zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Create actual BAM

This commit is contained in:
Joel Thibault 2012-12-01 11:08:34 -05:00
parent d69d1f8988
commit 72e2394b26
2 changed files with 33 additions and 16 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

49
public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java
View File

@ -2,6 +2,10 @@ package org.broadinstitute.sting.gatk.traversals;
import com.google.java.contract.PreconditionError;
import net.sf.samtools.*;
import org.broadinstitute.sting.commandline.Tags;
import org.broadinstitute.sting.gatk.datasources.reads.*;
import org.broadinstitute.sting.gatk.resourcemanagement.ThreadAllocation;
import org.broadinstitute.sting.utils.GenomeLocSortedSet;
import org.broadinstitute.sting.utils.activeregion.ActiveRegionReadState;
import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
import org.broadinstitute.sting.utils.interval.IntervalUtils;
@ -12,11 +16,8 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider;
import org.broadinstitute.sting.gatk.datasources.reads.MockLocusShard;
import org.broadinstitute.sting.gatk.datasources.reads.Shard;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.executive.WindowMaker;
import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.ActiveRegionWalker;
import org.broadinstitute.sting.utils.GenomeLoc;
@ -101,7 +102,8 @@ public class TraverseActiveRegionsTest extends BaseTest {
private GenomeLocParser genomeLocParser;
private List<GenomeLoc> intervals;
private List<GATKSAMRecord> reads;
private static final String testBAM = "TraverseActiveRegionsTest.bam";
@BeforeClass
private void init() throws FileNotFoundException {
@ -122,7 +124,7 @@ public class TraverseActiveRegionsTest extends BaseTest {
intervals.add(genomeLocParser.createGenomeLoc("20", 10000, 10100));
intervals = IntervalUtils.sortAndMergeIntervals(genomeLocParser, intervals, IntervalMergingRule.OVERLAPPING_ONLY).toList();
reads = new ArrayList<GATKSAMRecord>();
List<GATKSAMRecord> reads = new ArrayList<GATKSAMRecord>();
reads.add(buildSAMRecord("simple", "1", 100, 200));
reads.add(buildSAMRecord("overlap_equal", "1", 10, 20));
reads.add(buildSAMRecord("overlap_unequal", "1", 10, 21));
@ -133,8 +135,18 @@ public class TraverseActiveRegionsTest extends BaseTest {
reads.add(buildSAMRecord("end_of_chr1", "1", 249250600, 249250700));
reads.add(buildSAMRecord("simple20", "20", 10025, 10075));
// required by LocusIteratorByState, and I prefer to list them in test case order above
ReadUtils.sortReadsByCoordinate(reads);
createBAM(reads);
}
private void createBAM(List<GATKSAMRecord> reads) {
File outFile = new File(testBAM);
outFile.deleteOnExit();
SAMFileWriter out = new SAMFileWriterFactory().makeBAMWriter(reads.get(0).getHeader(), true, outFile);
for (GATKSAMRecord read : ReadUtils.sortReadsByCoordinate(reads)) {
out.addAlignment(read);
}
out.close();
}
@Test
@ -148,7 +160,7 @@ public class TraverseActiveRegionsTest extends BaseTest {
private List<GenomeLoc> getIsActiveIntervals(DummyActiveRegionWalker walker, List<GenomeLoc> intervals) {
List<GenomeLoc> activeIntervals = new ArrayList<GenomeLoc>();
for (LocusShardDataProvider dataProvider : createDataProviders(intervals)) {
for (LocusShardDataProvider dataProvider : createDataProviders(intervals, testBAM)) {
t.traverse(walker, dataProvider, 0);
activeIntervals.addAll(walker.isActiveCalls);
}
@ -350,7 +362,7 @@ public class TraverseActiveRegionsTest extends BaseTest {
}
private Map<GenomeLoc, ActiveRegion> getActiveRegions(DummyActiveRegionWalker walker, List<GenomeLoc> intervals) {
for (LocusShardDataProvider dataProvider : createDataProviders(intervals))
for (LocusShardDataProvider dataProvider : createDataProviders(intervals, testBAM))
t.traverse(walker, dataProvider, 0);
t.endTraversal(walker, 0);
@ -395,7 +407,7 @@ public class TraverseActiveRegionsTest extends BaseTest {
// copied from LocusViewTemplate
protected GATKSAMRecord buildSAMRecord(String readName, String contig, int alignmentStart, int alignmentEnd) {
SAMFileHeader header = new SAMFileHeader();
SAMFileHeader header = ArtificialSAMUtils.createDefaultReadGroup(new SAMFileHeader(), "test", "test");
header.setSequenceDictionary(dictionary);
GATKSAMRecord record = new GATKSAMRecord(header);
@ -407,23 +419,28 @@ public class TraverseActiveRegionsTest extends BaseTest {
int len = alignmentEnd - alignmentStart + 1;
cigar.add(new CigarElement(len, CigarOperator.M));
record.setCigar(cigar);
record.setReadBases(new byte[len]);
record.setReadString(new String(new char[len]).replace("\0", "A"));
record.setBaseQualities(new byte[len]);
return record;
}
private List<LocusShardDataProvider> createDataProviders(List<GenomeLoc> intervals) {
private List<LocusShardDataProvider> createDataProviders(List<GenomeLoc> intervals, String bamFile) {
GenomeAnalysisEngine engine = new GenomeAnalysisEngine();
engine.setGenomeLocParser(genomeLocParser);
t.initialize(engine);
StingSAMIterator iterator = ArtificialSAMUtils.createReadIterator(new ArrayList<SAMRecord>(reads));
Shard shard = new MockLocusShard(genomeLocParser, intervals);
Collection<SAMReaderID> samFiles = new ArrayList<SAMReaderID>();
SAMReaderID readerID = new SAMReaderID(new File(bamFile), new Tags());
samFiles.add(readerID);
SAMDataSource dataSource = new SAMDataSource(samFiles, new ThreadAllocation(), null, genomeLocParser);
List<LocusShardDataProvider> providers = new ArrayList<LocusShardDataProvider>();
for (WindowMaker.WindowMakerIterator window : new WindowMaker(shard, genomeLocParser, iterator, shard.getGenomeLocs())) {
providers.add(new LocusShardDataProvider(shard, shard.getReadProperties(), genomeLocParser, window.getLocus(), window, reference, new ArrayList<ReferenceOrderedDataSource>()));
for (Shard shard : dataSource.createShardIteratorOverIntervals(new GenomeLocSortedSet(genomeLocParser, intervals), new LocusShardBalancer())) {
for (WindowMaker.WindowMakerIterator window : new WindowMaker(shard, genomeLocParser, dataSource.seek(shard), shard.getGenomeLocs())) {
providers.add(new LocusShardDataProvider(shard, shard.getReadProperties(), genomeLocParser, window.getLocus(), window, reference, new ArrayList<ReferenceOrderedDataSource>()));
}
}
return providers;

BIN
public/java/test/org/broadinstitute/sting/gatk/traversals/resources/problem.bam 100644
View File

Binary file not shown.