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Refactored the BaseCounts classes so that they are safer and allow for calculations on the most probable base (which is not necessarily the most common base).

This commit is contained in:
Eric Banks 2012-10-04 10:37:11 -04:00
parent 2df5be702c
commit 0c46845c92
5 changed files with 75 additions and 50 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

15
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseAndQualsCounts.java
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@ -23,7 +23,7 @@ public class BaseAndQualsCounts extends BaseCounts {
}
}
public void incr(byte base, byte baseQual, byte insQual, byte delQual) {
public void incr(final byte base, final byte baseQual, final byte insQual, final byte delQual) {
super.incr(base, baseQual);
BaseIndex i = BaseIndex.byteToBase(base);
if (i != null) { // do not allow Ns
@ -32,7 +32,7 @@ public class BaseAndQualsCounts extends BaseCounts {
}
}
public void decr(byte base, byte baseQual, byte insQual, byte delQual) {
public void decr(final byte base, final byte baseQual, final byte insQual, final byte delQual) {
super.decr(base, baseQual);
BaseIndex i = BaseIndex.byteToBase(base);
if (i != null) { // do not allow Ns
@ -41,16 +41,15 @@ public class BaseAndQualsCounts extends BaseCounts {
}
}
public byte averageInsertionQualsOfMostCommonBase() {
return getGenericAverageQualOfMostCommonBase(sumInsertionQuals);
public byte averageInsertionQualsOfBase(final BaseIndex base) {
return getGenericAverageQualOfBase(base, sumInsertionQuals);
}
public byte averageDeletionQualsOfMostCommonBase() {
return getGenericAverageQualOfMostCommonBase(sumDeletionQuals);
public byte averageDeletionQualsOfBase(final BaseIndex base) {
return getGenericAverageQualOfBase(base, sumDeletionQuals);
}
private byte getGenericAverageQualOfMostCommonBase(Map<BaseIndex, Long> sumQuals) {
BaseIndex base = BaseIndex.byteToBase(baseWithMostCounts());
private byte getGenericAverageQualOfBase(final BaseIndex base, final Map<BaseIndex, Long> sumQuals) {
return (byte) (sumQuals.get(base) / getCount(base));
}
}

96
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseCounts.java
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@ -41,26 +41,26 @@ import java.util.Map;
@Requires("other != null")
public void add(BaseCounts other) {
for (BaseIndex i : BaseIndex.values())
for (final BaseIndex i : BaseIndex.values())
counts.put(i, counts.get(i) + other.counts.get(i));
}
@Requires("other != null")
public void sub(BaseCounts other) {
for (BaseIndex i : BaseIndex.values())
for (final BaseIndex i : BaseIndex.values())
counts.put(i, counts.get(i) - other.counts.get(i));
}
@Ensures("totalCount() == old(totalCount()) || totalCount() == old(totalCount()) + 1")
public void incr(byte base) {
BaseIndex i = BaseIndex.byteToBase(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) {
BaseIndex i = BaseIndex.byteToBase(base);
final BaseIndex i = BaseIndex.byteToBase(base);
if (i != null) { // no Ns
counts.put(i, counts.get(i) + 1);
sumQuals.put(i, sumQuals.get(i) + qual);
@ -69,14 +69,14 @@ import java.util.Map;
@Ensures("totalCount() == old(totalCount()) || totalCount() == old(totalCount()) - 1")
public void decr(byte base) {
BaseIndex i = BaseIndex.byteToBase(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) {
BaseIndex i = BaseIndex.byteToBase(base);
final BaseIndex i = BaseIndex.byteToBase(base);
if (i != null) { // no Ns
counts.put(i, counts.get(i) - 1);
sumQuals.put(i, sumQuals.get(i) - qual);
@ -84,52 +84,48 @@ import java.util.Map;
}
@Ensures("result >= 0")
public int getCount(byte base) {
public int getCount(final byte base) {
return getCount(BaseIndex.byteToBase(base));
}
@Ensures("result >= 0")
public int getCount(BaseIndex base) {
public int getCount(final BaseIndex base) {
return counts.get(base);
}
@Ensures("result >= 0")
public long getSumQuals(byte base) {
public long getSumQuals(final byte base) {
return getSumQuals(BaseIndex.byteToBase(base));
}
@Ensures("result >= 0")
public long getSumQuals(BaseIndex base) {
public long getSumQuals(final BaseIndex base) {
return sumQuals.get(base);
}
@Ensures("result >= 0")
public byte averageQuals(byte base) {
public byte averageQuals(final byte base) {
return (byte) (getSumQuals(base) / getCount(base));
}
@Ensures("result >= 0")
public byte averageQuals(BaseIndex base) {
public byte averageQuals(final BaseIndex base) {
return (byte) (getSumQuals(base) / getCount(base));
}
public byte baseWithMostCounts() {
return baseIndexWithMostCounts().getByte();
@Ensures("result >= 0")
public int countOfBase(final BaseIndex base) {
return counts.get(base);
}
@Ensures("result >= 0")
public int countOfMostCommonBase() {
return counts.get(baseIndexWithMostCounts());
public long sumQualsOfBase(final BaseIndex base) {
return sumQuals.get(base);
}
@Ensures("result >= 0")
public long sumQualsOfMostCommonBase() {
return sumQuals.get(baseIndexWithMostCounts());
}
@Ensures("result >= 0")
public byte averageQualsOfMostCommonBase() {
return (byte) (sumQualsOfMostCommonBase() / countOfMostCommonBase());
public byte averageQualsOfBase(final BaseIndex base) {
return (byte) (sumQualsOfBase(base) / countOfBase(base));
}
@ -149,7 +145,7 @@ import java.util.Map;
* @return the proportion of this base over all other bases
*/
@Ensures({"result >=0.0", "result<= 1.0"})
public double baseCountProportion(byte base) {
public double baseCountProportion(final byte base) {
return (double) counts.get(BaseIndex.byteToBase(base)) / totalCount();
}
@ -160,7 +156,7 @@ import java.util.Map;
* @return the proportion of this base over all other bases
*/
@Ensures({"result >=0.0", "result<= 1.0"})
public double baseCountProportion(BaseIndex baseIndex) {
public double baseCountProportion(final BaseIndex baseIndex) {
int total = totalCount();
if (total == 0)
return 0.0;
@ -177,22 +173,28 @@ import java.util.Map;
return b.toString();
}
public byte baseWithMostCounts() {
return baseIndexWithMostCounts().getByte();
}
@Ensures("result != null")
public BaseIndex baseIndexWithMostCounts() {
BaseIndex maxI = MAX_BASE_INDEX_WITH_NO_COUNTS;
for (BaseIndex i : counts.keySet())
if (hasHigherCount(i, maxI))
maxI = i;
for (Map.Entry<BaseIndex, Integer> entry : counts.entrySet()) {
if (entry.getValue() > counts.get(maxI))
maxI = entry.getKey();
}
return maxI;
}
@Ensures("result != null")
public BaseIndex baseIndexWithMostCountsWithoutIndels() {
BaseIndex mostCounts = MAX_BASE_INDEX_WITH_NO_COUNTS;
for (BaseIndex index : counts.keySet())
if (index.isNucleotide() && hasHigherCount(index, mostCounts))
mostCounts = index;
return mostCounts;
BaseIndex maxI = MAX_BASE_INDEX_WITH_NO_COUNTS;
for (Map.Entry<BaseIndex, Integer> entry : counts.entrySet()) {
if (entry.getKey().isNucleotide() && entry.getValue() > counts.get(maxI))
maxI = entry.getKey();
}
return maxI;
}
private boolean hasHigherCount(final BaseIndex targetIndex, final BaseIndex testIndex) {
@ -201,6 +203,30 @@ import java.util.Map;
return ( targetCount > testCount || (targetCount == testCount && sumQuals.get(targetIndex) > sumQuals.get(testIndex)) );
}
public byte baseWithMostProbability() {
return baseIndexWithMostProbability().getByte();
}
@Ensures("result != null")
public BaseIndex baseIndexWithMostProbability() {
BaseIndex maxI = MAX_BASE_INDEX_WITH_NO_COUNTS;
for (Map.Entry<BaseIndex, Long> entry : sumQuals.entrySet()) {
if (entry.getValue() > sumQuals.get(maxI))
maxI = entry.getKey();
}
return maxI;
}
@Ensures("result != null")
public BaseIndex baseIndexWithMostProbabilityWithoutIndels() {
BaseIndex maxI = MAX_BASE_INDEX_WITH_NO_COUNTS;
for (Map.Entry<BaseIndex, Long> entry : sumQuals.entrySet()) {
if (entry.getKey().isNucleotide() && entry.getValue() > sumQuals.get(maxI))
maxI = entry.getKey();
}
return maxI;
}
@Ensures("result >=0")
public int totalCountWithoutIndels() {
int sum = 0;
@ -218,8 +244,8 @@ import java.util.Map;
*/
@Requires("index.isNucleotide()")
@Ensures({"result >=0.0", "result<= 1.0"})
public double baseCountProportionWithoutIndels(BaseIndex index) {
int total = totalCountWithoutIndels();
public double baseCountProportionWithoutIndels(final BaseIndex index) {
final int total = totalCountWithoutIndels();
if (total == 0)
return 0.0;
return (double) counts.get(index) / totalCountWithoutIndels();

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/HeaderElement.java
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@ -182,7 +182,7 @@ public class HeaderElement {
* @return whether or not the HeaderElement is variant due to excess insertions
*/
private boolean isVariantFromMismatches(double minVariantProportion) {
BaseIndex mostCommon = consensusBaseCounts.baseIndexWithMostCountsWithoutIndels();
BaseIndex mostCommon = consensusBaseCounts.baseIndexWithMostProbabilityWithoutIndels();
double mostCommonProportion = consensusBaseCounts.baseCountProportionWithoutIndels(mostCommon);
return mostCommonProportion != 0.0 && mostCommonProportion < (1 - minVariantProportion);
}

10
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
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@ -472,11 +472,11 @@ public class SlidingWindow {
* @param rms the rms mapping quality in the header element
*/
private void genericAddBaseToConsensus(SyntheticRead syntheticRead, BaseAndQualsCounts baseCounts, double rms) {
BaseIndex base = baseCounts.baseIndexWithMostCounts();
byte count = (byte) Math.min(baseCounts.countOfMostCommonBase(), Byte.MAX_VALUE);
byte qual = baseCounts.averageQualsOfMostCommonBase();
byte insQual = baseCounts.averageInsertionQualsOfMostCommonBase();
byte delQual = baseCounts.averageDeletionQualsOfMostCommonBase();
BaseIndex base = baseCounts.baseIndexWithMostProbability();
byte count = (byte) Math.min(baseCounts.countOfBase(base), Byte.MAX_VALUE);
byte qual = baseCounts.averageQualsOfBase(base);
byte insQual = baseCounts.averageInsertionQualsOfBase(base);
byte delQual = baseCounts.averageDeletionQualsOfBase(base);
syntheticRead.add(base, count, qual, insQual, delQual, rms);
}

2
protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseCountsUnitTest.java
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@ -63,7 +63,7 @@ public class BaseCountsUnitTest extends BaseTest {
String name = String.format("Test-%s", params.bases);
Assert.assertEquals(counts.totalCount(), params.bases.length(), name);
Assert.assertEquals(counts.countOfMostCommonBase(), params.mostCommonCount, name);
Assert.assertEquals(counts.countOfBase(counts.baseIndexWithMostCounts()), params.mostCommonCount, name);
Assert.assertEquals((char)counts.baseWithMostCounts(), (char)params.mostCountBase, name);
}
}