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Revision as of 11:22, 3 August 2010
, 11:22, 3 August 2010no edit summary
== Enhancements/Updates/Fixes ==
== Enhancements/Updates/Fixes ==
=== 08/03/2010 ===
* Add methods to CigarRoller
** getNumOverlaps - takes a region and the query start position and returns the number of overlaps (cigar 'M') in that region
** getRefPosition - takes a query index and the query start position and returns the associated reference position or INDEX_NA
** getQueryIndex - takes a reference position and the query start position and returns the associated query index or INDEX_NA
=== 07/16/2010 ===
=== 07/16/2010 ===
* Cigar Roller: fix the way soft clips are interpreted for mapping between the reference and the read indices. They were being treated as if they did not exist in neither the reference nor the read. They are now treated like inserts, in the read, but not in the Reference.
* Cigar Roller: fix the way soft clips are interpreted for mapping between the reference and the read indices. They were being treated as if they did not exist in neither the reference nor the read. They are now treated like inserts, in the read, but not in the Reference.
