src/hg/hgc/hgc.c 1.1518

1.1518 2009/03/13 21:29:22 angie
Extra vertical whitespace between alt. pcr matches as suggested by Brooke. For HapMap SNPs (Phase III), show average of populations' allele frequencies instead of sum of all individual alleles.
Index: src/hg/hgc/hgc.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgc/hgc.c,v
retrieving revision 1.1517
retrieving revision 1.1518
diff -b -B -U 4 -r1.1517 -r1.1518
--- src/hg/hgc/hgc.c	12 Mar 2009 19:22:32 -0000	1.1517
+++ src/hg/hgc/hgc.c	13 Mar 2009 21:29:22 -0000	1.1518
@@ -5727,13 +5727,16 @@
     {
     puts("<HR>");
     printf("<B>Other matches for these primers:</B><BR>\n");
     for (psl = otherPsls;  psl != NULL;  psl = psl->next)
+	{
+	puts("<BR>");
 	if (target != NULL)
 	    printPcrTargetMatch(target, psl, FALSE);
 	else
 	    printPosOnChrom(psl->tName, psl->tStart, psl->tEnd,
 			    psl->strand, FALSE, NULL);
+	}
     puts("<HR>");
     }
 printPcrSequence(target, itemPsl, fPrimer, rPrimer);
 
@@ -18315,9 +18318,9 @@
 float freq2 = 0.0;
 
 if (majorCount == 0)
     {
-    printf("<TR><TD>%s</TD><TD>not available</TD><TD>not available</TD></TR>\n", pop);
+    printf("<TR><TD>%s</TD><TD align=center>-</TD><TD align=center>-</TD></TR>\n", pop);
     return;
     }
 
 if (sameString(allele1, majorAllele))
@@ -18354,8 +18357,29 @@
 printf("</TR>\n");
 
 }
 
+void showHapmapAverageRow(char *label, float freq1)
+{
+float freq2 = 1.0 - freq1;
+printf("<TR><TD>%s</TD>", label);
+if (freq1 > 0.5)
+    {
+    printf("<TD bgcolor = \"lightgrey\" align=right>(%3.2f%%)</TD>", freq1*100);
+    printf("<TD align=right>(%3.2f%%)</TD>", freq2*100);
+    }
+else if (freq1 < 0.5)
+    {
+    printf("<TD align=right>(%3.2f%%)</TD>", freq1*100);
+    printf("<TD bgcolor = \"lightgrey\" align=right>(%3.2f%%)</TD>", freq2*100);
+    }
+else
+    {
+    printf("<TD align=right>(%3.2f%%)</TD>", freq1*100);
+    printf("<TD align=right>(%3.2f%%)</TD>", freq2*100);
+    }
+printf("</TR>\n");
+}
 
 void doHapmapSnpsSummaryTable(struct sqlConnection *conn, struct trackDb *tdb, char *itemName,
 			      boolean showOrtho)
 /* Use the hapmapAllelesSummary table (caller checks for existence) to display allele
@@ -18441,8 +18465,9 @@
 char *majorAlleles[HAP_PHASEIII_POPCOUNT];
 int majorCounts[HAP_PHASEIII_POPCOUNT], haploCounts[HAP_PHASEIII_POPCOUNT];
 int totalA1Count = 0, totalA2Count = 0, totalHaploCount = 0;
 float sumHet = 0.0;
+int sumA1A1 = 0, sumA1A2 = 0, sumA2A2 = 0;
 int popCount = 0;
 char *allele1 = NULL, *allele2 = NULL;
 for (i=0;  i < HAP_PHASEIII_POPCOUNT;  i++)
     {
@@ -18488,18 +18513,19 @@
 	totalA2Count += 2*item->homoCount2 + item->heteroCount;
 	totalHaploCount += haploCounts[i];
 	sumHet += ((float)item->heteroCount /
 		   (item->homoCount1 + item->homoCount2 + item->heteroCount));
+	sumA1A1 += item->homoCount1;
+	sumA1A2 += item->heteroCount;
+	sumA2A2 += item->homoCount2;
 	popCount++;
 	}
     }
 printf("<TR><TH>Population</TH> <TH>%s</TH> <TH>%s</TH></TR>\n", allele1, allele2);
 for (i=0;  i < HAP_PHASEIII_POPCOUNT;  i++)
     showOneHapmapRow(hapmapPhaseIIIPops[i], allele1, allele2, majorAlleles[i],
 		     majorCounts[i], haploCounts[i]);
-char *totalMajorAllele = (totalA1Count >= totalA2Count) ? allele1 : allele2;
-int totalMajorCount = max(totalA1Count, totalA2Count);
-showOneHapmapRow("Total", allele1, allele2, totalMajorAllele, totalMajorCount, totalHaploCount);
+showHapmapAverageRow("Average", (float)totalA1Count / totalHaploCount);
 printf("</TABLE>\n");
 
 printf("<BR><B>Average of populations' observed heterozygosities:</B> %3.2f%%<BR>\n",
        (100.0 * sumHet/popCount));