xenial (1) HPCdaligner.1.gz

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)