org.broadinstitute.hellbender.testutils.testers.SamFileTester Maven / Gradle / Ivy
package org.broadinstitute.hellbender.testutils.testers;
import htsjdk.samtools.*;
import htsjdk.samtools.util.CloseableIterator;
import htsjdk.samtools.util.IOUtil;
import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
import org.broadinstitute.hellbender.testutils.CommandLineProgramTester;
import org.testng.Assert;
import java.io.File;
import java.util.*;
/**
* Abstract class for doing basic on the fly SAM file testing.
*/
public abstract class SamFileTester implements CommandLineProgramTester {
private final SAMRecordSetBuilder samRecordSetBuilder;
protected final Map duplicateFlags = new LinkedHashMap<>();
private File outputDir;
private File output;
private int readNameCounter = 0;
private boolean noMateCigars = false;
private boolean deleteOnExit = true;
protected final List args = new ArrayList<>();
public SamFileTester(final int readLength, final boolean deleteOnExit, final int defaultChromosomeLength, final DuplicateScoringStrategy.ScoringStrategy duplicateScoringStrategy, final SAMFileHeader.SortOrder sortOrder, final boolean recordsNeedSorting) {
this.deleteOnExit = deleteOnExit;
this.samRecordSetBuilder = new SAMRecordSetBuilder(recordsNeedSorting, sortOrder, true, defaultChromosomeLength, duplicateScoringStrategy);
samRecordSetBuilder.setReadLength(readLength);
setOutputDir();
}
public SamFileTester(final int readLength, final boolean deleteOnExit, final int defaultChromosomeLength, final DuplicateScoringStrategy.ScoringStrategy duplicateScoringStrategy, final SAMFileHeader.SortOrder sortOrder) {
this(readLength, deleteOnExit, defaultChromosomeLength, duplicateScoringStrategy, SAMFileHeader.SortOrder.coordinate, true);
}
public SamFileTester(final int readLength, final boolean deleteOnExit, final int defaultChromosomeLength, final DuplicateScoringStrategy.ScoringStrategy duplicateScoringStrategy) {
this(readLength, deleteOnExit, defaultChromosomeLength, duplicateScoringStrategy, SAMFileHeader.SortOrder.coordinate);
}
public SamFileTester(final int readLength, final boolean deleteOnExit, final int defaultChromosomeLength) {
this(readLength, deleteOnExit, defaultChromosomeLength, SAMRecordSetBuilder.DEFAULT_DUPLICATE_SCORING_STRATEGY);
}
public SamFileTester(final int readLength, final boolean deleteOnExit) {
this(readLength, deleteOnExit, SAMRecordSetBuilder.DEFAULT_CHROMOSOME_LENGTH);
}
public void setHeader(final SAMFileHeader header) {
this.samRecordSetBuilder.setHeader(header);
}
public SAMFileHeader getHeader() {
return this.samRecordSetBuilder.getHeader();
}
public void addRecord(final SAMRecord record) {
final String key = samRecordToDuplicatesFlagsKey(record);
Assert.assertFalse(this.duplicateFlags.containsKey(key));
this.duplicateFlags.put(key, record.getDuplicateReadFlag());
this.samRecordSetBuilder.addRecord(record);
}
public int getNumberOfRecords() {
return this.samRecordSetBuilder.size();
}
public CloseableIterator getRecordIterator() {
return this.samRecordSetBuilder.iterator();
}
public File getOutput() {
return output;
}
public void setOutput(final File output) {
this.output = output;
}
public void addArg(final String key) {
args.add(key);
}
public void addArg(final String key, final String value) {
args.add(key); args.add(value);
}
public List getArgs() {
return args;
}
public File getOutputDir() {
return outputDir;
}
private void setOutputDir() {
this.outputDir = IOUtil.createTempDir(this.getClass().getSimpleName() + ".", ".tmp");
if (deleteOnExit) {
outputDir.deleteOnExit();
}
}
public void setNoMateCigars(final boolean value) {
this.noMateCigars = value;
}
public boolean getDeleteOnExit() {
return deleteOnExit;
}
protected String samRecordToDuplicatesFlagsKey(final SAMRecord record) {
final StringBuilder nameBuilder = new StringBuilder();
nameBuilder.append(record.getReadName());
nameBuilder.append("-");
if (record.getReadUnmappedFlag()) {
nameBuilder.append("Unmapped");
} else {
nameBuilder.append(record.getContig())
.append("-")
.append(record.getAlignmentStart());
}
nameBuilder.append("-")
.append(record.getReadPairedFlag())
.append("-").append(record.isSecondaryAlignment())
.append("-");
if (record.getReadPairedFlag()) {
nameBuilder.append(record.getFirstOfPairFlag())
.append("-")
.append(record.getSecondOfPairFlag());
} else {
nameBuilder.append("false-false");
}
return nameBuilder.toString();
}
// Below are a bunch of utility methods for adding records to the SAMRecordSetBuilder
public void addUnmappedFragment(final int referenceSequenceIndex,
final int defaultQualityScore) {
addFragment(referenceSequenceIndex, -1, true, false, null, null, defaultQualityScore, false);
}
public void addUnmappedFragment(final int referenceSequenceIndex,
final String qualityString) {
addFragment(referenceSequenceIndex, -1, true, false, null, qualityString, -1, false);
}
public void addUnmappedPair(final int referenceSequenceIndex,
final int defaultQualityScore) {
addMatePair(referenceSequenceIndex, -1, -1, true, true, false, false, null, null, false, false, false, false, false, defaultQualityScore);
}
public void addMappedFragment(final int referenceSequenceIndex, final int alignmentStart, final boolean isDuplicate,
final int defaultQualityScore) {
addFragment(referenceSequenceIndex, alignmentStart, false, isDuplicate, null, null, defaultQualityScore, false);
}
public void addMappedFragment(final int referenceSequenceIndex, final int alignmentStart, final boolean isDuplicate,
final int defaultQualityScore, final boolean isSecondary) {
addFragment(referenceSequenceIndex, alignmentStart, false, isDuplicate, null, null, defaultQualityScore, isSecondary);
}
public void addMappedFragment(final int referenceSequenceIndex, final int alignmentStart, final boolean isDuplicate, final String cigar,
final int defaultQualityScore) {
addFragment(referenceSequenceIndex, alignmentStart, false, isDuplicate, cigar, null, defaultQualityScore, false);
}
public void addMappedFragment(final int referenceSequenceIndex, final int alignmentStart, final boolean isDuplicate, final String cigar,
final String qualityString,
final int defaultQualityScore) {
addFragment(referenceSequenceIndex, alignmentStart, false, isDuplicate, cigar, qualityString, defaultQualityScore, false);
}
public void addMappedFragment(final String readName, final int referenceSequenceIndex, final int alignmentStart, final boolean isDuplicate, final String cigar,
final String qualityString, final boolean isSecondary, final boolean isSupplementary,
final int defaultQualityScore) {
addFragment(readName, referenceSequenceIndex, alignmentStart, false, isDuplicate, cigar, qualityString, defaultQualityScore, isSecondary, isSupplementary);
}
public void addMappedPair(final int referenceSequenceIndex,
final int alignmentStart1,
final int alignmentStart2,
final boolean isDuplicate1,
final boolean isDuplicate2,
final int defaultQualityScore) {
addMappedPair(referenceSequenceIndex, alignmentStart1, alignmentStart2, isDuplicate1, isDuplicate2, null, null,
false, defaultQualityScore);
}
public void addMappedPair(final int referenceSequenceIndex,
final int alignmentStart1,
final int alignmentStart2,
final boolean isDuplicate1,
final boolean isDuplicate2,
final String cigar1,
final String cigar2,
final boolean firstOnly,
final int defaultQualityScore) {
addMappedPair(referenceSequenceIndex, alignmentStart1, alignmentStart2, isDuplicate1, isDuplicate2, cigar1,
cigar2, false, true, firstOnly, defaultQualityScore);
}
public void addMappedPair(final int referenceSequenceIndex,
final int alignmentStart1,
final int alignmentStart2,
final boolean isDuplicate1,
final boolean isDuplicate2,
final String cigar1,
final String cigar2,
final boolean strand1,
final boolean strand2,
final boolean firstOnly,
final int defaultQualityScore) {
addMatePair(referenceSequenceIndex, alignmentStart1, alignmentStart2, false, false, isDuplicate1, isDuplicate2, cigar1, cigar2,
strand1, strand2, firstOnly, false, false, defaultQualityScore);
}
public void addMatePair(final int referenceSequenceIndex,
final int alignmentStart1,
final int alignmentStart2,
final boolean record1Unmapped,
final boolean record2Unmapped,
final boolean isDuplicate1,
final boolean isDuplicate2,
final String cigar1,
final String cigar2,
final boolean strand1,
final boolean strand2,
final boolean firstOnly,
final boolean record1NonPrimary,
final boolean record2NonPrimary,
final int defaultQualityScore) {
addMatePair("READ" + readNameCounter++, referenceSequenceIndex, alignmentStart1, alignmentStart2, record1Unmapped, record2Unmapped,
isDuplicate1, isDuplicate2, cigar1, cigar2, strand1, strand2, firstOnly, record1NonPrimary, record2NonPrimary,
defaultQualityScore);
}
private void addFragment(final int referenceSequenceIndex, final int alignmentStart, final boolean recordUnmapped, final boolean isDuplicate, final String cigar,
final String qualityString, final int defaultQualityScore, final boolean isSecondary) {
addFragment("READ" + readNameCounter++, referenceSequenceIndex, alignmentStart, recordUnmapped, isDuplicate, cigar,
qualityString, defaultQualityScore, isSecondary, false);
}
private void addFragment(final String readName, final int referenceSequenceIndex, final int alignmentStart, final boolean recordUnmapped, final boolean isDuplicate, final String cigar,
final String qualityString, final int defaultQualityScore, final boolean isSecondary, final boolean isSupplementary) {
final SAMRecord record = samRecordSetBuilder.addFrag(readName, referenceSequenceIndex, alignmentStart, false,
recordUnmapped, cigar, qualityString, defaultQualityScore, isSecondary, isSupplementary);
final String key = samRecordToDuplicatesFlagsKey(record);
Assert.assertFalse(this.duplicateFlags.containsKey(key));
this.duplicateFlags.put(key, isDuplicate);
}
public void addMatePair(final String readName,
final int referenceSequenceIndex1,
final int referenceSequenceIndex2,
final int alignmentStart1,
final int alignmentStart2,
final boolean record1Unmapped,
final boolean record2Unmapped,
final boolean isDuplicate1,
final boolean isDuplicate2,
final String cigar1,
final String cigar2,
final boolean strand1,
final boolean strand2,
final boolean firstOnly,
final boolean record1NonPrimary,
final boolean record2NonPrimary,
final int defaultQuality,
final String readGroup) {
final List samRecordList = samRecordSetBuilder.addPair(readName, referenceSequenceIndex1, referenceSequenceIndex2, alignmentStart1, alignmentStart2,
record1Unmapped, record2Unmapped, cigar1, cigar2, strand1, strand2, record1NonPrimary, record2NonPrimary, defaultQuality);
final SAMRecord record1 = samRecordList.get(0);
final SAMRecord record2 = samRecordList.get(1);
if (this.noMateCigars) {
record1.setAttribute("MC", null);
record2.setAttribute("MC", null);
}
record1.setAttribute("RG", readGroup);
record2.setAttribute("RG", readGroup);
if (firstOnly) {
samRecordSetBuilder.getRecords().remove(record2);
}
final String key1 = samRecordToDuplicatesFlagsKey(record1);
Assert.assertFalse(this.duplicateFlags.containsKey(key1));
this.duplicateFlags.put(key1, isDuplicate1);
final String key2 = samRecordToDuplicatesFlagsKey(record2);
Assert.assertFalse(this.duplicateFlags.containsKey(key2));
this.duplicateFlags.put(key2, isDuplicate2);
}
public void addMatePair(final String readName,
final int referenceSequenceIndex,
final int alignmentStart1,
final int alignmentStart2,
final boolean record1Unmapped,
final boolean record2Unmapped,
final boolean isDuplicate1,
final boolean isDuplicate2,
final String cigar1,
final String cigar2,
final boolean strand1,
final boolean strand2,
final boolean firstOnly,
final boolean record1NonPrimary,
final boolean record2NonPrimary,
final int defaultQuality) {
addMatePair(readName, referenceSequenceIndex,referenceSequenceIndex, alignmentStart1, alignmentStart2, record1Unmapped, record2Unmapped,
isDuplicate1, isDuplicate2, cigar1, cigar2, strand1, strand2, firstOnly, record1NonPrimary, record2NonPrimary, defaultQuality, "1");
}
protected abstract void test();
/**
* Sets up the basic command line arguments for input and output and runs instanceMain.
*/
public void runTest() {
final File input = createInputFile();
output = new File(outputDir, "output.sam");
addArg("--" + StandardArgumentDefinitions.INPUT_LONG_NAME, input.getAbsolutePath());
addArg("--" + StandardArgumentDefinitions.OUTPUT_LONG_NAME, output.getAbsolutePath());
addArgs();
runCommandLine(args);
test();
}
protected void addArgs() {
// subclasses may override to add more arguments
}
private File createInputFile() {
// Create the input file
final File input = new File(outputDir, "input.bam");
try (final SAMFileWriter writer = new SAMFileWriterFactory().setCreateIndex(true).makeBAMWriter(samRecordSetBuilder.getHeader(), true, input)) {
samRecordSetBuilder.getRecords().forEach(writer::addAlignment);
}
return input;
}
public SamReader getInput() {
return samRecordSetBuilder.getSamReader();
}
public SAMRecordSetBuilder getSamRecordSetBuilder() { return samRecordSetBuilder; }
}
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