ebanks 48b15d42e0 More fixes and improvements. We no longer use any bases under Q20 because random ~Q5s were cluttering the graphs; instead we grab any contiguous segments of size at least MIN_SEQUENCE_LENGTH where all bases are above Q20. Also, I implemented a quick algorithm to traverse the graph (using DFS) to choose the two best scoring paths (haplotypes). Used it successfully at NA12878 HM3 SNP sites to determine whether they are homozygous (no distiction yet between ref and alt) or heterozygous! Indels are the next target. Still have some issues to work out. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5502 348d0f76-0448-11de-a6fe-93d51630548a		2011-03-24 03:51:19 +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	More fixes and improvements. We no longer use any bases under Q20 because random ~Q5s were cluttering the graphs; instead we grab any contiguous segments of size at least MIN_SEQUENCE_LENGTH where all bases are above Q20. Also, I implemented a quick algorithm to traverse the graph (using DFS) to choose the two best scoring paths (haplotypes). Used it successfully at NA12878 HM3 SNP sites to determine whether they are homozygous (no distiction yet between ref and alt) or heterozygous! Indels are the next target. Still have some issues to work out.	2011-03-24 03:51:19 +00:00
test	... and the corresponding integration test update	2011-03-23 01:58:07 +00:00