NAME

       slice_mercator_alignment  -  Extracts  the  corresponding  subalignment  from  a  Mercator
       multiple alignment

SYNOPSIS

       slice_mercator_alignment [options] <genome> <chromosome> <start> <end> <strand>

DESCRIPTION

       slice_mercator_alignment from FSA 1.15.9

       Extracts the corresponding subalignment from a Mercator multiple alignment.

OPTIONS

       -h, --help
              show this message

       -D, --data <directory>
              path to map, genome and alignment files

       -M, --map <directory>
              path to map and genome files

       -A, --align <directory>
              path to alignment files

       -L, --lazy
              warn, rather than die, if the subalignment can't be obtained

       -U, --truncate
              truncate unmappable sequence (rather than skipping) and show truncated subalignment

       -s, --stockholm
              use and display Stockholm-format alignments with conservation  statistics  (default
              is multi-FASTA)

       -0, --zerobased
              coordinates are 0-based (default is 1-based)

       -o, --halfopen
              end coordinate is open, i.e., [start, end)

       Assumes that coordinates are 1-based and fully-closed, therefore representing the interval
       [start, end].

       If requested, unmappable sequence will be truncated to the mappable portion; note that the
       truncation will favor the beginning of the requested sequence.

       If  the requested sequence is on the - strand, then the corresponding subalignment will be
       reverse-complemented.

AUTHOR

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