src/hg/hgTracks/bamTrack.c 1.7

1.7 2009/08/25 06:04:05 angie
Ignore strand -- seems to always be + and BAM inherently adjusts sequence and CIGAR to the positive strand when the alignment was -. Probably should test for inversion cases and make those appear minus strand.

Index: src/hg/hgTracks/bamTrack.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgTracks/bamTrack.c,v
retrieving revision 1.6
retrieving revision 1.7
diff -b -B -U 4 -r1.6 -r1.7
--- src/hg/hgTracks/bamTrack.c	18 Aug 2009 23:41:23 -0000	1.6
+++ src/hg/hgTracks/bamTrack.c	25 Aug 2009 06:04:05 -0000	1.7
@@ -118,12 +118,11 @@
 struct linkedFeaturesSeries *lfs;
 AllocVar(lfs);
 lfs->name = cloneString(lf->name);
 lfs->grayIx = lf->grayIx;
-if (!lf->next || lf->next->orientation == -lf->orientation)
-    lfs->orientation = lf->orientation;
 if (lf->next != NULL)
     slSort(&lf, linkedFeaturesCmpStart);
+lfs->orientation = 0;
 lfs->start = lf->start;
 lfs->end = lf->next ? lf->next->end : lf->end;
 lfs->features = lf;
 return lfs;