ebanks 3eea6e92b7 An extremely basic implementation of a deBruijn-based local assembler, using the jgrapht graph library. This is not at all optimized and has only been tested on my very simple 3-read test bams. I'm sure there are bugs in there - more testing coming soon. Insertions and deletions confirmed to generate identical graphs (except for the multiplicity of edges of course). Not worth using yet. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5455 348d0f76-0448-11de-a6fe-93d51630548a		2011-03-17 14:03:07 +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	An extremely basic implementation of a deBruijn-based local assembler, using the jgrapht graph library. This is not at all optimized and has only been tested on my very simple 3-read test bams. I'm sure there are bugs in there - more testing coming soon. Insertions and deletions confirmed to generate identical graphs (except for the multiplicity of edges of course). Not worth using yet.	2011-03-17 14:03:07 +00:00
test	Removing some debug code from VQSRv2. VariantEval can now be stratified by contig with -ST Contig. New hidden option in CombineVariants for overlapping records to take the info fields from the record with the highest AC (while still updating AC/AN/AF correctly) instead of dropping info fields which aren't exactly the same.	2011-03-15 21:28:10 +00:00