possible bug in full-gap detection #113
Description
In summarize_alignment.py line 219, "N" is used for full-gap classification. In CIGAR notation, "N" stands for intron, "D" for deletion. According to the minimap2 manual, minimap2 labels deletions as introns if the "splice" mode is used.
However, in map_reads.sh line 53, the "splice" mode is not used. Thus, introns marked "N" are not expected in the output.
In our data, we have observed "D" but not "N" in the BAM file CIGAR outputs from laava. Changing summarize_alignment.py line 219 "N" to "D" causes laava to classify some reads as "full-gap", which we have not otherwise observed.