NAME

       HPCmapper - generate a script to map reads

SYNOPSIS

       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]]

DESCRIPTION

       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.

SEE ALSO

       daligner(1) LAsort(1) LAmerge(1) LAshow(1) LAcat(1) LAsplit(1) LAcheck(1) HPCdaligner(1)

1.0                                                August 2015                                      HPCmapper(1)