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.