Extend transcript boundaries instead of skipping the transcript

This modifies the commit d6cf97b, it is better to include
such transcript and modify their boundaries instead of omitting
the transcripts entirely

Resolves #2323

NEWS

@@ -18,7 +18,8 @@ Changes affecting specific commands:
 
 * bcftools csq
 
-    - Check the input GFF for features outside transcript boundaries (#2323)
+    - Check the input GFF for features outside transcript boundaries and extend the transcript
+      to contain the feature fully (#2323)
 
 * bcftools query
 

gff.c

@@ -1017,9 +1017,9 @@ int gff_parse(gff_t *gff)
             if ( !gff->warned.ftr_out_of_bounds || gff->verbosity > 1 )
                 fprintf(stderr,"Warning: The GFF contains features outside the transcript boundaries .. %s\n",gff_id2string(gff,transcript,tr->id));
             gff->warned.ftr_out_of_bounds++;
-            continue;
+            if ( ftr->beg < tr->beg ) tr->beg = ftr->beg;
+            if ( ftr->end > tr->end ) tr->end = ftr->end;
         }
-
         tr->used = 1;
         tr->gene->used = 1;