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Refactored repeat covariates to eliminate duplicated code - now all inherit from basic RepeatCovariate abstract class. Comprehensive unit tests coming...

This commit is contained in:
Guillermo del Angel 2013-01-29 10:10:24 -05:00
parent 35543b9cba
commit c11197e361
4 changed files with 292 additions and 649 deletions
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281
protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatCovariate.java 100644
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@ -0,0 +1,281 @@
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package org.broadinstitute.sting.utils.recalibration.covariates;
import com.google.java.contract.Ensures;
import com.google.java.contract.Requires;
import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection;
import org.broadinstitute.sting.utils.recalibration.ReadCovariates;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.variant.utils.Pair;
import org.broadinstitute.variant.variantcontext.VariantContextUtils;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Map;
import java.util.Set;
public abstract class RepeatCovariate implements ExperimentalCovariate {
final int MAX_REPEAT_LENGTH = 20;
final int MAX_STR_UNIT_LENGTH = 8;
private final HashMap<String, Integer> repeatLookupTable = new HashMap<String, Integer>();
private final HashMap<Integer, String> repeatReverseLookupTable = new HashMap<Integer, String>();
private int nextId = 0;
// Initialize any member variables using the command-line arguments passed to the walkers
@Override
public void initialize(final RecalibrationArgumentCollection RAC) {
}
@Override
public void recordValues(final GATKSAMRecord read, final ReadCovariates values) {
// store the original bases and then write Ns over low quality ones
final byte[] originalBases = read.getReadBases().clone();
final boolean negativeStrand = read.getReadNegativeStrandFlag();
byte[] bases = read.getReadBases();
if (negativeStrand)
bases = BaseUtils.simpleReverseComplement(bases);
// don't record reads with N's
if (!BaseUtils.isAllRegularBases(bases))
return;
for (int i = 0; i < bases.length; i++) {
final Pair<byte[], Integer> res = findTandemRepeatUnits(bases, i);
// to merge repeat unit and repeat length to get covariate value:
final String repeatID = getCovariateValueFromUnitAndLength(res.first, res.second);
final int key = keyForRepeat(repeatID);
final int readOffset = (negativeStrand ? bases.length - i - 1 : i);
values.addCovariate(key, key, key, readOffset);
}
// put the original bases back in
read.setReadBases(originalBases);
}
private Pair<byte[], Integer> findTandemRepeatUnits(byte[] readBases, int offset) {
int maxBW = 0;
byte[] bestBWRepeatUnit = new byte[]{readBases[offset]};
for (int str = 1; str <= MAX_STR_UNIT_LENGTH; str++) {
// fix repeat unit length
//edge case: if candidate tandem repeat unit falls beyond edge of read, skip
if (offset+1-str < 0)
break;
// get backward repeat unit and # repeats
byte[] backwardRepeatUnit = Arrays.copyOfRange(readBases, offset - str + 1, offset + 1);
maxBW = VariantContextUtils.findNumberofRepetitions(backwardRepeatUnit, Arrays.copyOfRange(readBases, 0, offset + 1), false);
if (maxBW > 1) {
bestBWRepeatUnit = backwardRepeatUnit.clone();
break;
}
}
byte[] bestRepeatUnit = bestBWRepeatUnit;
int maxRL = maxBW;
if (offset < readBases.length-1) {
byte[] bestFWRepeatUnit = new byte[]{readBases[offset+1]};
int maxFW = 0;
for (int str = 1; str <= MAX_STR_UNIT_LENGTH; str++) {
// fix repeat unit length
//edge case: if candidate tandem repeat unit falls beyond edge of read, skip
if (offset+str+1 > readBases.length)
break;
// get forward repeat unit and # repeats
byte[] forwardRepeatUnit = Arrays.copyOfRange(readBases, offset +1, offset+str+1);
maxFW = VariantContextUtils.findNumberofRepetitions(forwardRepeatUnit,Arrays.copyOfRange(readBases, offset+1, readBases.length), true);
if (maxFW > 1) {
bestFWRepeatUnit = forwardRepeatUnit.clone();
break;
}
}
// if FW repeat unit = BW repeat unit it means we're in the middle of a tandem repeat - add FW and BW components
if (Arrays.equals(bestFWRepeatUnit, bestBWRepeatUnit)) {
maxRL = maxBW + maxFW;
bestRepeatUnit = bestFWRepeatUnit; // arbitrary
}
else {
// tandem repeat starting forward from current offset
maxRL = maxFW;
bestRepeatUnit = bestFWRepeatUnit;
}
/* if (maxFW > maxBW) {
// tandem repeat starting forward from current offset
maxRL = maxFW;
bestRepeatUnit = bestFWRepeatUnit;
}
else if (maxFW < maxBW) {
maxRL = maxBW;
bestRepeatUnit = bestBWRepeatUnit;
} */
/* else {
// maxFW = maxBW but repeat units different: not in a tandem repeat.
maxRL = 1;
bestRepeatUnit = bestBWRepeatUnit; // arbitrary
} */
}
if(maxRL > MAX_REPEAT_LENGTH) { maxRL = MAX_REPEAT_LENGTH; }
return new Pair<byte[], Integer>(bestRepeatUnit, maxRL);
}
@Override
public final Object getValue(final String str) {
return str;
}
@Override
public synchronized String formatKey(final int key) {
// This method is synchronized so that we don't attempt to do a get()
// from the reverse lookup table while that table is being updated
return repeatReverseLookupTable.get(key);
}
@Requires({"repeatLength>=0", "repeatFromUnitAndLength != null"})
@Ensures("result != null")
protected abstract String getCovariateValueFromUnitAndLength(final byte[] repeatFromUnitAndLength, final int repeatLength);
@Override
public int keyFromValue(final Object value) {
return keyForRepeat((String) value);
}
/**
* Get the mapping from read group names to integer key values for all read groups in this covariate
* @return a set of mappings from read group names -> integer key values
*/
public Set<Map.Entry<String, Integer>> getKeyMap() {
return repeatLookupTable.entrySet();
}
private int keyForRepeat(final String repeatID) {
// Rather than synchronize this entire method (which would be VERY expensive for walkers like the BQSR),
// synchronize only the table updates.
// Before entering the synchronized block, check to see if this read group is not in our tables.
// If it's not, either we will have to insert it, OR another thread will insert it first.
// This preliminary check avoids doing any synchronization most of the time.
if ( ! repeatLookupTable.containsKey(repeatID) ) {
synchronized ( this ) {
// Now we need to make sure the key is STILL not there, since another thread may have come along
// and inserted it while we were waiting to enter this synchronized block!
if ( ! repeatLookupTable.containsKey(repeatID) ) {
repeatLookupTable.put(repeatID, nextId);
repeatReverseLookupTable.put(nextId, repeatID);
nextId++;
}
}
}
return repeatLookupTable.get(repeatID);
}
/**
* Splits repeat unit and num repetitions from covariate value.
* For example, if value if "ATG4" it returns (ATG,4)
* @param value Covariate value
* @return Split pair
*/
@Requires("value != null")
@Ensures({"result.first != null","result.second>=0"})
public static Pair<String,Integer> getRUandNRfromCovariate(final String value) {
int k = 0;
for ( k=0; k < value.length(); k++ ) {
if (!BaseUtils.isRegularBase(value.getBytes()[k]))
break;
}
Integer nr = Integer.valueOf(value.substring(k,value.length())); // will throw NumberFormatException if format illegal
if (k == value.length() || nr <= 0)
throw new IllegalStateException("Covariate is not of form (Repeat Unit) + Integer");
return new Pair<String,Integer>(value.substring(0,k), nr);
}
/**
* Gets bases from tandem repeat representation (Repeat Unit),(Number of Repeats).
* For example, (AGC),3 returns AGCAGCAGC
* @param repeatUnit Tandem repeat unit
* @param numRepeats Number of repeats
* @return Expanded String
*/
@Requires({"numRepeats > 0","repeatUnit != null"})
@Ensures("result != null")
public static String getBasesFromRUandNR(final String repeatUnit, final int numRepeats) {
final StringBuilder sb = new StringBuilder();
for (int i=0; i < numRepeats; i++)
sb.append(repeatUnit);
return sb.toString();
}
// version given covariate key
public static String getBasesFromRUandNR(final String covariateValue) {
Pair<String,Integer> pair = getRUandNRfromCovariate(covariateValue);
return getBasesFromRUandNR(pair.getFirst(), pair.getSecond());
}
@Override
public abstract int maximumKeyValue();
}

232
protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatLengthCovariate.java
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@ -48,234 +48,13 @@ package org.broadinstitute.sting.utils.recalibration.covariates;
import com.google.java.contract.Ensures;
import com.google.java.contract.Requires;
import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection;
import org.broadinstitute.sting.utils.recalibration.ReadCovariates;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.variant.utils.Pair;
import org.broadinstitute.variant.variantcontext.VariantContextUtils;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Map;
import java.util.Set;
public class RepeatLengthCovariate implements ExperimentalCovariate {
final int MAX_REPEAT_LENGTH = 20;
final int MAX_STR_UNIT_LENGTH = 1; // =1 will restrict effectively to detecting homopolymer runs
public final boolean RECORD_REPUNIT_WITH_REPLENGTH = false;
private final HashMap<String, Integer> repeatLookupTable = new HashMap<String, Integer>();
private final HashMap<Integer, String> repeatReverseLookupTable = new HashMap<Integer, String>();
private int nextId = 0;
// Initialize any member variables using the command-line arguments passed to the walkers
@Override
public void initialize(final RecalibrationArgumentCollection RAC) {
}
@Override
public void recordValues(final GATKSAMRecord read, final ReadCovariates values) {
// store the original bases and then write Ns over low quality ones
final byte[] originalBases = read.getReadBases().clone();
final boolean negativeStrand = read.getReadNegativeStrandFlag();
byte[] bases = read.getReadBases();
if (negativeStrand)
bases = BaseUtils.simpleReverseComplement(bases);
// don't record reads with N's
if (!BaseUtils.isAllRegularBases(bases))
return;
for (int i = 0; i < bases.length; i++) {
final Pair<byte[], Integer> res = findTandemRepeatUnits(bases, i);
// merge repeat unit and repeat length to get covariate value
final String repeatID = repeatFromUnitAndLength(res.first, res.second);
final int key = keyForRepeat(repeatID);
final int readOffset = (negativeStrand ? bases.length - i - 1 : i);
values.addCovariate(key, key, key, readOffset);
}
// put the original bases back in
read.setReadBases(originalBases);
}
private Pair<byte[], Integer> findTandemRepeatUnits(byte[] readBases, int offset) {
int maxBW = 0;
byte[] bestBWRepeatUnit = new byte[]{readBases[offset]};
for (int str = 1; str <= MAX_STR_UNIT_LENGTH; str++) {
// fix repeat unit length
//edge case: if candidate tandem repeat unit falls beyond edge of read, skip
if (offset+1-str < 0)
break;
// get backward repeat unit and # repeats
byte[] backwardRepeatUnit = Arrays.copyOfRange(readBases, offset - str+1, offset+1);
maxBW = VariantContextUtils.findNumberofRepetitions(backwardRepeatUnit,Arrays.copyOfRange(readBases, 0, offset+1), false);
if (maxBW > 1) {
bestBWRepeatUnit = backwardRepeatUnit.clone();
break;
}
}
byte[] bestRepeatUnit = bestBWRepeatUnit;
int maxRL = maxBW;
if (offset < readBases.length-1) {
byte[] bestFWRepeatUnit = new byte[]{readBases[offset+1]};
int maxFW = 0;
for (int str = 1; str <= MAX_STR_UNIT_LENGTH; str++) {
// fix repeat unit length
//edge case: if candidate tandem repeat unit falls beyond edge of read, skip
if (offset+str+1 > readBases.length)
break;
// get forward repeat unit and # repeats
byte[] forwardRepeatUnit = Arrays.copyOfRange(readBases, offset +1, offset+str+1);
maxFW = VariantContextUtils.findNumberofRepetitions(forwardRepeatUnit,Arrays.copyOfRange(readBases, offset+1, readBases.length), true);
if (maxFW > 1) {
bestFWRepeatUnit = forwardRepeatUnit.clone();
break;
}
}
// if FW repeat unit = BW repeat unit it means we're in the middle of a tandem repeat - add FW and BW components
if (Arrays.equals(bestFWRepeatUnit, bestBWRepeatUnit)) {
maxRL = maxBW + maxFW;
bestRepeatUnit = bestFWRepeatUnit; // arbitrary
}
else {
// tandem repeat starting forward from current offset
maxRL = maxFW;
bestRepeatUnit = bestFWRepeatUnit;
}
/* if (maxFW > maxBW) {
// tandem repeat starting forward from current offset
maxRL = maxFW;
bestRepeatUnit = bestFWRepeatUnit;
}
else if (maxFW < maxBW) {
maxRL = maxBW;
bestRepeatUnit = bestBWRepeatUnit;
} */
/* else {
// maxFW = maxBW but repeat units different: not in a tandem repeat.
maxRL = 1;
bestRepeatUnit = bestBWRepeatUnit; // arbitrary
} */
}
if(maxRL > MAX_REPEAT_LENGTH) { maxRL = MAX_REPEAT_LENGTH; }
return new Pair<byte[], Integer>(bestRepeatUnit, maxRL);
}
@Override
public final Object getValue(final String str) {
return str;
}
@Override
public synchronized String formatKey(final int key) {
// This method is synchronized so that we don't attempt to do a get()
// from the reverse lookup table while that table is being updated
return repeatReverseLookupTable.get(key);
}
@Override
public int keyFromValue(final Object value) {
return keyForRepeat((String) value);
}
/**
* Get the mapping from read group names to integer key values for all read groups in this covariate
* @return a set of mappings from read group names -> integer key values
*/
public Set<Map.Entry<String, Integer>> getKeyMap() {
return repeatLookupTable.entrySet();
}
public class RepeatLengthCovariate extends RepeatCovariate {
@Requires({"repeatLength>=0", "repeatFromUnitAndLength != null"})
@Ensures("result != null")
private String repeatFromUnitAndLength(final byte[] repeatFromUnitAndLength, final int repeatLength) {
if (RECORD_REPUNIT_WITH_REPLENGTH)
return new String(repeatFromUnitAndLength) + String.format("%d",repeatLength);
else
return String.format("%d",repeatLength);
}
private int keyForRepeat(final String repeatID) {
// Rather than synchronize this entire method (which would be VERY expensive for walkers like the BQSR),
// synchronize only the table updates.
// Before entering the synchronized block, check to see if this read group is not in our tables.
// If it's not, either we will have to insert it, OR another thread will insert it first.
// This preliminary check avoids doing any synchronization most of the time.
if ( ! repeatLookupTable.containsKey(repeatID) ) {
synchronized ( this ) {
// Now we need to make sure the key is STILL not there, since another thread may have come along
// and inserted it while we were waiting to enter this synchronized block!
if ( ! repeatLookupTable.containsKey(repeatID) ) {
repeatLookupTable.put(repeatID, nextId);
repeatReverseLookupTable.put(nextId, repeatID);
nextId++;
}
}
}
return repeatLookupTable.get(repeatID);
}
/**
* Splits repeat unit and num repetitions from covariate value.
* For example, if value if "ATG4" it returns (ATG,4)
* @param value Covariate value
* @return Split pair
*/
@Requires("value != null")
@Ensures({"result.first != null","result.second>=0"})
public static Pair<String,Integer> getRUandNRfromCovariate(final String value) {
int k = 0;
for ( k=0; k < value.length(); k++ ) {
if (!BaseUtils.isRegularBase(value.getBytes()[k]))
break;
}
Integer nr = Integer.valueOf(value.substring(k,value.length())); // will throw NumberFormatException if format illegal
if (k == value.length() || nr <= 0)
throw new IllegalStateException("Covariate is not of form (Repeat Unit) + Integer");
return new Pair<String,Integer>(value.substring(0,k), nr);
}
/**
* Gets bases from tandem repeat representation (Repeat Unit),(Number of Repeats).
* For example, (AGC),3 returns AGCAGCAGC
* @param repeatUnit Tandem repeat unit
* @param numRepeats Number of repeats
* @return Expanded String
*/
@Requires({"numRepeats > 0","repeatUnit != null"})
@Ensures("result != null")
public static String getBasesFromRUandNR(final String repeatUnit, final int numRepeats) {
final StringBuilder sb = new StringBuilder();
for (int i=0; i < numRepeats; i++)
sb.append(repeatUnit);
return sb.toString();
}
// version given covariate key
public static String getBasesFromRUandNR(final String covariateValue) {
Pair<String,Integer> pair = getRUandNRfromCovariate(covariateValue);
return getBasesFromRUandNR(pair.getFirst(), pair.getSecond());
protected String getCovariateValueFromUnitAndLength(final byte[] repeatFromUnitAndLength, final int repeatLength) {
return String.format("%d",repeatLength);
}
@Override
@ -284,10 +63,7 @@ public class RepeatLengthCovariate implements ExperimentalCovariate {
//return repeatLookupTable.size() - 1;
// max possible values of covariate: for repeat unit, length is up to MAX_STR_UNIT_LENGTH,
// so we have 4^MAX_STR_UNIT_LENGTH * MAX_REPEAT_LENGTH possible values
if (RECORD_REPUNIT_WITH_REPLENGTH)
return (1<<(2*MAX_STR_UNIT_LENGTH)) * MAX_REPEAT_LENGTH +1;
else
return (1+MAX_REPEAT_LENGTH);
return (1+MAX_REPEAT_LENGTH);
}
}

221
protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatUnitAndLengthCovariate.java
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@ -62,222 +62,12 @@ import java.util.Map;
import java.util.Set;
public class RepeatUnitAndLengthCovariate implements ExperimentalCovariate {
final int MAX_REPEAT_LENGTH = 20;
final int MAX_STR_UNIT_LENGTH = 8;
public final boolean RECORD_REPUNIT_WITH_REPLENGTH = true;
private final HashMap<String, Integer> repeatLookupTable = new HashMap<String, Integer>();
private final HashMap<Integer, String> repeatReverseLookupTable = new HashMap<Integer, String>();
private int nextId = 0;
// Initialize any member variables using the command-line arguments passed to the walkers
@Override
public void initialize(final RecalibrationArgumentCollection RAC) {
}
@Override
public void recordValues(final GATKSAMRecord read, final ReadCovariates values) {
// store the original bases and then write Ns over low quality ones
final byte[] originalBases = read.getReadBases().clone();
final boolean negativeStrand = read.getReadNegativeStrandFlag();
byte[] bases = read.getReadBases();
if (negativeStrand)
bases = BaseUtils.simpleReverseComplement(bases);
// don't record reads with N's
if (!BaseUtils.isAllRegularBases(bases))
return;
for (int i = 0; i < bases.length; i++) {
final Pair<byte[], Integer> res = findTandemRepeatUnits(bases, i);
// merge repeat unit and repeat length to get covariate value
final String repeatID = repeatFromUnitAndLength(res.first, res.second);
final int key = keyForRepeat(repeatID);
final int readOffset = (negativeStrand ? bases.length - i - 1 : i);
values.addCovariate(key, key, key, readOffset);
}
// put the original bases back in
read.setReadBases(originalBases);
}
private Pair<byte[], Integer> findTandemRepeatUnits(byte[] readBases, int offset) {
int maxBW = 0;
byte[] bestBWRepeatUnit = new byte[]{readBases[offset]};
for (int str = 1; str <= MAX_STR_UNIT_LENGTH; str++) {
// fix repeat unit length
//edge case: if candidate tandem repeat unit falls beyond edge of read, skip
if (offset+1-str < 0)
break;
// get backward repeat unit and # repeats
byte[] backwardRepeatUnit = Arrays.copyOfRange(readBases, offset - str+1, offset+1);
maxBW = VariantContextUtils.findNumberofRepetitions(backwardRepeatUnit,Arrays.copyOfRange(readBases, 0, offset+1), false);
if (maxBW > 1) {
bestBWRepeatUnit = backwardRepeatUnit.clone();
break;
}
}
byte[] bestRepeatUnit = bestBWRepeatUnit;
int maxRL = maxBW;
if (offset < readBases.length-1) {
byte[] bestFWRepeatUnit = new byte[]{readBases[offset+1]};
int maxFW = 0;
for (int str = 1; str <= MAX_STR_UNIT_LENGTH; str++) {
// fix repeat unit length
//edge case: if candidate tandem repeat unit falls beyond edge of read, skip
if (offset+str+1 > readBases.length)
break;
// get forward repeat unit and # repeats
byte[] forwardRepeatUnit = Arrays.copyOfRange(readBases, offset +1, offset+str+1);
maxFW = VariantContextUtils.findNumberofRepetitions(forwardRepeatUnit,Arrays.copyOfRange(readBases, offset+1, readBases.length), true);
if (maxFW > 1) {
bestFWRepeatUnit = forwardRepeatUnit.clone();
break;
}
}
// if FW repeat unit = BW repeat unit it means we're in the middle of a tandem repeat - add FW and BW components
if (Arrays.equals(bestFWRepeatUnit, bestBWRepeatUnit)) {
maxRL = maxBW + maxFW;
bestRepeatUnit = bestFWRepeatUnit; // arbitrary
}
else {
// tandem repeat starting forward from current offset
maxRL = maxFW;
bestRepeatUnit = bestFWRepeatUnit;
}
/* if (maxFW > maxBW) {
// tandem repeat starting forward from current offset
maxRL = maxFW;
bestRepeatUnit = bestFWRepeatUnit;
}
else if (maxFW < maxBW) {
maxRL = maxBW;
bestRepeatUnit = bestBWRepeatUnit;
} */
/* else {
// maxFW = maxBW but repeat units different: not in a tandem repeat.
maxRL = 1;
bestRepeatUnit = bestBWRepeatUnit; // arbitrary
} */
}
if(maxRL > MAX_REPEAT_LENGTH) { maxRL = MAX_REPEAT_LENGTH; }
return new Pair<byte[], Integer>(bestRepeatUnit, maxRL);
}
@Override
public final Object getValue(final String str) {
return str;
}
@Override
public synchronized String formatKey(final int key) {
// This method is synchronized so that we don't attempt to do a get()
// from the reverse lookup table while that table is being updated
return repeatReverseLookupTable.get(key);
}
@Override
public int keyFromValue(final Object value) {
return keyForRepeat((String) value);
}
/**
* Get the mapping from read group names to integer key values for all read groups in this covariate
* @return a set of mappings from read group names -> integer key values
*/
public Set<Map.Entry<String, Integer>> getKeyMap() {
return repeatLookupTable.entrySet();
}
public class RepeatUnitAndLengthCovariate extends RepeatCovariate {
@Requires({"repeatLength>=0", "repeatFromUnitAndLength != null"})
@Ensures("result != null")
private String repeatFromUnitAndLength(final byte[] repeatFromUnitAndLength, final int repeatLength) {
if (RECORD_REPUNIT_WITH_REPLENGTH)
return new String(repeatFromUnitAndLength) + String.format("%d",repeatLength);
else
return String.format("%d",repeatLength);
}
private int keyForRepeat(final String repeatID) {
// Rather than synchronize this entire method (which would be VERY expensive for walkers like the BQSR),
// synchronize only the table updates.
// Before entering the synchronized block, check to see if this read group is not in our tables.
// If it's not, either we will have to insert it, OR another thread will insert it first.
// This preliminary check avoids doing any synchronization most of the time.
if ( ! repeatLookupTable.containsKey(repeatID) ) {
synchronized ( this ) {
// Now we need to make sure the key is STILL not there, since another thread may have come along
// and inserted it while we were waiting to enter this synchronized block!
if ( ! repeatLookupTable.containsKey(repeatID) ) {
repeatLookupTable.put(repeatID, nextId);
repeatReverseLookupTable.put(nextId, repeatID);
nextId++;
}
}
}
return repeatLookupTable.get(repeatID);
}
/**
* Splits repeat unit and num repetitions from covariate value.
* For example, if value if "ATG4" it returns (ATG,4)
* @param value Covariate value
* @return Split pair
*/
@Requires("value != null")
@Ensures({"result.first != null","result.second>=0"})
public static Pair<String,Integer> getRUandNRfromCovariate(final String value) {
int k = 0;
for ( k=0; k < value.length(); k++ ) {
if (!BaseUtils.isRegularBase(value.getBytes()[k]))
break;
}
Integer nr = Integer.valueOf(value.substring(k,value.length())); // will throw NumberFormatException if format illegal
if (k == value.length() || nr <= 0)
throw new IllegalStateException("Covariate is not of form (Repeat Unit) + Integer");
return new Pair<String,Integer>(value.substring(0,k), nr);
}
/**
* Gets bases from tandem repeat representation (Repeat Unit),(Number of Repeats).
* For example, (AGC),3 returns AGCAGCAGC
* @param repeatUnit Tandem repeat unit
* @param numRepeats Number of repeats
* @return Expanded String
*/
@Requires({"numRepeats > 0","repeatUnit != null"})
@Ensures("result != null")
public static String getBasesFromRUandNR(final String repeatUnit, final int numRepeats) {
final StringBuilder sb = new StringBuilder();
for (int i=0; i < numRepeats; i++)
sb.append(repeatUnit);
return sb.toString();
}
// version given covariate key
public static String getBasesFromRUandNR(final String covariateValue) {
Pair<String,Integer> pair = getRUandNRfromCovariate(covariateValue);
return getBasesFromRUandNR(pair.getFirst(), pair.getSecond());
protected String getCovariateValueFromUnitAndLength(final byte[] repeatFromUnitAndLength, final int repeatLength) {
return new String(repeatFromUnitAndLength) + String.format("%d",repeatLength);
}
@Override
@ -286,10 +76,7 @@ public class RepeatUnitAndLengthCovariate implements ExperimentalCovariate {
//return repeatLookupTable.size() - 1;
// max possible values of covariate: for repeat unit, length is up to MAX_STR_UNIT_LENGTH,
// so we have 4^MAX_STR_UNIT_LENGTH * MAX_REPEAT_LENGTH possible values
if (RECORD_REPUNIT_WITH_REPLENGTH)
return (1<<(2*MAX_STR_UNIT_LENGTH)) * MAX_REPEAT_LENGTH +1;
else
return (1+MAX_REPEAT_LENGTH);
return (1<<(2*MAX_STR_UNIT_LENGTH)) * MAX_REPEAT_LENGTH +1;
}
}

207
protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatUnitCovariate.java
View File

@ -66,214 +66,13 @@ import java.util.Set;
* Date: 11/3/12
*/
public class RepeatUnitCovariate implements ExperimentalCovariate {
final int MAX_REPEAT_LENGTH = 20;
final int MAX_STR_UNIT_LENGTH = 8;
private final HashMap<String, Integer> repeatLookupTable = new HashMap<String, Integer>();
private final HashMap<Integer, String> repeatReverseLookupTable = new HashMap<Integer, String>();
private int nextId = 0;
public class RepeatUnitCovariate extends RepeatCovariate {
// Initialize any member variables using the command-line arguments passed to the walkers
@Override
public void initialize(final RecalibrationArgumentCollection RAC) {
}
@Override
public void recordValues(final GATKSAMRecord read, final ReadCovariates values) {
// store the original bases and then write Ns over low quality ones
final byte[] originalBases = read.getReadBases().clone();
final boolean negativeStrand = read.getReadNegativeStrandFlag();
byte[] bases = read.getReadBases();
if (negativeStrand)
bases = BaseUtils.simpleReverseComplement(bases);
// don't record reads with N's
if (!BaseUtils.isAllRegularBases(bases))
return;
for (int i = 0; i < bases.length; i++) {
final Pair<byte[], Integer> res = findTandemRepeatUnits(bases, i);
// to merge repeat unit and repeat length to get covariate value:
//final String repeatID = repeatFromUnitAndLength(res.first, res.second);
final String repeatID = new String(res.first);
final int key = keyForRepeat(repeatID);
final int readOffset = (negativeStrand ? bases.length - i - 1 : i);
values.addCovariate(key, key, key, readOffset);
}
// put the original bases back in
read.setReadBases(originalBases);
protected String getCovariateValueFromUnitAndLength(final byte[] repeatFromUnitAndLength, final int repeatLength) {
return new String(repeatFromUnitAndLength);
}
private Pair<byte[], Integer> findTandemRepeatUnits(byte[] readBases, int offset) {
int maxBW = 0;
byte[] bestBWRepeatUnit = new byte[]{readBases[offset]};
for (int str = 1; str <= MAX_STR_UNIT_LENGTH; str++) {
// fix repeat unit length
//edge case: if candidate tandem repeat unit falls beyond edge of read, skip
if (offset+1-str < 0)
break;
// get backward repeat unit and # repeats
byte[] backwardRepeatUnit = Arrays.copyOfRange(readBases, offset - str+1, offset+1);
maxBW = VariantContextUtils.findNumberofRepetitions(backwardRepeatUnit,Arrays.copyOfRange(readBases, 0, offset+1), false);
if (maxBW > 1) {
bestBWRepeatUnit = backwardRepeatUnit.clone();
break;
}
}
byte[] bestRepeatUnit = bestBWRepeatUnit;
int maxRL = maxBW;
if (offset < readBases.length-1) {
byte[] bestFWRepeatUnit = new byte[]{readBases[offset+1]};
int maxFW = 0;
for (int str = 1; str <= MAX_STR_UNIT_LENGTH; str++) {
// fix repeat unit length
//edge case: if candidate tandem repeat unit falls beyond edge of read, skip
if (offset+str+1 > readBases.length)
break;
// get forward repeat unit and # repeats
byte[] forwardRepeatUnit = Arrays.copyOfRange(readBases, offset +1, offset+str+1);
maxFW = VariantContextUtils.findNumberofRepetitions(forwardRepeatUnit,Arrays.copyOfRange(readBases, offset+1, readBases.length), true);
if (maxFW > 1) {
bestFWRepeatUnit = forwardRepeatUnit.clone();
break;
}
}
// if FW repeat unit = BW repeat unit it means we're in the middle of a tandem repeat - add FW and BW components
if (Arrays.equals(bestFWRepeatUnit, bestBWRepeatUnit)) {
maxRL = maxBW + maxFW;
bestRepeatUnit = bestFWRepeatUnit; // arbitrary
}
else {
// tandem repeat starting forward from current offset
maxRL = maxFW;
bestRepeatUnit = bestFWRepeatUnit;
}
/* if (maxFW > maxBW) {
// tandem repeat starting forward from current offset
maxRL = maxFW;
bestRepeatUnit = bestFWRepeatUnit;
}
else if (maxFW < maxBW) {
maxRL = maxBW;
bestRepeatUnit = bestBWRepeatUnit;
} */
/* else {
// maxFW = maxBW but repeat units different: not in a tandem repeat.
maxRL = 1;
bestRepeatUnit = bestBWRepeatUnit; // arbitrary
} */
}
if(maxRL > MAX_REPEAT_LENGTH) { maxRL = MAX_REPEAT_LENGTH; }
return new Pair<byte[], Integer>(bestRepeatUnit, maxRL);
}
@Override
public final Object getValue(final String str) {
return str;
}
@Override
public synchronized String formatKey(final int key) {
// This method is synchronized so that we don't attempt to do a get()
// from the reverse lookup table while that table is being updated
return repeatReverseLookupTable.get(key);
}
@Override
public int keyFromValue(final Object value) {
return keyForRepeat((String) value);
}
/**
* Get the mapping from read group names to integer key values for all read groups in this covariate
* @return a set of mappings from read group names -> integer key values
*/
public Set<Map.Entry<String, Integer>> getKeyMap() {
return repeatLookupTable.entrySet();
}
private int keyForRepeat(final String repeatID) {
// Rather than synchronize this entire method (which would be VERY expensive for walkers like the BQSR),
// synchronize only the table updates.
// Before entering the synchronized block, check to see if this read group is not in our tables.
// If it's not, either we will have to insert it, OR another thread will insert it first.
// This preliminary check avoids doing any synchronization most of the time.
if ( ! repeatLookupTable.containsKey(repeatID) ) {
synchronized ( this ) {
// Now we need to make sure the key is STILL not there, since another thread may have come along
// and inserted it while we were waiting to enter this synchronized block!
if ( ! repeatLookupTable.containsKey(repeatID) ) {
repeatLookupTable.put(repeatID, nextId);
repeatReverseLookupTable.put(nextId, repeatID);
nextId++;
}
}
}
return repeatLookupTable.get(repeatID);
}
/**
* Splits repeat unit and num repetitions from covariate value.
* For example, if value if "ATG4" it returns (ATG,4)
* @param value Covariate value
* @return Split pair
*/
@Requires("value != null")
@Ensures({"result.first != null","result.second>=0"})
public static Pair<String,Integer> getRUandNRfromCovariate(final String value) {
int k = 0;
for ( k=0; k < value.length(); k++ ) {
if (!BaseUtils.isRegularBase(value.getBytes()[k]))
break;
}
Integer nr = Integer.valueOf(value.substring(k,value.length())); // will throw NumberFormatException if format illegal
if (k == value.length() || nr <= 0)
throw new IllegalStateException("Covariate is not of form (Repeat Unit) + Integer");
return new Pair<String,Integer>(value.substring(0,k), nr);
}
/**
* Gets bases from tandem repeat representation (Repeat Unit),(Number of Repeats).
* For example, (AGC),3 returns AGCAGCAGC
* @param repeatUnit Tandem repeat unit
* @param numRepeats Number of repeats
* @return Expanded String
*/
@Requires({"numRepeats > 0","repeatUnit != null"})
@Ensures("result != null")
public static String getBasesFromRUandNR(final String repeatUnit, final int numRepeats) {
final StringBuilder sb = new StringBuilder();
for (int i=0; i < numRepeats; i++)
sb.append(repeatUnit);
return sb.toString();
}
// version given covariate key
public static String getBasesFromRUandNR(final String covariateValue) {
Pair<String,Integer> pair = getRUandNRfromCovariate(covariateValue);
return getBasesFromRUandNR(pair.getFirst(), pair.getSecond());
}
@Override
public synchronized int maximumKeyValue() {