Steffen Möller pushed to branch upstream at Debian Med / gffread
Commits:
2148d2d5 by Steffen Moeller at 2020-01-27T11:04:01+01:00
New upstream version 0.11.7
- - - - -
1 changed file:
- gffread.cpp
Changes:
=====================================
gffread.cpp
=====================================
@@ -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, ".");
View it on GitLab:
https://salsa.debian.org/med-team/gffread/commit/2148d2d567ed992121ed34af206dfb6425e50f5b
--
View it on GitLab:
https://salsa.debian.org/med-team/gffread/commit/2148d2d567ed992121ed34af206dfb6425e50f5b
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