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Add some reads 

- Move intervals and reads to init
- Update intervals and reads
This commit is contained in:
Joel Thibault 2012-11-20 13:11:24 -05:00
parent 3fa3b00f4a
commit 3ad9128800
1 changed files with 53 additions and 20 deletions
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73
public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java
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@ -1,9 +1,10 @@
package org.broadinstitute.sting.gatk.traversals;
import org.testng.Assert;
import net.sf.samtools.*;
import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
import org.broadinstitute.sting.utils.interval.IntervalUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMSequenceDictionary;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@ -22,6 +23,7 @@ import org.broadinstitute.sting.utils.activeregion.ActiveRegion;
import org.broadinstitute.sting.utils.activeregion.ActivityProfileResult;
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
@ -43,8 +45,8 @@ public class TraverseActiveRegionsTest extends BaseTest {
private class DummyActiveRegionWalker extends ActiveRegionWalker<Integer, Integer> {
private final double prob;
public List<GenomeLoc> isActiveCalls = new ArrayList<GenomeLoc>();
public List<ActiveRegion> mappedActiveRegions = new ArrayList<ActiveRegion>();
protected List<GenomeLoc> isActiveCalls = new ArrayList<GenomeLoc>();
protected List<ActiveRegion> mappedActiveRegions = new ArrayList<ActiveRegion>();
public DummyActiveRegionWalker() {
this.prob = 1.0;
@ -76,30 +78,46 @@ public class TraverseActiveRegionsTest extends BaseTest {
private final TraverseActiveRegions<Integer, Integer> t = new TraverseActiveRegions<Integer, Integer>();
private IndexedFastaSequenceFile reference;
private SAMSequenceDictionary dictionary;
private GenomeLocParser genomeLocParser;
private List<GenomeLoc> intervals;
private List<SAMRecord> reads;
@BeforeClass
private void init() throws FileNotFoundException {
reference = new CachingIndexedFastaSequenceFile(new File(hg19Reference));
SAMSequenceDictionary dictionary = reference.getSequenceDictionary();
dictionary = reference.getSequenceDictionary();
genomeLocParser = new GenomeLocParser(dictionary);
intervals = new ArrayList<GenomeLoc>();
intervals.add(genomeLocParser.createGenomeLoc("1", 10, 20));
intervals.add(genomeLocParser.createGenomeLoc("1", 1, 999));
intervals.add(genomeLocParser.createGenomeLoc("1", 1000, 1999));
intervals.add(genomeLocParser.createGenomeLoc("1", 2000, 2999));
intervals.add(genomeLocParser.createGenomeLoc("1", 10000, 20000));
// TODO: this fails!
//intervals.add(genomeLocParser.createGenomeLoc("20", 10000, 20000));
intervals = IntervalUtils.sortAndMergeIntervals(genomeLocParser, intervals, IntervalMergingRule.OVERLAPPING_ONLY).toList();
reads = new ArrayList<SAMRecord>();
reads.add(buildSAMRecord("overlap_overlapped_equal", "1", 10, 20));
reads.add(buildSAMRecord("overlap_overlapped_unequal", "1", 10, 21));
reads.add(buildSAMRecord("overlap_boundary_equal", "1", 1990, 2009));
reads.add(buildSAMRecord("overlap_boundary_unequal", "1", 1995, 2050));
reads.add(buildSAMRecord("extended_only", "1", 3000, 3100));
reads.add(buildSAMRecord("extended_and_np", "1", 990, 1990));
reads.add(buildSAMRecord("simple", "20", 1000100, 1000150));
}
@Test
public void testAllBasesSeen() {
DummyActiveRegionWalker walker = new DummyActiveRegionWalker();
List<GenomeLoc> intervals = new ArrayList<GenomeLoc>();
intervals.add(genomeLocParser.createGenomeLoc("1", 1, 1));
List<GenomeLoc> activeIntervals = getIsActiveIntervals(walker, intervals);
// Contract: Every genome position in the analysis interval(s) is processed by the walker's isActive() call
verifyEqualIntervals(intervals, activeIntervals);
intervals.add(genomeLocParser.createGenomeLoc("1", 10, 20));
activeIntervals = getIsActiveIntervals(walker, intervals);
// Contract: Every genome position in the analysis interval(s) is processed by the walker's isActive() call
verifyEqualIntervals(intervals, activeIntervals);
// TODO: more tests and edge cases
}
@ -116,11 +134,6 @@ public class TraverseActiveRegionsTest extends BaseTest {
@Test
public void testActiveRegionCoverage() {
DummyActiveRegionWalker walker = new DummyActiveRegionWalker();
List<GenomeLoc> intervals = new ArrayList<GenomeLoc>();
intervals.add(genomeLocParser.createGenomeLoc("1", 1, 999));
intervals.add(genomeLocParser.createGenomeLoc("1", 1000, 1999));
intervals.add(genomeLocParser.createGenomeLoc("1", 2000, 2999));
List<ActiveRegion> activeRegions = getActiveRegions(walker, intervals);
verifyActiveRegionCoverage(intervals, activeRegions);
@ -212,17 +225,37 @@ public class TraverseActiveRegionsTest extends BaseTest {
}
}
// copied from LocusViewTemplate
protected GATKSAMRecord buildSAMRecord(String readName, String contig, int alignmentStart, int alignmentEnd) {
SAMFileHeader header = new SAMFileHeader();
header.setSequenceDictionary(dictionary);
GATKSAMRecord record = new GATKSAMRecord(header);
record.setReadName(readName);
record.setReferenceIndex(dictionary.getSequenceIndex(contig));
record.setAlignmentStart(alignmentStart);
Cigar cigar = new Cigar();
int len = alignmentEnd - alignmentStart + 1;
cigar.add(new CigarElement(len, CigarOperator.M));
record.setCigar(cigar);
record.setReadBases(new byte[len]);
record.setBaseQualities(new byte[len]);
return record;
}
private List<LocusShardDataProvider> createDataProviders(List<GenomeLoc> intervals) {
GenomeAnalysisEngine engine = new GenomeAnalysisEngine();
engine.setGenomeLocParser(genomeLocParser);
t.initialize(engine);
StingSAMIterator iterator = ArtificialSAMUtils.createReadIterator(new ArrayList<SAMRecord>());
StingSAMIterator iterator = ArtificialSAMUtils.createReadIterator(reads);
Shard shard = new MockLocusShard(genomeLocParser, intervals);
List<LocusShardDataProvider> providers = new ArrayList<LocusShardDataProvider>();
for (WindowMaker.WindowMakerIterator window : new WindowMaker(shard, genomeLocParser, iterator, shard.getGenomeLocs())) {
providers.add(new LocusShardDataProvider(shard, null, genomeLocParser, window.getLocus(), window, reference, new ArrayList<ReferenceOrderedDataSource>()));
providers.add(new LocusShardDataProvider(shard, shard.getReadProperties(), genomeLocParser, window.getLocus(), window, reference, new ArrayList<ReferenceOrderedDataSource>()));
}
return providers;