remove special handling of 50:50 mixtures for ordering

seppinho · Apr 27, 2018 · 29cf76f · 29cf76f
1 parent 3947ae4
commit 29cf76f
Showing 1 changed file with 2 additions and 50 deletions.
diff --git a/src/main/java/genepi/mut/objects/VariantLine.java b/src/main/java/genepi/mut/objects/VariantLine.java
@@ -260,30 +260,8 @@ public void parseLine(BasePosition base, double level) throws IOException {
 		char topBaseFWD = '-';
 		char minorBaseFWD = '-';
 
-		// prefer lexicographic order in case of 50/50
-		if (topBasePercentsFWD == minorBasePercentsFWD && topBasePercentsFWD > 0) {
-			if (aFWDPercents == gFWDPercents && gFWDPercents == topBasePercentsFWD) {
-				topBaseFWD = 'A';
-				minorBaseFWD = 'G';
-			} else if (aFWDPercents == cFWDPercents && cFWDPercents == topBasePercentsFWD) {
-				topBaseFWD = 'A';
-				minorBaseFWD = 'C';
-			} else if (aFWDPercents == tFWDPercents && tFWDPercents == topBasePercentsFWD) {
-				topBaseFWD = 'A';
-				minorBaseFWD = 'T';
-			} else if (cFWDPercents == tFWDPercents && tFWDPercents == topBasePercentsFWD) {
-				topBaseFWD = 'C';
-				minorBaseFWD = 'T';
-			} else if (cFWDPercents == gFWDPercents && gFWDPercents == topBasePercentsFWD) {
-				topBaseFWD = 'C';
-				minorBaseFWD = 'G';
-			} else if (gFWDPercents == tFWDPercents && tFWDPercents == topBasePercentsFWD) {
-				topBaseFWD = 'G';
-				minorBaseFWD = 'T';
-			}
-		}
 
-		else if (aFWD >= cFWD && aFWD >= gFWD && aFWD >= tFWD && aFWD >= dFWD && aFWD > 0) {
+		if (aFWD >= cFWD && aFWD >= gFWD && aFWD >= tFWD && aFWD >= dFWD && aFWD > 0) {
 			topBaseFWD = 'A';
 		}
 
@@ -306,34 +284,8 @@ else if (dFWD >= cFWD && dFWD >= gFWD && dFWD >= aFWD && dFWD >= tFWD && dFWD >
 		char topBaseREV = '-';
 		char minorBaseREV = '-';
 
-		if (topBasePercentsREV == minorBasePercentsREV) {
-			if (aREVPercents == gREVPercents && gREVPercents == topBasePercentsREV) {
-				topBaseREV = 'A';
-				minorBaseREV = 'G';
-			}
-			if (aREVPercents == cREVPercents && cREVPercents == topBasePercentsREV) {
-				topBaseREV = 'A';
-				minorBaseREV = 'C';
-			}
-			if (aREVPercents == tREVPercents && tREVPercents == topBasePercentsREV) {
-				topBaseREV = 'A';
-				minorBaseREV = 'T';
-			}
-			if (cREVPercents == tREVPercents && tREVPercents == topBasePercentsREV) {
-				topBaseREV = 'C';
-				minorBaseREV = 'T';
-			}
-			if (cREVPercents == gREVPercents && gREVPercents == topBasePercentsREV) {
-				topBaseREV = 'C';
-				minorBaseREV = 'G';
-			}
-			if (gREVPercents == tREVPercents && tREVPercents == topBasePercentsREV) {
-				topBaseREV = 'G';
-				minorBaseREV = 'T';
-			}
-		}
 
-		else if (aREV >= cREV && aREV >= gREV && aREV >= tREV && aREV >= dREV && aREV > 0) {
+		if (aREV >= cREV && aREV >= gREV && aREV >= tREV && aREV >= dREV && aREV > 0) {
 			topBaseREV = 'A';
 		}