HPCmapper [-vb] [-kint(20)] [-wint(6)] [-hint(50)] [-tint] [-Mint] [-edouble(.85)][-lint(1000)] [-sint(100)] [-Hint] [-mtrack]+ [-dalint(4)] [-degint(25)] ref:db|dam reads:db|dam [first:int[-last:int]]
HPCmapper writes a UNIX shell script to the standard output that consists of a sequence of commands that effectively "maps" every read in the DB reads against a reference set of sequences in the DB ref, recording all the found local alignments in the sequence of files ref.reads.1.las, ref.reads.2.las, and so on, where ref.reads.k.las contains the alignments between all of ref and the k'th block of reads. The parameters are exactly the same as for HPCdaligner(1) save that the -k, -h, and -e defaults are set appropriately for mapping, and the -A and -I options make no sense as ref and reads are expected to be distinct data sets.
If the integers first and last are missing, then the script produced is for every block in the database reads. If first is present then HPCmapper produces an script that compares blocks first through last (last = first if not present) against DAM ref.