Add --allow-multimapping

[EricKutschera]

Based on https://groups.google.com/g/rmats-user-group/c/qew7Olbs4sg and code from @leipzig

[ywang1993]

Would it be better to randomly assign the multi-mapped reads to one of the best alignments instead of counting them once for each alignment? (see reference Fig 3)

[leipzig]

those are determined by STAR option --outSAMmultNmax (max number of multiple alignments for a read that will be output to the SAM/BAM files) and --outFilterMultimapNmax (maximum number of loci the read is allowed to map to), and the reporting order is random

[leipzig]

for context this PR is necessary to actually see the effect of risdiplam on SMN1/2 in SMA