NAME

       HPCdaligner - generate a script to run daligner(1)

SYNOPSIS

       HPCdaligner  [-vbAI]  [-kint(14)]  [-wint(6)][-hint(35)]  [-tint]  [-Mint] [-edouble(.70)]
       [-lint(1000)]  [-sint(100)]  [-Hint]  [-mtrack]+  [-dalint(4)]  [-degint(25)]  path:db|dam
       [first:int[-last:int]]

DESCRIPTION

       HPCdaligner  writes a UNIX shell script to the standard output that consists of a sequence
       of commands that effectively run daligner(1) on all pairs of blocks of  a  split  database
       and then externally sorts and merges them using LAsort(1) and LAmerge(1) into a collection
       of alignment files with names path.#.las where # ranges from 1 to the number of blocks the
       database  is split into.  These sorted files if concatenated by say LAcat(1) would contain
       all the alignments in sorted order (of a-read, then b-read, and  so  on).   Moreover,  all
       overlaps  for  a  given a-read are guaranteed to not be split across files, so one can run
       artifact analyzers or error correction on each sorted file in parallel.

       The database must have been previously split by DBsplit(1) and all the parameters,  except
       -v,  -dal,  and  -deg,  are  passed through to the calls to daligner(1).  The defaults for
       these parameters are as for daligner(1).  The -v flag, for verbose-mode, is also passed to
       all calls to LAsort(1) and LAmerge(1).  -dal and -deg options are described later.

       For  a  database divided into N sub-blocks, the calls to daligner(1) will produce in total
       2TN^2 .las files assuming daligner runs with T threads.  These will  then  be  sorted  and
       merged  into  N^2  sorted  .las  files, one for each block pair.  These are then merged in
       ceil(log_deg N) phases where the number of files decreases  geometrically  in  -deg  until
       there  is  1  file per row of the N x N block matrix.  So at the end one has N sorted .las
       files that when concatenated would give a single large sorted overlap file.

       The -dal option (default 4) gives the desired number of  block  comparisons  per  call  to
       daligner(1).   Some  must contain dal-1 comparisons, and the first dal-2 block comparisons
       even less, but the HPCdaligner "planner" does the best it can to give an average  load  of
       dal  block comparisons per command.  The -deg option (default 25) gives the maximum number
       of files that will be merged in a single LAmerge(1) command.  The planner makes  the  most
       even k-ary tree of merges, where the number of levels is ceil(log_deg N).

       If the integers first and last are missing, then the script produced is for every block in
       the database.  If first is present, then HPCdaligner produces an incremental  script  that
       compares  blocks  first  through last (last = first if not present) against each other and
       all previous blocks 1 through first-1, and then incrementally updates the .las  files  for
       blocks 1 through first-1, and creates the .las files for blocks first through last.

       Each  UNIX  command  line  output  by  the  HPCdaligner  can be a batch job (we use the &&
       operator to combine several commands into one line to make this so).  Dependencies between
       jobs  can  be  maintained  simply  by first running all the daligner(1) jobs, then all the
       initial sort jobs, and then all the jobs in each phase of the external merge  sort.   Each
       of  these  phases  is  separated  by  an  informative  comment  line  for  your  scripting
       convenience.

SEE ALSO

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