PROGRAM:        refeature

DESCRIPTION:    Read a file representing a set of features, optionally
                alter the set in one or more of several possible ways, then
                output it in the desired format.  Input and output formats
                may be GFF, BED, or genepred.

                The input format is recognized automatically, but auto-
                recognition requires a 'seekable' input stream (e.g., an
                actual file rather than a pipe from stdin).

USAGE:          /home/mt269/phast/bin/refeature [OPTIONS] <infile>

OPTIONS:
    --include-only, -i <types>
        Include only features of the specified types (comma-delimited list);
        filter out everything else.

    --include-groups, -l <file>
        Include only groups whose names are listed in the specified file.
        Group names in file must be delimited by white-space (can be on
        any number of lines).

    --sort, -s
        Sort features primarily by start position and secondarily
        by end position (usually has desired effect in case of short
        overlapping features, e.g., start & stop codons).  Features
        will be sorted both across groups and within groups, but members
        of a group will be kept together.

    --unique, -u
        Ensures that output contains no overlapping groups (or
        subgroups, if -e).  If groups overlap, the one with the highest
        score (if available) or longest length (if no score) is kept and
        others are discarded.  Warning: long UTRs can have undesirable
        results; filter out UTR exons to avoid.

    --groupby, -g <tag>
        Group features according to specified tag (default "transcript_id")

    --exongroup, -e <tag>
        Sub-group features into contiguous sets, and define
        sub-groups using specified tag (e.g., "exon_id").  Can be
        used to group the features describing individual exons, e.g.,
        each CDS and its flanking splice sites.  Only features in the
        same major group will be included in the same minor group
        (e.g., exons of the same transcript).

    --fix-start-stop, -f
        Ensure that CDS features include start codons and exclude stop
        codons, as required by the GTF2 standard.  Assumes at most one
        start_codon and at most one stop_codon per group.

    --add-utrs, -U
        Create UTR features for portions of exons outside CDS (only
        useful with GFF output; features must be grouped at level
        of transcript).

    --add-introns, -I
        Create intron features between exons (only useful with GFF output;
        features must be grouped at level of transcript).

    --add-signals, -S
        Adds features for start and stop codons and 3' and 5' splice
        sites (only useful with GFF output; features must be grouped
        at level of transcript).  Start and stop codons will be added
        as required by the GTF2 standard (--fix-start-stop is not
        necessary).  Warning: does not correctly handle case of splice
        site in middle of start or stop codon.

    --output, -o gff|bed|genepred|wig
        Output format (default gff).  Note that wig output is fixedStep
        can only be used if all elements have a score and are of equal
        length.

    --simplebed, -b
        (for use with --output bed) Create a separate line for each
        feature in bed output (by default, all features of a group are
        described by a single line).

    --discards, -d <fname>
        Write any discarded features to specified file.

    --help, -h
        Print this help message.