Merge branch 'master' of ssh://gsa3.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
This commit is contained in:
Menachem Fromer
commit
5070304ef4
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@ -37,12 +37,6 @@ import java.util.*;
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public class AlleleBiasedDownsamplingUtils {
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private static final ArrayList<PileupElement>[] alleleStratifiedElements = new ArrayList[4];
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static {
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for ( int i = 0; i < 4; i++ )
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alleleStratifiedElements[i] = new ArrayList<PileupElement>();
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}
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/**
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* Computes an allele biased version of the given pileup
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*
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@ -51,13 +45,17 @@ public class AlleleBiasedDownsamplingUtils {
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* @param log logging output
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* @return allele biased pileup
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*/
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public synchronized static ReadBackedPileup createAlleleBiasedBasePileup(final ReadBackedPileup pileup, final double downsamplingFraction, final PrintStream log) {
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public static ReadBackedPileup createAlleleBiasedBasePileup(final ReadBackedPileup pileup, final double downsamplingFraction, final PrintStream log) {
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// special case removal of all or no reads
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if ( downsamplingFraction <= 0.0 )
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return pileup;
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if ( downsamplingFraction >= 1.0 )
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return new ReadBackedPileupImpl(pileup.getLocation(), new ArrayList<PileupElement>());
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final ArrayList<PileupElement>[] alleleStratifiedElements = new ArrayList[4];
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for ( int i = 0; i < 4; i++ )
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alleleStratifiedElements[i] = new ArrayList<PileupElement>();
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// start by stratifying the reads by the alleles they represent at this position
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for( final PileupElement pe : pileup ) {
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// abort if we have a reduced read - we do not want to remove it!
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@ -122,12 +122,12 @@ public class BQSRIntegrationTest extends WalkerTest {
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public Object[][] createPRTestData() {
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List<Object[]> tests = new ArrayList<Object[]>();
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tests.add(new Object[]{1, new PRTest(" -qq -1", "a1d87da5dcbde35170d6ba6bc3ee2812")});
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tests.add(new Object[]{1, new PRTest(" -qq 6", "a0fecae6d0e5ab9917862fa306186d10")});
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tests.add(new Object[]{1, new PRTest(" -qq -1", "5226c06237b213b9e9b25a32ed92d09a")});
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tests.add(new Object[]{1, new PRTest(" -qq 6", "b592a5c62b952a012e18adb898ea9c33")});
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tests.add(new Object[]{1, new PRTest(" -DIQ", "8977bea0c57b808e65e9505eb648cdf7")});
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for ( final int nct : Arrays.asList(1, 2, 4) ) {
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tests.add(new Object[]{nct, new PRTest("", "d1bbb4ce6aa93e866f106f8b11d888ed")});
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tests.add(new Object[]{nct, new PRTest("", "ab2f209ab98ad3432e208cbd524a4c4a")});
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}
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return tests.toArray(new Object[][]{});
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@ -406,7 +406,7 @@ public abstract class ArgumentTypeDescriptor {
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else
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throw new UserException.CommandLineException(
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String.format("Failed to parse value %s for argument %s. Message: %s",
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value.asString(), fieldName, e.getMessage()));
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value, fieldName, e.getMessage()));
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}
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}
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}
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@ -64,6 +64,7 @@ import org.broadinstitute.sting.utils.threading.ThreadEfficiencyMonitor;
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import java.io.File;
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import java.util.*;
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import java.util.concurrent.TimeUnit;
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/**
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* A GenomeAnalysisEngine that runs a specified walker.
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@ -73,6 +74,7 @@ public class GenomeAnalysisEngine {
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* our log, which we want to capture anything from this class
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*/
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private static Logger logger = Logger.getLogger(GenomeAnalysisEngine.class);
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public static final long NO_RUNTIME_LIMIT = -1;
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/**
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* The GATK command-line argument parsing code.
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@ -1090,6 +1092,33 @@ public class GenomeAnalysisEngine {
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public String createApproximateCommandLineArgumentString(Object... argumentProviders) {
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return CommandLineUtils.createApproximateCommandLineArgumentString(parsingEngine,argumentProviders);
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}
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/**
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* Does the current runtime in unit exceed the runtime limit, if one has been provided?
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*
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* @param runtime the runtime of this GATK instance in minutes
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* @param unit the time unit of runtime
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* @return false if not limit was requested or if runtime <= the limit, true otherwise
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*/
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public boolean exceedsRuntimeLimit(final long runtime, final TimeUnit unit) {
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if ( runtime < 0 ) throw new IllegalArgumentException("runtime must be >= 0 but got " + runtime);
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if ( getArguments().maxRuntime == NO_RUNTIME_LIMIT )
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return false;
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else {
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final long actualRuntimeNano = TimeUnit.NANOSECONDS.convert(runtime, unit);
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final long maxRuntimeNano = getRuntimeLimitInNanoseconds();
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return actualRuntimeNano > maxRuntimeNano;
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}
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}
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/**
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* @return the runtime limit in nanoseconds, or -1 if no limit was specified
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*/
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public long getRuntimeLimitInNanoseconds() {
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if ( getArguments().maxRuntime == NO_RUNTIME_LIMIT )
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return -1;
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else
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return TimeUnit.NANOSECONDS.convert(getArguments().maxRuntime, getArguments().maxRuntimeUnits);
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}
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}
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@ -31,6 +31,7 @@ import org.broadinstitute.sting.commandline.Argument;
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import org.broadinstitute.sting.commandline.Hidden;
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import org.broadinstitute.sting.commandline.Input;
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import org.broadinstitute.sting.commandline.IntervalBinding;
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import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
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import org.broadinstitute.sting.gatk.downsampling.DownsampleType;
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import org.broadinstitute.sting.gatk.downsampling.DownsamplingMethod;
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import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
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@ -44,6 +45,7 @@ import java.io.File;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.List;
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import java.util.concurrent.TimeUnit;
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/**
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* @author aaron
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@ -91,7 +93,7 @@ public class GATKArgumentCollection {
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// --------------------------------------------------------------------------------------------------------------
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//
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// XXX
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// General features
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//
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// --------------------------------------------------------------------------------------------------------------
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@ -143,6 +145,12 @@ public class GATKArgumentCollection {
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@Argument(fullName = "disableRandomization",doc="Completely eliminates randomization from nondeterministic methods. To be used mostly in the testing framework where dynamic parallelism can result in differing numbers of calls to the generator.")
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public boolean disableRandomization = false;
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@Argument(fullName = "maxRuntime", shortName = "maxRuntime", doc="If provided, that GATK will stop execution cleanly as soon after maxRuntime has been exceeded, truncating the run but not exiting with a failure. By default the value is interpreted in minutes, but this can be changed by maxRuntimeUnits", required = false)
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public long maxRuntime = GenomeAnalysisEngine.NO_RUNTIME_LIMIT;
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@Argument(fullName = "maxRuntimeUnits", shortName = "maxRuntimeUnits", doc="The TimeUnit for maxRuntime", required = false)
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public TimeUnit maxRuntimeUnits = TimeUnit.MINUTES;
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// --------------------------------------------------------------------------------------------------------------
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//
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// Downsampling Arguments
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@ -123,7 +123,7 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
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final ReduceTree reduceTree = new ReduceTree(this);
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initializeWalker(walker);
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while (isShardTraversePending() || isTreeReducePending()) {
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while (! abortExecution() && (isShardTraversePending() || isTreeReducePending())) {
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// Check for errors during execution.
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errorTracker.throwErrorIfPending();
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@ -63,7 +63,7 @@ public class LinearMicroScheduler extends MicroScheduler {
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final TraversalEngine traversalEngine = borrowTraversalEngine(this);
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for (Shard shard : shardStrategy ) {
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if ( done || shard == null ) // we ran out of shards that aren't owned
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if ( abortExecution() || done || shard == null ) // we ran out of shards that aren't owned
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break;
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if(shard.getShardType() == Shard.ShardType.LOCUS) {
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@ -39,6 +39,7 @@ import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
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import org.broadinstitute.sting.gatk.resourcemanagement.ThreadAllocation;
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import org.broadinstitute.sting.gatk.traversals.*;
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import org.broadinstitute.sting.gatk.walkers.*;
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import org.broadinstitute.sting.utils.AutoFormattingTime;
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import org.broadinstitute.sting.utils.MathUtils;
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import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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@ -52,6 +53,7 @@ import javax.management.ObjectName;
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import java.io.File;
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import java.lang.management.ManagementFactory;
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import java.util.*;
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import java.util.concurrent.TimeUnit;
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/**
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@ -269,6 +271,26 @@ public abstract class MicroScheduler implements MicroSchedulerMBean {
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this.threadEfficiencyMonitor = threadEfficiencyMonitor;
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}
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/**
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* Should we stop all execution work and exit gracefully?
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*
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* Returns true in the case where some external signal or time limit has been received, indicating
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* that this GATK shouldn't continue executing. This isn't a kill signal, it is really a "shutdown
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* gracefully at the next opportunity" signal. Concrete implementations of the MicroScheduler
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* examine this value as often as reasonable and, if it returns true, stop what they are doing
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* at the next available opportunity, shutdown their resources, call notify done, and return.
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*
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* @return true if we should abort execution, or false otherwise
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*/
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protected boolean abortExecution() {
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final boolean abort = engine.exceedsRuntimeLimit(progressMeter.getRuntimeInNanoseconds(), TimeUnit.NANOSECONDS);
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if ( abort ) {
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final AutoFormattingTime aft = new AutoFormattingTime(TimeUnit.SECONDS.convert(engine.getRuntimeLimitInNanoseconds(), TimeUnit.NANOSECONDS), 1, 4);
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logger.info("Aborting execution (cleanly) because the runtime has exceeded the requested maximum " + aft);
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}
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return abort;
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}
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/**
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* Walks a walker over the given list of intervals.
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*
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@ -364,7 +364,7 @@ public class VariantContextAdaptors {
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long end = hapmap.getEnd();
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if ( deletionLength > 0 )
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end += deletionLength;
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end += (deletionLength - 1);
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VariantContext vc = new VariantContextBuilder(name, hapmap.getChr(), hapmap.getStart(), end, alleles).id(hapmap.getName()).genotypes(genotypes).make();
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return vc;
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}
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@ -438,8 +438,6 @@ public class SomaticIndelDetector extends ReadWalker<Integer,Integer> {
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location = getToolkit().getGenomeLocParser().createGenomeLoc(getToolkit().getSAMFileHeader().getSequence(0).getSequenceName(),1);
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normalSamples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeaders().get(0));
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try {
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// we already checked that bedOutput and output_file are not set simultaneously
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if ( bedOutput != null ) bedWriter = new FileWriter(bedOutput);
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@ -1152,8 +1150,9 @@ public class SomaticIndelDetector extends ReadWalker<Integer,Integer> {
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GenotypesContext genotypes = GenotypesContext.create();
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for ( String sample : normalSamples ) {
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final GenotypeBuilder gb = new GenotypeBuilder(sample);
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gb.attributes(call.makeStatsAttributes(null));
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GenotypeBuilder gb = new GenotypeBuilder(sample);
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gb=call.addStatsAttributes(gb);
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gb.alleles(! discard_event
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? alleles // we made a call - put actual het genotype here:
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: homref_alleles); // no call: genotype is ref/ref (but alleles still contain the alt if we observed anything at all)
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@ -1200,8 +1199,11 @@ public class SomaticIndelDetector extends ReadWalker<Integer,Integer> {
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if ( start == 0 )
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return;
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Map<String,Object> attrsNormal = nCall.makeStatsAttributes(null);
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Map<String,Object> attrsTumor = tCall.makeStatsAttributes(null);
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GenotypeBuilder nGB = new GenotypeBuilder();
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GenotypeBuilder tGB = new GenotypeBuilder();
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nCall.addStatsAttributes(nGB);
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tCall.addStatsAttributes(tGB);
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Map<String,Object> attrs = new HashMap();
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@ -1242,11 +1244,11 @@ public class SomaticIndelDetector extends ReadWalker<Integer,Integer> {
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GenotypesContext genotypes = GenotypesContext.create();
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for ( String sample : normalSamples ) {
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genotypes.add(GenotypeBuilder.create(sample, homRefN ? homRefAlleles : alleles, attrsNormal));
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genotypes.add(nGB.name(sample).alleles(homRefN ? homRefAlleles : alleles).make());
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}
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for ( String sample : tumorSamples ) {
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genotypes.add(GenotypeBuilder.create(sample, homRefT ? homRefAlleles : alleles, attrsTumor));
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genotypes.add(tGB.name(sample).alleles(homRefT ? homRefAlleles : alleles).make());
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}
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Set<String> filters = null;
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@ -1254,14 +1256,6 @@ public class SomaticIndelDetector extends ReadWalker<Integer,Integer> {
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filters = new HashSet<String>();
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filters.add("NoCall");
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}
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if ( nCall.getCoverage() < minNormalCoverage ) {
|
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if ( filters == null ) filters = new HashSet<String>();
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filters.add("NCov");
|
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}
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if ( tCall.getCoverage() < minCoverage ) {
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if ( filters == null ) filters = new HashSet<String>();
|
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filters.add("TCov");
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}
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VariantContext vc = new VariantContextBuilder("IGv2_Indel_call", refName, start, stop, alleles)
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.genotypes(genotypes).filters(filters).attributes(attrs).make();
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@ -1844,6 +1838,38 @@ public class SomaticIndelDetector extends ReadWalker<Integer,Integer> {
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VCFIndelAttributes.recordStrandCounts(strand_cons.first,strand_cons.second,strand_ref.first,strand_ref.second,attr);
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return attr;
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}
|
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|
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|
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/**
|
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* Adds alignment statistics directly into the genotype builder object.
|
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*
|
||||
* @param gb
|
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* @return
|
||||
*/
|
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public GenotypeBuilder addStatsAttributes(GenotypeBuilder gb) {
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if ( gb == null ) gb = new GenotypeBuilder();
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|
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gb = VCFIndelAttributes.recordDepth(getConsensusVariantCount(),getAllVariantCount(),getCoverage(),gb);
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gb = VCFIndelAttributes.recordAvMM(getAvConsensusMismatches(),getAvRefMismatches(),gb);
|
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gb = VCFIndelAttributes.recordAvMapQ(getAvConsensusMapq(),getAvRefMapq(),gb);
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gb = VCFIndelAttributes.recordNQSMMRate(getNQSConsensusMMRate(),getNQSRefMMRate(),gb);
|
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gb = VCFIndelAttributes.recordNQSAvQ(getNQSConsensusAvQual(),getNQSRefAvQual(),gb);
|
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|
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gb = VCFIndelAttributes.recordOffsetFromStart(from_start_median,from_start_mad,gb);
|
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|
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gb = VCFIndelAttributes.recordOffsetFromEnd(from_end_median,from_end_mad,gb);
|
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|
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PrimitivePair.Int strand_cons = getConsensusStrandCounts();
|
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PrimitivePair.Int strand_ref = getRefStrandCounts();
|
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|
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gb = VCFIndelAttributes.recordStrandCounts(strand_cons.first,strand_cons.second,strand_ref.first,strand_ref.second,gb);
|
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return gb;
|
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}
|
||||
|
||||
}
|
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|
||||
interface IndelListener {
|
||||
|
|
@ -2170,18 +2196,18 @@ class VCFIndelAttributes {
|
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public static Set<? extends VCFHeaderLine> getAttributeHeaderLines() {
|
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Set<VCFHeaderLine> lines = new HashSet<VCFHeaderLine>();
|
||||
|
||||
lines.add(new VCFFormatHeaderLine(ALLELIC_DEPTH_KEY, 2, VCFHeaderLineType.Integer, "# of reads supporting consensus indel/reference at the site"));
|
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lines.add(new VCFFormatHeaderLine(ALLELIC_DEPTH_KEY, 2, VCFHeaderLineType.Integer, "# of reads supporting consensus reference/indel at the site"));
|
||||
lines.add(new VCFFormatHeaderLine(DEPTH_TOTAL_KEY, 1, VCFHeaderLineType.Integer, "Total coverage at the site"));
|
||||
|
||||
lines.add(new VCFFormatHeaderLine(MAPQ_KEY, 2, VCFHeaderLineType.Float, "Average mapping qualities of consensus indel-supporting reads/reference-supporting reads"));
|
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lines.add(new VCFFormatHeaderLine(MAPQ_KEY, 2, VCFHeaderLineType.Float, "Average mapping qualities of ref-/consensus indel-supporting reads"));
|
||||
|
||||
lines.add(new VCFFormatHeaderLine(MM_KEY, 2, VCFHeaderLineType.Float, "Average # of mismatches per consensus indel-supporting read/per reference-supporting read"));
|
||||
lines.add(new VCFFormatHeaderLine(MM_KEY, 2, VCFHeaderLineType.Float, "Average # of mismatches per ref-/consensus indel-supporting read"));
|
||||
|
||||
lines.add(new VCFFormatHeaderLine(NQS_MMRATE_KEY, 2, VCFHeaderLineType.Float, "Within NQS window: fraction of mismatching bases in consensus indel-supporting reads/in reference-supporting reads"));
|
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lines.add(new VCFFormatHeaderLine(NQS_MMRATE_KEY, 2, VCFHeaderLineType.Float, "Within NQS window: fraction of mismatching bases in ref/consensus indel-supporting reads"));
|
||||
|
||||
lines.add(new VCFFormatHeaderLine(NQS_AVQ_KEY, 2, VCFHeaderLineType.Float, "Within NQS window: average quality of bases from consensus indel-supporting reads/from reference-supporting reads"));
|
||||
lines.add(new VCFFormatHeaderLine(NQS_AVQ_KEY, 2, VCFHeaderLineType.Float, "Within NQS window: average quality of bases in ref-/consensus indel-supporting reads"));
|
||||
|
||||
lines.add(new VCFFormatHeaderLine(STRAND_COUNT_KEY, 4, VCFHeaderLineType.Integer, "Strandness: counts of forward-/reverse-aligned indel-supporting reads / forward-/reverse-aligned reference supporting reads"));
|
||||
lines.add(new VCFFormatHeaderLine(STRAND_COUNT_KEY, 4, VCFHeaderLineType.Integer, "Strandness: counts of forward-/reverse-aligned reference and indel-supporting reads (FwdRef,RevRef,FwdIndel,RevIndel)"));
|
||||
|
||||
lines.add(new VCFFormatHeaderLine(RSTART_OFFSET_KEY, 2, VCFHeaderLineType.Integer, "Median/mad of indel offsets from the starts of the reads"));
|
||||
lines.add(new VCFFormatHeaderLine(REND_OFFSET_KEY, 2, VCFHeaderLineType.Integer, "Median/mad of indel offsets from the ends of the reads"));
|
||||
|
|
@ -2194,39 +2220,72 @@ class VCFIndelAttributes {
|
|||
return attrs;
|
||||
}
|
||||
|
||||
public static GenotypeBuilder recordStrandCounts(int cnt_cons_fwd, int cnt_cons_rev, int cnt_ref_fwd, int cnt_ref_rev,
|
||||
GenotypeBuilder gb) {
|
||||
return gb.attribute(STRAND_COUNT_KEY, new Integer[] {cnt_ref_fwd, cnt_ref_rev,cnt_cons_fwd, cnt_cons_rev } );
|
||||
}
|
||||
|
||||
public static Map<String,Object> recordDepth(int cnt_cons, int cnt_indel, int cnt_total, Map<String,Object> attrs) {
|
||||
attrs.put(ALLELIC_DEPTH_KEY, new Integer[] {cnt_cons, cnt_indel} );
|
||||
attrs.put(ALLELIC_DEPTH_KEY, new Integer[] {cnt_total-cnt_indel, cnt_cons} );
|
||||
attrs.put(DEPTH_TOTAL_KEY, cnt_total);
|
||||
return attrs;
|
||||
}
|
||||
|
||||
public static GenotypeBuilder recordDepth(int cnt_cons, int cnt_indel, int cnt_total, GenotypeBuilder gb) {
|
||||
return gb.AD(new int[] {cnt_total-cnt_indel,cnt_cons} ).DP(cnt_total);
|
||||
}
|
||||
|
||||
public static Map<String,Object> recordAvMapQ(double cons, double ref, Map<String,Object> attrs) {
|
||||
attrs.put(MAPQ_KEY, new Float[] {(float)cons, (float)ref} );
|
||||
attrs.put(MAPQ_KEY, new Float[] {(float)ref, (float)cons} );
|
||||
return attrs;
|
||||
}
|
||||
|
||||
public static GenotypeBuilder recordAvMapQ(double cons, double ref, GenotypeBuilder gb) {
|
||||
return gb.attribute(MAPQ_KEY,new float[] {(float)ref, (float)cons} );
|
||||
}
|
||||
|
||||
public static Map<String,Object> recordAvMM(double cons, double ref, Map<String,Object> attrs) {
|
||||
attrs.put(MM_KEY, new Float[] {(float)cons, (float)ref} );
|
||||
attrs.put(MM_KEY, new Float[] {(float)ref, (float)cons} );
|
||||
return attrs;
|
||||
}
|
||||
|
||||
public static GenotypeBuilder recordAvMM(double cons, double ref, GenotypeBuilder gb) {
|
||||
return gb.attribute(MM_KEY, new float[] {(float)ref, (float)cons} );
|
||||
}
|
||||
|
||||
public static Map<String,Object> recordNQSMMRate(double cons, double ref, Map<String,Object> attrs) {
|
||||
attrs.put(NQS_MMRATE_KEY, new Float[] {(float)cons, (float)ref} );
|
||||
attrs.put(NQS_MMRATE_KEY, new Float[] {(float)ref, (float)cons} );
|
||||
return attrs;
|
||||
}
|
||||
|
||||
public static GenotypeBuilder recordNQSMMRate(double cons, double ref, GenotypeBuilder gb) {
|
||||
return gb.attribute(NQS_MMRATE_KEY, new float[] {(float)ref, (float)cons} );
|
||||
}
|
||||
|
||||
public static Map<String,Object> recordNQSAvQ(double cons, double ref, Map<String,Object> attrs) {
|
||||
attrs.put(NQS_AVQ_KEY, new Float[] {(float)cons, (float)ref} );
|
||||
attrs.put(NQS_AVQ_KEY, new float[] {(float)ref, (float)cons} );
|
||||
return attrs;
|
||||
}
|
||||
|
||||
public static GenotypeBuilder recordNQSAvQ(double cons, double ref, GenotypeBuilder gb) {
|
||||
return gb.attribute(NQS_AVQ_KEY, new float[] {(float)ref, (float)cons} );
|
||||
}
|
||||
|
||||
public static Map<String,Object> recordOffsetFromStart(int median, int mad, Map<String,Object> attrs) {
|
||||
attrs.put(RSTART_OFFSET_KEY, new Integer[] {median, mad} );
|
||||
return attrs;
|
||||
}
|
||||
|
||||
public static GenotypeBuilder recordOffsetFromStart(int median, int mad, GenotypeBuilder gb) {
|
||||
return gb.attribute(RSTART_OFFSET_KEY, new int[] {median, mad} );
|
||||
}
|
||||
|
||||
public static Map<String,Object> recordOffsetFromEnd(int median, int mad, Map<String,Object> attrs) {
|
||||
attrs.put(REND_OFFSET_KEY, new Integer[] {median, mad} );
|
||||
return attrs;
|
||||
}
|
||||
|
||||
public static GenotypeBuilder recordOffsetFromEnd(int median, int mad, GenotypeBuilder gb) {
|
||||
return gb.attribute(REND_OFFSET_KEY, new int[] {median, mad} );
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -55,8 +55,8 @@ public class AssessReducedQuals extends LocusWalker<GenomeLoc, GenomeLoc> implem
|
|||
@Argument(fullName = "qual_epsilon", shortName = "epsilon", doc = "when |Quals_reduced_bam - Quals_original_bam| > epsilon*Quals_original_bam we output this interval", required = false)
|
||||
public int qual_epsilon = 0;
|
||||
|
||||
@Argument(fullName = "debugLevel", shortName = "debug", doc = "debug mode on")
|
||||
public int debugLevel = 0;
|
||||
@Argument(fullName = "debugLevel", shortName = "debug", doc = "debug mode on") // TODO -- best to make this optional
|
||||
public int debugLevel = 0; // TODO -- best to make this an enum or boolean
|
||||
|
||||
@Output
|
||||
protected PrintStream out;
|
||||
|
|
@ -114,7 +114,11 @@ public class AssessReducedQuals extends LocusWalker<GenomeLoc, GenomeLoc> implem
|
|||
return quals;
|
||||
}
|
||||
|
||||
// TODO -- arguments/variables should be final, not method declaration
|
||||
private final boolean isGoodRead(PileupElement p, List<String> tags){
|
||||
// TODO -- this isn't quite right. You don't need the tags here. Instead, you want to check whether the read itself (which
|
||||
// TODO -- you can get from the PileupElement) is a reduced read (not all reads from the reduced bam are reduced) and only
|
||||
// TODO -- for them do you want to ignore that min mapping quality cutoff (but you *do* still want the min base cutoff).
|
||||
return !p.isDeletion() && (tags.contains(reduced) || (tags.contains(original) && (int)p.getQual() >= 20 && p.getMappingQual() >= 20));
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -160,7 +160,7 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
|
|||
|
||||
Map<String, Allele> alleleMap = new HashMap<String, Allele>(2);
|
||||
alleleMap.put(RawHapMapFeature.DELETION, Allele.create(ref.getBase(), dbsnpVC.isSimpleInsertion()));
|
||||
alleleMap.put(RawHapMapFeature.INSERTION, Allele.create(ref.getBase() + ((RawHapMapFeature)record).getAlleles()[1], !dbsnpVC.isSimpleInsertion()));
|
||||
alleleMap.put(RawHapMapFeature.INSERTION, Allele.create((char)ref.getBase() + ((RawHapMapFeature)record).getAlleles()[1], !dbsnpVC.isSimpleInsertion()));
|
||||
hapmap.setActualAlleles(alleleMap);
|
||||
|
||||
// also, use the correct positioning for insertions
|
||||
|
|
|
|||
|
|
@ -4,12 +4,21 @@ package org.broadinstitute.sting.utils;
|
|||
* Simple utility class that makes it convenient to print unit adjusted times
|
||||
*/
|
||||
public class AutoFormattingTime {
|
||||
double timeInSeconds; // in Seconds
|
||||
int precision; // for format
|
||||
private final int width; // for format
|
||||
private final int precision; // for format
|
||||
|
||||
public AutoFormattingTime(double timeInSeconds, int precision) {
|
||||
double timeInSeconds; // in Seconds
|
||||
private final String formatString;
|
||||
|
||||
public AutoFormattingTime(double timeInSeconds, final int width, int precision) {
|
||||
this.width = width;
|
||||
this.timeInSeconds = timeInSeconds;
|
||||
this.precision = precision;
|
||||
this.formatString = "%" + width + "." + precision + "f %s";
|
||||
}
|
||||
|
||||
public AutoFormattingTime(double timeInSeconds, int precision) {
|
||||
this(timeInSeconds, 6, precision);
|
||||
}
|
||||
|
||||
public AutoFormattingTime(double timeInSeconds) {
|
||||
|
|
@ -20,6 +29,20 @@ public class AutoFormattingTime {
|
|||
return timeInSeconds;
|
||||
}
|
||||
|
||||
/**
|
||||
* @return the precision (a la format's %WIDTH.PERCISIONf)
|
||||
*/
|
||||
public int getWidth() {
|
||||
return width;
|
||||
}
|
||||
|
||||
/**
|
||||
* @return the precision (a la format's %WIDTH.PERCISIONf)
|
||||
*/
|
||||
public int getPrecision() {
|
||||
return precision;
|
||||
}
|
||||
|
||||
/**
|
||||
* Instead of 10000 s, returns 2.8 hours
|
||||
* @return
|
||||
|
|
@ -48,6 +71,6 @@ public class AutoFormattingTime {
|
|||
}
|
||||
}
|
||||
|
||||
return String.format("%6."+precision+"f %s", unitTime, unit);
|
||||
return String.format(formatString, unitTime, unit);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -159,6 +159,7 @@ public class VCFHeader {
|
|||
*/
|
||||
public void addMetaDataLine(VCFHeaderLine headerLine) {
|
||||
mMetaData.add(headerLine);
|
||||
loadMetaDataMaps();
|
||||
}
|
||||
|
||||
/**
|
||||
|
|
@ -236,7 +237,6 @@ public class VCFHeader {
|
|||
+ VCFConstants.GENOTYPE_PL_KEY + " field. As the GATK now only manages PL fields internally"
|
||||
+ " automatically adding a corresponding PL field to your VCF header");
|
||||
addMetaDataLine(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_PL_KEY, VCFHeaderLineCount.G, VCFHeaderLineType.Integer, "Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"));
|
||||
loadMetaDataMaps();
|
||||
}
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -24,6 +24,7 @@
|
|||
|
||||
package org.broadinstitute.sting.utils.progressmeter;
|
||||
|
||||
import com.google.java.contract.Ensures;
|
||||
import com.google.java.contract.Invariant;
|
||||
import org.apache.log4j.Logger;
|
||||
import org.broadinstitute.sting.utils.*;
|
||||
|
|
@ -200,6 +201,14 @@ public class ProgressMeter {
|
|||
"Location", processingUnitName, processingUnitName));
|
||||
}
|
||||
|
||||
/**
|
||||
* @return the current runtime in nanoseconds
|
||||
*/
|
||||
@Ensures("result >= 0")
|
||||
public long getRuntimeInNanoseconds() {
|
||||
return timer.getElapsedTimeNano();
|
||||
}
|
||||
|
||||
/**
|
||||
* Utility routine that prints out process information (including timing) every N records or
|
||||
* every M seconds, for N and M set in global variables.
|
||||
|
|
|
|||
|
|
@ -0,0 +1,86 @@
|
|||
/*
|
||||
* Copyright (c) 2011, 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.gatk;
|
||||
|
||||
import org.broadinstitute.sting.WalkerTest;
|
||||
import org.broadinstitute.sting.utils.SimpleTimer;
|
||||
import org.testng.Assert;
|
||||
import org.testng.annotations.DataProvider;
|
||||
import org.testng.annotations.Test;
|
||||
|
||||
import java.util.Arrays;
|
||||
import java.util.Collections;
|
||||
import java.util.concurrent.TimeUnit;
|
||||
|
||||
/**
|
||||
*
|
||||
*/
|
||||
public class MaxRuntimeIntegrationTest extends WalkerTest {
|
||||
private static final long STARTUP_TIME = TimeUnit.NANOSECONDS.convert(20, TimeUnit.SECONDS);
|
||||
|
||||
private class MaxRuntimeTestProvider extends TestDataProvider {
|
||||
final long maxRuntime;
|
||||
final TimeUnit unit;
|
||||
|
||||
public MaxRuntimeTestProvider(final long maxRuntime, final TimeUnit unit) {
|
||||
super(MaxRuntimeTestProvider.class);
|
||||
this.maxRuntime = maxRuntime;
|
||||
this.unit = unit;
|
||||
setName(String.format("Max runtime test : %d of %s", maxRuntime, unit));
|
||||
}
|
||||
|
||||
public long expectedMaxRuntimeNano() {
|
||||
return TimeUnit.NANOSECONDS.convert(maxRuntime, unit) + STARTUP_TIME;
|
||||
}
|
||||
}
|
||||
|
||||
@DataProvider(name = "MaxRuntimeProvider")
|
||||
public Object[][] makeMaxRuntimeProvider() {
|
||||
for ( final TimeUnit requestedUnits : Arrays.asList(TimeUnit.NANOSECONDS, TimeUnit.MILLISECONDS, TimeUnit.SECONDS, TimeUnit.MINUTES) )
|
||||
new MaxRuntimeTestProvider(requestedUnits.convert(30, TimeUnit.SECONDS), requestedUnits);
|
||||
|
||||
return MaxRuntimeTestProvider.getTests(MaxRuntimeTestProvider.class);
|
||||
}
|
||||
|
||||
//
|
||||
// Loop over errors to throw, make sure they are the errors we get back from the engine, regardless of NT type
|
||||
//
|
||||
@Test(enabled = true, dataProvider = "MaxRuntimeProvider", timeOut = 60 * 1000)
|
||||
public void testMaxRuntime(final MaxRuntimeTestProvider cfg) {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-T UnifiedGenotyper -R " + hg18Reference
|
||||
+ " -I " + validationDataLocation + "NA12878.WEx.downsampled20x.bam -o /dev/null"
|
||||
+ " -maxRuntime " + cfg.maxRuntime + " -maxRuntimeUnits " + cfg.unit, 0,
|
||||
Collections.<String>emptyList());
|
||||
final SimpleTimer timer = new SimpleTimer().start();
|
||||
executeTest("Max runtime " + cfg, spec);
|
||||
final long actualRuntimeNano = timer.getElapsedTimeNano();
|
||||
|
||||
Assert.assertTrue(actualRuntimeNano < cfg.expectedMaxRuntimeNano(),
|
||||
"Actual runtime " + TimeUnit.SECONDS.convert(actualRuntimeNano, TimeUnit.NANOSECONDS)
|
||||
+ " exceeded max. tolerated runtime " + TimeUnit.SECONDS.convert(cfg.expectedMaxRuntimeNano(), TimeUnit.NANOSECONDS)
|
||||
+ " given requested runtime " + cfg.maxRuntime + " " + cfg.unit);
|
||||
}
|
||||
}
|
||||
|
|
@ -117,24 +117,24 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
|
||||
// Note that we need to turn off any randomization for this to work, so no downsampling and no annotations
|
||||
|
||||
String md5 = "3d25ea660275a455ca443a786bff3d32";
|
||||
String md5 = "d408b4661b820ed86272415b8ea08780";
|
||||
|
||||
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
|
||||
baseCommand + " -dt NONE -G none -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000", 1,
|
||||
baseCommand + " -dt NONE -G none --contamination_fraction_to_filter 0.0 -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000", 1,
|
||||
Arrays.asList(md5));
|
||||
executeTest("test parallelization (single thread)", spec1);
|
||||
|
||||
GenomeAnalysisEngine.resetRandomGenerator();
|
||||
|
||||
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
|
||||
baseCommand + " -dt NONE -G none -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000 -nt 2", 1,
|
||||
baseCommand + " -dt NONE -G none --contamination_fraction_to_filter 0.0 -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000 -nt 2", 1,
|
||||
Arrays.asList(md5));
|
||||
executeTest("test parallelization (2 threads)", spec2);
|
||||
|
||||
GenomeAnalysisEngine.resetRandomGenerator();
|
||||
|
||||
WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec(
|
||||
baseCommand + " -dt NONE -G none -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000 -nt 4", 1,
|
||||
baseCommand + " -dt NONE -G none --contamination_fraction_to_filter 0.0 -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000 -nt 4", 1,
|
||||
Arrays.asList(md5));
|
||||
executeTest("test parallelization (4 threads)", spec3);
|
||||
}
|
||||
|
|
@ -157,7 +157,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
public void testSLOD() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-T UnifiedGenotyper -R " + b36KGReference + " --computeSLOD --no_cmdline_in_header -glm BOTH --dbsnp " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
|
||||
Arrays.asList("9f95cfe14d53a697c58247833bfd72a6"));
|
||||
Arrays.asList("6ccb9bd88934e4272d0ce362dd35e603"));
|
||||
executeTest("test SLOD", spec);
|
||||
}
|
||||
|
||||
|
|
@ -451,13 +451,13 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
public void testReducedBam() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1,
|
||||
Arrays.asList("1b711c0966a2f76eb21801e73b76b758"));
|
||||
Arrays.asList("9a7cd58b9e3d5b72608c0d529321deba"));
|
||||
executeTest("test calling on a ReducedRead BAM", spec);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testReducedBamSNPs() {
|
||||
testReducedCalling("SNP", "9ba4867cadb366746ee63e7a4afdb95e");
|
||||
testReducedCalling("SNP", "e7fc11baf208a1bca7b462d3148c936e");
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
|
|||
|
|
@ -32,11 +32,12 @@ public class NanoSchedulerIntegrationTest extends WalkerTest {
|
|||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
buildCommandLine(
|
||||
"-T UnifiedGenotyper -R " + b37KGReference,
|
||||
"-nosl --no_cmdline_in_header -G",
|
||||
"--no_cmdline_in_header -G",
|
||||
//"--dbsnp " + b37dbSNP132,
|
||||
"-I " + privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam",
|
||||
"-L 20:10,000,000-10,100,000",
|
||||
"-glm " + glm,
|
||||
"--contamination_fraction_to_filter 0.0",
|
||||
"-nt " + nt,
|
||||
"-nct " + nct,
|
||||
"-o %s"
|
||||
|
|
|
|||
Loading…
Reference in New Issue