I am using Rsamtools to scan a BAM file generated with Bowtie2 (local alignment mode). I am interested in the insert sizes. Most of the time, everything works as expected. However, I noticed an issue with soft-clipped reads. If the fragment is smaller than read length and the reads go past the start of their mates, the reported insert size includes the soft-clipped ends and is actually bigger than the fragment.

Here is an example read pair:

A00427:5:H3CG5DSXX:1:1103:18078:10316    83    chr10    3740676    42    7S44M    =    3740677    59    AGAGACAGGGGTCGACTCAGGCAGGACCTGCTAGCCCGGCGCTCCCGCCCC    ,FFF:F,FFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF    AS:i:88    XN:i:0    XM:i:0    XO:i:0    XG:i:0    NM:i:0    MD:Z:44    YS:i:86    YT:Z:CP
A00427:5:H3CG5DSXX:1:1103:18078:10316    163    chr10    3740677    42    43M8S    =    3740676    -59    GGGTCGACTCAGGCAGGACCTGCTAGCCCGGCGCTCCCGCCCCCTGTCTCT    FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF    AS:i:86    XN:i:0    XM:i:0    XO:i:0    XG:i:0    NM:i:0    MD:Z:43    YS:i:88    YT:Z:CP

The reported insert size is 59, but the actual fragment (the aligned part) is 43.

I understand Rsamtools is just reading the `TLEN` column, but is there a way to adjust these lengths or at least filter them out?