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

This commit is contained in:
Guillermo del Angel 2011-09-07 13:21:26 -04:00
parent 5f22ef9a8c 3bcbfa6e06
commit 743bf7784c
7 changed files with 33 additions and 15 deletions
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1
public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
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@ -97,7 +97,6 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
if (!( walker instanceof TreeReducible ))
throw new IllegalArgumentException("The GATK can currently run in parallel only with TreeReducible walkers");
traversalEngine.startTimers();
ReduceTree reduceTree = new ReduceTree(this);
initializeWalker(walker);

2
public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
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@ -44,7 +44,6 @@ public class LinearMicroScheduler extends MicroScheduler {
* @param shardStrategy A strategy for sharding the data.
*/
public Object execute(Walker walker, ShardStrategy shardStrategy) {
traversalEngine.startTimers();
walker.initialize();
Accumulator accumulator = Accumulator.create(engine,walker);
@ -54,6 +53,7 @@ public class LinearMicroScheduler extends MicroScheduler {
if ( done || shard == null ) // we ran out of shards that aren't owned
break;
traversalEngine.startTimersIfNecessary();
if(shard.getShardType() == Shard.ShardType.LOCUS) {
LocusWalker lWalker = (LocusWalker)walker;
WindowMaker windowMaker = new WindowMaker(shard, engine.getGenomeLocParser(), getReadIterator(shard), shard.getGenomeLocs(), engine.getSampleMetadata());

1
public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
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@ -57,6 +57,7 @@ public class ShardTraverser implements Callable {
public Object call() {
try {
traversalEngine.startTimersIfNecessary();
long startTime = System.currentTimeMillis();
Object accumulator = walker.reduceInit();

19
public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
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@ -115,12 +115,13 @@ public abstract class TraversalEngine<M,T,WalkerType extends Walker<M,T>,Provide
LinkedList<ProcessingHistory> history = new LinkedList<ProcessingHistory>();
/** We use the SimpleTimer to time our run */
private SimpleTimer timer = new SimpleTimer("Traversal");
private SimpleTimer timer = null;
// How long can we go without printing some progress info?
private static final int PRINT_PROGRESS_CHECK_FREQUENCY_IN_CYCLES = 1000;
private int printProgressCheckCounter = 0;
private long lastProgressPrintTime = -1; // When was the last time we printed progress log?
private long MIN_ELAPSED_TIME_BEFORE_FIRST_PROGRESS = 120 * 1000; // in milliseconds
private long PROGRESS_PRINT_FREQUENCY = 10 * 1000; // in milliseconds
private final double TWO_HOURS_IN_SECONDS = 2.0 * 60.0 * 60.0;
private final double TWELVE_HOURS_IN_SECONDS = 12.0 * 60.0 * 60.0;
@ -209,11 +210,16 @@ public abstract class TraversalEngine<M,T,WalkerType extends Walker<M,T>,Provide
}
}
/**
* Should be called to indicate that we're going to process records and the timer should start ticking
* Should be called to indicate that we're going to process records and the timer should start ticking. This
* function should be called right before any traversal work is done, to avoid counting setup costs in the
* processing costs and inflating the estimated runtime.
*/
public void startTimers() {
timer.start();
lastProgressPrintTime = timer.currentTime();
public void startTimersIfNecessary() {
if ( timer == null ) {
timer = new SimpleTimer("Traversal");
timer.start();
lastProgressPrintTime = timer.currentTime();
}
}
/**
@ -224,7 +230,8 @@ public abstract class TraversalEngine<M,T,WalkerType extends Walker<M,T>,Provide
* @return true if the maximum interval (in millisecs) has passed since the last printing
*/
private boolean maxElapsedIntervalForPrinting(final long curTime, long lastPrintTime, long printFreq) {
return (curTime - lastPrintTime) > printFreq;
long elapsed = curTime - lastPrintTime;
return elapsed > printFreq && elapsed > MIN_ELAPSED_TIME_BEFORE_FIRST_PROGRESS;
}
/**

19
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
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@ -15,6 +15,7 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.gatk.walkers.Window;
import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator;
import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.JexlExpression;
import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.VariantStratifier;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.*;
import org.broadinstitute.sting.gatk.walkers.variantrecalibration.Tranche;
@ -24,6 +25,7 @@ import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
@ -224,12 +226,6 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
}
sampleNamesForStratification.add(ALL_SAMPLE_NAME);
// Initialize select expressions
for (VariantContextUtils.JexlVCMatchExp jexl : VariantContextUtils.initializeMatchExps(SELECT_NAMES, SELECT_EXPS)) {
SortableJexlVCMatchExp sjexl = new SortableJexlVCMatchExp(jexl.name, jexl.exp);
jexlExpressions.add(sjexl);
}
// Add select expressions for anything in the tranches file
if ( TRANCHE_FILENAME != null ) {
// we are going to build a few select names automatically from the tranches file
@ -240,16 +236,27 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
}
}
// Initialize select expressions
for (VariantContextUtils.JexlVCMatchExp jexl : VariantContextUtils.initializeMatchExps(SELECT_NAMES, SELECT_EXPS)) {
SortableJexlVCMatchExp sjexl = new SortableJexlVCMatchExp(jexl.name, jexl.exp);
jexlExpressions.add(sjexl);
}
// Initialize the set of stratifications and evaluations to use
stratificationObjects = variantEvalUtils.initializeStratificationObjects(this, NO_STANDARD_STRATIFICATIONS, STRATIFICATIONS_TO_USE);
Set<Class<? extends VariantEvaluator>> evaluationObjects = variantEvalUtils.initializeEvaluationObjects(NO_STANDARD_MODULES, MODULES_TO_USE);
boolean usingJEXL = false;
for ( VariantStratifier vs : getStratificationObjects() ) {
if ( vs.getClass().getSimpleName().equals("Filter") )
byFilterIsEnabled = true;
else if ( vs.getClass().getSimpleName().equals("Sample") )
perSampleIsEnabled = true;
usingJEXL = usingJEXL || vs.getClass().equals(JexlExpression.class);
}
if ( TRANCHE_FILENAME != null && ! usingJEXL )
throw new UserException.BadArgumentValue("tf", "Requires the JexlExpression ST to enabled");
// Initialize the evaluation contexts
evaluationContexts = variantEvalUtils.initializeEvaluationContexts(stratificationObjects, evaluationObjects, null, null);

2
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
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@ -277,7 +277,7 @@ public class VariantEvalUtils {
* @return a new VariantContext with just the requested samples
*/
public VariantContext getSubsetOfVariantContext(VariantContext vc, Collection<String> sampleNames) {
VariantContext vcsub = vc.subContextFromGenotypes(vc.getGenotypes(sampleNames).values(), vc.getAlleles());
VariantContext vcsub = vc.subContextFromGenotypes(vc.getGenotypes(sampleNames).values());
HashMap<String, Object> newAts = new HashMap<String, Object>(vcsub.getAttributes());

4
public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
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@ -63,6 +63,10 @@ public class ReadClipper {
if (start < 0 || stop > read.getReadLength() - 1)
throw new ReviewedStingException("Trying to clip before the start or after the end of a read");
// TODO add requires statement/check in the Hardclip function
if ( start > stop )
stop = ReadUtils.getReadCoordinateForReferenceCoordinate(read, ReadUtils.getRefCoordSoftUnclippedEnd(read));
//System.out.println("Clipping start/stop: " + start + "/" + stop);
this.addOp(new ClippingOp(start, stop));
SAMRecord clippedRead = clipRead(ClippingRepresentation.HARDCLIP_BASES);