NAME

       isect_mercator_alignment_gff  -  Extracts subalignments from a Mercator multiple alignment
       for the features in the GFF file

SYNOPSIS

       isect_mercator_alignment_gff [options] <genome> <GFF file>

DESCRIPTION

       isect_mercator_alignment_gff from FSA 1.15.9

       Extracts subalignments from a Mercator multiple alignment for  the  features  in  the  GFF
       file.

OPTIONS

       -h, --help
              show this message

       -v, --version
              show version information

       -t, --type <string>
              only look at features of particular type

       -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)

       -e, --verbose
              report progress

       PLEASE NOTE: While this program is reasonably fast if  the  GFF  is  properly  ordered  by
       chromosome  and  the  start and end coordinates of features, it will be *very slow* if the
       GFF is not sorted.  Assumes that the "seqid" or "name" field (the first field) of the  GFF
       entries holds the chromosome name.

       Note  that  the  GFF  specification  defines  coordinates  to be 1-based and fully-closed,
       therefore representing the interval [start, end].  Conformance to  this  specification  is
       assumed internally.

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

       If a GFF feature 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.