UPDATED: added binary files
UPDATE: naming convention
UPDATE: naming convention

genCigar becams samparser_mrfread_to_cigar
UPDATE: added binary files
UPDATE: dealing with Cigar

This version tackles the issue of Cigar including soft-clipped bases
and indels.
This version correctly identifies reads on the positive strand that are:
mM - genomic reads, all matches
m1MnNm2M - splice junction reads
sSm1MnNm2M - splice junction reads with soft clipped data at the
beginning of the query