src/hg/pslCDnaGenomeMatch/pslCDnaGenomeMatch.c 1.24

Index: src/hg/pslCDnaGenomeMatch/pslCDnaGenomeMatch.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/pslCDnaGenomeMatch/pslCDnaGenomeMatch.c,v
retrieving revision 1.23
retrieving revision 1.24
diff -b -B -U 4 -r1.23 -r1.24
--- src/hg/pslCDnaGenomeMatch/pslCDnaGenomeMatch.c	18 Aug 2009 22:31:32 -0000	1.23
+++ src/hg/pslCDnaGenomeMatch/pslCDnaGenomeMatch.c	18 Aug 2009 23:24:05 -0000	1.24
@@ -788,8 +788,9 @@
             name, score, nextBestScore, maxScore);
     if (maxScore == score)
         {
         maxHits ++;
+        nextBestScore = score;
         verbose(3,"%s score %d == maxScore %d next %d \n",
                 name, score, maxScore, nextBestScore);
         }
     else 
@@ -1329,8 +1330,9 @@
     if (psl->strand[0] == '+' && psl->strand[1] == '-')
         pslRc(psl);
     pslTabOut(psl, outFile);
     outputCount++;
+    filterCount++;
     return;
     }
 /* one loci for each place the mrna alignments to the genome */
 for (align = alignList ; align != NULL ; align= align->next)
@@ -1445,9 +1447,9 @@
 doOneMrna(lastName, subList);
 alignFreeList(&subList);
 //pslFreeList(&pslList);
 verbose(1,"Wrote %d alignments out of %d \n", outputCount, aliCount);
-verbose(1,"Filtered %d out of %d mRNAs \n", filterCount, mrnaCount);
+verbose(1,"Kept %d out of %d mRNAs \n", filterCount, mrnaCount);
 if (computeSS)
     {
     fprintf(outFile, "%8d %8d %8d %8d  %8d %8d %8d %8d  %8d %8d %8d %8d  %8d %8d %8d %8d \n",
             getHistogram('a','a'), getHistogram('a','c'), getHistogram('a','g'), getHistogram('a','t'),