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.