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Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Ryan Poplin 2012-06-28 12:57:59 -04:00
parent 5bb0693888 1ce0b9d519
commit d12ec92a55
49 changed files with 862 additions and 1382 deletions
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3
public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
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@ -345,7 +345,8 @@ public abstract class ArgumentTypeDescriptor {
FeatureManager manager = new FeatureManager();
if ( manager.getByName(tribbleType) == null )
throw new UserException.CommandLineException(
throw new UserException.UnknownTribbleType(
tribbleType,
String.format("Unable to find tribble type '%s' provided on the command line. " +
"Please select a correct type from among the supported types:%n%s",
tribbleType, manager.userFriendlyListOfAvailableFeatures(parameterType)));

6
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGatherer.java
View File

@ -71,11 +71,13 @@ public class BQSRGatherer extends Gatherer {
if (RAC.recalibrationReport != null && !RAC.NO_PLOTS) {
File recal_out = new File(output.getName() + ".original");
RecalibrationReport originalReport = new RecalibrationReport(RAC.recalibrationReport);
RecalDataManager.generateRecalibrationPlot(recal_out, originalReport.getKeysAndTablesMap(), generalReport.getKeysAndTablesMap(), RAC.KEEP_INTERMEDIATE_FILES);
// TODO -- fix me
//RecalDataManager.generateRecalibrationPlot(recal_out, originalReport.getKeysAndTablesMap(), generalReport.getKeysAndTablesMap(), RAC.KEEP_INTERMEDIATE_FILES);
}
else if (!RAC.NO_PLOTS) {
File recal_out = new File(output.getName() + ".recal");
RecalDataManager.generateRecalibrationPlot(recal_out, generalReport.getKeysAndTablesMap(), RAC.KEEP_INTERMEDIATE_FILES);
// TODO -- fix me
//RecalDataManager.generateRecalibrationPlot(recal_out, generalReport.getKeysAndTablesMap(), RAC.KEEP_INTERMEDIATE_FILES);
}
generalReport.output(outputFile);

329
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRKeyManager.java
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@ -1,329 +0,0 @@
package org.broadinstitute.sting.gatk.walkers.bqsr;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import java.util.*;
/**
* This class provides all the functionality for the BitSet representation of the keys to the hash table of BQSR
*
* It also handles the event type "covariate" which is not exactly a covariate, but is added as a key to the hashmap. The Key Manager will
* add the event type as a bitset to the end of the covariate bitset key. This way, it won't get int the way of masking the information
* out of the key for the actual covariates, and having the covariates handle it. The key manager handles the event type.
*
* The keys represented by this key manager will always have the same order:
*
* RequiredCovariate1, RequiredCovariate2, ..., RequiredCovariateN, OptionalCovariate1, OptionalCovariateID, EventType
* RequiredCovariate1, RequiredCovariate2, ..., RequiredCovariateN, OptionalCovariate2, OptionalCovariateID, EventType
* ...
* RequiredCovariate1, RequiredCovariate2, ..., RequiredCovariateN, OptionalCovariateN, OptionalCovariateID, EventType
*
*
* Note that Optional Covariates are optional, and the Key Manager should operate without them if necessary.
*
* @author Mauricio Carneiro
* @since 3/6/12
*/
public class BQSRKeyManager {
private final Covariate[] requiredCovariates;
private final Covariate[] optionalCovariates;
private final RequiredCovariateInfo[] requiredCovariatesInfo;
private final OptionalCovariateInfo[] optionalCovariatesInfo;
private final Map<String, Short> covariateNameToIDMap;
private int nRequiredBits; // Number of bits used to represent the required covariates
private final int optionalCovariateOffset;
private final int optionalCovariateIDOffset;
private final long optionalCovariateMask; // Standard mask for optional covariates key
private final long optionalCovariateIDMask; // Standard mask for optional covariates order key
private final long eventIDMask; // Standard mask for event ID
/**
* Initializes the KeyManager with the total number of covariates to use
*
* @param requiredCovariates the ordered list of required covariates
* @param optionalCovariates the ordered list of optional covariates
*/
public BQSRKeyManager(final List<Covariate> requiredCovariates, final List<Covariate> optionalCovariates) {
this.requiredCovariates = new Covariate[requiredCovariates.size()];
this.optionalCovariates = new Covariate[optionalCovariates.size()];
requiredCovariatesInfo = new RequiredCovariateInfo[requiredCovariates.size()]; // initialize the required covariates list
optionalCovariatesInfo = new OptionalCovariateInfo[optionalCovariates.size()]; // initialize the optional covariates list (size may be 0, it's okay)
covariateNameToIDMap = new HashMap<String, Short>(optionalCovariates.size()*2); // the map from covariate name to covariate id (when reading GATK Reports, we get the IDs as names of covariates)
nRequiredBits = 0;
for (int i = 0; i < requiredCovariates.size(); i++) { // create a list of required covariates with the extra information for key management
final Covariate required = requiredCovariates.get(i);
final int nBits = required.numberOfBits(); // number of bits used by this covariate
final long mask = genericMask(nRequiredBits, nBits); // create a mask for this covariate
this.requiredCovariates[i] = required;
requiredCovariatesInfo[i] = new RequiredCovariateInfo(nBits, nRequiredBits, mask, required); // Create an object for this required covariate
nRequiredBits += nBits;
}
final int bitsInEventType = numberOfBitsToRepresent(EventType.values().length);
eventIDMask = genericMask(nRequiredBits, bitsInEventType);
short id = 0;
int nOptionalBits = 0;
for (int i = 0; i < optionalCovariates.size(); i++) {
final Covariate optional = optionalCovariates.get(i);
nOptionalBits = Math.max(nOptionalBits, optional.numberOfBits()); // optional covariates are represented by the number of bits needed by biggest covariate
this.optionalCovariates[i] = optional;
optionalCovariatesInfo[i] = new OptionalCovariateInfo(id, optional);
final String covariateName = optional.getClass().getSimpleName().split("Covariate")[0]; // get the name of the covariate (without the "covariate" part of it) so we can match with the GATKReport
covariateNameToIDMap.put(covariateName, id);
id++;
}
optionalCovariateOffset = nRequiredBits + bitsInEventType;
optionalCovariateMask = genericMask(optionalCovariateOffset, nOptionalBits); // the generic mask to extract optional covariate bits from the combined bitset
optionalCovariateIDOffset = nRequiredBits + bitsInEventType + nOptionalBits;
final int nOptionalIDBits = numberOfBitsToRepresent(optionalCovariates.size()); // number of bits used to represent the covariate ID
optionalCovariateIDMask = genericMask(optionalCovariateIDOffset, nOptionalIDBits); // the generic mask to extract optional covariate ID bits from the combined bitset
final int totalNumberOfBits = optionalCovariateIDOffset + nOptionalIDBits; // total number of bits used in the final key
if ( totalNumberOfBits > 64 )
throw new UserException.BadInput("The total number of bits used for the master BQSR key is greater than 64 and cannot be represented in a long");
}
/**
* Generates one key given the optional covariate (or none if it is null)
*
* Keys include all required covariates, the standard covariate and the event type.
*
* @param allKeys The keys in long representation for each covariate (includes all optional covariates, not just the one requested)
* @param eventType The type of event described by this keyset (e.g. mismatches, insertions, deletions)
* @return one key in long representation (non-negative) or -1 for a bad key
*/
public long createMasterKey(final long[] allKeys, final EventType eventType, final int optionalCovariateIndex) {
int keyIndex = 0;
long masterKey = 0L; // This will be a master key holding all the required keys, to replicate later on
for (RequiredCovariateInfo infoRequired : requiredCovariatesInfo)
masterKey |= (allKeys[keyIndex++] << infoRequired.offset);
final long eventKey = keyFromEvent(eventType); // create a key for the event type
masterKey |= (eventKey << nRequiredBits);
if (optionalCovariateIndex >= 0 && optionalCovariateIndex < optionalCovariates.length) {
final long covariateKey = allKeys[keyIndex + optionalCovariateIndex];
if (covariateKey < 0) // do not add "nulls" to the final set of keys
return -1;
masterKey |= (covariateKey << optionalCovariateOffset);
masterKey |= (optionalCovariatesInfo[optionalCovariateIndex].covariateID << optionalCovariateIDOffset);
}
return masterKey;
}
/**
* Generates one key for the covariates represented in Object[] key
*
* The covariates will have the actual objects produced by the covariates (probably read from the recalibration data file)
* and will contain all required covariates and one (or none) optional covariates. Therefore, the product is one key, not many.
*
* Example key:
* RG, QUAL, CYCLE, CYCLE_ID, EventType
*
* @param key list of objects produced by the required covariates followed by one or zero optional covariates.
* @return a key representing these objects.
*/
public long longFromKey(Object[] key) {
int requiredCovariate = 0;
long masterKey = 0L; // This will be a master key holding all the required keys, to replicate later on
for (RequiredCovariateInfo infoRequired : requiredCovariatesInfo)
masterKey |= (infoRequired.covariate.longFromKey(key[requiredCovariate++]) << infoRequired.offset);
final int eventIndex = key.length - 1; // the event type is always the last key
final long eventKey = keyFromEvent((EventType) key[eventIndex]); // create a key for the event type
masterKey |= (eventKey << nRequiredBits);
if (optionalCovariatesInfo.length > 0) {
final int covariateIndex = requiredCovariatesInfo.length; // the optional covariate index in the key array
final int covariateIDIndex = covariateIndex + 1; // the optional covariate ID index is right after the optional covariate's
final short covariateID = parseCovariateID(key[covariateIDIndex]); // when reading the GATK Report the ID may come in a String instead of an index
final OptionalCovariateInfo infoOptional = optionalCovariatesInfo[covariateID]; // so we can get the optional covariate information
final long covariateKey = infoOptional.covariate.longFromKey(key[covariateIndex]); // convert the optional covariate key into a bitset using the covariate's interface
masterKey |= (covariateKey << optionalCovariateOffset);
masterKey |= (infoOptional.covariateID << optionalCovariateIDOffset);
}
return masterKey;
}
/**
* Covariate id can be either the covariate name (String) or the actual id (short). This method
* finds it's type and converts accordingly to the short notation.
*
* @param id the string or short representation of the optional covariate id
* @return the short representation of the optional covariate id.
*/
private short parseCovariateID(final Object id) {
return (id instanceof String) ? covariateNameToIDMap.get(id.toString()) : (Short) id;
}
/**
* Generates a key set of objects from a combined master key.
*
* Masks out each covariate independently and decodes their values (Object) into a keyset
*
* @param master the master representation of the keys
* @return an object array with the values for each key
*/
public List<Object> keySetFrom(final long master) {
final List<Object> objectKeys = new ArrayList<Object>();
for (RequiredCovariateInfo info : requiredCovariatesInfo) {
final long covariateKey = extractKeyFromMaster(master, info.mask, info.offset); // get the covariate's key
objectKeys.add(info.covariate.formatKey(covariateKey)); // convert the key to object using covariate's interface
}
if (optionalCovariatesInfo.length > 0) {
final long covKey = extractKeyFromMaster(master, optionalCovariateMask, optionalCovariateOffset); // get the covariate's key
final int covIDKey = (int)extractKeyFromMaster(master, optionalCovariateIDMask, optionalCovariateIDOffset); // get the covariate's id (to identify which covariate this is)
Covariate covariate = optionalCovariatesInfo[(short)covIDKey].covariate; // get the corresponding optional covariate object
objectKeys.add(covariate.formatKey(covKey)); // add the optional covariate key to the key set
objectKeys.add(covariate.getClass().getSimpleName().split("Covariate")[0]); // add the covariate name using the id
}
objectKeys.add(EventType.eventFrom((int)extractKeyFromMaster(master, eventIDMask, nRequiredBits))); // add the event type object to the key set
return objectKeys;
}
public Covariate[] getRequiredCovariates() {
return requiredCovariates;
}
public Covariate[] getOptionalCovariates() {
return optionalCovariates;
}
public int getNumRequiredCovariates() {
return requiredCovariates.length;
}
public int getNumOptionalCovariates() {
return optionalCovariates.length;
}
/**
* Creates a mask for the requested covariate to extract the relevant key from a combined master key
*
* @param offset the offset into the master key
* @param nBits the number of bits needed by the Covariate to represent its values
* @return the mask relevant to the covariate
*/
private long genericMask(final int offset, final int nBits) {
long mask = 0L;
for ( int i = 0; i < nBits; i++ )
mask |= 1L << (offset+i);
return mask;
}
private long extractKeyFromMaster(final long master, final long mask, final int offset) {
long key = master & mask;
return key >> offset;
}
// cache the key representing an event since it's otherwise created a massive amount of times
private static final long[] eventTypeCache = new long[EventType.values().length]; // event IDs must be longs so that bit-fiddling works
static {
for (final EventType eventType : EventType.values())
eventTypeCache[eventType.index] = (long)eventType.index;
}
private long keyFromEvent(final EventType eventType) {
return eventTypeCache[eventType.index];
}
@Override
public boolean equals(Object o) {
if (!(o instanceof BQSRKeyManager))
return false;
BQSRKeyManager other = (BQSRKeyManager) o;
if (this == other)
return true;
if (requiredCovariatesInfo.length != other.requiredCovariatesInfo.length ||
optionalCovariatesInfo.length != other.optionalCovariatesInfo.length)
return false;
for (int i = 0; i < requiredCovariates.length; i++) {
Covariate myRequiredCovariate = requiredCovariates[i];
Covariate otherRequiredCovariate = other.requiredCovariates[i];
String thisName = myRequiredCovariate.getClass().getSimpleName();
String otherName = otherRequiredCovariate.getClass().getSimpleName();
if (!thisName.equals(otherName))
return false;
}
for (int i = 0; i < optionalCovariates.length; i++) {
Covariate myOptionalCovariate = optionalCovariates[i];
Covariate otherOptionalCovariate = other.optionalCovariates[i];
String thisName = myOptionalCovariate.getClass().getSimpleName();
String otherName = otherOptionalCovariate.getClass().getSimpleName();
if (!thisName.equals(otherName))
return false;
}
return true;
}
/**
* Calculates the number of bits necessary to represent a given number of elements
*
* @param numberOfElements the number of elements to represent (must be positive)
* @return the number of bits necessary to represent this many elements
*/
public static int numberOfBitsToRepresent(long numberOfElements) {
if (numberOfElements < 0)
throw new ReviewedStingException("Number of elements must be positive: " + numberOfElements);
if (numberOfElements == 1L)
return 1; // special case
int n = 0;
numberOfElements--;
while (numberOfElements > 0) {
numberOfElements = numberOfElements >> 1;
n++;
}
return n;
}
/**
* Aggregate information for each Covariate
*/
private static class RequiredCovariateInfo {
public final int nBits; // number of bits for this key
public final int offset; // the offset into the master key
public final long mask; // the mask to pull out this covariate from the combined bitset key ( a mask made from bitsBefore and nBits )
public final Covariate covariate; // this allows reverse lookup of the Covariates in order
RequiredCovariateInfo(final int nBits, final int offset, final long mask, final Covariate covariate) {
this.nBits = nBits;
this.offset = offset;
this.mask = mask;
this.covariate = covariate;
}
}
private static class OptionalCovariateInfo {
public final long covariateID; // cache the covariate ID (must be a long so that bit-fiddling works)
public final Covariate covariate;
OptionalCovariateInfo(final long covariateID, final Covariate covariate) {
this.covariateID = covariateID;
this.covariate = covariate;
}
}
}

219
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ContextCovariate.java
View File

@ -32,6 +32,8 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import java.util.ArrayList;
/**
* Created by IntelliJ IDEA.
* User: rpoplin
@ -43,6 +45,19 @@ public class ContextCovariate implements StandardCovariate {
private int mismatchesContextSize;
private int indelsContextSize;
private int mismatchesKeyMask;
private int indelsKeyMask;
private static final int LENGTH_BITS = 4;
private static final int LENGTH_MASK = 15;
// temporary lists to use for creating context covariate keys
private final ArrayList<Integer> mismatchKeys = new ArrayList<Integer>(200);
private final ArrayList<Integer> indelKeys = new ArrayList<Integer>(200);
// the maximum context size (number of bases) permitted; we need to keep the leftmost base free so that values are
// not negative and we reserve 4 more bits to represent the length of the context; it takes 2 bits to encode one base.
static final private int MAX_DNA_CONTEXT = 13;
private byte LOW_QUAL_TAIL;
// Initialize any member variables using the command-line arguments passed to the walkers
@ -59,11 +74,15 @@ public class ContextCovariate implements StandardCovariate {
if (mismatchesContextSize <= 0 || indelsContextSize <= 0)
throw new UserException(String.format("Context size must be positive, if you don't want to use the context covariate, just turn it off instead. Mismatches: %d Indels: %d", mismatchesContextSize, indelsContextSize));
mismatchesKeyMask = createMask(mismatchesContextSize);
indelsKeyMask = createMask(indelsContextSize);
}
@Override
public void recordValues(final GATKSAMRecord read, final ReadCovariates values) {
// TODO -- wrong: fix me
final GATKSAMRecord clippedRead = ReadClipper.clipLowQualEnds(read, LOW_QUAL_TAIL, ClippingRepresentation.WRITE_NS); // Write N's over the low quality tail of the reads to avoid adding them into the context
final boolean negativeStrand = clippedRead.getReadNegativeStrandFlag();
@ -71,10 +90,15 @@ public class ContextCovariate implements StandardCovariate {
if (negativeStrand)
bases = BaseUtils.simpleReverseComplement(bases);
final int readLength = clippedRead.getReadLength();
mismatchKeys.clear();
indelKeys.clear();
contextWith(bases, mismatchesContextSize, mismatchKeys, mismatchesKeyMask);
contextWith(bases, indelsContextSize, indelKeys, indelsKeyMask);
final int readLength = bases.length;
for (int i = 0; i < readLength; i++) {
final long indelKey = contextWith(bases, i, indelsContextSize);
values.addCovariate(contextWith(bases, i, mismatchesContextSize), indelKey, indelKey, (negativeStrand ? readLength - i - 1 : i));
final int indelKey = indelKeys.get(i);
values.addCovariate(mismatchKeys.get(i), indelKey, indelKey, (negativeStrand ? readLength - i - 1 : i));
}
}
@ -85,7 +109,7 @@ public class ContextCovariate implements StandardCovariate {
}
@Override
public String formatKey(final long key) {
public String formatKey(final int key) {
if (key == -1) // this can only happen in test routines because we do not propagate null keys to the csv file
return null;
@ -93,147 +117,126 @@ public class ContextCovariate implements StandardCovariate {
}
@Override
public long longFromKey(Object key) {
return keyFromContext((String) key);
public int keyFromValue(final Object value) {
return keyFromContext((String) value);
}
@Override
public int numberOfBits() {
return Integer.bitCount(Integer.MAX_VALUE);
private static int createMask(final int contextSize) {
int mask = 0;
// create 2*contextSize worth of bits
for (int i = 0; i < contextSize; i++)
mask = (mask << 2) | 3;
// shift 4 bits to mask out the bits used to encode the length
return mask << LENGTH_BITS;
}
/**
* calculates the context of a base independent of the covariate mode (mismatch, insertion or deletion)
*
* @param bases the bases in the read to build the context from
* @param offset the position in the read to calculate the context for
* @param contextSize context size to use building the context
* @return the key representing the context
* @param keys list to store the keys
* @param mask mask for pulling out just the context bits
*/
private long contextWith(final byte[] bases, final int offset, final int contextSize) {
final int start = offset - contextSize + 1;
final long result;
if (start >= 0)
result = keyFromContext(bases, start, offset + 1);
else
result = -1L;
return result;
private static void contextWith(final byte[] bases, final int contextSize, final ArrayList<Integer> keys, final int mask) {
// the first contextSize-1 bases will not have enough previous context
for (int i = 1; i < contextSize && i <= bases.length; i++)
keys.add(-1);
if (bases.length < contextSize)
return;
final int newBaseOffset = 2 * (contextSize - 1) + LENGTH_BITS;
// get (and add) the key for the context starting at the first base
int currentKey = keyFromContext(bases, 0, contextSize);
keys.add(currentKey);
// if the first key was -1 then there was an N in the context; figure out how many more consecutive contexts it affects
int currentNPenalty = 0;
if (currentKey == -1) {
currentKey = 0;
currentNPenalty = contextSize - 1;
int offset = newBaseOffset;
while (bases[currentNPenalty] != 'N') {
final int baseIndex = BaseUtils.simpleBaseToBaseIndex(bases[currentNPenalty]);
currentKey |= (baseIndex << offset);
offset -= 2;
currentNPenalty--;
}
}
final int readLength = bases.length;
for (int currentIndex = contextSize; currentIndex < readLength; currentIndex++) {
final int baseIndex = BaseUtils.simpleBaseToBaseIndex(bases[currentIndex]);
if (baseIndex == -1) { // ignore non-ACGT bases
currentNPenalty = contextSize;
currentKey = 0; // reset the key
} else {
// push this base's contribution onto the key: shift everything 2 bits, mask out the non-context bits, and add the new base and the length in
currentKey = (currentKey >> 2) & mask;
currentKey |= (baseIndex << newBaseOffset);
currentKey |= contextSize;
}
if (currentNPenalty == 0) {
keys.add(currentKey);
} else {
currentNPenalty--;
keys.add(-1);
}
}
}
public static long keyFromContext(final String dna) {
public static int keyFromContext(final String dna) {
return keyFromContext(dna.getBytes(), 0, dna.length());
}
/**
* Creates a long representation of a given dna string.
* Creates a int representation of a given dna string.
*
* Warning: This conversion is limited to long precision, therefore the dna sequence cannot
* be longer than 31 bases.
*
* The bit representation of a dna string is the simple:
* 0 A 4 AA 8 CA
* 1 C 5 AC ...
* 2 G 6 AG 1343 TTGGT
* 3 T 7 AT 1364 TTTTT
*
* To convert from dna to number, we convert the dna string to base10 and add all combinations that
* preceded the string (with smaller lengths).
*
* @param dna the dna sequence
* @param dna the dna sequence
* @param start the start position in the byte array (inclusive)
* @param end the end position in the array (exclusive)
* @return the key representing the dna sequence
*/
public static long keyFromContext(final byte[] dna, final int start, final int end) {
final long preContext = combinationsPerLength[end - start - 1]; // the sum of all combinations that preceded the length of the dna string
long baseTen = 0L; // the number in base_10 that we are going to use to generate the bit set
private static int keyFromContext(final byte[] dna, final int start, final int end) {
int key = end - start;
int bitOffset = 4;
for (int i = start; i < end; i++) {
baseTen = (baseTen << 2); // multiply by 4
final int baseIndex = BaseUtils.simpleBaseToBaseIndex(dna[i]);
if (baseIndex == -1) // ignore non-ACGT bases
return -1L;
baseTen += (long)baseIndex;
return -1;
key |= (baseIndex << bitOffset);
bitOffset += 2;
}
return baseTen + preContext; // the number representing this DNA string is the base_10 representation plus all combinations that preceded this string length.
}
static final private int MAX_DNA_CONTEXT = 31; // the maximum context size (number of bases) permitted in the "long bitset" implementation of the DNA <=> BitSet conversion.
static final long[] combinationsPerLength = new long[MAX_DNA_CONTEXT + 1]; // keeps the memoized table with the number of combinations for each given DNA context length
static {
for (int i = 0; i < MAX_DNA_CONTEXT + 1; i++)
computeCombinationsFor(i);
}
/**
* The sum of all combinations of a context of a given length from length = 0 to length.
*
* Memoized implementation of sum(4^i) , where i=[0,length]
*
* @param length the length of the DNA context
*/
private static void computeCombinationsFor(final int length) {
long combinations = 0L;
for (int i = 1; i <= length; i++)
combinations += (1L << 2 * i); // add all combinations with 4^i ( 4^i is the same as 2^(2*i) )
combinationsPerLength[length] = combinations;
return key;
}
/**
* Converts a key into the dna string representation.
*
* Warning: This conversion is limited to long precision, therefore the dna sequence cannot
* be longer than 31 bases.
*
* We calculate the length of the resulting DNA sequence by looking at the sum(4^i) that exceeds the
* base_10 representation of the sequence. This is important for us to know how to bring the number
* to a quasi-canonical base_4 representation, and to fill in leading A's (since A's are represented
* as 0's and leading 0's are omitted).
*
* quasi-canonical because A is represented by a 0, therefore,
* instead of : 0, 1, 2, 3, 10, 11, 12, ...
* we have : 0, 1, 2, 3, 00, 01, 02, ...
*
* but we can correctly decode it because we know the final length.
*
* @param key the key representing the dna sequence
* @return the dna sequence represented by the key
*/
public static String contextFromKey(long key) {
public static String contextFromKey(final int key) {
if (key < 0)
throw new ReviewedStingException("dna conversion cannot handle negative numbers. Possible overflow?");
final int length = contextLengthFor(key); // the length of the context (the number of combinations is memoized, so costs zero to separate this into two method calls)
key -= combinationsPerLength[length - 1]; // subtract the the number of combinations of the preceding context from the number to get to the quasi-canonical representation
final int length = key & LENGTH_MASK; // the first bits represent the length (in bp) of the context
int mask = 48; // use the mask to pull out bases
int offset = 4;
StringBuilder dna = new StringBuilder();
while (key > 0) { // perform a simple base_10 to base_4 conversion (quasi-canonical)
final byte base = (byte) (key & 3); // equivalent to (key % 4)
dna.append((char)BaseUtils.baseIndexToSimpleBase(base));
key = key >> 2; // divide by 4
for (int i = 0; i < length; i++) {
final int baseIndex = (key & mask) >> offset;
dna.append((char)BaseUtils.baseIndexToSimpleBase(baseIndex));
mask = mask << 2; // move the mask over to the next 2 bits
offset += 2;
}
for (int j = dna.length(); j < length; j++)
dna.append('A'); // add leading A's as necessary (due to the "quasi" canonical status, see description above)
return dna.reverse().toString(); // make sure to reverse the string since we should have been pre-pending all along
}
/**
* Calculates the length of the DNA context for a given base 10 number
*
* It is important to know the length given the base 10 number to calculate the number of combinations
* and to disambiguate the "quasi-canonical" state.
*
* This method also calculates the number of combinations as a by-product, but since it memoizes the
* results, a subsequent call to combinationsFor(length) is O(1).
*
* @param number the base 10 representation of the key
* @return the length of the DNA context represented by this number
*/
private static int contextLengthFor(final long number) {
int length = 1; // the calculated length of the DNA sequence given the base_10 representation of its BitSet.
long combinations = combinationsPerLength[length]; // the next context (we advance it so we know which one was preceding it).
while (combinations <= number) { // find the length of the dna string (length)
length++;
combinations = combinationsPerLength[length]; // calculate the next context
}
return length;
return dna.toString();
}
}

14
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/Covariate.java
View File

@ -67,7 +67,7 @@ public interface Covariate {
* @param key the long representation of the key
* @return a string representation of the key
*/
public String formatKey(final long key);
public String formatKey(final int key);
/**
* Converts an Object key into a long key using only the lowest numberOfBits() bits
@ -75,18 +75,10 @@ public interface Covariate {
* Only necessary for on-the-fly recalibration when you have the object, but need to store it in memory in long format. For counting covariates
* the getValues method already returns all values in long format.
*
* @param key the object corresponding to the covariate
* @param value the object corresponding to the covariate
* @return a long representation of the object
*/
public long longFromKey(final Object key);
/**
* Each covariate should determine how many bits are necessary to encode it's data
*
* @return The number of bits used to represent the values of this covariate.
*/
public int numberOfBits();
public int keyFromValue(final Object value);
}
interface RequiredCovariate extends Covariate {}

39
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/CycleCovariate.java
View File

@ -79,7 +79,7 @@ public class CycleCovariate implements StandardCovariate {
final int CUSHION = 4;
final int MAX_CYCLE = readLength - CUSHION - 1;
for (int i = 0; i < readLength; i++) {
final long key = (i<CUSHION || i>MAX_CYCLE) ? -1L : keyFromCycle(cycle);
final int key = (i<CUSHION || i>MAX_CYCLE) ? -1 : keyFromCycle(cycle);
values.addCovariate(key, key, key, i);
cycle += increment;
}
@ -106,22 +106,22 @@ public class CycleCovariate implements StandardCovariate {
int iii = 0;
while (iii < readLength) {
while (iii < readLength && bases[iii] == (byte) 'T') {
final long key = keyFromCycle(cycle);
final int key = keyFromCycle(cycle);
values.addCovariate(key, key, key, iii);
iii++;
}
while (iii < readLength && bases[iii] == (byte) 'A') {
final long key = keyFromCycle(cycle);
final int key = keyFromCycle(cycle);
values.addCovariate(key, key, key, iii);
iii++;
}
while (iii < readLength && bases[iii] == (byte) 'C') {
final long key = keyFromCycle(cycle);
final int key = keyFromCycle(cycle);
values.addCovariate(key, key, key, iii);
iii++;
}
while (iii < readLength && bases[iii] == (byte) 'G') {
final long key = keyFromCycle(cycle);
final int key = keyFromCycle(cycle);
values.addCovariate(key, key, key, iii);
iii++;
}
@ -132,7 +132,7 @@ public class CycleCovariate implements StandardCovariate {
cycle++;
}
if (iii < readLength && !BaseUtils.isRegularBase(bases[iii])) {
final long key = keyFromCycle(cycle);
final int key = keyFromCycle(cycle);
values.addCovariate(key, key, key, iii);
iii++;
}
@ -143,22 +143,22 @@ public class CycleCovariate implements StandardCovariate {
int iii = readLength - 1;
while (iii >= 0) {
while (iii >= 0 && bases[iii] == (byte) 'T') {
final long key = keyFromCycle(cycle);
final int key = keyFromCycle(cycle);
values.addCovariate(key, key, key, iii);
iii--;
}
while (iii >= 0 && bases[iii] == (byte) 'A') {
final long key = keyFromCycle(cycle);
final int key = keyFromCycle(cycle);
values.addCovariate(key, key, key, iii);
iii--;
}
while (iii >= 0 && bases[iii] == (byte) 'C') {
final long key = keyFromCycle(cycle);
final int key = keyFromCycle(cycle);
values.addCovariate(key, key, key, iii);
iii--;
}
while (iii >= 0 && bases[iii] == (byte) 'G') {
final long key = keyFromCycle(cycle);
final int key = keyFromCycle(cycle);
values.addCovariate(key, key, key, iii);
iii--;
}
@ -169,7 +169,7 @@ public class CycleCovariate implements StandardCovariate {
cycle++;
}
if (iii >= 0 && !BaseUtils.isRegularBase(bases[iii])) {
final long key = keyFromCycle(cycle);
final int key = keyFromCycle(cycle);
values.addCovariate(key, key, key, iii);
iii--;
}
@ -190,26 +190,21 @@ public class CycleCovariate implements StandardCovariate {
}
@Override
public String formatKey(final long key) {
long cycle = key >> 1; // shift so we can remove the "sign" bit
public String formatKey(final int key) {
int cycle = key >> 1; // shift so we can remove the "sign" bit
if ( (key & 1) != 0 ) // is the last bit set?
cycle *= -1; // then the cycle is negative
return String.format("%d", cycle);
}
@Override
public long longFromKey(final Object key) {
return (key instanceof String) ? keyFromCycle(Integer.parseInt((String) key)) : keyFromCycle((Integer) key);
public int keyFromValue(final Object value) {
return (value instanceof String) ? keyFromCycle(Integer.parseInt((String) value)) : keyFromCycle((Integer) value);
}
@Override
public int numberOfBits() {
return Integer.bitCount(Integer.MAX_VALUE);
}
private static long keyFromCycle(final int cycle) {
private static int keyFromCycle(final int cycle) {
// no negative values because values must fit into the first few bits of the long
long result = Math.abs(cycle);
int result = Math.abs(cycle);
result = result << 1; // shift so we can add the "sign" bit
if ( cycle < 0 )
result++; // negative cycles get the lower-most bit set

16
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/QualityScoreCovariate.java
View File

@ -1,6 +1,5 @@
package org.broadinstitute.sting.gatk.walkers.bqsr;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
/*
@ -49,7 +48,7 @@ public class QualityScoreCovariate implements RequiredCovariate {
final byte[] baseDeletionQualities = read.getBaseDeletionQualities();
for (int i = 0; i < baseQualities.length; i++) {
values.addCovariate((long)baseQualities[i], (long)baseInsertionQualities[i], (long)baseDeletionQualities[i], i);
values.addCovariate((int)baseQualities[i], (int)baseInsertionQualities[i], (int)baseDeletionQualities[i], i);
}
}
@ -60,17 +59,12 @@ public class QualityScoreCovariate implements RequiredCovariate {
}
@Override
public String formatKey(final long key) {
public String formatKey(final int key) {
return String.format("%d", key);
}
@Override
public long longFromKey(final Object key) {
return (key instanceof String) ? (long)Byte.parseByte((String) key) : (long)(Byte) key;
public int keyFromValue(final Object value) {
return (value instanceof String) ? (int)Byte.parseByte((String) value) : (int)(Byte) value;
}
@Override
public int numberOfBits() {
return BQSRKeyManager.numberOfBitsToRepresent(QualityUtils.MAX_QUAL_SCORE);
}
}
}

25
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/QuantizationInfo.java
View File

@ -1,13 +1,14 @@
package org.broadinstitute.sting.gatk.walkers.bqsr;
import org.broadinstitute.sting.gatk.report.GATKReportTable;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.collections.NestedHashMap;
import org.broadinstitute.sting.utils.recalibration.QualQuantizer;
import org.broadinstitute.sting.utils.recalibration.RecalibrationTables;
import java.util.Arrays;
import java.util.List;
import java.util.Map;
/**
* Class that encapsulates the information necessary for quality score quantization for BQSR
@ -30,25 +31,17 @@ public class QuantizationInfo {
this(quantizedQuals, empiricalQualCounts, calculateQuantizationLevels(quantizedQuals));
}
public QuantizationInfo(Map<BQSRKeyManager, Map<Long, RecalDatum>> keysAndTablesMap, int quantizationLevels) {
public QuantizationInfo(final RecalibrationTables recalibrationTables, final int quantizationLevels) {
final Long [] qualHistogram = new Long[QualityUtils.MAX_QUAL_SCORE+1]; // create a histogram with the empirical quality distribution
for (int i = 0; i < qualHistogram.length; i++)
qualHistogram[i] = 0L;
Map<Long, RecalDatum> qualTable = null; // look for the quality score table
for (Map.Entry<BQSRKeyManager, Map<Long, RecalDatum>> entry : keysAndTablesMap.entrySet()) {
BQSRKeyManager keyManager = entry.getKey();
if (keyManager.getNumRequiredCovariates() == 2) // it should be the only one with 2 required covariates
qualTable = entry.getValue();
}
final NestedHashMap qualTable = recalibrationTables.getTable(RecalibrationTables.TableType.QUALITY_SCORE_TABLE); // get the quality score table
if (qualTable == null)
throw new ReviewedStingException("Could not find QualityScore table.");
for (RecalDatum datum : qualTable.values()) {
int empiricalQual = (int) Math.round(datum.getEmpiricalQuality()); // convert the empirical quality to an integer ( it is already capped by MAX_QUAL )
long nObservations = datum.numObservations;
qualHistogram[empiricalQual] += nObservations; // add the number of observations for every key
for (final Object value : qualTable.getAllValues()) {
final RecalDatum datum = (RecalDatum)value;
final int empiricalQual = MathUtils.fastRound(datum.getEmpiricalQuality()); // convert the empirical quality to an integer ( it is already capped by MAX_QUAL )
qualHistogram[empiricalQual] += datum.numObservations; // add the number of observations for every key
}
empiricalQualCounts = Arrays.asList(qualHistogram); // histogram with the number of observations of the empirical qualities
quantizeQualityScores(quantizationLevels);

61
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ReadCovariates.java
View File

@ -1,7 +1,5 @@
package org.broadinstitute.sting.gatk.walkers.bqsr;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
/**
* The object temporarily held by a read that describes all of it's covariates.
*
@ -11,65 +9,56 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
* @since 2/8/12
*/
public class ReadCovariates {
private final long[][] mismatchesKeySet;
private final long[][] insertionsKeySet;
private final long[][] deletionsKeySet;
private final int[][][] keys;
private int currentCovariateIndex = 0;
public ReadCovariates(int readLength, int numberOfCovariates) {
this.mismatchesKeySet = new long[readLength][numberOfCovariates];
this.insertionsKeySet = new long[readLength][numberOfCovariates];
this.deletionsKeySet = new long[readLength][numberOfCovariates];
public ReadCovariates(final int readLength, final int numberOfCovariates) {
keys = new int[EventType.values().length][readLength][numberOfCovariates];
}
public void setCovariateIndex(final int index) {
currentCovariateIndex = index;
}
public void addCovariate(final long mismatch, final long insertion, final long deletion, final int readOffset) {
mismatchesKeySet[readOffset][currentCovariateIndex] = mismatch;
insertionsKeySet[readOffset][currentCovariateIndex] = insertion;
deletionsKeySet[readOffset][currentCovariateIndex] = deletion;
public void addCovariate(final int mismatch, final int insertion, final int deletion, final int readOffset) {
keys[EventType.BASE_SUBSTITUTION.index][readOffset][currentCovariateIndex] = mismatch;
keys[EventType.BASE_INSERTION.index][readOffset][currentCovariateIndex] = insertion;
keys[EventType.BASE_DELETION.index][readOffset][currentCovariateIndex] = deletion;
}
public long[] getKeySet(final int readPosition, final EventType errorModel) {
switch (errorModel) {
case BASE_SUBSTITUTION:
return getMismatchesKeySet(readPosition);
case BASE_INSERTION:
return getInsertionsKeySet(readPosition);
case BASE_DELETION:
return getDeletionsKeySet(readPosition);
default:
throw new ReviewedStingException("Unrecognized Base Recalibration type: " + errorModel);
}
public int[] getKeySet(final int readPosition, final EventType errorModel) {
return keys[errorModel.index][readPosition];
}
public long[] getMismatchesKeySet(final int readPosition) {
return mismatchesKeySet[readPosition];
public int[][] getKeySet(final EventType errorModel) {
return keys[errorModel.index];
}
public long[] getInsertionsKeySet(final int readPosition) {
return insertionsKeySet[readPosition];
public int[] getMismatchesKeySet(final int readPosition) {
return keys[EventType.BASE_SUBSTITUTION.index][readPosition];
}
public long[] getDeletionsKeySet(final int readPosition) {
return deletionsKeySet[readPosition];
public int[] getInsertionsKeySet(final int readPosition) {
return keys[EventType.BASE_INSERTION.index][readPosition];
}
public int[] getDeletionsKeySet(final int readPosition) {
return keys[EventType.BASE_DELETION.index][readPosition];
}
/**
* Testing routines
*/
protected long[][] getMismatchesKeySet() {
return mismatchesKeySet;
protected int[][] getMismatchesKeySet() {
return keys[EventType.BASE_SUBSTITUTION.index];
}
protected long[][] getInsertionsKeySet() {
return insertionsKeySet;
protected int[][] getInsertionsKeySet() {
return keys[EventType.BASE_INSERTION.index];
}
protected long[][] getDeletionsKeySet() {
return deletionsKeySet;
protected int[][] getDeletionsKeySet() {
return keys[EventType.BASE_DELETION.index];
}
}

21
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ReadGroupCovariate.java
View File

@ -40,9 +40,9 @@ import java.util.HashMap;
public class ReadGroupCovariate implements RequiredCovariate {
private final HashMap<String, Long> readGroupLookupTable = new HashMap<String, Long>();
private final HashMap<Long, String> readGroupReverseLookupTable = new HashMap<Long, String>();
private long nextId = 0L;
private final HashMap<String, Integer> readGroupLookupTable = new HashMap<String, Integer>();
private final HashMap<Integer, String> readGroupReverseLookupTable = new HashMap<Integer, String>();
private int nextId = 0;
// Initialize any member variables using the command-line arguments passed to the walkers
@Override
@ -51,7 +51,7 @@ public class ReadGroupCovariate implements RequiredCovariate {
@Override
public void recordValues(final GATKSAMRecord read, final ReadCovariates values) {
final String readGroupId = readGroupValueFromRG(read.getReadGroup());
final long key = keyForReadGroup(readGroupId);
final int key = keyForReadGroup(readGroupId);
final int l = read.getReadLength();
for (int i = 0; i < l; i++)
@ -64,21 +64,16 @@ public class ReadGroupCovariate implements RequiredCovariate {
}
@Override
public String formatKey(final long key) {
public String formatKey(final int key) {
return readGroupReverseLookupTable.get(key);
}
@Override
public long longFromKey(Object key) {
return keyForReadGroup((String) key);
public int keyFromValue(final Object value) {
return keyForReadGroup((String) value);
}
@Override
public int numberOfBits() {
return BQSRKeyManager.numberOfBitsToRepresent(Short.MAX_VALUE);
}
private long keyForReadGroup(final String readGroupId) {
private int keyForReadGroup(final String readGroupId) {
if (!readGroupLookupTable.containsKey(readGroupId)) {
readGroupLookupTable.put(readGroupId, nextId);
readGroupReverseLookupTable.put(nextId, readGroupId);

312
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDataManager.java
View File

@ -32,11 +32,13 @@ import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.R.RScriptExecutor;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.collections.NestedHashMap;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.io.Resource;
import org.broadinstitute.sting.utils.recalibration.RecalibrationTables;
import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
@ -82,6 +84,14 @@ public class RecalDataManager {
private static final String SCRIPT_FILE = "BQSR.R";
private static final Pair<String, String> covariateValue = new Pair<String, String>(RecalDataManager.COVARIATE_VALUE_COLUMN_NAME, "%s");
private static final Pair<String, String> covariateName = new Pair<String, String>(RecalDataManager.COVARIATE_NAME_COLUMN_NAME, "%s");
private static final Pair<String, String> eventType = new Pair<String, String>(RecalDataManager.EVENT_TYPE_COLUMN_NAME, "%s");
private static final Pair<String, String> empiricalQuality = new Pair<String, String>(RecalDataManager.EMPIRICAL_QUALITY_COLUMN_NAME, "%.4f");
private static final Pair<String, String> estimatedQReported = new Pair<String, String>(RecalDataManager.ESTIMATED_Q_REPORTED_COLUMN_NAME, "%.4f");
private static final Pair<String, String> nObservations = new Pair<String, String>(RecalDataManager.NUMBER_OBSERVATIONS_COLUMN_NAME, "%d");
private static final Pair<String, String> nErrors = new Pair<String, String>(RecalDataManager.NUMBER_ERRORS_COLUMN_NAME, "%d");
public enum SOLID_RECAL_MODE {
/**
@ -141,30 +151,6 @@ public class RecalDataManager {
}
}
/**
* Initializes the recalibration table -> key manager map
*
* @param requiredCovariates list of required covariates (in order)
* @param optionalCovariates list of optional covariates (in order)
* @return a map with each key manager and it's corresponding recalibration table properly initialized
*/
public static LinkedHashMap<BQSRKeyManager, Map<Long, RecalDatum>> initializeTables(ArrayList<Covariate> requiredCovariates, ArrayList<Covariate> optionalCovariates) {
final LinkedHashMap<BQSRKeyManager, Map<Long, RecalDatum>> tablesAndKeysMap = new LinkedHashMap<BQSRKeyManager, Map<Long, RecalDatum>>();
final ArrayList<Covariate> requiredCovariatesToAdd = new ArrayList<Covariate>(requiredCovariates.size() + 1); // incrementally add the covariates to create the recal tables with 1, 2 and 3 covariates.
final ArrayList<Covariate> optionalCovariatesToAdd = new ArrayList<Covariate>(); // initialize an empty array of optional covariates to create the first few tables
for (Covariate covariate : requiredCovariates) {
requiredCovariatesToAdd.add(covariate);
final Map<Long, RecalDatum> recalTable = new HashMap<Long, RecalDatum>(); // initializing a new recal table for each required covariate (cumulatively)
final BQSRKeyManager keyManager = new BQSRKeyManager(requiredCovariatesToAdd, optionalCovariatesToAdd); // initializing it's corresponding key manager
tablesAndKeysMap.put(keyManager, recalTable); // adding the pair table+key to the map
}
final Map<Long, RecalDatum> recalTable = new HashMap<Long, RecalDatum>(Short.MAX_VALUE); // initializing a new recal table to hold all optional covariates
final BQSRKeyManager keyManager = new BQSRKeyManager(requiredCovariates, optionalCovariates); // initializing it's corresponding key manager
tablesAndKeysMap.put(keyManager, recalTable); // adding the pair table+key to the map
return tablesAndKeysMap;
}
/**
* Generates two lists : required covariates and optional covariates based on the user's requests.
*
@ -223,42 +209,29 @@ public class RecalDataManager {
logger.info("");
}
private static List<GATKReportTable> generateReportTables(Map<BQSRKeyManager, Map<Long, RecalDatum>> keysAndTablesMap) {
private static List<GATKReportTable> generateReportTables(final RecalibrationTables recalibrationTables, final Covariate[] requestedCovariates) {
List<GATKReportTable> result = new LinkedList<GATKReportTable>();
int tableIndex = 0;
final Pair<String, String> covariateValue = new Pair<String, String>(RecalDataManager.COVARIATE_VALUE_COLUMN_NAME, "%s");
final Pair<String, String> covariateName = new Pair<String, String>(RecalDataManager.COVARIATE_NAME_COLUMN_NAME, "%s");
final Pair<String, String> eventType = new Pair<String, String>(RecalDataManager.EVENT_TYPE_COLUMN_NAME, "%s");
final Pair<String, String> empiricalQuality = new Pair<String, String>(RecalDataManager.EMPIRICAL_QUALITY_COLUMN_NAME, "%.4f");
final Pair<String, String> estimatedQReported = new Pair<String, String>(RecalDataManager.ESTIMATED_Q_REPORTED_COLUMN_NAME, "%.4f");
final Pair<String, String> nObservations = new Pair<String, String>(RecalDataManager.NUMBER_OBSERVATIONS_COLUMN_NAME, "%d");
final Pair<String, String> nErrors = new Pair<String, String>(RecalDataManager.NUMBER_ERRORS_COLUMN_NAME, "%d");
final Map<Covariate, String> covariateNameMap = new HashMap<Covariate, String>(requestedCovariates.length);
for (final Covariate covariate : requestedCovariates)
covariateNameMap.put(covariate, parseCovariateName(covariate));
for (Map.Entry<BQSRKeyManager, Map<Long, RecalDatum>> entry : keysAndTablesMap.entrySet()) {
final BQSRKeyManager keyManager = entry.getKey();
final Map<Long, RecalDatum> recalTable = entry.getValue();
for (final RecalibrationTables.TableType type : RecalibrationTables.TableType.values()) {
final boolean isReadGroupTable = tableIndex == 0; // special case for the read group table so we can print the extra column it needs.
final Covariate[] requiredList = keyManager.getRequiredCovariates(); // ask the key manager what required covariates were used in this recal table
final Covariate[] optionalList = keyManager.getOptionalCovariates(); // ask the key manager what optional covariates were used in this recal table
final ArrayList<Pair<String, String>> columnNames = new ArrayList<Pair<String, String>>(); // initialize the array to hold the column names
for (final Covariate covariate : requiredList) {
final String name = covariate.getClass().getSimpleName().split("Covariate")[0]; // get the covariate names and put them in order
columnNames.add(new Pair<String,String>(name, "%s")); // save the required covariate name so we can reference it in the future
}
if (optionalList.length > 0) {
columnNames.add(covariateValue);
columnNames.add(covariateName);
final ArrayList<Pair<String, String>> columnNames = new ArrayList<Pair<String, String>>(); // initialize the array to hold the column names
columnNames.add(new Pair<String, String>(covariateNameMap.get(requestedCovariates[0]), "%s")); // save the required covariate name so we can reference it in the future
if (type != RecalibrationTables.TableType.READ_GROUP_TABLE) {
columnNames.add(new Pair<String, String>(covariateNameMap.get(requestedCovariates[1]), "%s")); // save the required covariate name so we can reference it in the future
if (type == RecalibrationTables.TableType.OPTIONAL_COVARIATE_TABLE) {
columnNames.add(covariateValue);
columnNames.add(covariateName);
}
}
columnNames.add(eventType); // the order of these column names is important here
columnNames.add(empiricalQuality);
if (isReadGroupTable)
if (type == RecalibrationTables.TableType.READ_GROUP_TABLE)
columnNames.add(estimatedQReported); // only the read group table needs the estimated Q reported
columnNames.add(nObservations);
columnNames.add(nErrors);
@ -269,42 +242,59 @@ public class RecalDataManager {
int rowIndex = 0;
for (Map.Entry<Long, RecalDatum> recalTableEntry : recalTable.entrySet()) { // create a map with column name => key value for all covariate keys
final Long bitSetKey = recalTableEntry.getKey();
final Map<String, Object> columnData = new HashMap<String, Object>(columnNames.size());
final Iterator<Pair<String, String>> iterator = columnNames.iterator();
for (final Object key : keyManager.keySetFrom(bitSetKey)) {
final String columnName = iterator.next().getFirst();
columnData.put(columnName, key);
}
final RecalDatum datum = recalTableEntry.getValue();
columnData.put(iterator.next().getFirst(), datum.getEmpiricalQuality());
if (isReadGroupTable)
columnData.put(iterator.next().getFirst(), datum.getEstimatedQReported()); // we only add the estimated Q reported in the RG table
columnData.put(iterator.next().getFirst(), datum.numObservations);
columnData.put(iterator.next().getFirst(), datum.numMismatches);
final NestedHashMap table = recalibrationTables.getTable(type);
for (final NestedHashMap.Leaf row : table.getAllLeaves()) {
final RecalDatum datum = (RecalDatum)row.value;
final List<Object> keys = row.keys;
for (final Map.Entry<String, Object> dataEntry : columnData.entrySet()) {
final String columnName = dataEntry.getKey();
final Object value = dataEntry.getValue();
reportTable.set(rowIndex, columnName, value.toString());
int columnIndex = 0;
setReportTableCell(reportTable, rowIndex, columnNames.get(columnIndex).getFirst(), requestedCovariates[0].formatKey((Integer)keys.get(columnIndex++)));
if (type != RecalibrationTables.TableType.READ_GROUP_TABLE) {
setReportTableCell(reportTable, rowIndex, columnNames.get(columnIndex).getFirst(), requestedCovariates[1].formatKey((Integer) keys.get(columnIndex++)));
if (type == RecalibrationTables.TableType.OPTIONAL_COVARIATE_TABLE) {
final int covariateIndex = (Integer)keys.get(columnIndex);
final Covariate covariate = requestedCovariates[2 + covariateIndex];
final int covariateKey = (Integer)keys.get(columnIndex+1);
setReportTableCell(reportTable, rowIndex, columnNames.get(columnIndex++).getFirst(), covariate.formatKey(covariateKey));
setReportTableCell(reportTable, rowIndex, columnNames.get(columnIndex++).getFirst(), covariateNameMap.get(covariate));
}
}
final EventType event = EventType.eventFrom((Integer)keys.get(columnIndex));
setReportTableCell(reportTable, rowIndex, columnNames.get(columnIndex++).getFirst(), event);
setReportTableCell(reportTable, rowIndex, columnNames.get(columnIndex++).getFirst(), datum.getEmpiricalQuality());
if (type == RecalibrationTables.TableType.READ_GROUP_TABLE)
setReportTableCell(reportTable, rowIndex, columnNames.get(columnIndex++).getFirst(), datum.getEstimatedQReported()); // we only add the estimated Q reported in the RG table
setReportTableCell(reportTable, rowIndex, columnNames.get(columnIndex++).getFirst(), datum.numObservations);
setReportTableCell(reportTable, rowIndex, columnNames.get(columnIndex).getFirst(), datum.numMismatches);
rowIndex++;
}
result.add(reportTable);
}
return result;
}
public static void outputRecalibrationReport(RecalibrationArgumentCollection RAC, QuantizationInfo quantizationInfo, Map<BQSRKeyManager, Map<Long, RecalDatum>> keysAndTablesMap, PrintStream outputFile) {
outputRecalibrationReport(RAC.generateReportTable(), quantizationInfo.generateReportTable(), generateReportTables(keysAndTablesMap), outputFile);
private static String parseCovariateName(final Covariate covariate) {
return covariate.getClass().getSimpleName().split("Covariate")[0];
}
public static void outputRecalibrationReport(GATKReportTable argumentTable, QuantizationInfo quantizationInfo, LinkedHashMap<BQSRKeyManager,Map<Long, RecalDatum>> keysAndTablesMap, PrintStream outputFile) {
outputRecalibrationReport(argumentTable, quantizationInfo.generateReportTable(), generateReportTables(keysAndTablesMap), outputFile);
private static void setReportTableCell(final GATKReportTable reportTable, final int rowIndex, final String columnName, final Object value) {
reportTable.set(rowIndex, columnName, value.toString());
}
private static void outputRecalibrationReport(GATKReportTable argumentTable, GATKReportTable quantizationTable, List<GATKReportTable> recalTables, PrintStream outputFile) {
public static void outputRecalibrationReport(final RecalibrationArgumentCollection RAC, final QuantizationInfo quantizationInfo, final RecalibrationTables recalibrationTables, final Covariate[] requestedCovariates, final PrintStream outputFile) {
outputRecalibrationReport(RAC.generateReportTable(), quantizationInfo.generateReportTable(), generateReportTables(recalibrationTables, requestedCovariates), outputFile);
}
public static void outputRecalibrationReport(final GATKReportTable argumentTable, final QuantizationInfo quantizationInfo, final RecalibrationTables recalibrationTables, final Covariate[] requestedCovariates, final PrintStream outputFile) {
outputRecalibrationReport(argumentTable, quantizationInfo.generateReportTable(), generateReportTables(recalibrationTables, requestedCovariates), outputFile);
}
private static void outputRecalibrationReport(final GATKReportTable argumentTable, final GATKReportTable quantizationTable, final List<GATKReportTable> recalTables, final PrintStream outputFile) {
final GATKReport report = new GATKReport();
report.addTable(argumentTable);
report.addTable(quantizationTable);
@ -340,108 +330,87 @@ public class RecalDataManager {
}
public static void generateRecalibrationPlot(File filename, LinkedHashMap<BQSRKeyManager, Map<Long, RecalDatum>> original, boolean keepIntermediates) {
public static void generateRecalibrationPlot(final File filename, final RecalibrationTables original, final Covariate[] requestedCovariates, final boolean keepIntermediates) {
final Pair<PrintStream, File> files = initializeRecalibrationPlot(filename);
writeCSV(files.getFirst(), original, "ORIGINAL", true);
writeCSV(files.getFirst(), original, "ORIGINAL", requestedCovariates, true);
outputRecalibrationPlot(files, keepIntermediates);
}
public static void generateRecalibrationPlot(File filename, LinkedHashMap<BQSRKeyManager, Map<Long, RecalDatum>> original, LinkedHashMap<BQSRKeyManager, Map<Long, RecalDatum>> recalibrated, boolean keepIntermediates) {
public static void generateRecalibrationPlot(final File filename, final RecalibrationTables original, final RecalibrationTables recalibrated, final Covariate[] requestedCovariates, final boolean keepIntermediates) {
final Pair<PrintStream, File> files = initializeRecalibrationPlot(filename);
writeCSV(files.getFirst(), recalibrated, "RECALIBRATED", true);
writeCSV(files.getFirst(), original, "ORIGINAL", false);
writeCSV(files.getFirst(), recalibrated, "RECALIBRATED", requestedCovariates, true);
writeCSV(files.getFirst(), original, "ORIGINAL", requestedCovariates, false);
outputRecalibrationPlot(files, keepIntermediates);
}
private static void writeCSV(PrintStream deltaTableFile, LinkedHashMap<BQSRKeyManager, Map<Long, RecalDatum>> map, String recalibrationMode, boolean printHeader) {
final int QUALITY_SCORE_COVARIATE_INDEX = 1;
final Map<Long, RecalDatum> deltaTable = new HashMap<Long, RecalDatum>();
BQSRKeyManager deltaKeyManager = null;
private static void writeCSV(final PrintStream deltaTableFile, final RecalibrationTables recalibrationTables, final String recalibrationMode, final Covariate[] requestedCovariates, final boolean printHeader) {
final NestedHashMap deltaTable = new NestedHashMap();
for (Map.Entry<BQSRKeyManager, Map<Long, RecalDatum>> tableEntry : map.entrySet()) {
final BQSRKeyManager keyManager = tableEntry.getKey();
if (keyManager.getNumOptionalCovariates() > 0) { // initialize with the 'all covariates' table
// create a key manager for the delta table
final List<Covariate> requiredCovariates = Arrays.asList(keyManager.getRequiredCovariates()[0]); // include the read group covariate as the only required covariate
final List<Covariate> optionalCovariates = new ArrayList<Covariate>();
optionalCovariates.add(keyManager.getRequiredCovariates()[1]); // include the quality score covariate as an optional covariate
optionalCovariates.addAll(Arrays.asList(keyManager.getOptionalCovariates())); // include all optional covariates
deltaKeyManager = new BQSRKeyManager(requiredCovariates, optionalCovariates); // initialize the key manager
}
// add the quality score table to the delta table
final NestedHashMap qualTable = recalibrationTables.getTable(RecalibrationTables.TableType.QUALITY_SCORE_TABLE);
for (final NestedHashMap.Leaf leaf : qualTable.getAllLeaves()) { // go through every element in the covariates table to create the delta table
final List<Object> newCovs = new ArrayList<Object>(4);
newCovs.add(leaf.keys.get(0));
newCovs.add(requestedCovariates.length); // replace the covariate name with an arbitrary (unused) index for QualityScore
newCovs.add(leaf.keys.get(1));
newCovs.add(leaf.keys.get(2));
addToDeltaTable(deltaTable, newCovs.toArray(), (RecalDatum)leaf.value); // add this covariate to the delta table
}
if (deltaKeyManager == null)
throw new ReviewedStingException ("Couldn't find the covariates table");
boolean readyToPrint = false;
for (Map.Entry<BQSRKeyManager, Map<Long, RecalDatum>> tableEntry : map.entrySet()) {
final BQSRKeyManager keyManager = tableEntry.getKey();
if (keyManager.getNumRequiredCovariates() == 2 && keyManager.getNumOptionalCovariates() == 0) { // look for the QualityScore table
final Map<Long, RecalDatum> table = tableEntry.getValue();
// add the quality score table to the delta table
for (final Map.Entry<Long, RecalDatum> entry : table.entrySet()) { // go through every element in the covariates table to create the delta table
final RecalDatum recalDatum = entry.getValue(); // the current element (recal datum)
final List<Object> covs = keyManager.keySetFrom(entry.getKey()); // extract the key objects from the bitset key
final List<Object> newCovs = new ArrayList<Object>(4);
newCovs.add(0, covs.get(0)); // replace the covariate value with the quality score
newCovs.add(1, covs.get(1));
newCovs.add(2, "QualityScore"); // replace the covariate name with QualityScore (for the QualityScore covariate)
newCovs.add(3, covs.get(2));
final long deltaKey = deltaKeyManager.longFromKey(newCovs.toArray()); // create a new bitset key for the delta table
addToDeltaTable(deltaTable, deltaKey, recalDatum); // add this covariate to the delta table
}
}
else if (keyManager.getNumOptionalCovariates() > 0) { // look for the optional covariates table
final Map<Long, RecalDatum> table = tableEntry.getValue();
// add the optional covariates to the delta table
for (final Map.Entry<Long, RecalDatum> entry : table.entrySet()) { // go through every element in the covariates table to create the delta table
final RecalDatum recalDatum = entry.getValue(); // the current element (recal datum)
final List<Object> covs = keyManager.keySetFrom(entry.getKey()); // extract the key objects from the bitset key
covs.remove(QUALITY_SCORE_COVARIATE_INDEX); // reset the quality score covariate to 0 from the keyset (so we aggregate all rows regardless of QS)
final long deltaKey = deltaKeyManager.longFromKey(covs.toArray()); // create a new bitset key for the delta table
addToDeltaTable(deltaTable, deltaKey, recalDatum); // add this covariate to the delta table
}
readyToPrint = true;
}
// output the csv file
if (readyToPrint) {
if (printHeader) {
final List<String> header = new LinkedList<String>();
header.add("ReadGroup");
header.add("CovariateValue");
header.add("CovariateName");
header.add("EventType");
header.add("Observations");
header.add("Errors");
header.add("EmpiricalQuality");
header.add("AverageReportedQuality");
header.add("Accuracy");
header.add("Recalibration");
deltaTableFile.println(Utils.join(",", header));
}
// print each data line
for (final Map.Entry<Long, RecalDatum> deltaEntry : deltaTable.entrySet()) {
final List<Object> deltaKeys = deltaKeyManager.keySetFrom(deltaEntry.getKey());
final RecalDatum deltaDatum = deltaEntry.getValue();
deltaTableFile.print(Utils.join(",", deltaKeys));
deltaTableFile.print("," + deltaDatum.stringForCSV());
deltaTableFile.println("," + recalibrationMode);
}
}
// add the optional covariates to the delta table
final NestedHashMap covTable = recalibrationTables.getTable(RecalibrationTables.TableType.OPTIONAL_COVARIATE_TABLE);
for (final NestedHashMap.Leaf leaf : covTable.getAllLeaves()) {
final List<Object> covs = new ArrayList<Object>(leaf.keys);
covs.remove(1); // reset the quality score covariate to 0 from the keyset (so we aggregate all rows regardless of QS)
addToDeltaTable(deltaTable, covs.toArray(), (RecalDatum)leaf.value); // add this covariate to the delta table
}
// output the csv file
if (printHeader) {
final List<String> header = new LinkedList<String>();
header.add("ReadGroup");
header.add("CovariateValue");
header.add("CovariateName");
header.add("EventType");
header.add("Observations");
header.add("Errors");
header.add("EmpiricalQuality");
header.add("AverageReportedQuality");
header.add("Accuracy");
header.add("Recalibration");
deltaTableFile.println(Utils.join(",", header));
}
final Map<Covariate, String> covariateNameMap = new HashMap<Covariate, String>(requestedCovariates.length);
for (final Covariate covariate : requestedCovariates)
covariateNameMap.put(covariate, parseCovariateName(covariate));
// print each data line
for (final NestedHashMap.Leaf leaf : deltaTable.getAllLeaves()) {
final List<Object> deltaKeys = generateValuesFromKeys(leaf.keys, requestedCovariates, covariateNameMap);
final RecalDatum deltaDatum = (RecalDatum)leaf.value;
deltaTableFile.print(Utils.join(",", deltaKeys));
deltaTableFile.print("," + deltaDatum.stringForCSV());
deltaTableFile.println("," + recalibrationMode);
}
}
private static List<Object> generateValuesFromKeys(final List<Object> keys, final Covariate[] covariates, final Map<Covariate, String> covariateNameMap) {
final List<Object> values = new ArrayList<Object>(4);
values.add(covariates[0].formatKey((Integer)keys.get(0)));
// TODO -- create static final variables to hold the indexes of the RG, qual, cov ID, etc.
final int covariateIndex = (Integer)keys.get(1);
final Covariate covariate = covariateIndex == covariates.length ? covariates[1] : covariates[2 + covariateIndex];
final int covariateKey = (Integer)keys.get(2);
values.add(covariate.formatKey(covariateKey));
values.add(covariateNameMap.get(covariate));
final EventType event = EventType.eventFrom((Integer)keys.get(3));
values.add(event);
return values;
}
/**
@ -453,15 +422,14 @@ public class RecalDataManager {
* @param deltaKey the key to the table
* @param recalDatum the recal datum to combine with the accuracyDatum element in the table
*/
private static void addToDeltaTable(Map<Long, RecalDatum> deltaTable, Long deltaKey, RecalDatum recalDatum) {
final RecalDatum deltaDatum = deltaTable.get(deltaKey); // check if we already have a RecalDatum for this key
private static void addToDeltaTable(final NestedHashMap deltaTable, final Object[] deltaKey, final RecalDatum recalDatum) {
final RecalDatum deltaDatum = (RecalDatum)deltaTable.get(deltaKey); // check if we already have a RecalDatum for this key
if (deltaDatum == null)
deltaTable.put(deltaKey, new RecalDatum(recalDatum)); // if we don't have a key yet, create a new one with the same values as the curent datum
deltaTable.put(new RecalDatum(recalDatum), deltaKey); // if we don't have a key yet, create a new one with the same values as the curent datum
else
deltaDatum.combine(recalDatum); // if we do have a datum, combine it with this one.
}
/**
* Section of code shared between the two recalibration walkers which uses the command line arguments to adjust attributes of the read such as quals or platform string
*
@ -627,13 +595,13 @@ public class RecalDataManager {
*
* @param read The read for which to compute covariate values.
* @param requestedCovariates The list of requested covariates.
* @param readCovariates The object to store the covariate values
* @param resultsStorage The object to store the covariate values
*/
public static void computeCovariates(final GATKSAMRecord read, final Covariate[] requestedCovariates, final ReadCovariates readCovariates) {
public static void computeCovariates(final GATKSAMRecord read, final Covariate[] requestedCovariates, final ReadCovariates resultsStorage) {
// Loop through the list of requested covariates and compute the values of each covariate for all positions in this read
for (int i = 0; i < requestedCovariates.length; i++) {
readCovariates.setCovariateIndex(i);
requestedCovariates[i].recordValues(read, readCovariates);
resultsStorage.setCovariateIndex(i);
requestedCovariates[i].recordValues(read, resultsStorage);
}
}

3
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDatum.java
View File

@ -113,8 +113,7 @@ public class RecalDatum extends Datum {
return String.format("%s,%d,%.2f", toString(), (byte) Math.floor(getEstimatedQReported()), getEmpiricalQuality() - getEstimatedQReported());
}
private double calcExpectedErrors() {
private double calcExpectedErrors() {
return (double) this.numObservations * qualToErrorProb(estimatedQReported);
}

247
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationReport.java
View File

@ -3,8 +3,9 @@ package org.broadinstitute.sting.gatk.walkers.bqsr;
import org.broadinstitute.sting.gatk.report.GATKReport;
import org.broadinstitute.sting.gatk.report.GATKReportTable;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.collections.NestedHashMap;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.recalibration.RecalibrationTables;
import java.io.File;
import java.io.PrintStream;
@ -18,14 +19,19 @@ import java.util.*;
*/
public class RecalibrationReport {
private QuantizationInfo quantizationInfo; // histogram containing the counts for qual quantization (calculated after recalibration is done)
private final LinkedHashMap<BQSRKeyManager, Map<Long, RecalDatum>> keysAndTablesMap; // quick access reference to the read group table and its key manager
private final RecalibrationTables recalibrationTables; // quick access reference to the tables
private final Covariate[] requestedCovariates; // list of all covariates to be used in this calculation
private final HashMap<String, Integer> optionalCovariateIndexes;
private final GATKReportTable argumentTable; // keep the argument table untouched just for output purposes
private final RecalibrationArgumentCollection RAC; // necessary for quantizing qualities with the same parameter
private final Object[] tempRGarray = new Object[2];
private final Object[] tempQUALarray = new Object[3];
private final Object[] tempCOVarray = new Object[5];
public RecalibrationReport(final File RECAL_FILE) {
GATKReport report = new GATKReport(RECAL_FILE);
final GATKReport report = new GATKReport(RECAL_FILE);
argumentTable = report.getTable(RecalDataManager.ARGUMENT_REPORT_TABLE_TITLE);
RAC = initializeArgumentCollectionTable(argumentTable);
@ -37,52 +43,39 @@ public class RecalibrationReport {
ArrayList<Covariate> requiredCovariates = covariates.getFirst();
ArrayList<Covariate> optionalCovariates = covariates.getSecond();
requestedCovariates = new Covariate[requiredCovariates.size() + optionalCovariates.size()];
optionalCovariateIndexes = new HashMap<String, Integer>(optionalCovariates.size());
int covariateIndex = 0;
for (final Covariate covariate : requiredCovariates)
requestedCovariates[covariateIndex++] = covariate;
for (final Covariate covariate : optionalCovariates)
requestedCovariates[covariateIndex++] = covariate;
for (final Covariate covariate : optionalCovariates) {
requestedCovariates[covariateIndex] = covariate;
final String covariateName = covariate.getClass().getSimpleName().split("Covariate")[0]; // get the name of the covariate (without the "covariate" part of it) so we can match with the GATKReport
optionalCovariateIndexes.put(covariateName, covariateIndex-2);
covariateIndex++;
}
for (Covariate cov : requestedCovariates)
cov.initialize(RAC); // initialize any covariate member variables using the shared argument collection
keysAndTablesMap = new LinkedHashMap<BQSRKeyManager, Map<Long, RecalDatum>>();
ArrayList<Covariate> requiredCovariatesToAdd = new ArrayList<Covariate>(requiredCovariates.size()); // incrementally add the covariates to create the recal tables with 1, 2 and 3 covariates.
ArrayList<Covariate> optionalCovariatesToAdd = new ArrayList<Covariate>(); // initialize an empty array of optional covariates to create the first few tables
for (Covariate covariate : requiredCovariates) {
requiredCovariatesToAdd.add(covariate);
final Map<Long, RecalDatum> table; // initializing a new recal table for each required covariate (cumulatively)
final BQSRKeyManager keyManager = new BQSRKeyManager(requiredCovariatesToAdd, optionalCovariatesToAdd); // initializing it's corresponding key manager
final GATKReportTable rgReportTable = report.getTable(RecalDataManager.READGROUP_REPORT_TABLE_TITLE);
final NestedHashMap rgTable = parseReadGroupTable(rgReportTable);
final int nRequiredCovariates = requiredCovariatesToAdd.size(); // the number of required covariates defines which table we are looking at (RG, QUAL or ALL_COVARIATES)
final String UNRECOGNIZED_REPORT_TABLE_EXCEPTION = "Unrecognized table. Did you add an extra required covariate? This is a hard check.";
if (nRequiredCovariates == 1) { // if there is only one required covariate, this is the read group table
final GATKReportTable reportTable = report.getTable(RecalDataManager.READGROUP_REPORT_TABLE_TITLE);
table = parseReadGroupTable(keyManager, reportTable);
}
else if (nRequiredCovariates == 2 && optionalCovariatesToAdd.isEmpty()) { // when we have both required covariates and no optional covariates we're at the QUAL table
final GATKReportTable reportTable = report.getTable(RecalDataManager.QUALITY_SCORE_REPORT_TABLE_TITLE);
table = parseQualityScoreTable(keyManager, reportTable);
}
else
throw new ReviewedStingException(UNRECOGNIZED_REPORT_TABLE_EXCEPTION);
final GATKReportTable qualReportTable = report.getTable(RecalDataManager.QUALITY_SCORE_REPORT_TABLE_TITLE);
final NestedHashMap qualTable = parseQualityScoreTable(qualReportTable);
keysAndTablesMap.put(keyManager, table); // adding the pair key+table to the map
}
final GATKReportTable covReportTable = report.getTable(RecalDataManager.ALL_COVARIATES_REPORT_TABLE_TITLE);
final NestedHashMap covTable = parseAllCovariatesTable(covReportTable);
final BQSRKeyManager keyManager = new BQSRKeyManager(requiredCovariates, optionalCovariates); // initializing it's corresponding key manager
final GATKReportTable reportTable = report.getTable(RecalDataManager.ALL_COVARIATES_REPORT_TABLE_TITLE);
final Map<Long, RecalDatum> table = parseAllCovariatesTable(keyManager, reportTable);
keysAndTablesMap.put(keyManager, table);
recalibrationTables = new RecalibrationTables(rgTable, qualTable, covTable);
}
protected RecalibrationReport(final QuantizationInfo quantizationInfo, final LinkedHashMap<BQSRKeyManager, Map<Long, RecalDatum>> keysAndTablesMap, final GATKReportTable argumentTable, final RecalibrationArgumentCollection RAC) {
protected RecalibrationReport(final QuantizationInfo quantizationInfo, final RecalibrationTables recalibrationTables, final GATKReportTable argumentTable, final RecalibrationArgumentCollection RAC) {
this.quantizationInfo = quantizationInfo;
this.keysAndTablesMap = keysAndTablesMap;
this.recalibrationTables = recalibrationTables;
this.argumentTable = argumentTable;
this.RAC = RAC;
this.requestedCovariates = null;
this.optionalCovariateIndexes = null;
}
/**
@ -98,29 +91,20 @@ public class RecalibrationReport {
*
* @param other the recalibration report to combine with this one
*/
public void combine(RecalibrationReport other) {
Iterator<Map.Entry<BQSRKeyManager, Map<Long, RecalDatum>>> thisIterator = keysAndTablesMap.entrySet().iterator();
public void combine(final RecalibrationReport other) {
for (Map.Entry<BQSRKeyManager, Map<Long, RecalDatum>> otherEntry : other.getKeysAndTablesMap().entrySet()) {
Map.Entry<BQSRKeyManager, Map<Long, RecalDatum>> thisEntry = thisIterator.next();
for (RecalibrationTables.TableType type : RecalibrationTables.TableType.values()) {
final NestedHashMap myTable = recalibrationTables.getTable(type);
final NestedHashMap otherTable = other.recalibrationTables.getTable(type);
final Map<Long, RecalDatum> thisTable = thisEntry.getValue();
final BQSRKeyManager thisKeyManager = thisEntry.getKey();
final BQSRKeyManager otherKeyManager = otherEntry.getKey();
for (final NestedHashMap.Leaf row : otherTable.getAllLeaves()) {
final RecalDatum myDatum = (RecalDatum)myTable.get(row.keys);
for (Map.Entry<Long, RecalDatum> otherTableEntry : otherEntry.getValue().entrySet()) {
final RecalDatum otherDatum = otherTableEntry.getValue();
final Long otherBitKey = otherTableEntry.getKey();
final List<Object> otherObjectKey = otherKeyManager.keySetFrom(otherBitKey);
final long thisKey = thisKeyManager.longFromKey(otherObjectKey.toArray());
final RecalDatum thisDatum = thisTable.get(thisKey);
if (thisDatum == null)
thisTable.put(thisKey, otherDatum);
if (myDatum == null)
myTable.put(row.value, row.keys);
else
thisDatum.combine(otherDatum);
}
myDatum.combine((RecalDatum)row.value);
}
}
}
@ -128,8 +112,8 @@ public class RecalibrationReport {
return quantizationInfo;
}
public LinkedHashMap<BQSRKeyManager, Map<Long, RecalDatum>> getKeysAndTablesMap() {
return keysAndTablesMap;
public RecalibrationTables getRecalibrationTables() {
return recalibrationTables;
}
public Covariate[] getRequestedCovariates() {
@ -139,82 +123,87 @@ public class RecalibrationReport {
/**
* Compiles the list of keys for the Covariates table and uses the shared parsing utility to produce the actual table
*
* @param keyManager the key manager for this table
* @param reportTable the GATKReport table containing data for this table
* @return a lookup table indexed by bitsets containing the empirical quality and estimated quality reported for every key.
*/
private Map<Long, RecalDatum> parseAllCovariatesTable(BQSRKeyManager keyManager, GATKReportTable reportTable) {
ArrayList<String> columnNamesOrderedList = new ArrayList<String>(5);
columnNamesOrderedList.add(RecalDataManager.READGROUP_COLUMN_NAME);
columnNamesOrderedList.add(RecalDataManager.QUALITY_SCORE_COLUMN_NAME);
columnNamesOrderedList.add(RecalDataManager.COVARIATE_VALUE_COLUMN_NAME);
columnNamesOrderedList.add(RecalDataManager.COVARIATE_NAME_COLUMN_NAME);
columnNamesOrderedList.add(RecalDataManager.EVENT_TYPE_COLUMN_NAME);
return genericRecalTableParsing(keyManager, reportTable, columnNamesOrderedList, false);
private NestedHashMap parseAllCovariatesTable(final GATKReportTable reportTable) {
final NestedHashMap result = new NestedHashMap();
for ( int i = 0; i < reportTable.getNumRows(); i++ ) {
final Object rg = reportTable.get(i, RecalDataManager.READGROUP_COLUMN_NAME);
tempCOVarray[0] = requestedCovariates[0].keyFromValue(rg);
final Object qual = reportTable.get(i, RecalDataManager.QUALITY_SCORE_COLUMN_NAME);
tempCOVarray[1] = requestedCovariates[1].keyFromValue(qual);
final String covName = (String)reportTable.get(i, RecalDataManager.COVARIATE_NAME_COLUMN_NAME);
final int covIndex = optionalCovariateIndexes.get(covName);
tempCOVarray[2] = covIndex;
final Object covValue = reportTable.get(i, RecalDataManager.COVARIATE_VALUE_COLUMN_NAME);
tempCOVarray[3] = requestedCovariates[covIndex + 2].keyFromValue(covValue);
final EventType event = EventType.eventFrom((String)reportTable.get(i, RecalDataManager.EVENT_TYPE_COLUMN_NAME));
tempCOVarray[4] = event.index;
result.put(getRecalDatum(reportTable, i, false), tempCOVarray);
}
return result;
}
/**
*
* Compiles the list of keys for the QualityScore table and uses the shared parsing utility to produce the actual table
* @param keyManager the key manager for this table
* @param reportTable the GATKReport table containing data for this table
* @return a lookup table indexed by bitsets containing the empirical quality and estimated quality reported for every key.
*/
private Map<Long, RecalDatum> parseQualityScoreTable(BQSRKeyManager keyManager, GATKReportTable reportTable) {
ArrayList<String> columnNamesOrderedList = new ArrayList<String>(3);
columnNamesOrderedList.add(RecalDataManager.READGROUP_COLUMN_NAME);
columnNamesOrderedList.add(RecalDataManager.QUALITY_SCORE_COLUMN_NAME);
columnNamesOrderedList.add(RecalDataManager.EVENT_TYPE_COLUMN_NAME);
return genericRecalTableParsing(keyManager, reportTable, columnNamesOrderedList, false);
private NestedHashMap parseQualityScoreTable(final GATKReportTable reportTable) {
final NestedHashMap result = new NestedHashMap();
for ( int i = 0; i < reportTable.getNumRows(); i++ ) {
final Object rg = reportTable.get(i, RecalDataManager.READGROUP_COLUMN_NAME);
tempQUALarray[0] = requestedCovariates[0].keyFromValue(rg);
final Object qual = reportTable.get(i, RecalDataManager.QUALITY_SCORE_COLUMN_NAME);
tempQUALarray[1] = requestedCovariates[1].keyFromValue(qual);
final EventType event = EventType.eventFrom((String)reportTable.get(i, RecalDataManager.EVENT_TYPE_COLUMN_NAME));
tempQUALarray[2] = event.index;
result.put(getRecalDatum(reportTable, i, false), tempQUALarray);
}
return result;
}
/**
* Compiles the list of keys for the ReadGroup table and uses the shared parsing utility to produce the actual table
*
* @param keyManager the key manager for this table
* @param reportTable the GATKReport table containing data for this table
* @return a lookup table indexed by bitsets containing the empirical quality and estimated quality reported for every key.
*/
private Map<Long, RecalDatum> parseReadGroupTable(BQSRKeyManager keyManager, GATKReportTable reportTable) {
ArrayList<String> columnNamesOrderedList = new ArrayList<String>(2);
columnNamesOrderedList.add(RecalDataManager.READGROUP_COLUMN_NAME);
columnNamesOrderedList.add(RecalDataManager.EVENT_TYPE_COLUMN_NAME);
return genericRecalTableParsing(keyManager, reportTable, columnNamesOrderedList, true);
}
/**
* Shared parsing functionality for all tables.
*
* @param keyManager the key manager for this table
* @param reportTable the GATKReport table containing data for this table
* @param columnNamesOrderedList a list of columns to read from the report table and build as key for this particular table
* @return a lookup table indexed by bitsets containing the empirical quality and estimated quality reported for every key.
*/
private Map<Long, RecalDatum> genericRecalTableParsing(BQSRKeyManager keyManager, GATKReportTable reportTable, ArrayList<String> columnNamesOrderedList, boolean hasEstimatedQReportedColumn) {
final Map<Long, RecalDatum> result = new HashMap<Long, RecalDatum>(reportTable.getNumRows()*2);
private NestedHashMap parseReadGroupTable(final GATKReportTable reportTable) {
final NestedHashMap result = new NestedHashMap();
for ( int i = 0; i < reportTable.getNumRows(); i++ ) {
final int nKeys = columnNamesOrderedList.size();
final Object [] keySet = new Object[nKeys];
for (int j = 0; j < nKeys; j++)
keySet[j] = reportTable.get(i, columnNamesOrderedList.get(j)); // all these objects are okay in String format, the key manager will handle them correctly (except for the event type (see below)
keySet[keySet.length-1] = EventType.eventFrom((String) keySet[keySet.length-1]); // the last key is always the event type. We convert the string ("M", "I" or "D") to an enum object (necessary for the key manager).
final long bitKey = keyManager.longFromKey(keySet);
final Object rg = reportTable.get(i, RecalDataManager.READGROUP_COLUMN_NAME);
tempRGarray[0] = requestedCovariates[0].keyFromValue(rg);
final EventType event = EventType.eventFrom((String)reportTable.get(i, RecalDataManager.EVENT_TYPE_COLUMN_NAME));
tempRGarray[1] = event.index;
final long nObservations = (Long) reportTable.get(i, RecalDataManager.NUMBER_OBSERVATIONS_COLUMN_NAME);
final long nErrors = (Long) reportTable.get(i, RecalDataManager.NUMBER_ERRORS_COLUMN_NAME);
final double empiricalQuality = (Double) reportTable.get(i, RecalDataManager.EMPIRICAL_QUALITY_COLUMN_NAME);
final double estimatedQReported = hasEstimatedQReportedColumn ? // the estimatedQreported column only exists in the ReadGroup table
(Double) reportTable.get(i, RecalDataManager.ESTIMATED_Q_REPORTED_COLUMN_NAME) : // we get it if we are in the read group table
Byte.parseByte((String) reportTable.get(i, RecalDataManager.QUALITY_SCORE_COLUMN_NAME)); // or we use the reported quality if we are in any other table
final RecalDatum recalDatum = new RecalDatum(nObservations, nErrors, estimatedQReported, empiricalQuality);
result.put(bitKey, recalDatum);
result.put(getRecalDatum(reportTable, i, true), tempRGarray);
}
return result;
}
private RecalDatum getRecalDatum(final GATKReportTable reportTable, final int row, final boolean hasEstimatedQReportedColumn) {
final long nObservations = (Long) reportTable.get(row, RecalDataManager.NUMBER_OBSERVATIONS_COLUMN_NAME);
final long nErrors = (Long) reportTable.get(row, RecalDataManager.NUMBER_ERRORS_COLUMN_NAME);
final double empiricalQuality = (Double) reportTable.get(row, RecalDataManager.EMPIRICAL_QUALITY_COLUMN_NAME);
final double estimatedQReported = hasEstimatedQReportedColumn ? // the estimatedQreported column only exists in the ReadGroup table
(Double) reportTable.get(row, RecalDataManager.ESTIMATED_Q_REPORTED_COLUMN_NAME) : // we get it if we are in the read group table
Byte.parseByte((String) reportTable.get(row, RecalDataManager.QUALITY_SCORE_COLUMN_NAME)); // or we use the reported quality if we are in any other table
return new RecalDatum(nObservations, nErrors, estimatedQReported, empiricalQuality);
}
/**
* Parses the quantization table from the GATK Report and turns it into a map of original => quantized quality scores
*
@ -308,55 +297,21 @@ public class RecalibrationReport {
* and quantization of the quality scores during every call of combine(). Very useful for the BQSRGatherer.
*/
public void calculateEmpiricalAndQuantizedQualities() {
for (Map<Long, RecalDatum> table : keysAndTablesMap.values())
for (RecalDatum datum : table.values())
datum.calcCombinedEmpiricalQuality();
for (RecalibrationTables.TableType type : RecalibrationTables.TableType.values()) {
final NestedHashMap table = recalibrationTables.getTable(type);
for (final Object value : table.getAllValues()) {
((RecalDatum)value).calcCombinedEmpiricalQuality();
}
}
quantizationInfo = new QuantizationInfo(keysAndTablesMap, RAC.QUANTIZING_LEVELS);
quantizationInfo = new QuantizationInfo(recalibrationTables, RAC.QUANTIZING_LEVELS);
}
public void output(PrintStream output) {
RecalDataManager.outputRecalibrationReport(argumentTable, quantizationInfo, keysAndTablesMap, output);
RecalDataManager.outputRecalibrationReport(argumentTable, quantizationInfo, recalibrationTables, requestedCovariates, output);
}
public RecalibrationArgumentCollection getRAC() {
return RAC;
}
@Override
public boolean equals(Object o) {
if (!(o instanceof RecalibrationReport))
return false;
RecalibrationReport other = (RecalibrationReport) o;
if (this == o)
return true;
return isEqualTable(this.keysAndTablesMap, other.keysAndTablesMap);
}
private boolean isEqualTable(LinkedHashMap<BQSRKeyManager, Map<Long, RecalDatum>> t1, LinkedHashMap<BQSRKeyManager, Map<Long, RecalDatum>> t2) {
if (t1.size() != t2.size())
return false;
final Iterator<Map.Entry<BQSRKeyManager, Map<Long, RecalDatum>>> t1Iterator = t1.entrySet().iterator();
final Iterator<Map.Entry<BQSRKeyManager, Map<Long, RecalDatum>>> t2Iterator = t2.entrySet().iterator();
while (t1Iterator.hasNext() && t2Iterator.hasNext()) {
Map.Entry<BQSRKeyManager, Map<Long, RecalDatum>> t1MapEntry = t1Iterator.next();
Map.Entry<BQSRKeyManager, Map<Long, RecalDatum>> t2MapEntry = t2Iterator.next();
if (!(t1MapEntry.getKey().equals(t2MapEntry.getKey())))
return false;
final Map<Long, RecalDatum> table2 = t2MapEntry.getValue();
for (Map.Entry<Long, RecalDatum> t1TableEntry : t1MapEntry.getValue().entrySet()) {
final Long t1Key = t1TableEntry.getKey();
if (!table2.containsKey(t1Key))
return false;
final RecalDatum t1Datum = t1TableEntry.getValue();
if (!t1Datum.equals(table2.get(t1Key)))
return false;
}
}
return true;
}
}

15
public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java
View File

@ -266,13 +266,13 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
alleles.add(refAllele);
alleles.add(SYMBOLIC_ALLELE);
VariantContextBuilder vcb = new VariantContextBuilder("DiagnoseTargets", interval.getContig(), interval.getStart(), interval.getStart(), alleles);
VariantContextBuilder vcb = new VariantContextBuilder("DiagnoseTargets", interval.getContig(), interval.getStart(), interval.getStop(), alleles);
vcb = vcb.log10PError(VariantContext.NO_LOG10_PERROR); // QUAL field makes no sense in our VCF
vcb.filters(new HashSet<String>(statusesToStrings(stats.callableStatuses(thresholds))));
vcb.filters(new HashSet<String>(statusesToStrings(stats.callableStatuses(thresholds), true)));
attributes.put(VCFConstants.END_KEY, interval.getStop());
attributes.put(VCFConstants.DEPTH_KEY, stats.averageCoverage());
attributes.put(ThresHolder.AVG_INTERVAL_DP_KEY, stats.averageCoverage());
vcb = vcb.attributes(attributes);
if (debug) {
@ -282,7 +282,7 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
final GenotypeBuilder gb = new GenotypeBuilder(sample);
SampleStatistics sampleStat = stats.getSample(sample);
gb.DP((int)sampleStat.averageCoverage());
gb.attribute(ThresHolder.AVG_INTERVAL_DP_KEY, sampleStat.averageCoverage());
gb.attribute("Q1", sampleStat.getQuantileDepth(0.25));
gb.attribute("MED", sampleStat.getQuantileDepth(0.50));
gb.attribute("Q3", sampleStat.getQuantileDepth(0.75));
@ -290,7 +290,7 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
if (debug) {
System.out.printf("Found %d bad mates out of %d reads %n", sampleStat.getnBadMates(), sampleStat.getnReads());
}
gb.filters(statusesToStrings(stats.getSample(sample).getCallableStatuses(thresholds)));
gb.filters(statusesToStrings(stats.getSample(sample).getCallableStatuses(thresholds), false));
genotypes.add(gb.make());
}
@ -307,11 +307,12 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
* @param statuses the set of statuses to be converted
* @return a matching set of strings
*/
private List<String> statusesToStrings(Set<CallableStatus> statuses) {
private List<String> statusesToStrings(Set<CallableStatus> statuses, final boolean includePASS) {
List<String> output = new ArrayList<String>(statuses.size());
for (CallableStatus status : statuses)
output.add(status.name());
if ( includePASS || status != CallableStatus.PASS ) // adding pass => results in a filter for genotypes
output.add(status.name());
return output;
}

6
public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/ThresHolder.java
View File

@ -31,6 +31,7 @@ import java.util.HashSet;
import java.util.Set;
class ThresHolder {
public static final String AVG_INTERVAL_DP_KEY = "AVG_INTERVAL_DP";
public static final ThresHolder DEFAULTS = new ThresHolder(20, 20, 5, 700, 20, 50, 0.5, 0.2, 0.5, 0.2, 0.2, 0.5);
private final int minimumBaseQuality;
@ -129,12 +130,13 @@ class ThresHolder {
// INFO fields for overall data
headerLines.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.END_KEY));
headerLines.add(new VCFInfoHeaderLine("AVG_INTERVAL_DP", 1, VCFHeaderLineType.Float, "Average depth across the interval. Sum of the depth in a loci divided by interval size."));
headerLines.add(new VCFInfoHeaderLine(AVG_INTERVAL_DP_KEY, 1, VCFHeaderLineType.Float, "Average depth across the interval. Sum of the depth in a loci divided by interval size."));
headerLines.add(new VCFInfoHeaderLine("Diagnose Targets", 0, VCFHeaderLineType.Flag, "DiagnoseTargets mode"));
// FORMAT fields for each genotype
// todo -- find the appropriate VCF constants
headerLines.add(new VCFFormatHeaderLine("AVG_INTERVAL_DP", 1, VCFHeaderLineType.Float, "Average depth across the interval. Sum of the depth in a loci divided by interval size."));
headerLines.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.GENOTYPE_FILTER_KEY));
headerLines.add(new VCFFormatHeaderLine(AVG_INTERVAL_DP_KEY, 1, VCFHeaderLineType.Float, "Average depth across the interval. Sum of the depth in a loci divided by interval size."));
headerLines.add(new VCFFormatHeaderLine("Q1", 1, VCFHeaderLineType.Float, "Lower Quartile of depth distribution."));
headerLines.add(new VCFFormatHeaderLine("MED", 1, VCFHeaderLineType.Float, "Median of depth distribution."));
headerLines.add(new VCFFormatHeaderLine("Q3", 1, VCFHeaderLineType.Float, "Upper Quartile of depth Distribution."));

2
public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
View File

@ -176,7 +176,7 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
hInfo.add(new VCFFilterHeaderLine(exp.name, exp.exp.toString()));
if ( genotypeFilterExps.size() > 0 )
hInfo.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_FILTER_KEY, 1, VCFHeaderLineType.String, "Genotype-level filter"));
hInfo.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.GENOTYPE_FILTER_KEY));
if ( mask.isBound() ) {
hInfo.add(new VCFFilterHeaderLine(MASK_NAME, "Overlaps a user-input mask"));

6
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
View File

@ -187,6 +187,8 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
// the annotation engine
private VariantAnnotatorEngine annotationEngine;
private Set<String> samples;
// enable deletions in the pileup
@Override
public boolean includeReadsWithDeletionAtLoci() { return true; }
@ -231,7 +233,7 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
logger.warn("WARNING: note that the EMIT_ALL_SITES option is intended only for point mutations (SNPs) in DISCOVERY mode or generally when running in GENOTYPE_GIVEN_ALLELES mode; it will by no means produce a comprehensive set of indels in DISCOVERY mode");
// get all of the unique sample names
Set<String> samples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader());
samples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader());
// initialize the verbose writer
if ( verboseWriter != null )
@ -298,7 +300,7 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
* @return the VariantCallContext object
*/
public List<VariantCallContext> map(RefMetaDataTracker tracker, ReferenceContext refContext, AlignmentContext rawContext) {
return UG_engine.calculateLikelihoodsAndGenotypes(tracker, refContext, rawContext);
return UG_engine.calculateLikelihoodsAndGenotypes(tracker, refContext, rawContext, samples);
}
public UGStatistics reduceInit() { return new UGStatistics(); }

55
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
View File

@ -140,14 +140,39 @@ public class UnifiedGenotyperEngine {
}
/**
* Compute full calls at a given locus. Entry point for engine calls from the UnifiedGenotyper.
* @see #calculateLikelihoodsAndGenotypes(org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker, org.broadinstitute.sting.gatk.contexts.ReferenceContext, org.broadinstitute.sting.gatk.contexts.AlignmentContext, java.util.Set)
*
* @param tracker the meta data tracker
* @param refContext the reference base
* @param rawContext contextual information around the locus
* @return the VariantCallContext object
* same as the full call but with allSamples == null
*
* @param tracker
* @param refContext
* @param rawContext
* @return
*/
public List<VariantCallContext> calculateLikelihoodsAndGenotypes(RefMetaDataTracker tracker, ReferenceContext refContext, AlignmentContext rawContext) {
public List<VariantCallContext> calculateLikelihoodsAndGenotypes(final RefMetaDataTracker tracker,
final ReferenceContext refContext,
final AlignmentContext rawContext) {
return calculateLikelihoodsAndGenotypes(tracker, refContext, rawContext, null);
}
/**
* Compute full calls at a given locus. Entry point for engine calls from the UnifiedGenotyper.
*
* If allSamples != null, then the output variantCallContext is guarenteed to contain a genotype
* for every sample in allSamples. If it's null there's no such guarentee. Providing this
* argument is critical when the resulting calls will be written to a VCF file.
*
* @param tracker the meta data tracker
* @param refContext the reference base
* @param rawContext contextual information around the locus
* @param allSamples set of all sample names that we might call (i.e., those in the VCF header)
* @return the VariantCallContext object
*/
public List<VariantCallContext> calculateLikelihoodsAndGenotypes(final RefMetaDataTracker tracker,
final ReferenceContext refContext,
final AlignmentContext rawContext,
final Set<String> allSamples) {
final List<VariantCallContext> results = new ArrayList<VariantCallContext>(2);
final List<GenotypeLikelihoodsCalculationModel.Model> models = getGLModelsToUse(tracker, refContext, rawContext);
@ -168,7 +193,23 @@ public class UnifiedGenotyperEngine {
}
}
return results;
return addMissingSamples(results, allSamples);
}
private List<VariantCallContext> addMissingSamples(final List<VariantCallContext> calls, final Set<String> allSamples) {
if ( calls.isEmpty() || allSamples == null ) return calls;
final List<VariantCallContext> withAllSamples = new ArrayList<VariantCallContext>(calls.size());
for ( final VariantCallContext call : calls ) {
if ( call == null )
withAllSamples.add(call);
else {
final VariantContext withoutMissing = VariantContextUtils.addMissingSamples(call, allSamples);
withAllSamples.add(new VariantCallContext(withoutMissing, call.confidentlyCalled, call.shouldEmit));
}
}
return withAllSamples;
}
/**

3
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java
View File

@ -261,6 +261,7 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
private UnifiedGenotyperEngine snpEngine;
private UnifiedGenotyperEngine indelEngine;
private Set<String> samples;
public static class CountedData {
private long nAltCalledAlt = 0L;
@ -307,7 +308,7 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
// Initialize VCF header
if (vcfWriter != null) {
Map<String, VCFHeader> header = VCFUtils.getVCFHeadersFromRodPrefix(getToolkit(), alleles.getName());
Set<String> samples = SampleUtils.getSampleList(header, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE);
samples = SampleUtils.getSampleList(header, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE);
Set<VCFHeaderLine> headerLines = VCFUtils.smartMergeHeaders(header.values(), logger);
headerLines.add(new VCFHeaderLine("source", "GenotypeAndValidate"));
vcfWriter.writeHeader(new VCFHeader(headerLines, samples));

19
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
View File

@ -174,17 +174,24 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
/** Optimization to strip out genotypes before merging if we are doing a sites_only output */
private boolean sitesOnlyVCF = false;
private Set<String> samples;
public void initialize() {
Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit());
if ( vcfWriter instanceof VariantContextWriterStub) {
sitesOnlyVCF = ((VariantContextWriterStub)vcfWriter).getWriterOptions().contains(Options.DO_NOT_WRITE_GENOTYPES);
if ( sitesOnlyVCF ) logger.info("Pre-stripping genotypes for performance");
} else
logger.warn("VCF output file not an instance of VCFWriterStub; cannot enable sites only output option");
if ( PRIORITY_STRING == null ) {
PRIORITY_STRING = Utils.join(",", vcfRods.keySet());
logger.info("Priority string not provided, using arbitrary genotyping order: " + PRIORITY_STRING);
}
validateAnnotateUnionArguments();
Set<String> samples = SampleUtils.getSampleList(vcfRods, genotypeMergeOption);
samples = sitesOnlyVCF ? Collections.<String>emptySet() : SampleUtils.getSampleList(vcfRods, genotypeMergeOption);
if ( SET_KEY.toLowerCase().equals("null") )
SET_KEY = null;
@ -194,15 +201,9 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
headerLines.add(new VCFInfoHeaderLine(SET_KEY, 1, VCFHeaderLineType.String, "Source VCF for the merged record in CombineVariants"));
if ( !ASSUME_IDENTICAL_SAMPLES )
headerLines.addAll(Arrays.asList(ChromosomeCounts.descriptions));
VCFHeader vcfHeader = new VCFHeader(headerLines, sitesOnlyVCF ? Collections.<String>emptySet() : samples);
VCFHeader vcfHeader = new VCFHeader(headerLines, samples);
vcfHeader.setWriteCommandLine(!SUPPRESS_COMMAND_LINE_HEADER);
vcfWriter.writeHeader(vcfHeader);
if ( vcfWriter instanceof VariantContextWriterStub) {
sitesOnlyVCF = ((VariantContextWriterStub)vcfWriter).getWriterOptions().contains(Options.DO_NOT_WRITE_GENOTYPES);
if ( sitesOnlyVCF ) logger.info("Pre-stripping genotypes for performance");
} else
logger.warn("VCF output file not an instance of VCFWriterStub; cannot enable sites only output option");
}
private void validateAnnotateUnionArguments() {
@ -296,7 +297,7 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
VariantContextUtils.calculateChromosomeCounts(builder, false);
if ( minimalVCF )
VariantContextUtils.pruneVariantContext(builder, Arrays.asList(SET_KEY));
vcfWriter.add(builder.make());
vcfWriter.add(VariantContextUtils.addMissingSamples(builder.make(), samples));
}
return vcs.isEmpty() ? 0 : 1;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
View File

@ -108,6 +108,7 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
private Set<String> allowedGenotypeFormatStrings = new HashSet<String>();
private boolean wroteHeader = false;
private Set<String> samples;
// for dealing with indels in hapmap
CloseableIterator<GATKFeature> dbsnpIterator = null;
@ -228,7 +229,7 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
}
}
Set<String> samples = new LinkedHashSet<String>();
samples = new LinkedHashSet<String>();
if ( sampleName != null ) {
samples.add(sampleName);
} else {
@ -252,6 +253,7 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
}
vc = VariantContextUtils.purgeUnallowedGenotypeAttributes(vc, allowedGenotypeFormatStrings);
vc = VariantContextUtils.addMissingSamples(vc, samples);
vcfwriter.add(vc);
}

65
public/java/src/org/broadinstitute/sting/utils/BaseUtils.java
View File

@ -2,6 +2,8 @@ package org.broadinstitute.sting.utils;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import java.util.Arrays;
/**
* BaseUtils contains some basic utilities for manipulating nucleotides.
*/
@ -47,6 +49,20 @@ public class BaseUtils {
public boolean sameBase(int i) { return index == i; }
}
static private final int[] baseIndexMap = new int[256];
static {
Arrays.fill(baseIndexMap, -1);
baseIndexMap['A'] = 0;
baseIndexMap['a'] = 0;
baseIndexMap['*'] = 0; // the wildcard character counts as an A
baseIndexMap['C'] = 1;
baseIndexMap['c'] = 1;
baseIndexMap['G'] = 2;
baseIndexMap['g'] = 2;
baseIndexMap['T'] = 3;
baseIndexMap['t'] = 3;
}
// todo -- fix me (enums?)
public static final byte DELETION_INDEX = 4;
public static final byte NO_CALL_INDEX = 5; // (this is 'N')
@ -182,27 +198,7 @@ public class BaseUtils {
* @return 0, 1, 2, 3, or -1 if the base can't be understood
*/
static public int simpleBaseToBaseIndex(byte base) {
switch (base) {
case '*': // the wildcard character counts as an A
case 'A':
case 'a':
return 0;
case 'C':
case 'c':
return 1;
case 'G':
case 'g':
return 2;
case 'T':
case 't':
return 3;
default:
return -1;
}
return baseIndexMap[base];
}
/**
@ -213,27 +209,7 @@ public class BaseUtils {
*/
@Deprecated
static public int simpleBaseToBaseIndex(char base) {
switch (base) {
case '*': // the wildcard character counts as an A
case 'A':
case 'a':
return 0;
case 'C':
case 'c':
return 1;
case 'G':
case 'g':
return 2;
case 'T':
case 't':
return 3;
default:
return -1;
}
return baseIndexMap[base];
}
static public int extendedBaseToBaseIndex(byte base) {
@ -284,11 +260,6 @@ public class BaseUtils {
}
}
@Deprecated
static public char baseIndexToSimpleBaseAsChar(int baseIndex) {
return (char) baseIndexToSimpleBase(baseIndex);
}
/**
* Converts a base index to a base index representing its cross-talk partner
*

7
public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Decoder.java
View File

@ -136,6 +136,10 @@ public final class BCF2Decoder {
public final Object decodeTypedValue(final byte typeDescriptor) {
final int size = decodeNumberOfElements(typeDescriptor);
return decodeTypedValue(typeDescriptor, size);
}
public final Object decodeTypedValue(final byte typeDescriptor, final int size) {
final BCF2Type type = BCF2Utils.decodeType(typeDescriptor);
assert size >= 0;
@ -285,8 +289,7 @@ public final class BCF2Decoder {
}
}
public final int[] decodeIntArray(final byte typeDescriptor) {
final int size = decodeNumberOfElements(typeDescriptor);
public final int[] decodeIntArray(final byte typeDescriptor, final int size) {
final BCF2Type type = BCF2Utils.decodeType(typeDescriptor);
return decodeIntArray(size, type, null);
}

30
public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2GenotypeFieldDecoders.java
View File

@ -104,19 +104,17 @@ public class BCF2GenotypeFieldDecoders {
final String field,
final BCF2Decoder decoder,
final byte typeDescriptor,
final int numElements,
final GenotypeBuilder[] gbs);
}
private class GTDecoder implements Decoder {
@Override
public void decode(final List<Allele> siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final GenotypeBuilder[] gbs) {
// we have to do a bit of low-level processing here as we want to know the size upfronta
final int ploidy = decoder.decodeNumberOfElements(typeDescriptor);
if ( ENABLE_FASTPATH_GT && siteAlleles.size() == 2 && ploidy == 2 && gbs.length >= MIN_SAMPLES_FOR_FASTPATH_GENOTYPES )
public void decode(final List<Allele> siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final int numElements, final GenotypeBuilder[] gbs) {
if ( ENABLE_FASTPATH_GT && siteAlleles.size() == 2 && numElements == 2 && gbs.length >= MIN_SAMPLES_FOR_FASTPATH_GENOTYPES )
fastBiallelicDiploidDecode(siteAlleles, decoder, typeDescriptor, gbs);
else {
generalDecode(siteAlleles, ploidy, decoder, typeDescriptor, gbs);
generalDecode(siteAlleles, numElements, decoder, typeDescriptor, gbs);
}
}
@ -218,7 +216,7 @@ public class BCF2GenotypeFieldDecoders {
private class DPDecoder implements Decoder {
@Override
public void decode(final List<Allele> siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final GenotypeBuilder[] gbs) {
public void decode(final List<Allele> siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final int numElements, final GenotypeBuilder[] gbs) {
for ( final GenotypeBuilder gb : gbs ) {
// the -1 is for missing
gb.DP(decoder.decodeInt(typeDescriptor, -1));
@ -228,7 +226,7 @@ public class BCF2GenotypeFieldDecoders {
private class GQDecoder implements Decoder {
@Override
public void decode(final List<Allele> siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final GenotypeBuilder[] gbs) {
public void decode(final List<Allele> siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final int numElements, final GenotypeBuilder[] gbs) {
for ( final GenotypeBuilder gb : gbs ) {
// the -1 is for missing
gb.GQ(decoder.decodeInt(typeDescriptor, -1));
@ -238,27 +236,27 @@ public class BCF2GenotypeFieldDecoders {
private class ADDecoder implements Decoder {
@Override
public void decode(final List<Allele> siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final GenotypeBuilder[] gbs) {
public void decode(final List<Allele> siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final int numElements, final GenotypeBuilder[] gbs) {
for ( final GenotypeBuilder gb : gbs ) {
gb.AD(decoder.decodeIntArray(typeDescriptor));
gb.AD(decoder.decodeIntArray(typeDescriptor, numElements));
}
}
}
private class PLDecoder implements Decoder {
@Override
public void decode(final List<Allele> siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final GenotypeBuilder[] gbs) {
public void decode(final List<Allele> siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final int numElements, final GenotypeBuilder[] gbs) {
for ( final GenotypeBuilder gb : gbs ) {
gb.PL(decoder.decodeIntArray(typeDescriptor));
gb.PL(decoder.decodeIntArray(typeDescriptor, numElements));
}
}
}
private class GenericDecoder implements Decoder {
@Override
public void decode(final List<Allele> siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final GenotypeBuilder[] gbs) {
public void decode(final List<Allele> siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final int numElements, final GenotypeBuilder[] gbs) {
for ( final GenotypeBuilder gb : gbs ) {
Object value = decoder.decodeTypedValue(typeDescriptor);
Object value = decoder.decodeTypedValue(typeDescriptor, numElements);
if ( value != null ) { // don't add missing values
if ( value instanceof List && ((List)value).size() == 1) {
// todo -- I really hate this, and it suggests that the code isn't completely right
@ -275,9 +273,9 @@ public class BCF2GenotypeFieldDecoders {
private class FTDecoder implements Decoder {
@Override
public void decode(final List<Allele> siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final GenotypeBuilder[] gbs) {
public void decode(final List<Allele> siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final int numElements, final GenotypeBuilder[] gbs) {
for ( final GenotypeBuilder gb : gbs ) {
Object value = decoder.decodeTypedValue(typeDescriptor);
Object value = decoder.decodeTypedValue(typeDescriptor, numElements);
if ( value != null ) { // don't add missing values
gb.filters(value instanceof String ? Collections.singletonList((String)value) : (List<String>)value);
}

3
public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2LazyGenotypesDecoder.java
View File

@ -77,9 +77,10 @@ class BCF2LazyGenotypesDecoder implements LazyGenotypesContext.LazyParser {
// the type of each element
final byte typeDescriptor = decoder.readTypeDescriptor();
final int numElements = decoder.decodeNumberOfElements(typeDescriptor);
final BCF2GenotypeFieldDecoders.Decoder fieldDecoder = codec.getGenotypeFieldDecoder(field);
try {
fieldDecoder.decode(siteAlleles, field, decoder, typeDescriptor, builders);
fieldDecoder.decode(siteAlleles, field, decoder, typeDescriptor, numElements, builders);
} catch ( ClassCastException e ) {
throw new UserException.MalformedBCF2("BUG: expected encoding of field " + field
+ " inconsistent with the value observed in the decoded value");

18
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCompoundHeaderLine.java
View File

@ -75,22 +75,24 @@ public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCF
* If the count is a fixed count, return that. For example, a field with size of 1 in the header returns 1
* If the count is of type A, return vc.getNAlleles - 1
* If the count is of type G, return the expected number of genotypes given the number of alleles in VC and the
* max ploidy among all samples
* max ploidy among all samples. Note that if the max ploidy of the VC is 0 (there's no GT information
* at all, then implicitly assume diploid samples when computing G values.
* If the count is UNBOUNDED return -1
*
* @param vc
* @return
*/
public int getCount(final VariantContext vc) {
int myCount;
switch ( countType ) {
case INTEGER: myCount = count; break;
case UNBOUNDED: myCount = -1; break;
case A: myCount = vc.getNAlleles() - 1; break;
case G: myCount = GenotypeLikelihoods.numLikelihoods(vc.getNAlleles(), vc.getMaxPloidy()); break;
default: throw new ReviewedStingException("Unknown count type: " + countType);
case INTEGER: return count;
case UNBOUNDED: return -1;
case A: return vc.getNAlleles() - 1;
case G:
final int ploidy = vc.getMaxPloidy();
return GenotypeLikelihoods.numLikelihoods(vc.getNAlleles(), ploidy == 0 ? 2 : ploidy);
default:
throw new ReviewedStingException("Unknown count type: " + countType);
}
return myCount;
}
public void setNumberToUnbounded() {

1
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFStandardHeaderLines.java
View File

@ -183,6 +183,7 @@ public class VCFStandardHeaderLines {
registerStandard(new VCFFormatHeaderLine(VCFConstants.DEPTH_KEY, 1, VCFHeaderLineType.Integer, "Approximate read depth (reads with MQ=255 or with bad mates are filtered)"));
registerStandard(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_PL_KEY, VCFHeaderLineCount.G, VCFHeaderLineType.Integer, "Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"));
registerStandard(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_ALLELE_DEPTHS, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "Allelic depths for the ref and alt alleles in the order listed"));
registerStandard(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_FILTER_KEY, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "Genotype-level filter"));
// INFO lines
registerStandard(new VCFInfoHeaderLine(VCFConstants.END_KEY, 1, VCFHeaderLineType.Integer, "Stop position of the interval"));

51
public/java/src/org/broadinstitute/sting/utils/collections/NestedHashMap.java
View File

@ -25,7 +25,9 @@
package org.broadinstitute.sting.utils.collections;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
@ -83,4 +85,53 @@ public class NestedHashMap {
return value; // todo -- should never reach this point
}
public List<Object> getAllValues() {
List<Object> result = new ArrayList<Object>();
fillAllValues(data, result);
return result;
}
private void fillAllValues(final Map map, final List<Object> result) {
for ( Object value : map.values() ) {
if ( value == null )
continue;
if ( value instanceof Map )
fillAllValues((Map)value, result);
else
result.add(value);
}
}
public static class Leaf {
public final List<Object> keys;
public final Object value;
public Leaf(final List<Object> keys, final Object value) {
this.keys = keys;
this.value = value;
}
}
public List<Leaf> getAllLeaves() {
List<Leaf> result = new ArrayList<Leaf>();
List<Object> path = new ArrayList<Object>();
fillAllLeaves(data, path, result);
return result;
}
private void fillAllLeaves(final Map map, final List<Object> path, final List<Leaf> result) {
for ( final Object key : map.keySet() ) {
final Object value = map.get(key);
if ( value == null )
continue;
final List<Object> newPath = new ArrayList<Object>(path);
newPath.add(key);
if ( value instanceof Map ) {
fillAllLeaves((Map) value, newPath, result);
} else {
result.add(new Leaf(newPath, value));
}
}
}
}

100
public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
View File

@ -28,10 +28,10 @@ package org.broadinstitute.sting.utils.recalibration;
import org.broadinstitute.sting.gatk.walkers.bqsr.*;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.collections.NestedHashMap;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import java.io.File;
import java.util.*;
/**
* Utility methods to facilitate on-the-fly base quality score recalibration.
@ -45,39 +45,15 @@ public class BaseRecalibration {
private final ReadCovariates readCovariates;
private final QuantizationInfo quantizationInfo; // histogram containing the map for qual quantization (calculated after recalibration is done)
private final KeysAndTables keysAndTables;
private final RecalibrationTables recalibrationTables;
private final Covariate[] requestedCovariates; // list of all covariates to be used in this calculation
static class KeysAndTables {
private final Object[] tempKeySet;
public enum Type {
READ_GROUP_TABLE(0),
QUALITY_SCORE_TABLE(1),
OPTIONAL_COVARIATE_TABLE(2);
private final int index;
private Type(int index) {
this.index = index;
}
}
public final BQSRKeyManager[] managers = new BQSRKeyManager[Type.values().length];
public final Map<Long, RecalDatum>[] tables = new Map[Type.values().length];
public KeysAndTables(final Map<BQSRKeyManager, Map<Long, RecalDatum>> keysAndTablesMap) {
for (Map.Entry<BQSRKeyManager, Map<Long, RecalDatum>> mapEntry : keysAndTablesMap.entrySet()) {
Type type;
if (mapEntry.getKey().getNumRequiredCovariates() == 1)
type = Type.READ_GROUP_TABLE;
else if (mapEntry.getKey().getNumOptionalCovariates() == 0)
type = Type.QUALITY_SCORE_TABLE;
else
type = Type.OPTIONAL_COVARIATE_TABLE;
managers[type.index] = mapEntry.getKey();
tables[type.index] = mapEntry.getValue();
}
}
private static final NestedHashMap[] qualityScoreByFullCovariateKey = new NestedHashMap[EventType.values().length]; // Caches the result of performSequentialQualityCalculation(..) for all sets of covariate values.
static {
for (int i = 0; i < EventType.values().length; i++)
qualityScoreByFullCovariateKey[i] = new NestedHashMap();
}
/**
@ -89,7 +65,7 @@ public class BaseRecalibration {
public BaseRecalibration(final File RECAL_FILE, int quantizationLevels) {
RecalibrationReport recalibrationReport = new RecalibrationReport(RECAL_FILE);
keysAndTables = new KeysAndTables(recalibrationReport.getKeysAndTablesMap());
recalibrationTables = recalibrationReport.getRecalibrationTables();
requestedCovariates = recalibrationReport.getRequestedCovariates();
quantizationInfo = recalibrationReport.getQuantizationInfo();
if (quantizationLevels == 0) // quantizationLevels == 0 means no quantization, preserve the quality scores
@ -98,20 +74,22 @@ public class BaseRecalibration {
quantizationInfo.quantizeQualityScores(quantizationLevels);
readCovariates = new ReadCovariates(MAXIMUM_RECALIBRATED_READ_LENGTH, requestedCovariates.length);
tempKeySet = new Integer[requestedCovariates.length];
}
/**
* This constructor only exists for testing purposes.
*
* @param quantizationInfo the quantization info object
* @param keysAndTablesMap the map of key managers and recalibration tables
* @param recalibrationTables the map of key managers and recalibration tables
* @param requestedCovariates the list of requested covariates
*/
protected BaseRecalibration(final QuantizationInfo quantizationInfo, final LinkedHashMap<BQSRKeyManager, Map<Long, RecalDatum>> keysAndTablesMap, final Covariate[] requestedCovariates) {
protected BaseRecalibration(final QuantizationInfo quantizationInfo, final RecalibrationTables recalibrationTables, final Covariate[] requestedCovariates) {
this.quantizationInfo = quantizationInfo;
keysAndTables = new KeysAndTables(keysAndTablesMap);
this.recalibrationTables = recalibrationTables;
this.requestedCovariates = requestedCovariates;
readCovariates = new ReadCovariates(MAXIMUM_RECALIBRATED_READ_LENGTH, requestedCovariates.length);
tempKeySet = new Integer[requestedCovariates.length];
}
/**
@ -125,13 +103,20 @@ public class BaseRecalibration {
RecalDataManager.computeCovariates(read, requestedCovariates, readCovariates); // compute all covariates for the read
for (final EventType errorModel : EventType.values()) { // recalibrate all three quality strings
final byte[] quals = read.getBaseQualities(errorModel);
final int[][] fullReadKeySet = readCovariates.getKeySet(errorModel); // get the keyset for this base using the error model
final int readLength = read.getReadLength();
for (int offset = 0; offset < readLength; offset++) { // recalibrate all bases in the read
for (int offset = 0; offset < read.getReadLength(); offset++) { // recalibrate all bases in the read
final byte originalQualityScore = quals[offset];
if (originalQualityScore >= QualityUtils.MIN_USABLE_Q_SCORE) { // only recalibrate usable qualities (the original quality will come from the instrument -- reported quality)
final long[] keySet = readCovariates.getKeySet(offset, errorModel); // get the keyset for this base using the error model
final byte recalibratedQualityScore = performSequentialQualityCalculation(keySet, errorModel); // recalibrate the base
final int[] keySet = fullReadKeySet[offset]; // get the keyset for this base using the error model
Byte recalibratedQualityScore = (Byte) qualityScoreByFullCovariateKey[errorModel.index].get(wrapKeySet(keySet));
if (recalibratedQualityScore == null) {
recalibratedQualityScore = performSequentialQualityCalculation(keySet, errorModel); // recalibrate the base
qualityScoreByFullCovariateKey[errorModel.index].put(recalibratedQualityScore, keySet);
}
quals[offset] = recalibratedQualityScore;
}
}
@ -139,7 +124,11 @@ public class BaseRecalibration {
}
}
private Object[] wrapKeySet(final int[] keySet) {
for (int i = 0; i < keySet.length; i++)
tempKeySet[i] = keySet[i];
return tempKeySet;
}
/**
* Implements a serial recalibration of the reads using the combinational table.
@ -158,24 +147,23 @@ public class BaseRecalibration {
* @param errorModel the event type
* @return A recalibrated quality score as a byte
*/
protected byte performSequentialQualityCalculation(final long[] key, final EventType errorModel) {
protected byte performSequentialQualityCalculation(final int[] key, final EventType errorModel) {
final double globalDeltaQ = calculateGlobalDeltaQ(keysAndTables.managers[KeysAndTables.Type.READ_GROUP_TABLE.index], keysAndTables.tables[KeysAndTables.Type.READ_GROUP_TABLE.index], key, errorModel);
final double deltaQReported = calculateDeltaQReported(keysAndTables.managers[KeysAndTables.Type.QUALITY_SCORE_TABLE.index], keysAndTables.tables[KeysAndTables.Type.QUALITY_SCORE_TABLE.index], key, errorModel, globalDeltaQ);
final double deltaQCovariates = calculateDeltaQCovariates(keysAndTables.managers[KeysAndTables.Type.OPTIONAL_COVARIATE_TABLE.index], keysAndTables.tables[KeysAndTables.Type.OPTIONAL_COVARIATE_TABLE.index], key, errorModel, globalDeltaQ, deltaQReported);
final byte qualFromRead = (byte)(long)key[1];
final double globalDeltaQ = calculateGlobalDeltaQ(recalibrationTables.getTable(RecalibrationTables.TableType.READ_GROUP_TABLE), key, errorModel);
final double deltaQReported = calculateDeltaQReported(recalibrationTables.getTable(RecalibrationTables.TableType.QUALITY_SCORE_TABLE), key, errorModel, globalDeltaQ, qualFromRead);
final double deltaQCovariates = calculateDeltaQCovariates(recalibrationTables.getTable(RecalibrationTables.TableType.OPTIONAL_COVARIATE_TABLE), key, errorModel, globalDeltaQ, deltaQReported, qualFromRead);
final byte qualFromRead = (byte)key[1];
double recalibratedQual = qualFromRead + globalDeltaQ + deltaQReported + deltaQCovariates; // calculate the recalibrated qual using the BQSR formula
recalibratedQual = QualityUtils.boundQual(MathUtils.fastRound(recalibratedQual), QualityUtils.MAX_RECALIBRATED_Q_SCORE); // recalibrated quality is bound between 1 and MAX_QUAL
return quantizationInfo.getQuantizedQuals().get((int) recalibratedQual); // return the quantized version of the recalibrated quality
}
private double calculateGlobalDeltaQ(final BQSRKeyManager keyManager, final Map<Long, RecalDatum> table, final long[] key, final EventType errorModel) {
private double calculateGlobalDeltaQ(final NestedHashMap table, final int[] key, final EventType errorModel) {
double result = 0.0;
final long masterKey = keyManager.createMasterKey(key, errorModel, -1);
final RecalDatum empiricalQualRG = table.get(masterKey);
final RecalDatum empiricalQualRG = (RecalDatum)table.get(key[0], errorModel.index);
if (empiricalQualRG != null) {
final double globalDeltaQEmpirical = empiricalQualRG.getEmpiricalQuality();
final double aggregrateQReported = empiricalQualRG.getEstimatedQReported();
@ -185,32 +173,28 @@ public class BaseRecalibration {
return result;
}
private double calculateDeltaQReported(final BQSRKeyManager keyManager, final Map<Long, RecalDatum> table, final long[] key, final EventType errorModel, final double globalDeltaQ) {
private double calculateDeltaQReported(final NestedHashMap table, final int[] key, final EventType errorModel, final double globalDeltaQ, final byte qualFromRead) {
double result = 0.0;
final long masterKey = keyManager.createMasterKey(key, errorModel, -1);
final RecalDatum empiricalQualQS = table.get(masterKey);
final RecalDatum empiricalQualQS = (RecalDatum)table.get(key[0], key[1], errorModel.index);
if (empiricalQualQS != null) {
final double deltaQReportedEmpirical = empiricalQualQS.getEmpiricalQuality();
final byte qualFromRead = (byte)key[1];
result = deltaQReportedEmpirical - qualFromRead - globalDeltaQ;
}
return result;
}
private double calculateDeltaQCovariates(final BQSRKeyManager keyManager, final Map<Long, RecalDatum> table, final long[] key, final EventType errorModel, final double globalDeltaQ, final double deltaQReported) {
private double calculateDeltaQCovariates(final NestedHashMap table, final int[] key, final EventType errorModel, final double globalDeltaQ, final double deltaQReported, final byte qualFromRead) {
double result = 0.0;
final int numOptionalCovariates = keyManager.getNumOptionalCovariates();
for (int i = 0; i < numOptionalCovariates; i++) {
final long masterKey = keyManager.createMasterKey(key, errorModel, i);
if (masterKey < 0)
// for all optional covariates
for (int i = 2; i < requestedCovariates.length; i++) {
if (key[i] < 0)
continue;
final RecalDatum empiricalQualCO = table.get(masterKey);
final RecalDatum empiricalQualCO = (RecalDatum)table.get(key[0], key[1], (i-2), key[i], errorModel.index);
if (empiricalQualCO != null) {
final double deltaQCovariateEmpirical = empiricalQualCO.getEmpiricalQuality();
final byte qualFromRead = (byte)key[1];
result += (deltaQCovariateEmpirical - qualFromRead - (globalDeltaQ + deltaQReported));
}
}

62
public/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationTables.java 100644
View File

@ -0,0 +1,62 @@
/*
* Copyright (c) 2012 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.recalibration;
import org.broadinstitute.sting.utils.collections.NestedHashMap;
/**
* Utility class to facilitate on-the-fly base quality score recalibration.
*
* User: ebanks
* Date: 6/20/12
*/
public class RecalibrationTables {
public enum TableType {
READ_GROUP_TABLE(0),
QUALITY_SCORE_TABLE(1),
OPTIONAL_COVARIATE_TABLE(2);
private final int index;
private TableType(final int index) {
this.index = index;
}
}
private final NestedHashMap[] tables = new NestedHashMap[TableType.values().length];
public RecalibrationTables(final NestedHashMap rgMap, final NestedHashMap qualMap, final NestedHashMap covMap) {
tables[TableType.READ_GROUP_TABLE.index] = rgMap;
tables[TableType.QUALITY_SCORE_TABLE.index] = qualMap;
tables[TableType.OPTIONAL_COVARIATE_TABLE.index] = covMap;
}
public NestedHashMap getTable(final TableType type) {
return tables[type.index];
}
}

1
public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
View File

@ -58,7 +58,6 @@ public class GenotypeLikelihoods {
static {
// must be done before PLIndexToAlleleIndex
for ( int numAlleles = 1; numAlleles < NUM_LIKELIHOODS_CACHE_N_ALLELES; numAlleles++ ) {
//numLikelihoodCache[numAlleles] = new int[NUM_LIKELIHOODS_CACHE_PLOIDY];
for ( int ploidy = 1; ploidy < NUM_LIKELIHOODS_CACHE_PLOIDY; ploidy++ ) {
numLikelihoodCache[numAlleles][ploidy] = calcNumLikelihoods(numAlleles, ploidy);
}

1
public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypesContext.java
View File

@ -416,6 +416,7 @@ public class GenotypesContext implements List<Genotype> {
@Ensures("result >= 0")
public int getMaxPloidy() {
if ( maxPloidy == -1 ) {
maxPloidy = 0; // necessary in the case where there are no genotypes
for ( final Genotype g : getGenotypes() ) {
maxPloidy = Math.max(g.getPloidy(), maxPloidy);
}

26
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
View File

@ -46,6 +46,7 @@ public class VariantContextUtils {
public final static String MERGE_FILTER_IN_ALL = "FilteredInAll";
public final static String MERGE_REF_IN_ALL = "ReferenceInAll";
public final static String MERGE_FILTER_PREFIX = "filterIn";
private static final List<Allele> DIPLOID_NO_CALL = Arrays.asList(Allele.NO_CALL, Allele.NO_CALL);
final public static JexlEngine engine = new JexlEngine();
public static final int DEFAULT_PLOIDY = 2;
@ -57,6 +58,31 @@ public class VariantContextUtils {
engine.setDebug(false);
}
/**
* Ensures that VC contains all of the samples in allSamples by adding missing samples to
* the resulting VC with default diploid ./. genotypes
*
* @param vc
* @param allSamples
* @return
*/
public static VariantContext addMissingSamples(final VariantContext vc, final Set<String> allSamples) {
// TODO -- what's the fastest way to do this calculation?
final Set<String> missingSamples = new HashSet<String>(allSamples);
missingSamples.removeAll(vc.getSampleNames());
if ( missingSamples.isEmpty() )
return vc;
else {
//logger.warn("Adding " + missingSamples.size() + " missing samples to called context");
final GenotypesContext gc = GenotypesContext.copy(vc.getGenotypes());
for ( final String missing : missingSamples ) {
gc.add(new GenotypeBuilder(missing).alleles(DIPLOID_NO_CALL).make());
}
return new VariantContextBuilder(vc).genotypes(gc).make();
}
}
/**
* Update the attributes of the attributes map given the VariantContext to reflect the
* proper chromosome-based VCF tags

4
public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java
View File

@ -302,9 +302,7 @@ class BCF2Writer extends IndexingVariantContextWriter {
writer.start(encoder, vc);
for ( final String name : sampleNames ) {
Genotype g = vc.getGenotype(name);
if ( g == null )
// we don't have any data about g at all
g = new GenotypeBuilder(name).alleles(MISSING_GENOTYPE).make();
if ( g == null ) VCFWriter.missingSampleError(vc, header);
writer.addGenotype(encoder, vc, g);
}
writer.done(encoder, vc);

21
public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java
View File

@ -27,6 +27,7 @@ package org.broadinstitute.sting.utils.variantcontext.writer;
import net.sf.samtools.SAMSequenceDictionary;
import org.broad.tribble.TribbleException;
import org.broad.tribble.util.ParsingUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
@ -339,23 +340,12 @@ class VCFWriter extends IndexingVariantContextWriter {
*/
private void addGenotypeData(VariantContext vc, Map<Allele, String> alleleMap, List<String> genotypeFormatKeys)
throws IOException {
// if ( ! mHeader.getGenotypeSamples().containsAll(vc.getSampleNames()) ) {
// final List<String> badSampleNames = new ArrayList<String>();
// for ( final Genotype g : vc.getGenotypes() )
// if ( ! mHeader.getGenotypeSamples().contains(g.getSampleName()) )
// badSampleNames.add(g.getSampleName());
// throw new ReviewedStingException("BUG: VariantContext contains some samples not in the VCF header: bad samples are " + Utils.join(",",badSampleNames));
// }
for ( String sample : mHeader.getGenotypeSamples() ) {
mWriter.write(VCFConstants.FIELD_SEPARATOR);
Genotype g = vc.getGenotype(sample);
if ( g == null ) {
// TODO -- The VariantContext needs to know what the general ploidy is of the samples
// TODO -- We shouldn't be assuming diploid genotypes here!
mWriter.write(VCFConstants.EMPTY_GENOTYPE);
continue;
missingSampleError(vc, mHeader);
}
List<String> attrs = new ArrayList<String>(genotypeFormatKeys.size());
@ -439,6 +429,13 @@ class VCFWriter extends IndexingVariantContextWriter {
}
}
public static final void missingSampleError(final VariantContext vc, final VCFHeader header) {
final List<String> badSampleNames = new ArrayList<String>();
for ( final String x : header.getGenotypeSamples() )
if ( ! vc.hasGenotype(x) ) badSampleNames.add(x);
throw new ReviewedStingException("BUG: we now require all samples in VCFheader to have genotype objects. Missing samples are " + Utils.join(",", badSampleNames));
}
private boolean isMissingValue(String s) {
// we need to deal with the case that it's a list of missing values
return (countOccurrences(VCFConstants.MISSING_VALUE_v4.charAt(0), s) + countOccurrences(',', s) == s.length());

158
public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRKeyManagerUnitTest.java
View File

@ -1,158 +0,0 @@
package org.broadinstitute.sting.gatk.walkers.bqsr;
import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
import java.util.ArrayList;
import java.util.LinkedList;
import java.util.List;
/**
* @author Mauricio Carneiro
* @since 3/7/12
*/
public class BQSRKeyManagerUnitTest {
RecalibrationArgumentCollection RAC;
@BeforeClass
public void init() {
RAC = new RecalibrationArgumentCollection();
}
@Test(enabled = false)
public void testCombineBitSets() {
final int nRequired = 2;
final ArrayList<Covariate> covariates = new ArrayList<Covariate>();
covariates.add(new ReadGroupCovariate());
covariates.add(new QualityScoreCovariate());
covariates.add(new CycleCovariate());
covariates.add(new ContextCovariate());
createReadAndTest(covariates, nRequired);
}
@Test(enabled = true)
public void testOnlyRequiredCovariates() {
final int nRequired = 2;
final ArrayList<Covariate> covariates = new ArrayList<Covariate>(2);
covariates.add(new ReadGroupCovariate());
covariates.add(new QualityScoreCovariate());
createReadAndTest(covariates, nRequired);
}
@Test(enabled = true)
public void testOnlyOneCovariate() {
final int nRequired = 1;
final ArrayList<Covariate> covariates = new ArrayList<Covariate>(2);
covariates.add(new ReadGroupCovariate());
createReadAndTest(covariates, nRequired);
}
@Test(enabled = false)
public void testOneCovariateWithOptionalCovariates() {
final int nRequired = 1;
final ArrayList<Covariate> covariates = new ArrayList<Covariate>(4);
covariates.add(new ReadGroupCovariate());
covariates.add(new QualityScoreCovariate());
covariates.add(new CycleCovariate());
covariates.add(new ContextCovariate());
createReadAndTest(covariates, nRequired);
}
private void createReadAndTest(List<Covariate> covariates, int nRequired) {
int readLength = 1000;
GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(ReadUtils.createRandomReadBases(readLength, true), ReadUtils.createRandomReadQuals(readLength), readLength + "M");
read.setReadGroup(new GATKSAMReadGroupRecord("ID"));
read.getReadGroup().setPlatform("illumina");
runTestOnRead(read, covariates, nRequired);
read.setReadNegativeStrandFlag(true);
runTestOnRead(read, covariates, nRequired);
read.setReadPairedFlag(true);
read.setSecondOfPairFlag(true);
runTestOnRead(read, covariates, nRequired);
read.setReadNegativeStrandFlag(false);
runTestOnRead(read, covariates, nRequired);
}
private void runTestOnRead(GATKSAMRecord read, List<Covariate> covariateList, int nRequired) {
final long[][][] covariateKeys = new long[covariateList.size()][EventType.values().length][read.getReadLength()];
ReadCovariates readCovariates = new ReadCovariates(read.getReadLength(), covariateList.size());
for (int i = 0; i < covariateList.size(); i++) {
final Covariate cov = covariateList.get(i);
cov.initialize(RAC);
readCovariates.setCovariateIndex(i);
cov.recordValues(read, readCovariates);
}
for (int i = 0; i < read.getReadLength(); i++) {
for (EventType eventType : EventType.values()) {
final long[] vals = readCovariates.getKeySet(i, eventType);
for (int j = 0; j < vals.length; j++)
covariateKeys[j][eventType.index][i] = vals[j];
}
}
List<Covariate> requiredCovariates = new LinkedList<Covariate>();
List<Covariate> optionalCovariates = new LinkedList<Covariate>();
for (int j=0; j<nRequired; j++)
requiredCovariates.add(covariateList.get(j));
for (int j=nRequired; j<covariateList.size(); j++)
optionalCovariates.add(covariateList.get(j));
BQSRKeyManager keyManager = new BQSRKeyManager(requiredCovariates, optionalCovariates);
for (int l = 0; l < read.getReadLength(); l++) {
for (EventType eventType : EventType.values()) {
long[] keySet = new long[covariateList.size()];
Object[] expectedRequired = new Object[covariateList.size()];
Object[] expectedCovariate = new Object[covariateList.size()];
for (int j = 0; j < covariateList.size(); j++) {
keySet[j] = covariateKeys[j][eventType.index][l];
if (j < nRequired)
expectedRequired[j] = covariateList.get(j).formatKey(keySet[j]);
else
expectedCovariate[j - nRequired] = covariateList.get(j).formatKey(keySet[j]);
}
if (optionalCovariates.size() == 0) {
final long masterKey = keyManager.createMasterKey(keySet, eventType, -1);
testKeys(keyManager, masterKey, nRequired, optionalCovariates, expectedRequired, expectedCovariate, eventType, -1);
} else {
for (int j = 0; j < optionalCovariates.size(); j++) {
final long masterKey = keyManager.createMasterKey(keySet, eventType, j);
testKeys(keyManager, masterKey, nRequired, optionalCovariates, expectedRequired, expectedCovariate, eventType, j);
}
}
}
}
}
private void testKeys(final BQSRKeyManager keyManager, final long key, final int nRequired, final List<Covariate> optionalCovariates,
final Object[] expectedRequired, final Object[] expectedCovariate, final EventType eventType, final int index) {
Object[] actual = keyManager.keySetFrom(key).toArray();
// Build the expected array
Object[] expected = new Object[nRequired + (optionalCovariates.size() > 0 ? 3 : 1)];
System.arraycopy(expectedRequired, 0, expected, 0, nRequired);
if (optionalCovariates.size() > 0) {
expected[expected.length-3] = expectedCovariate[index];
expected[expected.length-2] = optionalCovariates.get(index).getClass().getSimpleName().split("Covariate")[0];
}
expected[expected.length-1] = eventType;
// System.out.println("Actual : " + Utils.join(",", Arrays.asList(actual)));
// System.out.println("Expected: " + Utils.join(",", Arrays.asList(expected)));
// System.out.println();
for (int k = 0; k < expected.length; k++)
Assert.assertEquals(actual[k], expected[k]);
}
}

2
public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/ContextCovariateUnitTest.java
View File

@ -36,7 +36,7 @@ public class ContextCovariateUnitTest {
verifyCovariateArray(readCovariates.getDeletionsKeySet(), RAC.INDELS_CONTEXT_SIZE, clippedRead, covariate);
}
public static void verifyCovariateArray(long[][] values, int contextSize, GATKSAMRecord read, Covariate contextCovariate) {
public static void verifyCovariateArray(int[][] values, int contextSize, GATKSAMRecord read, Covariate contextCovariate) {
for (int i = 0; i < values.length; i++)
Assert.assertEquals(contextCovariate.formatKey(values[i][0]), expectedContext(read, i, contextSize));

2
public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/CycleCovariateUnitTest.java
View File

@ -47,7 +47,7 @@ public class CycleCovariateUnitTest {
verifyCovariateArray(readCovariates.getMismatchesKeySet(), -1, -1);
}
private void verifyCovariateArray(long[][] values, int init, int increment) {
private void verifyCovariateArray(int[][] values, int init, int increment) {
for (short i = 0; i < values.length; i++) {
short actual = Short.decode(covariate.formatKey(values[i][0]));
int expected = init + (increment * i);

4
public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/ReadGroupCovariateUnitTest.java
View File

@ -46,8 +46,8 @@ public class ReadGroupCovariateUnitTest {
}
private void verifyCovariateArray(long[][] values, String expected) {
for (long[] value : values) {
private void verifyCovariateArray(int[][] values, String expected) {
for (int[] value : values) {
String actual = covariate.formatKey(value[0]);
Assert.assertEquals(actual, expected);
}

48
public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationReportUnitTest.java
View File

@ -1,7 +1,9 @@
package org.broadinstitute.sting.gatk.walkers.bqsr;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.collections.NestedHashMap;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.recalibration.RecalibrationTables;
import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
@ -32,7 +34,6 @@ public class RecalibrationReportUnitTest {
final QuantizationInfo quantizationInfo = new QuantizationInfo(quals, counts);
final RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection();
final LinkedHashMap<BQSRKeyManager, Map<Long, RecalDatum>> keysAndTablesMap = new LinkedHashMap<BQSRKeyManager, Map<Long, RecalDatum>>();
quantizationInfo.noQuantization();
final List<Covariate> requiredCovariates = new LinkedList<Covariate>();
@ -41,14 +42,10 @@ public class RecalibrationReportUnitTest {
final ReadGroupCovariate rgCovariate = new ReadGroupCovariate();
rgCovariate.initialize(RAC);
requiredCovariates.add(rgCovariate);
final BQSRKeyManager rgKeyManager = new BQSRKeyManager(requiredCovariates, optionalCovariates);
keysAndTablesMap.put(rgKeyManager, new HashMap<Long, RecalDatum>());
final QualityScoreCovariate qsCovariate = new QualityScoreCovariate();
qsCovariate.initialize(RAC);
requiredCovariates.add(qsCovariate);
final BQSRKeyManager qsKeyManager = new BQSRKeyManager(requiredCovariates, optionalCovariates);
keysAndTablesMap.put(qsKeyManager, new HashMap<Long, RecalDatum>());
final ContextCovariate cxCovariate = new ContextCovariate();
cxCovariate.initialize(RAC);
@ -56,8 +53,6 @@ public class RecalibrationReportUnitTest {
final CycleCovariate cyCovariate = new CycleCovariate();
cyCovariate.initialize(RAC);
optionalCovariates.add(cyCovariate);
BQSRKeyManager cvKeyManager = new BQSRKeyManager(requiredCovariates, optionalCovariates);
keysAndTablesMap.put(cvKeyManager, new HashMap<Long, RecalDatum>());
final Covariate[] requestedCovariates = new Covariate[requiredCovariates.size() + optionalCovariates.size()];
int covariateIndex = 0;
@ -75,34 +70,35 @@ public class RecalibrationReportUnitTest {
readQuals[i] = 20;
read.setBaseQualities(readQuals);
final int expectedKeys = expectedNumberOfKeys(4, length, RAC.INDELS_CONTEXT_SIZE, RAC.MISMATCHES_CONTEXT_SIZE);
int nKeys = 0; // keep track of how many keys were produced
final ReadCovariates rc = RecalDataManager.computeCovariates(read, requestedCovariates);
for (int offset = 0; offset < length; offset++) {
for (Map.Entry<BQSRKeyManager, Map<Long, RecalDatum>> entry : keysAndTablesMap.entrySet()) {
BQSRKeyManager keyManager = entry.getKey();
Map<Long, RecalDatum> table = entry.getValue();
final int numOptionalCovariates = keyManager.getNumOptionalCovariates();
if (numOptionalCovariates == 0) {
table.put(keyManager.createMasterKey(rc.getMismatchesKeySet(offset), EventType.BASE_SUBSTITUTION, -1), RecalDatum.createRandomRecalDatum(10000, 10));
table.put(keyManager.createMasterKey(rc.getMismatchesKeySet(offset), EventType.BASE_INSERTION, -1), RecalDatum.createRandomRecalDatum(100000, 10));
table.put(keyManager.createMasterKey(rc.getMismatchesKeySet(offset), EventType.BASE_DELETION, -1), RecalDatum.createRandomRecalDatum(100000, 10));
nKeys += 3;
} else {
for (int j = 0; j < numOptionalCovariates; j++) {
table.put(keyManager.createMasterKey(rc.getMismatchesKeySet(offset), EventType.BASE_SUBSTITUTION, j), RecalDatum.createRandomRecalDatum(10000, 10));
table.put(keyManager.createMasterKey(rc.getMismatchesKeySet(offset), EventType.BASE_INSERTION, j), RecalDatum.createRandomRecalDatum(100000, 10));
table.put(keyManager.createMasterKey(rc.getMismatchesKeySet(offset), EventType.BASE_DELETION, j), RecalDatum.createRandomRecalDatum(100000, 10));
nKeys += 3;
}
final NestedHashMap rgTable = new NestedHashMap();
final NestedHashMap qualTable = new NestedHashMap();
final NestedHashMap covTable = new NestedHashMap();
for (int offset = 0; offset < length; offset++) {
for (EventType errorMode : EventType.values()) {
final int[] covariates = rc.getKeySet(offset, errorMode);
final int randomMax = errorMode == EventType.BASE_SUBSTITUTION ? 10000 : 100000;
rgTable.put(RecalDatum.createRandomRecalDatum(randomMax, 10), covariates[0], errorMode.index);
qualTable.put(RecalDatum.createRandomRecalDatum(randomMax, 10), covariates[0], covariates[1], errorMode.index);
nKeys += 2;
for (int j = 0; j < optionalCovariates.size(); j++) {
covTable.put(RecalDatum.createRandomRecalDatum(randomMax, 10), covariates[0], covariates[1], j, covariates[2 + j], errorMode.index);
nKeys++;
}
}
}
Assert.assertEquals(nKeys, expectedKeys);
RecalibrationReport report = new RecalibrationReport(quantizationInfo, keysAndTablesMap, RAC.generateReportTable(), RAC);
final RecalibrationTables recalibrationTables = new RecalibrationTables(rgTable, qualTable, covTable);
final RecalibrationReport report = new RecalibrationReport(quantizationInfo, recalibrationTables, RAC.generateReportTable(), RAC);
File output = new File("RecalibrationReportUnitTestOutuput.grp");
PrintStream out;

7
public/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargetsIntegrationTest.java
View File

@ -36,18 +36,19 @@ public class DiagnoseTargetsIntegrationTest extends WalkerTest {
final String L = validationDataLocation + "DT-itest.interval_list";
private void DTTest(String testName, String args, String md5) {
String base = String.format("-T DiagnoseTargets -R %s -L %s", REF, L) + " -o %s ";
String base = String.format("-T DiagnoseTargets --no_cmdline_in_header -R %s -L %s", REF, L) + " -o %s ";
WalkerTestSpec spec = new WalkerTestSpec(base + args, Arrays.asList(md5));
spec.disableShadowBCF();
executeTest(testName, spec);
}
@Test(enabled = true)
public void testSingleSample() {
DTTest("testSingleSample ", "-I " + singleSample + " -max 75", "2df47009571fe83ead779c94be97fe96");
DTTest("testSingleSample ", "-I " + singleSample + " -max 75", "ef71a569a48697c89e642cdda7bfb766");
}
@Test(enabled = true)
public void testMultiSample() {
DTTest("testMultiSample ", "-I " + multiSample, "6f0c070b9671e1d007ce6374c3183014");
DTTest("testMultiSample ", "-I " + multiSample, "1e6e15156e01e736274898fdac77d911");
}
}

4
public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
View File

@ -80,7 +80,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testGenotypeFilters1() {
WalkerTestSpec spec1 = new WalkerTestSpec(
baseTestString() + " -G_filter 'GQ == 0.60' -G_filterName foo --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("060e9e7b6faf8b2f7b3291594eb6b39c"));
Arrays.asList("c5ed9dd3975b3602293bb484b4fda5f4"));
executeTest("test genotype filter #1", spec1);
}
@ -88,7 +88,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testGenotypeFilters2() {
WalkerTestSpec spec2 = new WalkerTestSpec(
baseTestString() + " -G_filter 'isHomVar == 1' -G_filterName foo --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("00f90028a8c0d56772c47f039816b585"));
Arrays.asList("979ccdf484259117aa31305701075602"));
executeTest("test genotype filter #2", spec2);
}

6
public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
View File

@ -7,10 +7,6 @@ import org.testng.annotations.DataProvider;
import java.util.*;
public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
static HashMap<String, String> clusterFiles = new HashMap<String, String>();
static HashMap<String, String> tranchesFiles = new HashMap<String, String>();
static HashMap<String, String> inputVCFFiles = new HashMap<String, String>();
private static class VRTest {
String inVCF;
String tranchesMD5;
@ -77,7 +73,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
VRTest indel = new VRTest("combined.phase1.chr20.raw.indels.sites.vcf",
"da4458d05f6396f5c4ab96f274e5ccdc", // tranches
"a04a9001f62eff43d363f4d63769f3ee", // recal file
"05e88052e0798f1c1e83f0a8938bce56"); // cut VCF
"b9936d2432d3c85b2d8b5b7aa17d0950"); // cut VCF
@DataProvider(name = "VRIndelTest")
public Object[][] createData2() {

2
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java
View File

@ -60,7 +60,7 @@ public class VCFStreamingIntegrationTest extends WalkerTest {
" --no_cmdline_in_header " +
" -o %s",
1,
Arrays.asList("2cdcd9e140eb1b6da7e365e37dd7d859")
Arrays.asList("283f434b3efbebb8e10ed6347f97d104")
);
executeTest("testSimpleVCFStreaming", spec);

17
public/java/test/org/broadinstitute/sting/utils/BitSetUtilsUnitTest.java
View File

@ -1,8 +1,6 @@
package org.broadinstitute.sting.utils;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.walkers.bqsr.BQSRKeyManager;
import org.broadinstitute.sting.gatk.walkers.bqsr.ContextCovariate;
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
@ -59,19 +57,4 @@ public class BitSetUtilsUnitTest {
//for (String d : dna)
// Assert.assertEquals(BitSetUtils.dnaFrom(BitSetUtils.bitSetFrom(d)), d);
}
@Test(enabled = true)
public void testNumberOfBitsToRepresent() {
Assert.assertEquals(BQSRKeyManager.numberOfBitsToRepresent(0), 0); // Make sure 0 elements need 0 bits to be represented
Assert.assertEquals(BQSRKeyManager.numberOfBitsToRepresent(1), 1); // Make sure 1 element needs 1 bit to be represented
Assert.assertEquals(BQSRKeyManager.numberOfBitsToRepresent(3), 2); // Make sure 3 elements need 2 bit to be represented
for (int i = 1; i < 63; i++) { // Can't test i == 63 because n1 is a negative number
long n1 = 1L << i;
long n2 = Math.abs(random.nextLong()) % n1;
long n3 = n1 | n2;
Assert.assertEquals(BQSRKeyManager.numberOfBitsToRepresent(n3), (n3 == n1) ? i : i + 1);
Assert.assertEquals(BQSRKeyManager.numberOfBitsToRepresent(n1), i);
}
}
}

3
public/java/test/org/broadinstitute/sting/utils/codecs/bcf2/BCF2EncoderDecoderUnitTest.java
View File

@ -480,7 +480,8 @@ public class BCF2EncoderDecoderUnitTest extends BaseTest {
final byte typeDescriptor = decoder.readTypeDescriptor();
// read the int[] with the low-level version
final int[] decoded = decoder.decodeIntArray(typeDescriptor);
final int size = decoder.decodeNumberOfElements(typeDescriptor);
final int[] decoded = decoder.decodeIntArray(typeDescriptor, size);
if ( isMissing(ints) ) {
// we expect that the result is null in this case

2
public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java
View File

@ -34,7 +34,7 @@ public class VCFIntegrationTest extends WalkerTest {
String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s ";
String test1 = baseCommand + "-T SelectVariants -V " + testVCF;
WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("355b029487c3b4c499140d71310ca37e"));
WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("13329ba7360a8beb3afc02569e5a20c4"));
executeTest("Test reading and writing breakpoint VCF", spec1);
}

91
public/java/test/org/broadinstitute/sting/utils/recalibration/BaseRecalibrationUnitTest.java
View File

@ -2,7 +2,6 @@ package org.broadinstitute.sting.utils.recalibration;
import org.broadinstitute.sting.gatk.walkers.bqsr.*;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.collections.NestedHashMap;
import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
@ -22,7 +21,7 @@ import java.util.*;
public class BaseRecalibrationUnitTest {
private org.broadinstitute.sting.gatk.walkers.recalibration.RecalDataManager dataManager;
private LinkedHashMap<BQSRKeyManager, Map<Long, RecalDatum>> keysAndTablesMap;
private RecalibrationTables recalibrationTables;
private ReadGroupCovariate rgCovariate;
private QualityScoreCovariate qsCovariate;
@ -50,19 +49,14 @@ public class BaseRecalibrationUnitTest {
List<Covariate> optionalCovariates = new ArrayList<Covariate>();
dataManager = new org.broadinstitute.sting.gatk.walkers.recalibration.RecalDataManager(true, 4);
keysAndTablesMap = new LinkedHashMap<BQSRKeyManager, Map<Long, RecalDatum>>();
rgCovariate = new ReadGroupCovariate();
rgCovariate.initialize(RAC);
requiredCovariates.add(rgCovariate);
BQSRKeyManager rgKeyManager = new BQSRKeyManager(requiredCovariates, optionalCovariates);
keysAndTablesMap.put(rgKeyManager, new HashMap<Long, RecalDatum>());
qsCovariate = new QualityScoreCovariate();
qsCovariate.initialize(RAC);
requiredCovariates.add(qsCovariate);
BQSRKeyManager qsKeyManager = new BQSRKeyManager(requiredCovariates, optionalCovariates);
keysAndTablesMap.put(qsKeyManager, new HashMap<Long, RecalDatum>());
cxCovariate = new ContextCovariate();
cxCovariate.initialize(RAC);
@ -70,8 +64,6 @@ public class BaseRecalibrationUnitTest {
cyCovariate = new CycleCovariate();
cyCovariate.initialize(RAC);
optionalCovariates.add(cyCovariate);
BQSRKeyManager cvKeyManager = new BQSRKeyManager(requiredCovariates, optionalCovariates);
keysAndTablesMap.put(cvKeyManager, new HashMap<Long, RecalDatum>());
final Covariate[] requestedCovariates = new Covariate[requiredCovariates.size() + optionalCovariates.size()];
int covariateIndex = 0;
@ -82,10 +74,13 @@ public class BaseRecalibrationUnitTest {
readCovariates = RecalDataManager.computeCovariates(read, requestedCovariates);
for (int i=0; i<read.getReadLength(); i++) {
long[] bitKeys = readCovariates.getMismatchesKeySet(i);
final NestedHashMap rgTable = new NestedHashMap();
final NestedHashMap qualTable = new NestedHashMap();
final NestedHashMap covTable = new NestedHashMap();
Object[] objKey = buildObjectKey(bitKeys);
for (int i=0; i<read.getReadLength(); i++) {
final int[] bitKeys = readCovariates.getMismatchesKeySet(i);
final Object[] objKey = buildObjectKey(bitKeys);
Random random = new Random();
int nObservations = random.nextInt(10000);
@ -97,21 +92,17 @@ public class BaseRecalibrationUnitTest {
dataManager.addToAllTables(objKey, oldDatum, QualityUtils.MIN_USABLE_Q_SCORE);
RecalDatum newDatum = new RecalDatum(nObservations, nErrors, estimatedQReported, empiricalQuality);
for (Map.Entry<BQSRKeyManager, Map<Long, RecalDatum>> mapEntry : keysAndTablesMap.entrySet()) {
final BQSRKeyManager keyManager = mapEntry.getKey();
final int numOptionalCovariates = keyManager.getNumOptionalCovariates();
if (numOptionalCovariates == 0) {
final long masterKey = keyManager.createMasterKey(bitKeys, EventType.BASE_SUBSTITUTION, -1);
updateCovariateWithKeySet(mapEntry.getValue(), masterKey, newDatum);
} else {
for (int j = 0; j < numOptionalCovariates; j++) {
final long masterKey = keyManager.createMasterKey(bitKeys, EventType.BASE_SUBSTITUTION, j);
updateCovariateWithKeySet(mapEntry.getValue(), masterKey, newDatum);
}
}
rgTable.put(newDatum, bitKeys[0], EventType.BASE_SUBSTITUTION.index);
qualTable.put(newDatum, bitKeys[0], bitKeys[1], EventType.BASE_SUBSTITUTION.index);
for (int j = 0; j < optionalCovariates.size(); j++) {
covTable.put(newDatum, bitKeys[0], bitKeys[1], j, bitKeys[2 + j], EventType.BASE_SUBSTITUTION.index);
}
}
dataManager.generateEmpiricalQualities(1, QualityUtils.MAX_RECALIBRATED_Q_SCORE);
recalibrationTables = new RecalibrationTables(rgTable, qualTable, covTable);
dataManager.generateEmpiricalQualities(1, QualityUtils.MAX_RECALIBRATED_Q_SCORE);
List<Byte> quantizedQuals = new ArrayList<Byte>();
List<Long> qualCounts = new ArrayList<Long>();
@ -121,16 +112,15 @@ public class BaseRecalibrationUnitTest {
}
QuantizationInfo quantizationInfo = new QuantizationInfo(quantizedQuals, qualCounts);
quantizationInfo.noQuantization();
baseRecalibration = new BaseRecalibration(quantizationInfo, keysAndTablesMap, requestedCovariates);
baseRecalibration = new BaseRecalibration(quantizationInfo, recalibrationTables, requestedCovariates);
}
@Test(enabled=false)
public void testGoldStandardComparison() {
debugTables();
for (int i = 0; i < read.getReadLength(); i++) {
long [] bitKey = readCovariates.getKeySet(i, EventType.BASE_SUBSTITUTION);
int [] bitKey = readCovariates.getKeySet(i, EventType.BASE_SUBSTITUTION);
Object [] objKey = buildObjectKey(bitKey);
byte v2 = baseRecalibration.performSequentialQualityCalculation(bitKey, EventType.BASE_SUBSTITUTION);
byte v1 = goldStandardSequentialCalculation(objKey);
@ -138,7 +128,7 @@ public class BaseRecalibrationUnitTest {
}
}
private Object[] buildObjectKey(long[] bitKey) {
private Object[] buildObjectKey(final int[] bitKey) {
Object[] key = new Object[bitKey.length];
key[0] = rgCovariate.formatKey(bitKey[0]);
key[1] = qsCovariate.formatKey(bitKey[1]);
@ -147,49 +137,6 @@ public class BaseRecalibrationUnitTest {
return key;
}
private void debugTables() {
System.out.println("\nV1 Table\n");
System.out.println("ReadGroup Table:");
NestedHashMap nestedTable = dataManager.getCollapsedTable(0);
printNestedHashMap(nestedTable.data, "");
System.out.println("\nQualityScore Table:");
nestedTable = dataManager.getCollapsedTable(1);
printNestedHashMap(nestedTable.data, "");
System.out.println("\nCovariates Table:");
nestedTable = dataManager.getCollapsedTable(2);
printNestedHashMap(nestedTable.data, "");
nestedTable = dataManager.getCollapsedTable(3);
printNestedHashMap(nestedTable.data, "");
int i = 0;
System.out.println("\nV2 Table\n");
for (Map.Entry<BQSRKeyManager, Map<Long, RecalDatum>> mapEntry : keysAndTablesMap.entrySet()) {
BQSRKeyManager keyManager = mapEntry.getKey();
Map<Long, RecalDatum> table = mapEntry.getValue();
switch(i++) {
case 0 :
System.out.println("ReadGroup Table:");
break;
case 1 :
System.out.println("QualityScore Table:");
break;
case 2 :
System.out.println("Covariates Table:");
break;
}
for (Map.Entry<Long, RecalDatum> entry : table.entrySet()) {
Long key = entry.getKey();
RecalDatum datum = entry.getValue();
List<Object> keySet = keyManager.keySetFrom(key);
System.out.println(String.format("%s => %s", Utils.join(",", keySet), datum) + "," + datum.getEstimatedQReported());
}
System.out.println();
}
}
private static void printNestedHashMap(Map table, String output) {
for (Object key : table.keySet()) {
String ret;

103
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java
View File

@ -56,18 +56,23 @@ public class VariantContextTestProvider {
final private static boolean ENABLE_VARARRAY_TESTS = true;
final private static boolean ENABLE_PLOIDY_TESTS = true;
final private static boolean ENABLE_PL_TESTS = true;
final private static boolean ENABLE_SYMBOLIC_ALLELE_TESTS = false;
final private static boolean ENABLE_SOURCE_VCF_TESTS = true;
final private static boolean ENABLE_VARIABLE_LENGTH_GENOTYPE_STRING_TESTS = true;
final private static List<Integer> TWENTY_INTS = Arrays.asList(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20);
private static VCFHeader syntheticHeader;
final static List<VariantContextTestData> TEST_DATAs = new ArrayList<VariantContextTestData>();
private static VariantContext ROOT;
private final static List<File> testSourceVCFs = Arrays.asList(
new File(BaseTest.privateTestDir + "ILLUMINA.wex.broad_phase2_baseline.20111114.both.exome.genotypes.1000.vcf"),
new File(BaseTest.privateTestDir + "ex2.vcf"),
new File(BaseTest.privateTestDir + "dbsnp_135.b37.1000.vcf")
);
private final static List<File> testSourceVCFs = new ArrayList<File>();
static {
testSourceVCFs.add(new File(BaseTest.privateTestDir + "ILLUMINA.wex.broad_phase2_baseline.20111114.both.exome.genotypes.1000.vcf"));
testSourceVCFs.add(new File(BaseTest.privateTestDir + "ex2.vcf"));
testSourceVCFs.add(new File(BaseTest.privateTestDir + "dbsnp_135.b37.1000.vcf"));
if ( ENABLE_SYMBOLIC_ALLELE_TESTS )
testSourceVCFs.add(new File(BaseTest.privateTestDir + "diagnosis_targets_testfile.vcf"));
}
public abstract static class VariantContextIOTest {
public String toString() {
@ -245,7 +250,7 @@ public class VariantContextTestProvider {
add(builder().attribute("INT3", Arrays.asList(1000, 2000, 3000)));
add(builder().attribute("INT3", Arrays.asList(100000, 200000, 300000)));
add(builder().attribute("INT3", null));
add(builder().attribute("INT20", Arrays.asList(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20)));
add(builder().attribute("INT20", TWENTY_INTS));
add(builder().attribute("FLOAT1", 1.0));
add(builder().attribute("FLOAT1", 100.0));
@ -449,6 +454,11 @@ public class VariantContextTestProvider {
attr("g1", ref, "INT3", 1, 2, 3),
attr("g2", ref, "INT3"));
addGenotypeTests(site,
attr("g1", ref, "INT20", TWENTY_INTS),
attr("g2", ref, "INT20", TWENTY_INTS));
if (ENABLE_VARARRAY_TESTS) {
addGenotypeTests(site,
attr("g1", ref, "INT.VAR", 1, 2, 3),
@ -693,20 +703,23 @@ public class VariantContextTestProvider {
* @param expected
*/
public static void assertEquals( final VariantContext actual, final VariantContext expected ) {
Assert.assertNotNull(actual);
Assert.assertEquals(actual.getChr(), expected.getChr());
Assert.assertEquals(actual.getStart(), expected.getStart());
Assert.assertEquals(actual.getEnd(), expected.getEnd());
Assert.assertEquals(actual.getID(), expected.getID());
Assert.assertEquals(actual.getAlleles(), expected.getAlleles());
Assert.assertNotNull(actual, "VariantContext expected not null");
Assert.assertEquals(actual.getChr(), expected.getChr(), "chr");
Assert.assertEquals(actual.getStart(), expected.getStart(), "start");
Assert.assertEquals(actual.getEnd(), expected.getEnd(), "end");
Assert.assertEquals(actual.getID(), expected.getID(), "id");
Assert.assertEquals(actual.getAlleles(), expected.getAlleles(), "alleles");
assertAttributesEquals(actual.getAttributes(), expected.getAttributes());
Assert.assertEquals(actual.getFilters(), expected.getFilters());
Assert.assertEquals(actual.getFilters(), expected.getFilters(), "filters");
BaseTest.assertEqualsDoubleSmart(actual.getPhredScaledQual(), expected.getPhredScaledQual());
Assert.assertEquals(actual.hasGenotypes(), expected.hasGenotypes());
Assert.assertEquals(actual.hasGenotypes(), expected.hasGenotypes(), "hasGenotypes");
if ( expected.hasGenotypes() ) {
Assert.assertEquals(actual.getSampleNames(), expected.getSampleNames());
final Set<String> actualSampleSet = new HashSet<String>(actual.getSampleNames());
final Set<String> expectedSampleSet = new HashSet<String>(expected.getSampleNames());
Assert.assertTrue(actualSampleSet.equals(expectedSampleSet), "sample names"); // note this is necessary due to testng bug for set comps
Assert.assertEquals(actual.getSampleNamesOrderedByName(), expected.getSampleNamesOrderedByName(), "sample names");
final Set<String> samples = expected.getSampleNames();
for ( final String sample : samples ) {
assertEquals(actual.getGenotype(sample), expected.getGenotype(sample));
@ -715,33 +728,33 @@ public class VariantContextTestProvider {
}
public static void assertEquals(final Genotype actual, final Genotype expected) {
Assert.assertEquals(actual.getSampleName(), expected.getSampleName());
Assert.assertEquals(actual.getAlleles(), expected.getAlleles());
Assert.assertEquals(actual.getGenotypeString(), expected.getGenotypeString());
Assert.assertEquals(actual.getType(), expected.getType());
Assert.assertEquals(actual.getSampleName(), expected.getSampleName(), "Genotype names");
Assert.assertEquals(actual.getAlleles(), expected.getAlleles(), "Genotype alleles");
Assert.assertEquals(actual.getGenotypeString(), expected.getGenotypeString(), "Genotype string");
Assert.assertEquals(actual.getType(), expected.getType(), "Genotype type");
// filters are the same
Assert.assertEquals(actual.getFilters(), expected.getFilters());
Assert.assertEquals(actual.isFiltered(), expected.isFiltered());
Assert.assertEquals(actual.getFilters(), expected.getFilters(), "Genotype fields");
Assert.assertEquals(actual.isFiltered(), expected.isFiltered(), "Genotype isFiltered");
// inline attributes
Assert.assertEquals(actual.getDP(), expected.getDP());
Assert.assertEquals(actual.getAD(), expected.getAD());
Assert.assertEquals(actual.getGQ(), expected.getGQ());
Assert.assertEquals(actual.hasPL(), expected.hasPL());
Assert.assertEquals(actual.hasAD(), expected.hasAD());
Assert.assertEquals(actual.hasGQ(), expected.hasGQ());
Assert.assertEquals(actual.hasDP(), expected.hasDP());
Assert.assertEquals(actual.getDP(), expected.getDP(), "Genotype dp");
Assert.assertEquals(actual.getAD(), expected.getAD(), "Genotype ad");
Assert.assertEquals(actual.getGQ(), expected.getGQ(), "Genotype gq");
Assert.assertEquals(actual.hasPL(), expected.hasPL(), "Genotype hasPL");
Assert.assertEquals(actual.hasAD(), expected.hasAD(), "Genotype hasAD");
Assert.assertEquals(actual.hasGQ(), expected.hasGQ(), "Genotype hasGQ");
Assert.assertEquals(actual.hasDP(), expected.hasDP(), "Genotype hasDP");
Assert.assertEquals(actual.hasLikelihoods(), expected.hasLikelihoods());
Assert.assertEquals(actual.getLikelihoodsString(), expected.getLikelihoodsString());
Assert.assertEquals(actual.getLikelihoods(), expected.getLikelihoods());
Assert.assertEquals(actual.getPL(), expected.getPL());
Assert.assertEquals(actual.hasLikelihoods(), expected.hasLikelihoods(), "Genotype haslikelihoods");
Assert.assertEquals(actual.getLikelihoodsString(), expected.getLikelihoodsString(), "Genotype getlikelihoodsString");
Assert.assertEquals(actual.getLikelihoods(), expected.getLikelihoods(), "Genotype getLikelihoods");
Assert.assertEquals(actual.getPL(), expected.getPL(), "Genotype getPL");
Assert.assertEquals(actual.getPhredScaledQual(), expected.getPhredScaledQual());
Assert.assertEquals(actual.getPhredScaledQual(), expected.getPhredScaledQual(), "Genotype phredScaledQual");
assertAttributesEquals(actual.getExtendedAttributes(), expected.getExtendedAttributes());
Assert.assertEquals(actual.isPhased(), expected.isPhased());
Assert.assertEquals(actual.getPloidy(), expected.getPloidy());
Assert.assertEquals(actual.isPhased(), expected.isPhased(), "Genotype isPhased");
Assert.assertEquals(actual.getPloidy(), expected.getPloidy(), "Genotype getPloidy");
}
private static void assertAttributesEquals(final Map<String, Object> actual, Map<String, Object> expected) {
@ -753,16 +766,16 @@ public class VariantContextTestProvider {
final Object expectedValue = expected.get(act.getKey());
if ( expectedValue instanceof List ) {
final List<Object> expectedList = (List<Object>)expectedValue;
Assert.assertTrue(actualValue instanceof List);
Assert.assertTrue(actualValue instanceof List, act.getKey() + " should be a list but isn't");
final List<Object> actualList = (List<Object>)actualValue;
Assert.assertEquals(actualList.size(), expectedList.size());
Assert.assertEquals(actualList.size(), expectedList.size(), act.getKey() + " size");
for ( int i = 0; i < expectedList.size(); i++ )
assertAttributesEquals(actualList.get(i), expectedList.get(i));
assertAttributeEquals(act.getKey(), actualList.get(i), expectedList.get(i));
} else
assertAttributesEquals(actualValue, expectedValue);
assertAttributeEquals(act.getKey(), actualValue, expectedValue);
} else {
// it's ok to have a binding in x -> null that's absent in y
Assert.assertNull(actualValue);
Assert.assertNull(actualValue, act.getKey() + " present in one but not in the other");
}
expectedKeys.remove(act.getKey());
}
@ -771,7 +784,7 @@ public class VariantContextTestProvider {
// and they must all be null
for ( final String missingExpected : expectedKeys ) {
final Object value = expected.get(missingExpected);
Assert.assertTrue(isMissing(value));
Assert.assertTrue(isMissing(value), "Attribute " + missingExpected + " missing in one but not in other" );
}
}
@ -788,12 +801,12 @@ public class VariantContextTestProvider {
return false;
}
private static void assertAttributesEquals(final Object actual, final Object expected) {
private static void assertAttributeEquals(final String key, final Object actual, final Object expected) {
if ( expected instanceof Double ) {
// must be very tolerant because doubles are being rounded to 2 sig figs
BaseTest.assertEqualsDoubleSmart(actual, (Double)expected, 1e-2);
} else
Assert.assertEquals(actual, expected);
Assert.assertEquals(actual, expected, "Attribute " + key);
}
public static void addComplexGenotypesTest() {
@ -863,14 +876,14 @@ public class VariantContextTestProvider {
}
public static void assertEquals(final VCFHeader actual, final VCFHeader expected) {
Assert.assertEquals(actual.getMetaData().size(), expected.getMetaData().size());
Assert.assertEquals(actual.getMetaData().size(), expected.getMetaData().size(), "No VCF header lines");
// for some reason set.equals() is returning false but all paired elements are .equals(). Perhaps compare to is busted?
//Assert.assertEquals(actual.getMetaData(), expected.getMetaData());
final List<VCFHeaderLine> actualLines = new ArrayList<VCFHeaderLine>(actual.getMetaData());
final List<VCFHeaderLine> expectedLines = new ArrayList<VCFHeaderLine>(expected.getMetaData());
for ( int i = 0; i < actualLines.size(); i++ ) {
Assert.assertEquals(actualLines.get(i), expectedLines.get(i));
Assert.assertEquals(actualLines.get(i), expectedLines.get(i), "VCF header lines");
}
}