0aad47f5ee3160c1f1f6eff3324fe8e20a774efe
hartera
  Thu Feb 28 10:44:29 2013 -0800
Removed oldScore column as no longer needed and renamed oldIntronCount to alignGapCount in ucscRetroInfo table so change code and variable names to match for details page display.
diff --git src/hg/hgc/retroClick.c src/hg/hgc/retroClick.c
index 776990c..1ab2ca9 100644
--- src/hg/hgc/retroClick.c
+++ src/hg/hgc/retroClick.c
@@ -514,31 +514,31 @@
     }
 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, 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>Possible Introns (or gaps) in Retro<TD>%d + %d\n", pg->intronCount, pg->alignGapCount);
 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;
     }
 wt[0] = 0; wt[1] = 0.85; wt[2] = 0.2; wt[3] = 0.3; wt[4] = 0.8; 
 wt[5] = 1; wt[6] = 1  ; wt[7] = 0.5; wt[8] = 0.5; wt[9] = 1; wt[10] = 1;
 #ifdef debug
@@ -574,43 +574,43 @@
 printf("<TR><TH>score function<TD>1:xon %d %4.1f conSS %d 2: ax %4.1f 3: pA %4.1f 4: net + %4.1f max (%d, %d) 5: procIntrons %d %4.1f 6:in.cnt %d -%4.1f 7:overlap - %4.1f  8:cov %d*(qe %d- qsz %d)/%d=%4.1f 9:tRep - %4.1f 10:oldintron %d %4.1f </td></TR>\n",
                 pg->exonCover,
                 wt[1]*(log(pg->exonCover+1)/log(2))*200 , 
                 pg->conservedSpliceSites,
                 wt[2]*(((log(pg->axtScore>0?pg->axtScore:1)/log(2))*170)-1000),
                 wt[3]*(log(pg->polyAlen+2)*200) ,
                 wt[4]*overlapOrtholog*10 , pg->overlapMouse, pg->overlapDog,
                 pg->processedIntrons,
                 wt[5]*(((log(pg->processedIntrons > 0 ? pg->processedIntrons : 1))/log(2))*600) ,
                 pg->intronCount, 
                 wt[6]*pow(pg->intronCount,0.5)*750 ,
                 wt[7]*(maxOverlap*300),
                 pg->coverage, pg->qEnd, pg->qSize , pg->qSize,
                 wt[8]*((pg->coverage/100.0)*(1.0-coverFactor)*300.0),
                 wt[9]*(pg->tReps*10), 
-                pg->oldIntronCount,
-                wt[10]*pg->oldIntronCount);
+                pg->alignGapCount,
+                wt[10]*pg->alignGapCount);
 printf("<TR><TH>score function<TD>%4.1f+ %4.1f+ %4.1f+ %4.1f+ %4.1f - %4.1f - %4.1f+ %4.1f - %4.1f - %4.1f</td></TR>\n",
                 wt[1]*(log(pg->exonCover+1)/log(2))*200 , 
                 wt[2]*(((log(pg->axtScore>0?pg->axtScore:1)/log(2))*170)-1000),
                 wt[3]*(log(pg->polyAlen+2)*200) ,
                 wt[4]*overlapOrtholog*10 , 
                 wt[5]*(((log(pg->processedIntrons > 0 ? pg->processedIntrons : 1))/log(2))*600) ,
                 (float)wt[6]*pow(pg->intronCount,0.5)*750 ,
                 (float)wt[7]*(maxOverlap*300),
                 wt[8]*((pg->coverage/100.0)*(1.0-coverFactor)*300.0),
                 wt[9]*(pg->tReps*10), 
-                wt[10]*pg->oldIntronCount);
+                wt[10]*pg->alignGapCount);
 if (pg->kaku > 0 && pg->kaku < 1000000)
     printf("<TR><TH>KA/KU mutation rate in non-syn sites vs utr with repect to parent gene<TD>%4.2f</TR>\n",  pg->kaku);
 #endif
 #ifdef xxx
 safef(query, sizeof(query), "select * from refGene where chrom = '%d' and txEnd > %d and txStart %d and name = '%s'", 
         pg->chrom, pg->gStart, pg->gEnd , pg->overName );
 sr = sqlGetResult(conn, query);
 if ((row = sqlNextRow(sr)) != NULL)
     overlappingGene = genePredLoad(row);
 if (overlappingGene != NULL)
     {
     printf ("CDS exons %d ",genePredcountCdsExons(overlappingGene));
     }
 
 #endif