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Added command-line flag to disble FPGA 

Completed integration with FPGA driver
This commit is contained in:
sathibault 2013-06-03 07:30:32 -05:00
parent 195f0c3e98
commit de2a2a4cc7
4 changed files with 159 additions and 26 deletions
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6
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
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@ -315,6 +315,10 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
@Argument(fullName="allowCyclesInKmerGraphToGeneratePaths", shortName="allowCyclesInKmerGraphToGeneratePaths", doc="If specified, we will allow cycles in the kmer graphs to generate paths with multiple copies of the path sequenece rather than just the shortest paths", required = false)
protected boolean allowCyclesInKmerGraphToGeneratePaths = false;
@Hidden
@Argument(fullName="noFpga", shortName="noFpga", doc="If provided, disables the use of the FPGA HMM implementation", required = false)
protected boolean noFpga = false;
// the UG engines
private UnifiedGenotyperEngine UG_engine = null;
@ -435,7 +439,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
if ( graphWriter != null ) assemblyEngine.setGraphWriter(graphWriter);
if ( useLowQualityBasesForAssembly ) assemblyEngine.setMinBaseQualityToUseInAssembly((byte)1);
likelihoodCalculationEngine = new LikelihoodCalculationEngine( (byte)gcpHMM, DEBUG, pairHMM );
likelihoodCalculationEngine = new LikelihoodCalculationEngine( (byte)gcpHMM, DEBUG, pairHMM, noFpga );
final MergeVariantsAcrossHaplotypes variantMerger = mergeVariantsViaLD ? new LDMerger(DEBUG, 10, 1) : new MergeVariantsAcrossHaplotypes();

13
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
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@ -80,7 +80,11 @@ public class LikelihoodCalculationEngine {
*/
private final double EXPECTED_ERROR_RATE_PER_BASE = 0.02;
public LikelihoodCalculationEngine( final byte constantGCP, final boolean debug, final PairHMM.HMM_IMPLEMENTATION hmmType ) {
public LikelihoodCalculationEngine( final byte constantGCP, final boolean debug, final PairHMM.HMM_IMPLEMENTATION hmmType) {
this(constantGCP, debug, hmmType, false);
}
public LikelihoodCalculationEngine( final byte constantGCP, final boolean debug, final PairHMM.HMM_IMPLEMENTATION hmmType, final boolean noFpga) {
switch (hmmType) {
case EXACT:
@ -90,7 +94,7 @@ public class LikelihoodCalculationEngine {
pairHMM = new Log10PairHMM(false);
break;
case LOGLESS_CACHING:
if (CnyPairHMM.isAvailable())
if (!noFpga && CnyPairHMM.isAvailable())
pairHMM = new CnyPairHMM();
else
pairHMM = new LoglessPairHMM();
@ -191,16 +195,17 @@ public class LikelihoodCalculationEngine {
final boolean isFirstHaplotype = jjj == 0;
final double log10l = pairHMM.computeReadLikelihoodGivenHaplotypeLog10(haplotype.getBases(),
read.getReadBases(), readQuals, readInsQuals, readDelQuals, overallGCP, isFirstHaplotype);
System.err.println(Integer.toString(jjj) + ": " + Double.toString(log10l));
perReadAlleleLikelihoodMap.add(read, alleleVersions.get(haplotype), log10l);
}
}
}
if ( batchPairHMM != null ) {
for( final GATKSAMRecord read : batchedReads ) {
final double[] likelihoods = batchPairHMM.batchResult();
final double[] likelihoods = batchPairHMM.batchGetResult();
for( int jjj = 0; jjj < numHaplotypes; jjj++ ) {
final Haplotype haplotype = haplotypes.get(jjj);
System.err.println(Integer.toString(jjj) + ": " + Double.toString(likelihoods[jjj]));
perReadAlleleLikelihoodMap.add(read, alleleVersions.get(haplotype), likelihoods[jjj]);
}
}

164
protected/java/src/org/broadinstitute/sting/utils/pairhmm/CnyPairHMM.java
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@ -1,33 +1,91 @@
package org.broadinstitute.sting.utils.pairhmm;
import java.io.File;
import java.util.*;
import java.lang.reflect.*;
import org.broadinstitute.sting.utils.haplotype.Haplotype;
public final class CnyPairHMM extends PairHMM implements BatchPairHMM {
private static class HmmInput {
public List<Haplotype> haplotypes;
public byte[] readBases;
public byte[] readQuals;
public byte[] insertionGOP;
public byte[] deletionGOP;
public byte[] overallGCP;
public List<Haplotype> haplotypes;
};
private static class ResultQueue {
private int offset;
private List<double[]> batchResults;
public ResultQueue() {
batchResults = new LinkedList<double[]>();
offset = 0;
}
public void push(double[] results) {
batchResults.add(results);
}
public double pop() {
double[] results = batchResults.get(0);
double top = results[offset++];
if (offset == results.length) {
batchResults.remove(0);
offset = 0;
}
return top;
}
}
final static String libPath = "/opt/convey/personalities/32100.1.1.1.0";
final static String libName = "gmvhdl_gatk_hmm";
private static boolean loaded = false;
private List<HmmInput> pending = new LinkedList<HmmInput>();
private List<HmmInput> batchRequests = new LinkedList<HmmInput>();
private ResultQueue resultQueue = new ResultQueue();
static public boolean isAvailable() {
return false;
if (!loaded) {
File library = new File(libPath + "/lib" + libName + ".so");
return library.exists();
}
return true;
}
private native void initFpga();
private native int dequeueRequirement(int reflen, int readlen);
private native int enqueue(byte[] haplotypeBases,
byte[] readBases,
byte[] readQuals,
byte[] insertionGOP,
byte[] deletionGOP,
byte[] overallGCP,
int hapStartIndex,
boolean recacheReadValues);
private native int flushQueue();
private native int dequeue(double[] results);
private native double softHmm(byte[] haplotypeBases,
byte[] readBases,
byte[] readQuals,
byte[] insertionGOP,
byte[] deletionGOP,
byte[] overallGCP,
int hapStartIndex,
boolean recacheReadValues);
public native void reportStats();
public void initialize( final int READ_MAX_LENGTH, final int HAPLOTYPE_MAX_LENGTH ) {
if (!loaded) {
// System.loadLibrary("gmvhdl_gatk_hmm");
// initFpga();
addLibraryPath(libPath);
System.loadLibrary(libName);
initFpga();
loaded = true;
System.out.println("FPGA HMM Initialized");
}
System.out.println("FPGA HMM Initialized");
}
public void batchAdd(final List<Haplotype> haplotypes,
@ -36,21 +94,44 @@ public final class CnyPairHMM extends PairHMM implements BatchPairHMM {
final byte[] insertionGOP,
final byte[] deletionGOP,
final byte[] overallGCP) {
HmmInput test=new HmmInput();
test.haplotypes=haplotypes;
test.readBases=readBases;
test.readQuals=readQuals;
test.insertionGOP=insertionGOP;
test.deletionGOP=deletionGOP;
test.overallGCP=overallGCP;
pending.add(test);
final int numHaplotypes = haplotypes.size();
HmmInput test = new HmmInput();
test.readBases = readBases;
test.readQuals = readQuals;
test.insertionGOP = insertionGOP;
test.deletionGOP = deletionGOP;
test.overallGCP = overallGCP;
test.haplotypes = haplotypes;
batchRequests.add(test);
for (int jjj = 0; jjj < numHaplotypes; jjj++) {
final boolean recacheReadValues = (jjj == 0);
final Haplotype haplotype = haplotypes.get(jjj);
enqueuePrepare(haplotype.getBases(), readBases);
if (enqueue(haplotype.getBases(), readBases, readQuals, insertionGOP, deletionGOP, overallGCP, 0, recacheReadValues) == 0)
throw new RuntimeException("FPGA queue overflow in batchAdd");
}
}
public double[] batchResult() {
HmmInput test=pending.remove(0);
double[] results=new double[test.haplotypes.size()];
for (int i=0; i<results.length; i++) {
results[i]=0.0;
public double[] batchGetResult() {
double[] results;
int n = flushQueue();
if (n > 0) {
results = new double[n];
if (dequeue(results) != n)
System.out.println("queue underflow in enqueuePrepare");
resultQueue.push(results);
}
final HmmInput test = batchRequests.remove(0);
final int numHaplotypes = test.haplotypes.size();
results = new double[numHaplotypes];
for (int jjj = 0; jjj < numHaplotypes; jjj++) {
results[jjj] = resultQueue.pop();
if (results[jjj]<-60.0) {
final Haplotype haplotype = test.haplotypes.get(jjj);
results[jjj]=softHmm(haplotype.getBases(), test.readBases, test.readQuals, test.insertionGOP, test.deletionGOP, test.overallGCP, 0, true);
}
}
return results;
}
@ -64,5 +145,48 @@ public final class CnyPairHMM extends PairHMM implements BatchPairHMM {
final int hapStartIndex,
final boolean recacheReadValues ) {
return 0.0;
}
}
private void enqueuePrepare(byte[] haplotypeBases, byte[] readBases) {
double[] results = null;
int n = dequeueRequirement(haplotypeBases.length, readBases.length);
if (n>0) {
results = new double[n];
if (dequeue(results)!=n)
System.out.println("queue underflow in enqueuePrepare");
} else if (n<0) {
n = flushQueue();
if (n > 0) {
results = new double[n];
if (dequeue(results) != n)
System.out.println("queue underflow in enqueuePrepare");
}
}
if (results != null)
resultQueue.push(results);
}
public static void addLibraryPath(String pathToAdd) {
try {
final Field usrPathsField = ClassLoader.class.getDeclaredField("usr_paths");
usrPathsField.setAccessible(true);
//get array of paths
final String[] paths = (String[])usrPathsField.get(null);
//check if the path to add is already present
for(String path : paths) {
if(path.equals(pathToAdd)) {
return;
}
}
//add the new path
final String[] newPaths = Arrays.copyOf(paths, paths.length + 1);
newPaths[newPaths.length-1] = pathToAdd;
usrPathsField.set(null, newPaths);
} catch (Exception ex) {
}
}
}

2
public/java/src/org/broadinstitute/sting/utils/pairhmm/BatchPairHMM.java
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@ -12,5 +12,5 @@ public interface BatchPairHMM {
final byte[] deletionGOP,
final byte[] overallGCP);
public double[] batchResult();
public double[] batchGetResult();
}