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RR optimization: since total count in BaseCounts is requested so often, don't keep computing it from scratch each time.

This commit is contained in:
Eric Banks 2012-10-17 00:44:23 -04:00
parent b30e2a5b7d
commit 19e2b5f0d5
2 changed files with 44 additions and 36 deletions
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72
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseCounts.java
View File

@ -20,6 +20,7 @@ import java.util.Map;
private final Map<BaseIndex, Integer> counts; // keeps track of the base counts
private final Map<BaseIndex, Long> sumQuals; // keeps track of the quals of each base
private int totalCount = 0; // keeps track of total count since this is requested so often
public BaseCounts() {
counts = new EnumMap<BaseIndex, Integer>(BaseIndex.class);
@ -36,49 +37,62 @@ import java.util.Map;
baseCounts.counts.put(BaseIndex.C, countsACGT[1]);
baseCounts.counts.put(BaseIndex.G, countsACGT[2]);
baseCounts.counts.put(BaseIndex.T, countsACGT[3]);
baseCounts.totalCount = countsACGT[0] + countsACGT[1] + countsACGT[2] + countsACGT[3];
return baseCounts;
}
@Requires("other != null")
public void add(BaseCounts other) {
for (final BaseIndex i : BaseIndex.values())
counts.put(i, counts.get(i) + other.counts.get(i));
public void add(final BaseCounts other) {
for (final BaseIndex i : BaseIndex.values()) {
final int otherCount = other.counts.get(i);
counts.put(i, counts.get(i) + otherCount);
totalCount += otherCount;
}
}
@Requires("other != null")
public void sub(BaseCounts other) {
for (final BaseIndex i : BaseIndex.values())
counts.put(i, counts.get(i) - other.counts.get(i));
public void sub(final BaseCounts other) {
for (final BaseIndex i : BaseIndex.values()) {
final int otherCount = other.counts.get(i);
counts.put(i, counts.get(i) - otherCount);
totalCount -= otherCount;
}
}
@Ensures("totalCount() == old(totalCount()) || totalCount() == old(totalCount()) + 1")
public void incr(byte base) {
final BaseIndex i = BaseIndex.byteToBase(base);
if (i != null) // no Ns
counts.put(i, counts.get(i) + 1);
}
@Ensures("totalCount() == old(totalCount()) || totalCount() == old(totalCount()) + 1")
public void incr(byte base, byte qual) {
public void incr(final byte base) {
final BaseIndex i = BaseIndex.byteToBase(base);
if (i != null) { // no Ns
counts.put(i, counts.get(i) + 1);
totalCount++;
}
}
@Ensures("totalCount() == old(totalCount()) || totalCount() == old(totalCount()) + 1")
public void incr(final byte base, final byte qual) {
final BaseIndex i = BaseIndex.byteToBase(base);
if (i != null) { // no Ns
counts.put(i, counts.get(i) + 1);
totalCount++;
sumQuals.put(i, sumQuals.get(i) + qual);
}
}
@Ensures("totalCount() == old(totalCount()) || totalCount() == old(totalCount()) - 1")
public void decr(byte base) {
final BaseIndex i = BaseIndex.byteToBase(base);
if (i != null) // no Ns
counts.put(i, counts.get(i) - 1);
}
@Ensures("totalCount() == old(totalCount()) || totalCount() == old(totalCount()) - 1")
public void decr(byte base, byte qual) {
public void decr(final byte base) {
final BaseIndex i = BaseIndex.byteToBase(base);
if (i != null) { // no Ns
counts.put(i, counts.get(i) - 1);
totalCount--;
}
}
@Ensures("totalCount() == old(totalCount()) || totalCount() == old(totalCount()) - 1")
public void decr(final byte base, final byte qual) {
final BaseIndex i = BaseIndex.byteToBase(base);
if (i != null) { // no Ns
counts.put(i, counts.get(i) - 1);
totalCount--;
sumQuals.put(i, sumQuals.get(i) - qual);
}
}
@ -131,11 +145,7 @@ import java.util.Map;
@Ensures("result >= 0")
public int totalCount() {
int sum = 0;
for (int c : counts.values())
sum += c;
return sum;
return totalCount;
}
/**
@ -146,7 +156,7 @@ import java.util.Map;
*/
@Ensures({"result >=0.0", "result<= 1.0"})
public double baseCountProportion(final byte base) {
return (double) counts.get(BaseIndex.byteToBase(base)) / totalCount();
return baseCountProportion(BaseIndex.byteToBase(base));
}
/**
@ -157,10 +167,10 @@ import java.util.Map;
*/
@Ensures({"result >=0.0", "result<= 1.0"})
public double baseCountProportion(final BaseIndex baseIndex) {
int total = totalCount();
final int total = totalCount();
if (total == 0)
return 0.0;
return (double) counts.get(baseIndex) / totalCount();
return (double) counts.get(baseIndex) / total;
}
@ -248,7 +258,7 @@ import java.util.Map;
final int total = totalCountWithoutIndels();
if (total == 0)
return 0.0;
return (double) counts.get(index) / totalCountWithoutIndels();
return (double) counts.get(index) / total;
}
public Object[] countsArray() {

8
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/HeaderElement.java
View File

@ -157,11 +157,9 @@ public class HeaderElement {
* @return whether or not the HeaderElement is variant due to excess insertions
*/
private boolean isVariantFromInsertions(double minIndelProportion) {
int numberOfBases = consensusBaseCounts.totalCount();
if (numberOfBases == 0 && insertionsToTheRight > 0)
return true; // we only have insertions
else if (numberOfBases == 0)
return false; // we don't have anything
final int numberOfBases = consensusBaseCounts.totalCount();
if (numberOfBases == 0)
return (insertionsToTheRight > 0); // do we only have insertions?
// if we have bases and insertions, check the ratio
return ((double) insertionsToTheRight / numberOfBases) > minIndelProportion;