Christopher Hartl 339ef92eac Goodbye SW by default. Now aligned reads that overlap intron-exon junctions are scored where they are by default, but warns the user (and flags the record in the VCF) if there's evidence to suggest that there is an indel throwing off the scoring (e.g. if the best score of a realigned unmapped read is >5 log orders better than the best score of a scored mapped read). Unmapped reads are still SW-aligned to the junction-junction sequence. This should result in a rather massive speedup, so far untested. ... UGBoundAF has to go in at some point. In the process of rewriting the math for bounding the allele frequency (it was assuming uniform tails, which is silly since i derived the posterior distribution in closed form sometime back, just need to find it)		2011-12-19 12:18:18 -05:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	Goodbye SW by default. Now aligned reads that overlap intron-exon junctions are scored where they are by default, but warns the user (and flags the record in the VCF) if there's evidence to suggest that there is an indel throwing off the scoring (e.g. if the best score of a realigned unmapped read is >5 log orders better than the best score of a scored mapped read). Unmapped reads are still SW-aligned to the junction-junction sequence. This should result in a rather massive speedup, so far untested.	2011-12-19 12:18:18 -05:00
test	- Corrected bug causing cases where both parents are HET to be accounted twice in the TDT calculation - Adapted TDT Integration test to corrected version of TDT	2011-12-19 10:30:59 -05:00