Convert GAlignmentPairs to GAlignments using CIGAR to mark flanked portion of the pairs as 'N'.
Each proper read pairs is combined into a single alignment record making use of the CIGAR flag ‘N’ to indicate the number of bases between the mate pairs (i.e., the difference between the start of the right mate pair and the end of the left mate pair). In other words, the paired-end alignments are treated as gapped alignments of long fragments. The function is used within
getAlignGal but can be used as a stand-alone function as well.
GAlignments object containing for each paired alignments a single alignment record.
P. Aboyoun, H. Pages and M. Lawrence. GenomicRanges: Representation and manipulation of genomic intervals. R package version 1.8.9.
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