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Fixing test bugs for WindowMaker that required empty sample list

This commit is contained in:
Mark DePristo 2011-09-30 14:18:27 -04:00
parent 810e8ad011
commit 56f10b40a8
7 changed files with 39 additions and 25 deletions
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3
public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
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@ -56,7 +56,8 @@ public class LinearMicroScheduler extends MicroScheduler {
traversalEngine.startTimersIfNecessary();
if(shard.getShardType() == Shard.ShardType.LOCUS) {
LocusWalker lWalker = (LocusWalker)walker;
WindowMaker windowMaker = new WindowMaker(shard, engine.getGenomeLocParser(), getReadIterator(shard), shard.getGenomeLocs(), engine.getSampleDB());
WindowMaker windowMaker = new WindowMaker(shard, engine.getGenomeLocParser(),
getReadIterator(shard), shard.getGenomeLocs(), engine.getSampleDB().getSampleNames());
for(WindowMaker.WindowMakerIterator iterator: windowMaker) {
ShardDataProvider dataProvider = new LocusShardDataProvider(shard,iterator.getSourceInfo(),engine.getGenomeLocParser(),iterator.getLocus(),iterator,reference,rods);
Object result = traversalEngine.traverse(walker, dataProvider, accumulator.getReduceInit());

5
public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
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@ -62,7 +62,10 @@ public class ShardTraverser implements Callable {
Object accumulator = walker.reduceInit();
LocusWalker lWalker = (LocusWalker)walker;
WindowMaker windowMaker = new WindowMaker(shard,microScheduler.getEngine().getGenomeLocParser(),microScheduler.getReadIterator(shard),shard.getGenomeLocs(), microScheduler.engine.getSampleDB()); // todo: microScheduler.engine is protected - is it okay to user it here?
WindowMaker windowMaker = new WindowMaker(shard,microScheduler.getEngine().getGenomeLocParser(),
microScheduler.getReadIterator(shard),
shard.getGenomeLocs(),
microScheduler.engine.getSampleDB().getSampleNames()); // todo: microScheduler.engine is protected - is it okay to user it here?
ShardDataProvider dataProvider = null;
for(WindowMaker.WindowMakerIterator iterator: windowMaker) {

12
public/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java
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@ -12,6 +12,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.Collection;
import java.util.Iterator;
import java.util.List;
import java.util.NoSuchElementException;
@ -63,17 +64,20 @@ public class WindowMaker implements Iterable<WindowMaker.WindowMakerIterator>, I
* the given intervals.
* @param iterator The data source for this window.
* @param intervals The set of intervals over which to traverse.
* @param sampleData SampleDataSource that we can reference reads with
* @param sampleNames The complete set of sample names in the reads in shard
*/
public WindowMaker(Shard shard, GenomeLocParser genomeLocParser, StingSAMIterator iterator, List<GenomeLoc> intervals, SampleDataSource sampleData ) {
public WindowMaker(Shard shard, GenomeLocParser genomeLocParser, StingSAMIterator iterator, List<GenomeLoc> intervals, Collection<String> sampleNames) {
this.sourceInfo = shard.getReadProperties();
this.readIterator = iterator;
this.sourceIterator = new PeekableIterator<AlignmentContext>(new LocusIteratorByState(iterator,sourceInfo,genomeLocParser,sampleData.getSampleNames()));
this.sourceIterator = new PeekableIterator<AlignmentContext>(new LocusIteratorByState(iterator,sourceInfo,genomeLocParser, sampleNames));
this.intervalIterator = intervals.size()>0 ? new PeekableIterator<GenomeLoc>(intervals.iterator()) : null;
}
public WindowMaker(Shard shard, GenomeLocParser genomeLocParser, StingSAMIterator iterator, List<GenomeLoc> intervals ) {
this(shard, genomeLocParser, iterator, intervals, LocusIteratorByState.sampleListForSAMWithoutReadGroups());
}
public Iterator<WindowMakerIterator> iterator() {
return this;
}

10
public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
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@ -284,6 +284,16 @@ public class LocusIteratorByState extends LocusIterator {
throw new IllegalArgumentException("samples list must not be empty");
}
/**
* For testing only. Assumes that the incoming SAMRecords have no read groups, so creates a dummy sample list
* for the system.
*/
public final static Collection<String> sampleListForSAMWithoutReadGroups() {
List<String> samples = new ArrayList<String>();
samples.add(null);
return samples;
}
public Iterator<AlignmentContext> iterator() {
return this;
}

26
public/java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusViewTemplate.java
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@ -50,7 +50,7 @@ public abstract class LocusViewTemplate extends BaseTest {
GenomeLoc shardBounds = genomeLocParser.createGenomeLoc("chr1", 1, 5);
Shard shard = new LocusShard(genomeLocParser, new SAMDataSource(Collections.<SAMReaderID>emptyList(),genomeLocParser),Collections.singletonList(shardBounds),Collections.<SAMReaderID,SAMFileSpan>emptyMap());
WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs(), new SampleDataSource());
WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
WindowMaker.WindowMakerIterator window = windowMaker.next();
LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, null, genomeLocParser, window.getLocus(), window, null, null);
@ -66,7 +66,7 @@ public abstract class LocusViewTemplate extends BaseTest {
GenomeLoc shardBounds = genomeLocParser.createGenomeLoc("chr1", 1, 5);
Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(shardBounds));
WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs(), new SampleDataSource());
WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
WindowMaker.WindowMakerIterator window = windowMaker.next();
LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
@ -81,7 +81,7 @@ public abstract class LocusViewTemplate extends BaseTest {
SAMRecordIterator iterator = new SAMRecordIterator(read);
Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 1, 10)));
WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs(),new SampleDataSource());
WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
WindowMaker.WindowMakerIterator window = windowMaker.next();
LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
LocusView view = createView(dataProvider);
@ -95,7 +95,7 @@ public abstract class LocusViewTemplate extends BaseTest {
SAMRecordIterator iterator = new SAMRecordIterator(read);
Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 1, 10)));
WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs(), new SampleDataSource());
WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
WindowMaker.WindowMakerIterator window = windowMaker.next();
LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
LocusView view = createView(dataProvider);
@ -109,7 +109,7 @@ public abstract class LocusViewTemplate extends BaseTest {
SAMRecordIterator iterator = new SAMRecordIterator(read);
Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 1, 10)));
WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs(), new SampleDataSource());
WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
WindowMaker.WindowMakerIterator window = windowMaker.next();
LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
LocusView view = createView(dataProvider);
@ -123,7 +123,7 @@ public abstract class LocusViewTemplate extends BaseTest {
SAMRecordIterator iterator = new SAMRecordIterator(read);
Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 5, 5)));
WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs(),new SampleDataSource());
WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
WindowMaker.WindowMakerIterator window = windowMaker.next();
LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
LocusView view = createView(dataProvider);
@ -137,7 +137,7 @@ public abstract class LocusViewTemplate extends BaseTest {
SAMRecordIterator iterator = new SAMRecordIterator(read);
Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 6, 15)));
WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs(), new SampleDataSource());
WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
WindowMaker.WindowMakerIterator window = windowMaker.next();
LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
LocusView view = createView(dataProvider);
@ -151,7 +151,7 @@ public abstract class LocusViewTemplate extends BaseTest {
SAMRecordIterator iterator = new SAMRecordIterator(read);
Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 1, 10)));
WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs(),new SampleDataSource());
WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
WindowMaker.WindowMakerIterator window = windowMaker.next();
LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
LocusView view = createView(dataProvider);
@ -166,7 +166,7 @@ public abstract class LocusViewTemplate extends BaseTest {
SAMRecordIterator iterator = new SAMRecordIterator(read1, read2);
Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 1, 10)));
WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs(),new SampleDataSource());
WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
WindowMaker.WindowMakerIterator window = windowMaker.next();
LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
LocusView view = createView(dataProvider);
@ -185,7 +185,7 @@ public abstract class LocusViewTemplate extends BaseTest {
SAMRecordIterator iterator = new SAMRecordIterator(read1, read2, read3, read4);
Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 1, 10)));
WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs(),new SampleDataSource());
WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
WindowMaker.WindowMakerIterator window = windowMaker.next();
LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
LocusView view = createView(dataProvider);
@ -204,7 +204,7 @@ public abstract class LocusViewTemplate extends BaseTest {
SAMRecordIterator iterator = new SAMRecordIterator(read1, read2, read3, read4);
Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 1, 10)));
WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs(),new SampleDataSource());
WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
WindowMaker.WindowMakerIterator window = windowMaker.next();
LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
LocusView view = createView(dataProvider);
@ -225,7 +225,7 @@ public abstract class LocusViewTemplate extends BaseTest {
SAMRecordIterator iterator = new SAMRecordIterator(read1, read2, read3, read4, read5, read6);
Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 1, 10)));
WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs(), new SampleDataSource());
WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
WindowMaker.WindowMakerIterator window = windowMaker.next();
LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
LocusView view = createView(dataProvider);
@ -253,7 +253,7 @@ public abstract class LocusViewTemplate extends BaseTest {
read07, read08, read09, read10, read11, read12);
Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 6, 15)));
WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs(), new SampleDataSource());
WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
WindowMaker.WindowMakerIterator window = windowMaker.next();
LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
LocusView view = createView(dataProvider);

2
public/java/test/org/broadinstitute/sting/gatk/datasources/reads/DownsamplerBenchmark.java
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@ -89,7 +89,7 @@ public class DownsamplerBenchmark extends ReadProcessingBenchmark {
// Filter unmapped reads. TODO: is this always strictly necessary? Who in the GATK normally filters these out?
Iterator<SAMRecord> readIterator = new FilteringIterator(reader.iterator(),new UnmappedReadFilter());
LocusIteratorByState locusIteratorByState = new LocusIteratorByState(readIterator,readProperties,genomeLocParser,sampleDataSource.getSampleNames());
LocusIteratorByState locusIteratorByState = new LocusIteratorByState(readIterator,readProperties,genomeLocParser, LocusIteratorByState.sampleListForSAMWithoutReadGroups());
while(locusIteratorByState.hasNext()) {
locusIteratorByState.next().getLocation();
}

6
public/java/test/org/broadinstitute/sting/gatk/iterators/LocusIteratorByStateUnitTest.java
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@ -11,7 +11,6 @@ import org.testng.Assert;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.gatk.ReadProperties;
import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
import org.broadinstitute.sting.gatk.samples.SampleDataSource;
import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.utils.GenomeLocParser;
@ -39,11 +38,8 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
}
private final LocusIteratorByState makeLTBS(List<SAMRecord> reads, ReadProperties readAttributes) {
List<String> samples = new ArrayList<String>();
samples.add(null);
return new LocusIteratorByState(new FakeCloseableIterator<SAMRecord>(reads.iterator()),
readAttributes,genomeLocParser, samples);
readAttributes, genomeLocParser, LocusIteratorByState.sampleListForSAMWithoutReadGroups());
}
@Test