This is the first pull request for the integration of the changes from cigar-strings branch to develop branch. This pull request includes only improvements regarding the performance of the alignment computation step in PuffAligner. These improvements mostly consist of early exits during the between-Mem alignment procedure, that is, by knowing the alignment score computed for a query up to a position sometimes we can guarantee aligning the rest of the query, even if it's going to be a perfect match, is not going to make any difference in terms of that alignment be acceptable by the alignment score threshold condition. The early exits occur both between every aligner call, and also during the DP procedure of KSW2.
This is the first pull request for the integration of the changes from cigar-strings branch to develop branch. This pull request includes only improvements regarding the performance of the alignment computation step in PuffAligner. These improvements mostly consist of early exits during the between-Mem alignment procedure, that is, by knowing the alignment score computed for a query up to a position sometimes we can guarantee aligning the rest of the query, even if it's going to be a perfect match, is not going to make any difference in terms of that alignment be acceptable by the alignment score threshold condition. The early exits occur both between every aligner call, and also during the DP procedure of KSW2.