Options for damapper.
If the -b option is set, then the daligner assumes the data has a strong compositional bias (e.g. >65% AT rich).
Search code looks for a pair of diagonal bands of width 2^^w (default 26 = 64) that contain a collection of exact matching k-mers (default 14) between the two reads, such that the total number of bases covered by the k-mer hits is h (default 35).
Suppresses the use of any k-mer that occurs more than t times in either the subject or target block.
Let the program automatically select a value of t that meets a given memory usage limit specified (in Gb) by the -M parameter.
The local alignments found will be output in a sparse encoding where a trace point on the alignment is recorded every -s base pairs of the a-read (default 100bp).
The program runs with 4 threads by default, but this may be set to any power of 2 with the -T option.
If there are one or more interval tracks specified with the -m option (m for mask), then the reads of the DB or DB’s to which the track applies are soft masked with the union of the intervals of all the interval tracks that apply, that is any k-mers that contain any bases in any of the masked intervals are ignored for the purposes of seeding a match.
If the -n option is given then all chains that are within the given fraction of the best are also reported, e.g. -n.95 reports all matches within 95% of the top match.
The -p option requests that damapper produce a repeat profile track for each read.
The parameter -z asks that LAs are sorted in pile order as opposed to map order (see the -a option of daligner for which this is the negation).
If the -C option is set, then damapper also outputs a file Y.X.las for a given block pair that contains all the same matches as in X.Y.las but where the A-read is a contig of the reference and the B-read is a mapped read. And if the -N options is set, then the file Y.X.las is not produced.