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)