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Next intermediate commit in the pool caller. Lots of bug fixes and now we can emit true vcf's with calls in discovery mode (still of unknown quality) - old validation mode is temporarily broken,will be fixed in next refactoring.

This commit is contained in:
Guillermo del Angel 2012-01-23 09:22:31 -05:00
parent b123416c4c
commit 966387ca0b
1 changed files with 23 additions and 9 deletions
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32
public/java/src/org/broadinstitute/sting/utils/MathUtils.java
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@ -1572,34 +1572,37 @@ public class MathUtils {
/** /**
* Vector operations * Vector operations
* @param v1 first numerical array
* @param v2 second numerical array
* @return a new array with the elements added
*/ */
public static double[] vectorSum(double v1[], double v2[]) { public static <E extends Number> Double[] vectorSum(E v1[], E v2[]) {
if (v1.length != v2.length) if (v1.length != v2.length)
throw new UserException("BUG: vectors v1, v2 of different size in vectorSum()"); throw new UserException("BUG: vectors v1, v2 of different size in vectorSum()");
double result[] = new double[v1.length]; Double[] result = new Double[v1.length];
for (int k=0; k < v1.length; k++) for (int k=0; k < v1.length; k++)
result[k] = v1[k]+v2[k]; result[k] = v1[k].doubleValue()+v2[k].doubleValue();
return result; return result;
} }
public static double[] scalarTimesIntVector(double a, int[] v1) { public static <E extends Number> Double[] scalarTimesVector(E a, E[] v1) {
double result[] = new double[v1.length]; Double result[] = new Double[v1.length];
for (int k=0; k < v1.length; k++) for (int k=0; k < v1.length; k++)
result[k] = a*v1[k]; result[k] = a.doubleValue()*v1[k].doubleValue();
return result; return result;
} }
public static double dotProduct(double v1[], double v2[]) { public static <E extends Number> Double dotProduct(E[] v1, E[] v2) {
if (v1.length != v2.length) if (v1.length != v2.length)
throw new UserException("BUG: vectors v1, v2 of different size in vectorSum()"); throw new UserException("BUG: vectors v1, v2 of different size in vectorSum()");
double result = 0.0; Double result = 0.0;
for (int k=0; k < v1.length; k++) for (int k=0; k < v1.length; k++)
result += v1[k]*v2[k]; result += v1[k].doubleValue() *v2[k].doubleValue();
return result; return result;
@ -1613,4 +1616,15 @@ public class MathUtils {
return result; return result;
} }
// todo - silly overloading, just because Java can't unbox/box arrays of primitive types, and we can't do generics with primitive types!
public static Double[] vectorLog10(Double v1[]) {
Double result[] = new Double[v1.length];
for (int k=0; k < v1.length; k++)
result[k] = Math.log10(v1[k]);
return result;
}
} }