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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Guillermo del Angel 2012-03-26 15:15:50 -04:00
parent ce617b2dfc 8f0828daa6
commit 1c424c0daf
3 changed files with 32 additions and 28 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
View File

@ -500,7 +500,7 @@ public class PairHMMIndelErrorModel {
if (stop > ref.getWindow().getStop())
stop = ref.getWindow().getStop();
// if there's an insertion in the read, the read stop position will be less than start + read legnth,
// if there's an insertion in the read, the read stop position will be less than start + read length,
// but we want to compute likelihoods in the whole region that a read might overlap
if (stop <= start + readLength) {
stop = start + readLength-1;

5
public/java/src/org/broadinstitute/sting/utils/Haplotype.java
View File

@ -72,6 +72,11 @@ public class Haplotype {
public boolean equals( Object h ) {
return h instanceof Haplotype && Arrays.equals(bases, ((Haplotype) h).bases);
}
@Override
public int hashCode() {
return Arrays.hashCode(bases);
}
public void addReadLikelihoods( final String sample, final double[] readLikelihoods ) {
if( readLikelihoodsPerSample == null ) {

53
public/java/src/org/broadinstitute/sting/utils/MathUtils.java
View File

@ -51,7 +51,8 @@ public class MathUtils {
public static final double[] log10Cache;
private static final double[] jacobianLogTable;
private static final double JACOBIAN_LOG_TABLE_STEP = 0.001;
private static final double MAX_JACOBIAN_TOLERANCE = 10.0;
private static final double JACOBIAN_LOG_TABLE_INV_STEP = 1.0 / 0.001;
private static final double MAX_JACOBIAN_TOLERANCE = 8.0;
private static final int JACOBIAN_LOG_TABLE_SIZE = (int) (MAX_JACOBIAN_TOLERANCE / JACOBIAN_LOG_TABLE_STEP) + 1;
private static final int MAXN = 11000;
private static final int LOG10_CACHE_SIZE = 4 * MAXN; // we need to be able to go up to 2*(2N) when calculating some of the coefficients
@ -74,7 +75,7 @@ public class MathUtils {
// under/overflow checking, so this shouldn't be used in the general case (but is fine
// if one is already make those checks before calling in to the rounding).
public static int fastRound(double d) {
return (d > 0) ? (int) (d + 0.5d) : (int) (d - 0.5d);
return (d > 0.0) ? (int) (d + 0.5d) : (int) (d - 0.5d);
}
public static double approximateLog10SumLog10(final double[] vals) {
@ -85,8 +86,6 @@ public class MathUtils {
final int maxElementIndex = MathUtils.maxElementIndex(vals, endIndex);
double approxSum = vals[maxElementIndex];
if (approxSum == Double.NEGATIVE_INFINITY)
return approxSum;
for (int i = 0; i < endIndex; i++) {
if (i == maxElementIndex || vals[i] == Double.NEGATIVE_INFINITY)
@ -95,7 +94,7 @@ public class MathUtils {
final double diff = approxSum - vals[i];
if (diff < MathUtils.MAX_JACOBIAN_TOLERANCE) {
// See notes from the 2-inout implementation below
final int ind = fastRound(diff / MathUtils.JACOBIAN_LOG_TABLE_STEP); // hard rounding
final int ind = fastRound(diff * MathUtils.JACOBIAN_LOG_TABLE_INV_STEP); // hard rounding
approxSum += MathUtils.jacobianLogTable[ind];
}
}
@ -124,7 +123,7 @@ public class MathUtils {
// max(x,y) + log10(1+10^-abs(x-y))
// we compute the second term as a table lookup with integer quantization
// we have pre-stored correction for 0,0.1,0.2,... 10.0
final int ind = fastRound(diff / MathUtils.JACOBIAN_LOG_TABLE_STEP); // hard rounding
final int ind = fastRound(diff * MathUtils.JACOBIAN_LOG_TABLE_INV_STEP); // hard rounding
return big + MathUtils.jacobianLogTable[ind];
}
@ -206,7 +205,7 @@ public class MathUtils {
/**
* Calculates the log10 cumulative sum of an array with log10 probabilities
*
* @param log10p the array with log10 probabilites
* @param log10p the array with log10 probabilities
* @param upTo index in the array to calculate the cumsum up to
* @return the log10 of the cumulative sum
*/
@ -592,12 +591,12 @@ public class MathUtils {
}
public static int maxElementIndex(final double[] array, final int endIndex) {
if (array == null)
if (array == null || array.length == 0)
throw new IllegalArgumentException("Array cannot be null!");
int maxI = -1;
for (int i = 0; i < endIndex; i++) {
if (maxI == -1 || array[i] > array[maxI])
int maxI = 0;
for (int i = 1; i < endIndex; i++) {
if (array[i] > array[maxI])
maxI = i;
}
@ -609,12 +608,12 @@ public class MathUtils {
}
public static int maxElementIndex(final int[] array, int endIndex) {
if (array == null)
if (array == null || array.length == 0)
throw new IllegalArgumentException("Array cannot be null!");
int maxI = -1;
for (int i = 0; i < endIndex; i++) {
if (maxI == -1 || array[i] > array[maxI])
int maxI = 0;
for (int i = 1; i < endIndex; i++) {
if (array[i] > array[maxI])
maxI = i;
}
@ -638,12 +637,12 @@ public class MathUtils {
}
public static int minElementIndex(double[] array) {
if (array == null)
if (array == null || array.length == 0)
throw new IllegalArgumentException("Array cannot be null!");
int minI = -1;
for (int i = 0; i < array.length; i++) {
if (minI == -1 || array[i] < array[minI])
int minI = 0;
for (int i = 1; i < array.length; i++) {
if (array[i] < array[minI])
minI = i;
}
@ -651,12 +650,12 @@ public class MathUtils {
}
public static int minElementIndex(byte[] array) {
if (array == null)
if (array == null || array.length == 0)
throw new IllegalArgumentException("Array cannot be null!");
int minI = -1;
for (int i = 0; i < array.length; i++) {
if (minI == -1 || array[i] < array[minI])
int minI = 0;
for (int i = 1; i < array.length; i++) {
if (array[i] < array[minI])
minI = i;
}
@ -664,12 +663,12 @@ public class MathUtils {
}
public static int minElementIndex(int[] array) {
if (array == null)
if (array == null || array.length == 0)
throw new IllegalArgumentException("Array cannot be null!");
int minI = -1;
for (int i = 0; i < array.length; i++) {
if (minI == -1 || array[i] < array[minI])
int minI = 0;
for (int i = 1; i < array.length; i++) {
if (array[i] < array[minI])
minI = i;
}