3c07e0899280b85976b6fcff458970e8166c4248
baertsch
  Sun May 29 19:19:12 2011 -0700
use version number in retro click score calc
diff --git src/hg/hgc/retroClick.c src/hg/hgc/retroClick.c
index 527fabc..07a9c56 100644
--- src/hg/hgc/retroClick.c
+++ src/hg/hgc/retroClick.c
@@ -486,49 +486,56 @@
     if ( (gp->cdsStart <= gp->exonEnds[i]) &&  
          (gp->cdsEnd >= gp->exonStarts[i]) )
          count++;
     }
 return count;
 
 }
 static void displayMappingInfo(struct sqlConnection *conn, struct mappingInfo *mi)
 /* display information from a transMap table */
 {
 struct ucscRetroInfo *pg = mi->pg;
 double  wt[12];     /* weights on score function*/
 char query[512];
 char *name;
 char alignTbl[128];
+char scoreSql[128];
 struct psl *psl;
 float coverFactor = 0;
 float maxOverlap = 0;
 if (mi->suffix == NULL)
+    {
     safef(alignTbl, sizeof(alignTbl), "%s%sAli", mi->tblPre, mi->geneSet);
+    safef(scoreSql, sizeof(scoreSql), "select max(score) from %s%sInfo", mi->tblPre, mi->geneSet);
+    }
 else
+    {
     safef(alignTbl, sizeof(alignTbl), "%s%sAli%s", mi->tblPre, mi->geneSet, mi->suffix);
+    safef(scoreSql, sizeof(scoreSql), "select max(score) from %s%sInfo%s", mi->tblPre, mi->geneSet, mi->suffix);
+    }
 printf("<TABLE class=\"transMap\">\n");
 printf("<CAPTION>Retrogene stats</CAPTION>\n");
 printf("<THEAD>\n");
 printf("<TR><TH>Feature<TH>Value </TR>\n");
 printf("</THEAD><TBODY>\n");
 if (sameString(pg->type, "singleExon"))
     printf("<TR><TH>Type of Parent<TD>%s</tr>\n",pg->type);
 else 
     printf("<TR><TH>Expression of Retrocopy<TD>%s</TR>\n",pg->type);
 printf("<TR><TH>Score <TD>%d (range from 0 - %d)</TR>\n",  
         pg->score,
-        sqlQuickNum(conn, "select max(score) from ucscRetroInfo") );
+        sqlQuickNum(conn, scoreSql) );
 printf("<TR><TH>Alignment Coverage of parent gene (Bases&nbsp;matching Parent) <TD>%d %% &nbsp;(%d bp) </TR>\n", pg->coverage, pg->matches);
 printf("<TR><TH>Introns Procesed Out <TD>%d out of %d (%d exons covered)\n", pg->processedIntrons, (pg->parentSpliceCount/2), pg->exonCover);
 printf("<TR><TH>Possible Introns (or gaps) in Retro<TD>%d + %d\n", pg->intronCount, pg->oldIntronCount);
 printf("<TR><TH>Conserved Splice Sites<TD>%d</TR>\n",  pg->conservedSpliceSites);
 printf("<TR><TH>Parent Splice Sites<TD>%d</TR>\n",  pg->parentSpliceCount);
 psl = getAlignments(conn, alignTbl, mi->pg->name);
 if (psl != NULL)
     {
     maxOverlap = (float)pg->maxOverlap/(float)(psl->match+psl->misMatch+psl->repMatch)  ;
     coverFactor = ((float)(psl->qSize-psl->qEnd)/(float)psl->qSize);
     }
 else 
     {
     maxOverlap = 0;
     }