asivache 52eedaf22d Subtle but very annoying bug due to incorrect exit condition on backward traversal. Example of incorrect old behavior (found by Martha Borkan, this normally would NOT happen with the combination of match/mismatch/open/extend parameters we have been using; use match=10.0, mismatch= -9.0, open= -15.0, extend= -6.66 in older builds in order to reproduce): ... let's align two sequences (shown below, good alignment) AAATTTGGTAAAA-GT AAATTTGGTAAAAGGT now let's reverse the same very sequences and align again TGAAAATGGTTTAAA TGGAAAATGGTTTAAA Note how we lost the deletion and got a mismatch instead at the very first letter of the upper sequence. The overall score of any particular alignment does not depend on the direction of the traversal, so the best alignment (with the highest score) should stay the same too. New version fixes this issue and produces correct alignment of reverse sequences (up to the different choice of redundant position for the deletion): T-GAAAATGGTTTAAA TGGAAAATGGTTTAAA This version also has the main() method reinstated, so the aligner can be run on its own as a little app. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5255 348d0f76-0448-11de-a6fe-93d51630548a		2011-02-17 00:02:32 +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	Subtle but very annoying bug due to incorrect exit condition on backward traversal. Example of incorrect old behavior (found by Martha Borkan, this normally would NOT happen with the combination of match/mismatch/open/extend parameters we have been using; use match=10.0, mismatch= -9.0, open= -15.0, extend= -6.66 in older builds in order to reproduce):	2011-02-17 00:02:32 +00:00
test	Added pipeline for calling FCP in batches called MultiFullCallingPipeline.	2011-02-15 18:26:14 +00:00