NAME

       damapper - long read to reference genome mapping tool

DESCRIPTION

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

SYNOPSIS

       damapper  [-vpzCN]  [-k<int(20)>]   [-t<int>]   [-M<int>]   [-T<int(4)>]   [-P<dir(/tmp)>]
       [-e<double(.85)] [-s<int(100)>] [-n<double(1.00)>] [-m<track>]+ <reference:dam> <reads:db>
       ...

       -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.

       -v: Verbose mode, output statistics as proceed.

       -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.