Hi Bio-Samtools Team,
I have noticed a problem of getting coverage of RNA-Seq reads. These reads usually have long skips in middle (i.e. long “N” in CIGAR string) to cross introns. However, if I use the _coverage function on an intron, I still get very high coverage because the function counts the reads that cross the introns to map to exons at both ends . The solution, as you already mentioned in the function, is to use pileup instead in the _coverage function. The latest samtools pileup function returns bam_pileup1_t data structure with is_refskip and is_del flags to be used to ignore reads that skip the region.
I am using Bio-Samtools 1.27 by Perl 5.8.9 on Linux64.
Thanks,
Yi-Shiou Chen
Accelrys
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