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("<td> "); if (geneLabel != NULL) prApprisTdAnchor(transAttrs->geneId, geneLabel, apprisGeneUrl); else printf("<td> "); printf("</tr>\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("<table class=\"hgcCcds\" style=\"white-space: nowrap;\"><thead>\n"); printf("<tr><th><th>Transcript<th>Gene</tr>\n"); printf("</thead><tbody>\n"); printf("<tr><th>Gencode id"); prTdEnsIdAnchor(transAttrs->transcriptId, ensemblTranscriptIdUrl); prTdEnsIdAnchor(transAttrs->geneId, ensemblGeneIdUrl); printf("</tr>\n"); printf("<tr><th>HAVANA manual id"); prTdEnsIdAnchor(transAttrs->havanaTranscriptId, vegaTranscriptIdUrl); prTdEnsIdAnchor(transAttrs->havanaGeneId, vegaGeneIdUrl); printf("</tr>\n"); printf("<tr><th>Position"); printf("<td>"); writePosLink(transAnno->chrom, transAnno->txStart, transAnno->txEnd); printf("<td>"); writePosLink(transAnno->chrom, geneChromStart, geneChromEnd); printf("</tr>\n"); printf("<tr><th>Strand<td>%s<td></tr>\n", transAnno->strand); printf("<tr><th><a href=\"%s\" target = _blank>Biotype</a><td>%s<td>%s</tr>\n", gencodeBiotypesUrl, transAttrs->transcriptType, transAttrs->geneType); -printf("<tr><th>Status<td>%s<td>%s</tr>\n", transAttrs->transcriptStatus, transAttrs->geneStatus); - printf("<tr><th>Annotation Level<td>%s (%d)<td></tr>\n", getLevelDesc(transAttrs->level), transAttrs->level); printf("<tr><th>Annotation Method<td>%s<td>%s</tr>\n", getMethodDesc(transcriptSource->source), getMethodDesc(geneSource->source)); if (haveTsl) { char *tslDesc = getSupportLevelDesc(tsl); printf("<tr><th><a href=\"#tsl\">Transcription Support Level</a><td><a href=\"#%s\">%s</a><td></tr>\n", tslDesc, tslDesc); } printf("<tr><th>HGNC gene symbol<td colspan=2>"); prExtIdAnchor(transAttrs->geneName, hgncUrl); printf("</tr>\n"); printf("<tr><th>CCDS<td>"); if (!isEmpty(transAttrs->ccdsId))