delangel da2e879bbc Miscellaneous improvements to indel genotyper: ... - Add a simple calculation model for Pr(R|H) that doesn't rely on Dindel's HMM model. MUCH faster, at a cost of slightly worse performance since we're more sensitive to bad reads coming from sequencing artifacts (add -simple to command line to activate). - Add debug option to calculation model so that we can optionally output useful info on current read being evaluated. (add -debugout to commandline). - Small performance improvement: instead of evaluating haplotype to the right of indel (just with a 5 base addition to the left), it seems better to center the indel and to add context evenly around event. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4257 348d0f76-0448-11de-a6fe-93d51630548a		2010-09-12 13:50:28 +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	Miscellaneous improvements to indel genotyper:	2010-09-12 13:50:28 +00:00
test	Damnit. Enabling the Picard code to recalculate all of the relevant SAMRecord attribute tags means that I need to have reference bases over all read bases even after realignment (and there are some big indels in dbsnp). Fortunately, I have my trusty IndexedFastaSequenceFile reader handy! Re-enabling the previously broken performance test.	2010-09-12 05:06:37 +00:00