diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java b/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java index 59fb4aa9e..3b9e35311 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java +++ b/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java @@ -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); diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java b/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java index 65ff27497..09ab4bd44 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java +++ b/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java @@ -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()); diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java b/public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java index 6136bd68d..2b6488ada 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java +++ b/public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java @@ -57,6 +57,7 @@ public class ShardTraverser implements Callable { public Object call() { try { + traversalEngine.startTimersIfNecessary(); long startTime = System.currentTimeMillis(); Object accumulator = walker.reduceInit(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java index 89a179d0e..27fd173cb 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java @@ -115,12 +115,13 @@ public abstract class TraversalEngine,Provide LinkedList history = new LinkedList(); /** 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,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,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; } /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java index fe4729bdc..65e3d3e5a 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java @@ -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 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 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> 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); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java index 92e7c6554..3cc039141 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java @@ -277,7 +277,7 @@ public class VariantEvalUtils { * @return a new VariantContext with just the requested samples */ public VariantContext getSubsetOfVariantContext(VariantContext vc, Collection sampleNames) { - VariantContext vcsub = vc.subContextFromGenotypes(vc.getGenotypes(sampleNames).values(), vc.getAlleles()); + VariantContext vcsub = vc.subContextFromGenotypes(vc.getGenotypes(sampleNames).values()); HashMap newAts = new HashMap(vcsub.getAttributes()); diff --git a/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java b/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java index be045309a..26c25850a 100644 --- a/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java +++ b/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java @@ -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);