NAME

       HPC.damapper: - long read to reference genome mapping tool

DESCRIPTION

       Recognised as the Damapper Library, this is a long read to reference genome mapping tool.

       Compared to damapper, this writes a UNIX shell script to the standard output that maps
       every read in blocks <first> to <last> of database <reads> to a reference sequence <ref>.

SYNOPSIS

       HPC.damapper [-vpzCN] [-k<int(20)>] [-t<int>] [-M<int>] [-e<double(.85)] [-s<int(100)]

DESCRIPTION

       [-n<double(1.)] [-m<track>]+ [-B<int( 4)>] [-T<int(4)>] [-f<name>]
              <ref:db|dam> <reads:db|dam> [<first:int>[-<last:int>]]

              Passed through to damapper.

       -k: k-mer size (must be <= 32).

       -t: Ignore k-mers that occur >= -t times in a block.

       -M: Use only -M GB of memory by ignoring most frequent k-mers.

       -e: Look for alignments with -e percent similarity.

       -s: Use -s as the trace point spacing for encoding alignments.

       -n: Output all matches within this % of the best

       -T: Use -T threads.

       -P: Do sorts and merges in directory -P.

       -m: Soft mask the blocks with the specified mask.

       -b: For AT/GC biased data, compensate k-mer counts (deprecated).

       -z: sort .las by A,B-read pairs (overlap piles)

              off => sort .las by A-read,A-position pairs (default for mapping)

       -p: Output repeat profile track

       -C: Output reference vs reads .las.

       -N: Do not output reads vs reference .las.

              Script control.

       -v: Verbose mode, output statistics as proceed.

       -B: # of block compares per daligner job

       -f: Place script bundles in separate files with prefix <name>