NAME

       rapmap_quasimap - rapmap module to map reads using the SA-based index

SYNOPSIS

       rapmap quasimap [-c] [-f] [-s] [-m <positive integer>] [-t <positive integer>] [-o <path>]
       [-r <path>] [-2 <path>] [-1 <path>] [-n] -i <path> [--] [--version] [-h]

DESCRIPTION

       RapMap Mapper (SA-based)

       RapMap  is  a  testing  ground  for  ideas  in  quasi-mapping  /  (lightweight  /  pseudo)
       transcriptome  alignment. That means that, at this point, it is somewhat experimental. The
       develop branch will have the latest improvements and additions, but is not  guaranteed  to
       be  stable between commits. Breaking changes to the master branch will be accompanied by a
       tag to the version before the breaking change. Currently, RapMap is a  stand-alone  quasi-
       mapper  that  can  be used with other tools. It is also being used as part of Sailfish and
       Salmon. Eventually, the hope is to create and stabilize an API so that it can be used as a
       library from other tools.

OPTIONS

       -c, --consistentHits
              Ensure that the hits collected are consistent (co-linear)

       -f, --fuzzyIntersection
              Find paired-end mapping locations using fuzzy intersection

       -s, --strictCheck
              Perform extra checks to try and assure that only equally "best" mappings for a read
              are reported

       -m, --maxNumHits <positive integer>
              Reads mapping to more than this many loci are discarded

       -t, --numThreads <positive integer>
              Number of threads to use

       -o, --output <path>
              The output file (default: stdout)

       -r, --unmatedReads <path>
              The location of single-end reads

       -2, --rightMates <path>
              The location of the right paired-end reads

       -1, --leftMates <path>
              The location of the left paired-end reads

       -n, --noOutput
              Don't write out any alignments (for speed testing purposes)

       -i, --index <path>
              (required) The location of the quasiindex

       --, --ignore_rest
              Ignores the rest of the labeled arguments following this flag.

       --version
              Displays version information and exits.

       -h,  --help
              Displays usage information and exits.

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used  for
       any other usage of the program.