5452c9b2c8cd95c39600fdae1858cb58403530c7
markd
  Mon Jun 29 05:30:15 2015 -0700
fix pslStats computation of query coverage.  It was not counting based aligned to Ns (no redmine)

diff --git src/hg/pslStats/pslStats.c src/hg/pslStats/pslStats.c
index 1bd4b15..b8f4162 100644
--- src/hg/pslStats/pslStats.c
+++ src/hg/pslStats/pslStats.c
@@ -126,31 +126,31 @@
 {
 struct hash* querySizesTbl = hashNew(queryHashPowTwo);
 struct lineFile *lf = lineFileOpen(querySizeFile, TRUE);
 char *row[2];
 
 while (lineFileNextRowTab(lf, row, ArraySize(row)))
     sumStatsGetForQuery(querySizesTbl, row[0], sqlUnsigned(row[1]));
 
 lineFileClose(&lf);
 return querySizesTbl;
 }
 
 static unsigned calcAligned(struct psl *psl)
 /* compute the number of bases aligned */
 {
-return psl->match + psl->misMatch + psl->repMatch;
+return psl->match + psl->misMatch + psl->repMatch + psl->nCount;
 }
 
 static unsigned calcMatch(struct psl *psl)
 /* compute the number of bases matching */
 {
 return psl->match + psl->repMatch;
 }
 
 static float calcIdent(struct psl *psl)
 /* get fraction ident for a psl */
 {
 unsigned aligned = calcAligned(psl);
 if (aligned == 0)
     return 0.0;
 else