gatk-3.8/public/java
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
..
config Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
src Reworking of the dangling tails merging code. 2013-06-11 12:53:04 -04:00
test Reworking of the dangling tails merging code. 2013-06-11 12:53:04 -04:00