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)

1.0+20151214                                      January 2016                                        LAindex(1)