40a345b04f483a7e67494e62afc8528675eb587e
braney
  Mon Mar 6 12:06:43 2023 -0800
make sure alignment blockse are single coverage over the query.

diff --git src/hg/hgTracks/pslTrack.c src/hg/hgTracks/pslTrack.c
index d56d367..e8cad8b 100644
--- src/hg/hgTracks/pslTrack.c
+++ src/hg/hgTracks/pslTrack.c
@@ -286,30 +286,31 @@
 }
 
 struct linkedFeatures *lfFromPslx(struct psl *psl,
 	int sizeMul, boolean isXeno, boolean nameGetsPos, struct track *tg)
 /* Create a linked feature item from pslx.  Pass in sizeMul=1 for DNA,
  * sizeMul=3 for protein.
  * Don't free psl afterwards! */
 {
 int grayIx = pslGrayIx(psl, isXeno, maxShade);
 struct linkedFeatures *lf;
 boolean rcTarget = (psl->strand[1] == '-');
 
 AllocVar(lf);
 lf->score = (psl->match - psl->misMatch - psl->repMatch);
 lf->grayIx = grayIx;
+lf->qSize = psl->qSize;
 if (nameGetsPos)
     {
     char buf[256];
     safef(buf, sizeof(buf), "%s:%d-%d %s:%d-%d", psl->qName, psl->qStart, psl->qEnd,
     	psl->tName, psl->tStart, psl->tEnd);
     lf->extra = cloneString(buf);
     int len = strlen(psl->qName) + 32;
     lf->name = needMem(len);
     safef(lf->name, len, "%s %s %dk", psl->qName, psl->strand, psl->qStart/1000);
     }
 else
     lf->name = cloneString(psl->qName);
 lf->orientation = orientFromChar(psl->strand[0]);
 if (rcTarget)
     lf->orientation = -lf->orientation;