Commit 2148d2d5 authored by Steffen Möller's avatar Steffen Möller
Browse files

New upstream version 0.11.7

parent 6d79d533

gffread.cpp

+15 −4
Original line number Diff line number Diff line
@@ -4,7 +4,7 @@ 
#define __STDC_FORMAT_MACROS

#include <inttypes.h>



#define VERSION "0.11.6"

#define VERSION "0.11.7"



#define USAGE "gffread v" VERSION ". Usage:\n\

gffread <input_gff> [-g <genomic_seqs_fasta> | <dir>][-s <seq_info.fsize>] \n\
@@ -126,7 +126,8 @@ Output options:\n\ 
 --table output a simple tab delimited format instead of GFF, with columns\n\

       having the values of GFF attributes given in <attrlist>; special\n\

       pseudo-attributes (prefixed by @) are recognized:\n\

       @chr, @start, @end, @strand, @numexons, @exons, @cds, @covlen, @cdslen\n\

       @id, @geneid, @chr, @start, @end, @strand, @numexons, @exons, \n\

       @cds, @covlen, @cdslen\n\

 -v,-E expose (warn about) duplicate transcript IDs and other potential\n\

       problems with the given GFF/GTF records\n\

"
@@ -159,7 +160,8 @@ class RefTran { 


enum ETableFieldType {

  ctfGFF_Attr=0, // attribute name as is

  ctfGFF_ID, //ID or @id

  ctfGFF_ID, //ID or @id or transcript_id

  ctfGFF_geneID, //geneID or @gene_id

  ctfGFF_Parent, //Parent or @parent

  ctfGFF_chr, //@chr

  ctfGFF_feature, //@feature
@@ -293,6 +295,7 @@ void setTableFormat(GStr& s) { 
	 GHash<ETableFieldType> specialFields;

	 specialFields.Add("chr", new ETableFieldType(ctfGFF_chr));

	 specialFields.Add("id", new ETableFieldType(ctfGFF_ID));

	 specialFields.Add("geneid", new ETableFieldType(ctfGFF_geneID));

	 specialFields.Add("parent", new ETableFieldType(ctfGFF_Parent));

	 specialFields.Add("feature", new ETableFieldType(ctfGFF_feature));

	 specialFields.Add("start", new ETableFieldType(ctfGFF_start));
@@ -317,11 +320,16 @@ void setTableFormat(GStr& s) { 
    	  else GMessage("Warning: table field '@%s' not recognized!\n",w.chars());

    	  continue;

      }

      if (w=="ID") {

      if (w=="ID" || w=="transcript_id") {

    	  CTableField tcol(ctfGFF_ID);

    	  tableCols.Add(tcol);

    	  continue;

      }

      if (w=="geneID" || w=="gene_id") {

    	  CTableField tcol(ctfGFF_geneID);

    	  tableCols.Add(tcol);

    	  continue;

      }

      if (w=="Parent") {

    	  CTableField tcol(ctfGFF_Parent);

    	  tableCols.Add(tcol);
@@ -951,6 +959,9 @@ void printGxfTab(FILE* f, GffObj& g) { 
		case ctfGFF_ID:

			fprintf(f,"%s",g.getID());

			break;

		case ctfGFF_geneID:

			fprintf(f,"%s",g.getGeneID());

			break;

		case ctfGFF_Parent:

			if (g.parent!=NULL) fprintf(f,"%s",g.parent->getID());

			else fprintf(f, ".");