Once corrected to catch the -t option, current implementation applies trimming only to a subset of reads that match existing cases in trim_pair. Others fall through untrimmed. Also, trim_pair contains redundant "if (alignment_start > 0)" test at line 230.
Once corrected to catch the -t option, current implementation applies trimming only to a subset of reads that match existing cases in trim_pair. Others fall through untrimmed. Also, trim_pair contains redundant "if (alignment_start > 0)" test at line 230.