+1, this would be really useful to have!

Isn't -M mostly for compatibility with a long-outdated version of Picard (cf #26)? I'm curious why you're finding it useful.

@jmarshall I do believe that this is resolved on the updated version of Picard; if you want to close this, we can always reopen the PR if that is not the case.

"bwa mem -M" means the flag value which is 2048 is converted to 256. Firstly, you must understand the difference between supplementary alignment and secondary alignment. Officially, "Typically, one
of the linear alignments in a chimeric alignment is considered the “representative” alignment, and the
others are called “supplementary” and are distinguished by the supplementary alignment flag." defines the supplementary alignment. And "The correct placement of a read may be ambiguous, e.g. due to repeats. In this case, there may be multiple read alignments for the same read. One of these alignments is considered primary. All the other alignments have the secondary alignment flag set in the SAM records that represent them." defines the secondary alignment.

We were using the -M option for compatibility with Picard version 1.95.