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Ran 21 Aug 2014 04:27PM UTC

Files 68

Run time 31s

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Committed 21 Aug 2014 04:19PM UTC coverage: 87.548% (+0.1%) from 87.441%

Job # 776.1

Build Type

push

travis-ci

Committed by

MauricioCarneiro

Commit Message

Sam: implementation of mate operations

* add mate_alignment_stop, mate_unclipped_start, mate_unclipped_stop
* add mate operations overloads for performance and tests
* fix off-by-one bug on Sam::alignment_stop (it was reporting the base after the last inclusive base, contradicting the docs)
* refactor cigar operator parsing routine from SamBuilder to Cigar class for mutual use
* add consumes_read_bases and consumes_reference_bases as static methods to the Cigar class
* add tests to the new API and all new functions

fixes #6

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