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root/gclib/gffread/gffread.cpp
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# Line 9 | Line 9
9  
10   #define USAGE "Usage:\n\
11   gffread <input_gff> [-g <genomic_seqs_fasta> | <dir>][-s <seq_info.fsize>] \n\
12 < [-o <outfile.gff>] [-t <tname>] [-r [[<strand>]<chr>:]<start>..<end>] \n\
13 < [-CTVNJMKQAFGRUVBHZWTOLE] [-w <spl_exons.fa>] [-x <spl_cds.fa>] [-y <tr_cds.fa>]\n\
12 > [-o <outfile.gff>] [-t <tname>] [-r [[<strand>]<chr>:]<start>..<end> [-R]]\n\
13 > [-CTVNJMKQAFGUBHZWTOLE] [-w <exons.fa>] [-x <cds.fa>] [-y <tr_cds.fa>]\n\
14   [-i <maxintron>] \n\
15   Filters and/or converts GFF3/GTF2 records.\n\
16   <input_gff> is a GFF file, use '-' if the GFF records will be given at stdin\n\
# Line 24 | Line 24
24        <seq-name> <seq-length> <seq-description>\n\
25        (useful for -A option with mRNA/EST/protein mappings)\n\
26    -i  discard transcripts having an intron larger than <maxintron>\n\
27 <  -r  only show transcripts crossing coordinate range <start>..<end>\n\
27 >  -r  only show transcripts overlapping coordinate range <start>..<end>\n\
28        (on chromosome/contig <chr>, strand <strand> if provided)\n\
29    -R  for -r option, discard all transcripts that are not fully \n\
30 <      contained within given range\n\
30 >      contained within the given range\n\
31    -U  discard single-exon transcripts\n\
32    -C  coding only: discard mRNAs that have no CDS feature\n\
33    -F  full GFF attribute preservation (all attributes are shown)\n\
# Line 639 | Line 639
639       if (rfltStart!=0 || rfltEnd!=MAX_UINT) {
640         if (rfltWithin) {
641           if (gffrec->start<rfltStart || gffrec->end>rfltEnd) {
642 <            return false;
642 >            return false; //not within query range
643              }
644           }
645         else {
# Line 713 | Line 713
713        exit(1);
714        }
715      }
716 //protmap=(args.getOpt('P')!=NULL);
716   if (fullCDSonly) validCDSonly=true;
717   if (verbose) {
718       fprintf(stderr, "Command line was:\n");
# Line 786 | Line 785
785        rfltEnd=(uint)gsend.asInt();
786        if (rfltEnd==0) rfltEnd=MAX_UINT;
787        }
789  
788     } //gseq/range filtering
789   else {
790     if (rfltWithin)
791 <     GError("Error: option -R doesn't make sense without -r!\n");
791 >     GError("Error: option -R requires -r!\n");
792 >   //if (rfltWholeTranscript)
793 >   //  GError("Error: option -P requires -r!\n");
794     }
795   s=args.getOpt('m');
796   if (!s.is_empty()) {

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