2b5eb866f050d964d8964ec5a84f7b63889cc6b1 angie Mon Jun 3 14:39:36 2013 -0700 New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene predictions to identify which part of a gene, if any, is hit by each variant; several additional sources of annotations/predictions e.g. dbNSFP scores and conserved elements/scores; and several filters to constrain output to the variants most likely to have a functional effect. Along with the new CGI, there are various lib bugfixes and improvements, a new hg/lib/tests/ testcase, and some test file changes to accomodate data updates to both knownGene and the pg* tables in knownGene. refs #6152 diff --git src/hg/lib/annoStreamWig.c src/hg/lib/annoStreamWig.c index 3e944e7..f1274e4 100644 --- src/hg/lib/annoStreamWig.c +++ src/hg/lib/annoStreamWig.c @@ -122,24 +122,24 @@ { if (pVSelf == NULL) return; struct annoStreamWig *self = *(struct annoStreamWig **)pVSelf; carefulClose(&(self->wibF)); freeMem(self->wibFile); annoStreamerFree(pVSelf); } struct annoStreamer *annoStreamWigDbNew(char *db, char *table, struct annoAssembly *aa, int maxOutput) /* Create an annoStreamer (subclass) object from a wiggle database table. */ { struct annoStreamWig *self = NULL; AllocVar(self); -self->wigStr = annoStreamDbNew(db, table, aa, asParseText(wiggleAsText)); +self->wigStr = annoStreamDbNew(db, table, aa, asParseText(wiggleAsText), maxOutput); struct annoStreamer *streamer = &(self->streamer); annoStreamerInit(streamer, aa, asParseText(annoRowWigAsText), self->wigStr->name); streamer->rowType = arWig; streamer->setRegion = aswSetRegion; streamer->nextRow = aswNextRow; streamer->close = aswClose; return (struct annoStreamer *)self; }