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README.md

The Damapper Library

Author: Gene Myers

First: July 11, 2016

For typeset documentation, examples of use, and design philosophy please go to my blog.

The commands below permit one to find the best, or several good alternative, locations that a read may have been sampled from in a reference genome. The code is designed for PACBIO reads with an assumption of a 15% average error rate and occational large drop out regions where the quality is exceedingly low.

1. damapper [-vpzCN] [-k<int(20)>] [-t<int>] [-M<int>] [-T<int(4)>]
                     [-e<double(.85)] [-s<int(100)>] [-n<double(1.)>]
                     [-m<track>]+ <ref:db|dam> <reads:db|dam> ...

Search the reference data base <ref> for the best matches to each read in the list of databases or database blocks <reads>. The parameters -v, -k, -t, -M, -T -e, -s, and -m are exactly as for the daligner (see here). 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). Matches at the expected correlation given by -e are sought and unlike daligner they can be of any length (i.e. short). Alignments at much lower rates are not forced in order to report a single matching interval, but rather when a read has bad stretches, the result is a chain of local alignments over the good segments of the read. Damapper reports the best chain covering a segment of a read, and may report several chains covering disjoint segments (e.g. the case of a chimeric read). If the -n option is given then all chains that are within given fraction of optimal are also reported, e.g. -n.95 reports all matches within 95% of the top match.

For a given reference data base X and read block Y, damapper produces the single file Y.X..las. Note the order of X and Y is reversed from that on the command line (which is different than the conventions for daligner). The reversal of the order of the blocks emphasizes that in the result, the A-reads are the mapped reads, and the B-reads are contigs of the reference. Each file is sorted in order of the A-reads, and if a match is a chain of local alignments the la's in the chain occur in increasing order of A-coordinate. Moreover, if several near optimal matches are reported, matches appear in order of score starting with the best.

Itf the -C option is set, then damapper also outputs a file X.Y.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 files Y.X.las is not produced.

The -p option requests that damapper produce a repeat profile track for each read. For each trace-point sized interval (established by the -s parameter) the number of times, c, this segment is involved in a distinct alignment to the reference is estimated. 0 is recorded for segments that don't match anything in the reference, 1 for segments that match uniquely, and otherwise floor(log10c/10) up to a cap of 40 corresponding to 10,000 copies. Observe carefully that the track has the same form as intrinsic quality values. They can be output by DBdump and DaViewer is able to graphically display them. These profiles should make it obvious when a read does not have a unique location in a reference sequence due to its being entirely or almost entirely repetitive.

2. HPC.damapper [-vbpzCN]
                [-k<int(20)>] [-t<int>] [-M<int>] [-e<double(.85)] [-s<int(100)]
                [-n<double(1.)>] [-m<track>]+ [-B<int(4)>] [-T<int(4)>] [-f<name>]
                <ref:db|dam> <reads:db|dam> [<first:int>[-<last:int>]]

HPC.damapper 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>. If <last> is missing then only the single block <first> is mapped, and if <first> is also missing then all blocks of the database are mapped. Except for the -B and -f options, all other options are passed through to damapper, save of -v which is passed to every program in the script. The -B option determines the maximum number of blocks mapped per call to damapper in the script.

The command script output by HPC.damapper and other HPC.<x> programs consists of command blocks each of which begins with a comment line (begins with #) followed by a potentially long list of lines each containing a shell command. Command blocks whose comment mentions "jobs" and gives the number of said in parenthesis, we call parallel blocks because each command line in the block can be sent to a node in a cluster for independent execution, i.e. none of the commands in a block depend on another in the block. The remaining command blocks we call house-keeping blocks because they can be executed by the shell on the launch/server node and the commands are either checking the integrity of .las files with LAcheck, or removing intermediate files with rm. Each block should be performed in the order given and should complete before the next block is performed.

If the -f option is set, then each command block is written to a file with a name of the form <name>.#.<description> where <name> is specified by the user in the -f option argument, # gives the order in which the command block in the given file is to be performed in relation to other command block files, and <description> is a (very) short symbolic reminder of what the block is doing. For example, "HPC.damapper -fJOBS REF DB" would produce the files:

    JOBS.01.OVL
    JOBS.02.CHECK.OPT

The files with the suffix .OPT are optional and need not be executed albeit we highly recommend that one run the CHECK block.

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