Provided by: daligner_1.0+20151214-1_amd64 bug


       HPCmapper - generate a script to map reads


       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.


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