LAindex(1) index Daligner alignment files


LAindex -v source:las ...


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.