cf56097b1e6a5f61ba03b882cdf885a913c08c48
markd
Wed Dec 14 11:29:32 2016 -0800
remove status field from gencode hgc display; this is being dropped by gencode and ensembl
diff --git src/hg/hgc/gencodeClick.c src/hg/hgc/gencodeClick.c
index 4e3e14c..2f7a2fa 100644
--- src/hg/hgc/gencodeClick.c
+++ src/hg/hgc/gencodeClick.c
@@ -321,64 +321,56 @@
printf("
");
if (geneLabel != NULL)
prApprisTdAnchor(transAttrs->geneId, geneLabel, apprisGeneUrl);
else
printf(" | ");
printf("\n");
}
static void writeBasicInfoHtml(struct sqlConnection *conn, struct trackDb *tdb, char *gencodeId, struct genePred *transAnno,
struct wgEncodeGencodeAttrs *transAttrs,
int geneChromStart, int geneChromEnd,
struct wgEncodeGencodeGeneSource *geneSource, struct wgEncodeGencodeTranscriptSource *transcriptSource,
struct wgEncodeGencodeTag *tags, bool haveTsl, struct wgEncodeGencodeTranscriptionSupportLevel *tsl)
/* write basic HTML info for all genes */
{
-/*
- * notes:
- * - According to Steve: `status' is not the same for ensembl and havana. So either avoid displaying it
- * or display it as `automatic status' or `manual status'.
- */
-
// basic gene and transcript information
printf("\n");
printf(" | Transcript | Gene | \n");
printf("\n");
printf("Gencode id");
prTdEnsIdAnchor(transAttrs->transcriptId, ensemblTranscriptIdUrl);
prTdEnsIdAnchor(transAttrs->geneId, ensemblGeneIdUrl);
printf(" | \n");
printf("HAVANA manual id");
prTdEnsIdAnchor(transAttrs->havanaTranscriptId, vegaTranscriptIdUrl);
prTdEnsIdAnchor(transAttrs->havanaGeneId, vegaGeneIdUrl);
printf(" | \n");
printf("Position");
printf(" | ");
writePosLink(transAnno->chrom, transAnno->txStart, transAnno->txEnd);
printf(" | ");
writePosLink(transAnno->chrom, geneChromStart, geneChromEnd);
printf(" | \n");
printf("Strand | %s | | \n", transAnno->strand);
printf("Biotype | %s | %s | \n", gencodeBiotypesUrl, transAttrs->transcriptType, transAttrs->geneType);
-printf("Status | %s | %s | \n", transAttrs->transcriptStatus, transAttrs->geneStatus);
-
printf("Annotation Level | %s (%d) | | \n", getLevelDesc(transAttrs->level), transAttrs->level);
printf("Annotation Method | %s | %s | \n", getMethodDesc(transcriptSource->source), getMethodDesc(geneSource->source));
if (haveTsl)
{
char *tslDesc = getSupportLevelDesc(tsl);
printf("Transcription Support Level | %s | | \n", tslDesc, tslDesc);
}
printf("HGNC gene symbol | ");
prExtIdAnchor(transAttrs->geneName, hgncUrl);
printf(" | \n");
printf("CCDS | ");
if (!isEmpty(transAttrs->ccdsId))
|
---|
|