Opened 8 years ago

Closed 8 years ago

#830 closed request (fixed)

calculate BAM's alignment score from cigar and reference

Reported by: Peter Owned by: Peter
Priority: major Milestone: yat 0.13
Component: omic Version: trunk
Keywords: Cc:

Description

Something like this

template<typename RandomAccessIterator>
double alignment_score(const yat::omic::BamRead& bam,
                       RandomAccessIterator ref, double mismatch,
                       double gap, double open_gap=0.0)

where the ref argument is just needed to check CIGAR elements BAM_CMATCH to differentiate equal from diff.

Change History (2)

comment:1 Changed 8 years ago by Peter

Milestone: yat 0.x+yat 0.13
Status: newassigned

comment:2 Changed 8 years ago by Peter

Resolution: fixed
Status: assignedclosed

(In [3395]) closes #830. New function that calculates alignment_score of a bam alignment. Also a new function that returns bams one char in bam's query sequence. Using this function in sequence function. This might slow down the code slightly when building against old libbam, but speed is not a priority in that case.

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