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shortRNAhub / shortRNA

short RNA-seq analysis package
GNU General Public License v3.0
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wrong overlaps with spliced reads #15

Closed plger closed 5 years ago

plger commented 5 years ago

findoverlaps.bam.featureAnnotation returns wrong overlaps (as well as wrong values for the length and percentage of overlap) for reads with gapped alignment (i.e. spliced reads). Example of gapped alignment:

r551360 256 chr1    1234653 0   9M302102N9M *   0   0   CCCGTGGGACCCGCGGGC  *   NH:i:14 HI:i:12 NM:i:0

(cigar contains N, i.e. skipped nucleotides)

plger commented 5 years ago

Fixed long ago...