Secondary Alignments with BWA-MEM

[H_Peckham]

When I have split reads originating from repetitive sequences I must use the -a flag to get the secondary alignments. The problem with this is that with the -a flag there can be multiple secondary alignments and I can't easily tell which secondary alignments are part of a split alignment and which are from a single alignment.

Is there any way to flag the secondary alignments as to whether or not they are also split alignments or is this something that can be added to bwa-mem?

Thanks!