04a89671eb368a9fac4b5b1999ff4b55b13337a8
angie
  Tue Sep 17 07:17:49 2013 -0700
Yikes, when querying at the cart position instead of the whole genome,annoStreamVcf was skipping rows that it shouldn't have!

diff --git src/lib/annoStreamVcf.c src/lib/annoStreamVcf.c
index 2ed7b19..6626be4 100644
--- src/lib/annoStreamVcf.c
+++ src/lib/annoStreamVcf.c
@@ -114,31 +114,31 @@
 	regionStart = minEnd;
 	regionEnd = annoAssemblySeqSize(sSelf->assembly, minChrom);
 	}
     else
 	{
 	regionStart = max(regionStart, minEnd);
 	}
     }
 char **words = nextRowRaw(self);
 if (regionChrom != NULL && words != NULL)
     {
     if (self->isTabix && strcmp(getProperChromName(self, words[0]), regionChrom) < 0)
 	lineFileSetTabixRegion(self->vcff->lf, regionChrom, regionStart, regionEnd);
     while (words != NULL &&
 	   (strcmp(getProperChromName(self, words[0]), regionChrom) < 0 ||
-	    (sameString(words[0], regionChrom) && self->record->chromEnd < regionEnd)))
+	    (sameString(words[0], regionChrom) && self->record->chromEnd < regionStart)))
 	words = nextRowRaw(self);
     }
 return words;
 }
 
 static struct annoRow *asvNextRow(struct annoStreamer *sSelf, char *minChrom, uint minEnd,
 				  struct lm *callerLm)
 /* Return an annoRow encoding the next VCF record, or NULL if there are no more items. */
 {
 struct annoStreamVcf *self = (struct annoStreamVcf *)sSelf;
 if (minChrom != NULL && sSelf->chrom != NULL && differentString(minChrom, sSelf->chrom))
     errAbort("annoStreamVcf %s: nextRow minChrom='%s' but region chrom='%s'",
 	     sSelf->name, minChrom, sSelf->chrom);
 if (self->maxRecords > 0 && self->recordCount >= self->maxRecords)
     return NULL;