xenial (1) LAindex.1.gz

NAME

       LAindex - index Daligner alignment files

SYNOPSIS

       LAindex -v source:las ...

DESCRIPTION

       LAindex takes a series of one or more sorted .las files and produces a "pile index" for each one.  If the
       input file has name X.las, then the name of its index file is .X.las.idx.  For each A-read  pile  encoded
       in  the  .las  file,  the index contains the offset to the first local alignment with A in the file.  The
       index starts with four 64-bit integers that encode the numbers % P, + T, %  T,  and  @  T  described  for
       LAdump(1), and then an offset for each pile beginning with the first A-read in the file (which may not be
       read 0).  The index is meant to allow programs that process piles to more efficiently read just the piles
       they need at any momment int time, as opposed to having to sequentially scan through the .las file.

SEE ALSO

       daligner(1)