37608a22d891c5febb6c0dad94ef859258aea5b8
markd
  Mon Nov 7 16:24:09 2016 -0800
add geneType and transcriptType to gtfToGenePred info output file

diff --git src/lib/gff.c src/lib/gff.c
index 5cae55c..03c409b 100644
--- src/lib/gff.c
+++ src/lib/gff.c
@@ -228,30 +228,34 @@
        gl->intronId = gffFileGetStr(gff, val);
    else if (sameString("intron_status", type))
        gl->intronStatus = gffFileGetStr(gff, val);
    else if (sameString("protein_id", type))
        gl->proteinId = gffFileGetStr(gff, val);
    else if (sameString("gene_name", type))
        gl->geneName = gffFileGetStr(gff, val);
    else if (sameString("transcript_name", type))
        gl->transcriptName = gffFileGetStr(gff, val);
    else if (sameString("gene_version", type))
        gl->geneVersion = gffFileGetStr(gff, val);
    else if (sameString("transcript_version", type))
        gl->transcriptVersion = gffFileGetStr(gff, val);
    else if (sameString("protein_version", type))
        gl->proteinVersion = gffFileGetStr(gff, val);
+   else if (sameString("gene_type", type) || sameString("gene_biotype", type))
+       gl->geneType = gffFileGetStr(gff, val);
+   else if (sameString("transcript_type", type)|| sameString("transcript_biotype", type))
+       gl->transcriptType = gffFileGetStr(gff, val);
    }
 }
 
 void gffFileAddRow(struct gffFile *gff, int baseOffset, char *words[], int wordCount, 
     char *fileName, int lineIx)
 /* Process one row of GFF file (a non-comment line parsed by tabs normally). */
 {
 struct hashEl *hel;
 struct gffLine *gl;
 
 if (wordCount < 8)
     gffSyntaxError(fileName, lineIx, "Word count less than 8 ");
 AllocVar(gl);
 
 if ((hel = hashLookup(gff->seqHash, words[0])) == NULL)