asivache dd0085c428 1) now is tolerant to sloppy cigar strings with 0-length elements (at the price of extra recursive call) ... 2) when reads with deletions are requested, adds to the pile just those: reads with 'D' over the current reference base, but not 'N' 3) next() now implements a loop: recursive forward iteration calls to next() until ref. position with non-zero coverage is encountered were OK for (short) deletions, but with long stretches of N's they end up with stack overflow git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1568 348d0f76-0448-11de-a6fe-93d51630548a		2009-09-09 20:04:04 +00:00
..
config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src/org/broadinstitute/sting	1) now is tolerant to sloppy cigar strings with 0-length elements (at the price of extra recursive call)	2009-09-09 20:04:04 +00:00
test/org/broadinstitute/sting	Adding cleaner test	2009-09-09 16:05:56 +00:00