying test	2013-05-01 01:02:01 -04:00
org/broadinstitute/sting	Reworking of the dangling tails merging code.	2013-06-11 12:53:04 -04:00