SYNOPSIS

LAmerge [-v] merge:las parts:las ...

DESCRIPTION

Merge the .las files parts into a singled sorted file merge, where it is assumed that the input parts files are sorted. Due to operating system limits, the number of parts files must be <= 252. With the -v option set, the program reports the number of records read and written.

Used correctly, LAmerge and LAsort(1) together allow one to perform an "external" sort that produces a collection of sorted files containing in aggregate all the local alignments found by the daligner(1), such that their concatenation is sorted in order of (a,b,o,ab). In particular, this means that all the alignments for a given a-read will be found consecutively in one of the files. So computations that need to look at all the alignments for a given read can operate in simple sequential scans of these sorted files.