NAME

       refeature - Read a file representing a set of features, optionally

SYNOPSIS

       refeature [OPTIONS] <infile>

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 autorecognition requires a 'seekable'
       input stream (e.g., an actual file rather than a pipe from stdin).

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.