updated to turn XA alternative mapping locations from BWA output sam file into their own respective lines to allow for greater mapping flexibility. updated to allow mauriceville mapping with BWA. updated 03.remove_mv_snps subscript to allow for multiple sam lines per unique read
forced uniq on 03.remove_MV_snps.sh to avoid conficts when searching for duplicate lines (previous logic would report everything that had multiple alignment locations as an MV snp). changed final else on 03.sub_script bak to more correct elif to ensureerror reporting if anything goes wrong
updated master script to submit to zcluster run
end of day. left changing bwa to have -a option, want to confirm that -a option is the same as bwa mem | xa2multi pipeline