-M parameter for BWA MEM alignment #144

Thanks a lot for developing this pipeline. I have a question about BWA MEM alignment. In your main paper you mention that:

SpeedSeq aligns paired-end FASTQ files to the human GRCh37 reference genome with BWA-MEM, using the “-M” flag to mark shorter alignments as secondary

However by looking into the code it seems that you just use BWA MEM with the -t -R and -I options