58828cd10787ef70000e7cfd999a3458f0492141
braney
  Thu Nov 20 10:41:41 2014 -0800
backout change to allow gff3 files to not specify phase on exons (perMark)

diff --git src/lib/gff3.c src/lib/gff3.c
index c2cc424..f32a90a 100644
--- src/lib/gff3.c
+++ src/lib/gff3.c
@@ -316,31 +316,31 @@
 g3a->seqid = unescapeStrPooled(g3a, words[0]);
 g3a->source = unescapeStrPooled(g3a, words[1]);
 g3a->type = unescapeStrPooled(g3a, words[2]);
 g3a->start = gff3FileStrToInt(g3a->file, words[3])-1;
 g3a->end = gff3FileStrToInt(g3a->file, words[4]);
 if (!sameString(words[5], "."))
     {
     g3a->score = gff3FileStrToFloat(g3a->file, words[5]);
     g3a->haveScore = TRUE;
     }
 g3a->strand = parseStrand(g3a, words[6]);
 g3a->phase = parsePhase(g3a, words[7]);
 if (sameString(g3a->type, "CDS"))
     {
     if (g3a->phase < 0)
-	g3a->phase = 0;  // assume the phase is 0
+	gff3AnnErr(g3a, "CDS feature must have phase");
     }
 else
     {
 #if 0 // spec unclear; bug report filed
     // spec currently doesn't restrict phase, unclear if it's allowed on start/stop codon features
     if (g3a->phase >= 0)
         gff3AnnErr(g3a, "phase only allowed on CDS features");
 #endif
     }
 }
 
 /* check that an attribute tag name is valid. */
 static boolean checkAttrTag(struct gff3Ann *g3a, char *tag)
 {
 // FIXME: spec is not clear on what is a valid tag.