zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Eliminate 7-element arrays in BaseCounts and BaseAndQualsCount and replace with in-line primitive attributes. This is ugly but reduces heap overhead, and changes are localized. When used in conjunction with Mauricio's FastUtil changes it saves and additional 9% or so of execution time.

This commit is contained in:
Alec Wysoker 2013-02-26 16:23:12 -05:00
parent 69f6d53494
commit c8368ae2a5
2 changed files with 160 additions and 66 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

75
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseAndQualsCounts.java
View File

@ -53,39 +53,82 @@ package org.broadinstitute.sting.gatk.walkers.compression.reducereads;
* @since 6/15/12 * @since 6/15/12
*/ */
public class BaseAndQualsCounts extends BaseCounts { public class BaseAndQualsCounts extends BaseCounts {
private final long[] sumInsertionQuals;
private final long[] sumDeletionQuals;
public BaseAndQualsCounts() { private long sumInsertionQual_A = 0;
super(); private long sumDeletionQual_A = 0;
this.sumInsertionQuals = new long[BaseIndex.values().length]; private long sumInsertionQual_C = 0;
this.sumDeletionQuals = new long[BaseIndex.values().length]; private long sumDeletionQual_C = 0;
// Java primitive arrays comes zero-filled, so no need to do it explicitly. private long sumInsertionQual_G = 0;
} private long sumDeletionQual_G = 0;
private long sumInsertionQual_T = 0;
private long sumDeletionQual_T = 0;
private long sumInsertionQual_D = 0;
private long sumDeletionQual_D = 0;
private long sumInsertionQual_I = 0;
private long sumDeletionQual_I = 0;
private long sumInsertionQual_N = 0;
private long sumDeletionQual_N = 0;
public void incr(final byte base, final byte baseQual, final byte insQual, final byte delQual) { public void incr(final byte base, final byte baseQual, final byte insQual, final byte delQual) {
final BaseIndex i = BaseIndex.byteToBase(base); final BaseIndex i = BaseIndex.byteToBase(base);
super.incr(i, baseQual); super.incr(i, baseQual);
sumInsertionQuals[i.index] += insQual; switch (i) {
sumDeletionQuals[i.index] += delQual; case A: sumInsertionQual_A += insQual; sumDeletionQual_A += delQual; break;
case C: sumInsertionQual_C += insQual; sumDeletionQual_C += delQual; break;
case G: sumInsertionQual_G += insQual; sumDeletionQual_G += delQual; break;
case T: sumInsertionQual_T += insQual; sumDeletionQual_T += delQual; break;
case D: sumInsertionQual_D += insQual; sumDeletionQual_D += delQual; break;
case I: sumInsertionQual_I += insQual; sumDeletionQual_I += delQual; break;
case N: sumInsertionQual_N += insQual; sumDeletionQual_N += delQual; break;
}
} }
public void decr(final byte base, final byte baseQual, final byte insQual, final byte delQual) { public void decr(final byte base, final byte baseQual, final byte insQual, final byte delQual) {
final BaseIndex i = BaseIndex.byteToBase(base); final BaseIndex i = BaseIndex.byteToBase(base);
super.decr(i, baseQual); super.decr(i, baseQual);
sumInsertionQuals[i.index] -= insQual; switch (i) {
sumDeletionQuals[i.index] -= delQual; case A: sumInsertionQual_A -= insQual; sumDeletionQual_A -= delQual; break;
case C: sumInsertionQual_C -= insQual; sumDeletionQual_C -= delQual; break;
case G: sumInsertionQual_G -= insQual; sumDeletionQual_G -= delQual; break;
case T: sumInsertionQual_T -= insQual; sumDeletionQual_T -= delQual; break;
case D: sumInsertionQual_D -= insQual; sumDeletionQual_D -= delQual; break;
case I: sumInsertionQual_I -= insQual; sumDeletionQual_I -= delQual; break;
case N: sumInsertionQual_N -= insQual; sumDeletionQual_N -= delQual; break;
}
} }
public byte averageInsertionQualsOfBase(final BaseIndex base) { public byte averageInsertionQualsOfBase(final BaseIndex base) {
return getGenericAverageQualOfBase(base, sumInsertionQuals); return (byte) (getInsertionQual(base) / countOfBase(base));
} }
public byte averageDeletionQualsOfBase(final BaseIndex base) { public byte averageDeletionQualsOfBase(final BaseIndex base) {
return getGenericAverageQualOfBase(base, sumDeletionQuals); return (byte) (getDeletionQual(base) / countOfBase(base));
} }
private byte getGenericAverageQualOfBase(final BaseIndex base, final long[] sumQuals) { private long getInsertionQual(final BaseIndex base) {
return (byte) (sumQuals[base.index] / countOfBase(base)); switch (base) {
case A: return sumInsertionQual_A;
case C: return sumInsertionQual_C;
case G: return sumInsertionQual_G;
case T: return sumInsertionQual_T;
case D: return sumInsertionQual_D;
case I: return sumInsertionQual_I;
case N: return sumInsertionQual_N;
default: throw new IllegalArgumentException(base.name());
}
}
private long getDeletionQual(final BaseIndex base) {
switch (base) {
case A: return sumDeletionQual_A;
case C: return sumDeletionQual_C;
case G: return sumDeletionQual_G;
case T: return sumDeletionQual_T;
case D: return sumDeletionQual_D;
case I: return sumDeletionQual_I;
case N: return sumDeletionQual_N;
default: throw new IllegalArgumentException(base.name());
}
} }
} }

151
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseCounts.java
View File

@ -62,70 +62,107 @@ import com.google.java.contract.Requires;
public final static BaseIndex MAX_BASE_INDEX_WITH_NO_COUNTS = BaseIndex.N; public final static BaseIndex MAX_BASE_INDEX_WITH_NO_COUNTS = BaseIndex.N;
public final static byte MAX_BASE_WITH_NO_COUNTS = MAX_BASE_INDEX_WITH_NO_COUNTS.getByte(); public final static byte MAX_BASE_WITH_NO_COUNTS = MAX_BASE_INDEX_WITH_NO_COUNTS.getByte();
private final int[] counts; // keeps track of the base counts
private final long[] sumQuals; // keeps track of the quals of each base private int count_A = 0; // keeps track of the base counts
private int sumQual_A = 0; // keeps track of the quals of each base
private int count_C = 0;
private int sumQual_C = 0;
private int count_G = 0;
private int sumQual_G = 0;
private int count_T = 0;
private int sumQual_T = 0;
private int count_D = 0;
private int sumQual_D = 0;
private int count_I = 0;
private int sumQual_I = 0;
private int count_N = 0;
private int sumQual_N = 0;
private int totalCount = 0; // keeps track of total count since this is requested so often private int totalCount = 0; // keeps track of total count since this is requested so often
public BaseCounts() {
counts = new int[BaseIndex.values().length];
sumQuals = new long[BaseIndex.values().length];
// Java primitive arrays comes zero-filled, so no need to do it explicitly.
}
public static BaseCounts createWithCounts(int[] countsACGT) { public static BaseCounts createWithCounts(int[] countsACGT) {
BaseCounts baseCounts = new BaseCounts(); BaseCounts baseCounts = new BaseCounts();
baseCounts.counts[BaseIndex.A.index] = countsACGT[0]; baseCounts.count_A = countsACGT[0];
baseCounts.counts[BaseIndex.C.index] = countsACGT[1]; baseCounts.count_C = countsACGT[1];
baseCounts.counts[BaseIndex.G.index] = countsACGT[2]; baseCounts.count_G = countsACGT[2];
baseCounts.counts[BaseIndex.T.index] = countsACGT[3]; baseCounts.count_T = countsACGT[3];
baseCounts.totalCount = countsACGT[0] + countsACGT[1] + countsACGT[2] + countsACGT[3]; baseCounts.totalCount = countsACGT[0] + countsACGT[1] + countsACGT[2] + countsACGT[3];
return baseCounts; return baseCounts;
} }
@Requires("other != null") @Requires("other != null")
public void add(final BaseCounts other) { public void add(final BaseCounts other) {
for (final BaseIndex i : BaseIndex.values()) { this.count_A += other.count_A;
final int otherCount = other.counts[i.index]; this.count_C += other.count_C;
counts[i.index] += otherCount; this.count_G += other.count_G;
totalCount += otherCount; this.count_T += other.count_T;
} this.count_D += other.count_D;
this.count_I += other.count_I;
this.count_N += other.count_N;
this.totalCount += other.totalCount;
} }
@Requires("other != null") @Requires("other != null")
public void sub(final BaseCounts other) { public void sub(final BaseCounts other) {
for (final BaseIndex i : BaseIndex.values()) { this.count_A -= other.count_A;
final int otherCount = other.counts[i.index]; this.count_C -= other.count_C;
counts[i.index] -= otherCount; this.count_G -= other.count_G;
totalCount -= otherCount; this.count_T -= other.count_T;
} this.count_D -= other.count_D;
this.count_I -= other.count_I;
this.count_N -= other.count_N;
this.totalCount -= other.totalCount;
} }
@Ensures("totalCount() == old(totalCount()) || totalCount() == old(totalCount()) + 1") @Ensures("totalCount() == old(totalCount()) || totalCount() == old(totalCount()) + 1")
public void incr(final byte base) { public void incr(final byte base) {
final BaseIndex i = BaseIndex.byteToBase(base); add(BaseIndex.byteToBase(base), 1);
counts[i.index]++;
totalCount++;
} }
@Ensures("totalCount() == old(totalCount()) || totalCount() == old(totalCount()) + 1") @Ensures("totalCount() == old(totalCount()) || totalCount() == old(totalCount()) + 1")
public void incr(final BaseIndex base, final byte qual) { public void incr(final BaseIndex base, final byte qual) {
counts[base.index]++; switch (base) {
totalCount++; case A: ++count_A; sumQual_A += qual; break;
sumQuals[base.index] += qual; case C: ++count_C; sumQual_C += qual; break;
case G: ++count_G; sumQual_G += qual; break;
case T: ++count_T; sumQual_T += qual; break;
case D: ++count_D; sumQual_D += qual; break;
case I: ++count_I; sumQual_I += qual; break;
case N: ++count_N; sumQual_N += qual; break;
}
++totalCount;
} }
@Ensures("totalCount() == old(totalCount()) || totalCount() == old(totalCount()) - 1") @Ensures("totalCount() == old(totalCount()) || totalCount() == old(totalCount()) - 1")
public void decr(final byte base) { public void decr(final byte base) {
final BaseIndex i = BaseIndex.byteToBase(base); add(BaseIndex.byteToBase(base), -1);
counts[i.index]--; }
totalCount--;
private void add(final BaseIndex base, int amount) {
switch(base) {
case A: count_A += amount; break;
case C: count_C += amount; break;
case G: count_G += amount; break;
case T: count_T += amount; break;
case D: count_D += amount; break;
case I: count_I += amount; break;
case N: count_N += amount; break;
}
totalCount += amount;
} }
@Ensures("totalCount() == old(totalCount()) || totalCount() == old(totalCount()) - 1") @Ensures("totalCount() == old(totalCount()) || totalCount() == old(totalCount()) - 1")
public void decr(final BaseIndex base, final byte qual) { public void decr(final BaseIndex base, final byte qual) {
counts[base.index]--; switch (base) {
totalCount--; case A: --count_A; sumQual_A -= qual; break;
sumQuals[base.index] -= qual; case C: --count_C; sumQual_C -= qual; break;
case G: --count_G; sumQual_G -= qual; break;
case T: --count_T; sumQual_T -= qual; break;
case D: --count_D; sumQual_D -= qual; break;
case I: --count_I; sumQual_I -= qual; break;
case N: --count_N; sumQual_N -= qual; break;
}
--totalCount;
} }
@Ensures("result >= 0") @Ensures("result >= 0")
@ -135,7 +172,16 @@ import com.google.java.contract.Requires;
@Ensures("result >= 0") @Ensures("result >= 0")
public long getSumQuals(final BaseIndex base) { public long getSumQuals(final BaseIndex base) {
return sumQuals[base.index]; switch (base) {
case A: return sumQual_A;
case C: return sumQual_C;
case G: return sumQual_G;
case T: return sumQual_T;
case D: return sumQual_D;
case I: return sumQual_I;
case N: return sumQual_N;
default: throw new IllegalArgumentException(base.name());
}
} }
@Ensures("result >= 0") @Ensures("result >= 0")
@ -155,12 +201,21 @@ import com.google.java.contract.Requires;
@Ensures("result >= 0") @Ensures("result >= 0")
public int countOfBase(final BaseIndex base) { public int countOfBase(final BaseIndex base) {
return counts[base.index]; switch (base) {
case A: return count_A;
case C: return count_C;
case G: return count_G;
case T: return count_T;
case D: return count_D;
case I: return count_I;
case N: return count_N;
default: throw new IllegalArgumentException(base.name());
}
} }
@Ensures("result >= 0") @Ensures("result >= 0")
public long sumQualsOfBase(final BaseIndex base) { public long sumQualsOfBase(final BaseIndex base) {
return sumQuals[base.index]; return getSumQuals(base);
} }
@Ensures("result >= 0") @Ensures("result >= 0")
@ -193,14 +248,14 @@ import com.google.java.contract.Requires;
*/ */
@Ensures({"result >=0.0", "result<= 1.0"}) @Ensures({"result >=0.0", "result<= 1.0"})
public double baseCountProportion(final BaseIndex baseIndex) { public double baseCountProportion(final BaseIndex baseIndex) {
return (totalCount == 0) ? 0.0 : (double)counts[baseIndex.index] / (double)totalCount; return (totalCount == 0) ? 0.0 : (double)countOfBase(baseIndex) / (double)totalCount;
} }
@Ensures("result != null") @Ensures("result != null")
public String toString() { public String toString() {
StringBuilder b = new StringBuilder(); StringBuilder b = new StringBuilder();
for (final BaseIndex i : BaseIndex.values()) { for (final BaseIndex i : BaseIndex.values()) {
b.append(i.toString()).append("=").append(counts[i.index]).append(","); b.append(i.toString()).append("=").append(countOfBase(i)).append(",");
} }
return b.toString(); return b.toString();
} }
@ -213,7 +268,7 @@ import com.google.java.contract.Requires;
public BaseIndex baseIndexWithMostCounts() { public BaseIndex baseIndexWithMostCounts() {
BaseIndex maxI = MAX_BASE_INDEX_WITH_NO_COUNTS; BaseIndex maxI = MAX_BASE_INDEX_WITH_NO_COUNTS;
for (final BaseIndex i : BaseIndex.values()) { for (final BaseIndex i : BaseIndex.values()) {
if (counts[i.index] > counts[maxI.index]) if (countOfBase(i) > countOfBase(maxI))
maxI = i; maxI = i;
} }
return maxI; return maxI;
@ -223,7 +278,7 @@ import com.google.java.contract.Requires;
public BaseIndex baseIndexWithMostCountsWithoutIndels() { public BaseIndex baseIndexWithMostCountsWithoutIndels() {
BaseIndex maxI = MAX_BASE_INDEX_WITH_NO_COUNTS; BaseIndex maxI = MAX_BASE_INDEX_WITH_NO_COUNTS;
for (final BaseIndex i : BaseIndex.values()) { for (final BaseIndex i : BaseIndex.values()) {
if (i.isNucleotide() && counts[i.index] > counts[maxI.index]) if (i.isNucleotide() && countOfBase(i) > countOfBase(maxI))
maxI = i; maxI = i;
} }
return maxI; return maxI;
@ -237,25 +292,25 @@ import com.google.java.contract.Requires;
public BaseIndex baseIndexWithMostProbability() { public BaseIndex baseIndexWithMostProbability() {
BaseIndex maxI = MAX_BASE_INDEX_WITH_NO_COUNTS; BaseIndex maxI = MAX_BASE_INDEX_WITH_NO_COUNTS;
for (final BaseIndex i : BaseIndex.values()) { for (final BaseIndex i : BaseIndex.values()) {
if (sumQuals[i.index] > sumQuals[maxI.index]) if (getSumQuals(i) > getSumQuals(maxI))
maxI = i; maxI = i;
} }
return (sumQuals[maxI.index] > 0L ? maxI : baseIndexWithMostCounts()); return (getSumQuals(maxI) > 0L ? maxI : baseIndexWithMostCounts());
} }
@Ensures("result != null") @Ensures("result != null")
public BaseIndex baseIndexWithMostProbabilityWithoutIndels() { public BaseIndex baseIndexWithMostProbabilityWithoutIndels() {
BaseIndex maxI = MAX_BASE_INDEX_WITH_NO_COUNTS; BaseIndex maxI = MAX_BASE_INDEX_WITH_NO_COUNTS;
for (final BaseIndex i : BaseIndex.values()) { for (final BaseIndex i : BaseIndex.values()) {
if (i.isNucleotide() && sumQuals[i.index] > sumQuals[maxI.index]) if (i.isNucleotide() && getSumQuals(i) > getSumQuals(maxI))
maxI = i; maxI = i;
} }
return (sumQuals[maxI.index] > 0L ? maxI : baseIndexWithMostCountsWithoutIndels()); return (getSumQuals(maxI) > 0L ? maxI : baseIndexWithMostCountsWithoutIndels());
} }
@Ensures("result >=0") @Ensures("result >=0")
public int totalCountWithoutIndels() { public int totalCountWithoutIndels() {
return totalCount - counts[BaseIndex.D.index] - counts[BaseIndex.I.index]; return totalCount - countOfBase(BaseIndex.D) - countOfBase(BaseIndex.I);
} }
/** /**
@ -268,10 +323,6 @@ import com.google.java.contract.Requires;
@Ensures({"result >=0.0", "result<= 1.0"}) @Ensures({"result >=0.0", "result<= 1.0"})
public double baseCountProportionWithoutIndels(final BaseIndex base) { public double baseCountProportionWithoutIndels(final BaseIndex base) {
final int total = totalCountWithoutIndels(); final int total = totalCountWithoutIndels();
return (total == 0) ? 0.0 : (double)counts[base.index] / (double)total; return (total == 0) ? 0.0 : (double)countOfBase(base) / (double)total;
}
public int[] countsArray() {
return counts.clone();
} }
} }