/htsjdk

Increased test coverage for SamFileValidator #743

Merged
merged 1 commit into from Nov 19, 2016
Commits
Jump to file or symbol
Failed to load files and symbols.
+119 −28
Split
View
39 src/main/java/htsjdk/samtools/SamFileValidator.java
@@ -1,7 +1,7 @@
/*
* The MIT License
*
- * Copyright (c) 2009 The Broad Institute
+ * Copyright (c) 2009-2016 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
@@ -81,25 +81,40 @@
* @see SAMRecord#isValid()
*/
public class SamFileValidator {
- private Histogram<Type> errorsByType = new Histogram<Type>();
+
+ private final static Log log = Log.getInstance(SamFileValidator.class);
+
private final PrintWriter out;
+ private Histogram<Type> errorsByType;
private PairEndInfoMap pairEndInfoByName;
- private ReferenceSequenceFileWalker refFileWalker = null;
- private boolean verbose = false;
- private int maxVerboseOutput = 100;
+ private ReferenceSequenceFileWalker refFileWalker;
+ private boolean verbose;
+ private int maxVerboseOutput;
private SAMSortOrderChecker orderChecker;
- private Set<Type> errorsToIgnore = EnumSet.noneOf(Type.class);
- private boolean ignoreWarnings = false;
- private boolean bisulfiteSequenced = false;
- private IndexValidationStringency indexValidationStringency = IndexValidationStringency.NONE;
- private boolean sequenceDictionaryEmptyAndNoWarningEmitted = false;
- private final int maxTempFiles;
+ private Set<Type> errorsToIgnore;
+ private boolean ignoreWarnings;
+ private boolean bisulfiteSequenced;
+ private IndexValidationStringency indexValidationStringency;
+ private boolean sequenceDictionaryEmptyAndNoWarningEmitted;
- private final static Log log = Log.getInstance(SamFileValidator.class);
+ private final int maxTempFiles;
public SamFileValidator(final PrintWriter out, final int maxTempFiles) {
this.out = out;
this.maxTempFiles = maxTempFiles;
+ this.errorsByType = new Histogram<>();
+ this.refFileWalker = null;
+ this.maxVerboseOutput = 100;
+ this.indexValidationStringency = IndexValidationStringency.NONE;
+ this.errorsToIgnore = EnumSet.noneOf(Type.class);
+ this.verbose = false;
+ this.ignoreWarnings = false;
+ this.bisulfiteSequenced = false;
+ this.sequenceDictionaryEmptyAndNoWarningEmitted = false;
+ }
+
+ Histogram<Type> getErrorsByType() {
+ return errorsByType;
}
/**
View
108 src/test/java/htsjdk/samtools/ValidateSamFileTest.java
@@ -1,7 +1,7 @@
/*
* The MIT License
*
- * Copyright (c) 2009 The Broad Institute
+ * Copyright (c) 2009-2016 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
@@ -36,6 +36,8 @@
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
+import java.nio.channels.FileChannel;
+import java.nio.file.StandardOpenOption;
import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.FileReader;
@@ -45,6 +47,8 @@
import java.io.PrintWriter;
import java.io.StringWriter;
import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
import java.util.Iterator;
/**
@@ -55,6 +59,8 @@
*/
public class ValidateSamFileTest {
private static final File TEST_DATA_DIR = new File("src/test/resources/htsjdk/samtools/ValidateSamFileTest");
+ private static final int TERMINATION_GZIP_BLOCK_SIZE = 28;
+ private static final int RANDOM_NUMBER_TRUNC_BYTE = 128;
@Test
public void testValidSamFile() throws Exception {
@@ -412,21 +418,6 @@ public void testIndexFileValidation() throws Exception {
}
- private Histogram<String> executeValidation(final SamReader samReader, final ReferenceSequenceFile reference, final IndexValidationStringency stringency) throws IOException {
- final File outFile = File.createTempFile("validation", ".txt");
- outFile.deleteOnExit();
- final PrintWriter out = new PrintWriter(outFile);
- new SamFileValidator(out, 8000).setIndexValidationStringency(stringency).validateSamFileSummary(samReader, reference);
- final LineNumberReader reader = new LineNumberReader(new FileReader(outFile));
- if (reader.readLine().equals("No errors found")) {
- return new Histogram<String>();
- }
- final MetricsFile<MetricBase, String> outputFile = new MetricsFile<MetricBase, String>();
- outputFile.read(new FileReader(outFile));
- Assert.assertNotNull(outputFile.getHistogram());
- return outputFile.getHistogram();
- }
-
private void testHeaderVersion(final String version, final boolean expectValid) throws Exception {
final File samFile = File.createTempFile("validateHeader.", ".sam");
samFile.deleteOnExit();
@@ -468,4 +459,89 @@ public void duplicateReadsOutOfOrder() throws Exception {
Assert.assertFalse(results.isEmpty());
Assert.assertEquals(results.get(SAMValidationError.Type.MATES_ARE_SAME_END.getHistogramString()).getValue(), 2.0);
}
+
+
+ @DataProvider(name = "TagCorrectlyProcessData")
+ public Object[][] tagCorrectlyProcessData() throws IOException {
+ final String E2TagCorrectlyProcessTestData =
+ "@HD\tVN:1.0\tSO:unsorted\n" +
+ "@SQ\tSN:chr1\tLN:101\n" +
+ "@RG\tID:0\tSM:Hi,Mom!\n" +
+ "E\t147\tchr1\t15\t255\t10M\t=\t2\t-30\tCAACAGAAGC\t)'.*.+2,))\tE2:Z:CAA";
+
+ final String U2TagCorrectlyProcessTestData =
+ "@HD\tVN:1.0\tSO:unsorted\n" +
+ "@SQ\tSN:chr1\tLN:101\n" +
+ "@RG\tID:0\tSM:Hi,Mom!\n" +
+ "E\t147\tchr1\t15\t255\t10M\t=\t2\t-30\tCAACAGAAGC\t)'.*.+2,))\tU2:Z:CAA";
+
+ return new Object[][]{
+ {E2TagCorrectlyProcessTestData.getBytes(), SAMValidationError.Type.E2_BASE_EQUALS_PRIMARY_BASE},
+ {E2TagCorrectlyProcessTestData.getBytes(), SAMValidationError.Type.MISMATCH_READ_LENGTH_AND_E2_LENGTH},
+ {U2TagCorrectlyProcessTestData.getBytes(), SAMValidationError.Type.MISMATCH_READ_LENGTH_AND_U2_LENGTH}
+ };
+ }
+
+ @Test(dataProvider = "TagCorrectlyProcessData")
+ public void tagCorrectlyProcessTest(byte[] bytesFromFile,
+ SAMValidationError.Type errorType) throws Exception {
+ final SamReader samReader = SamReaderFactory
+ .makeDefault()
+ .validationStringency(ValidationStringency.SILENT)
+ .open(
+ SamInputResource.of(
+ new ByteArrayInputStream(bytesFromFile)
+ )
+ );
+ final Histogram<String> results = executeValidation(samReader, null, IndexValidationStringency.EXHAUSTIVE);
+ Assert.assertEquals(results.get(errorType.getHistogramString()).getValue(), 1.0);
+ }
+
+ @DataProvider(name = "validateBamFileTerminationData")
+ public Object[][] validateBamFileTerminationData() throws IOException {
+ return new Object[][]{
+ {getBrokenFile(TERMINATION_GZIP_BLOCK_SIZE), SAMValidationError.Type.BAM_FILE_MISSING_TERMINATOR_BLOCK},
+ {getBrokenFile(RANDOM_NUMBER_TRUNC_BYTE), SAMValidationError.Type.TRUNCATED_FILE}
+ };
+ }
+
+ @Test(dataProvider = "validateBamFileTerminationData")
+ public void validateBamFileTerminationTest(File file, SAMValidationError.Type errorType) throws IOException {
+ final SamFileValidator samFileValidator = new SamFileValidator(new PrintWriter(System.out), 8000);
+ samFileValidator.validateBamFileTermination(file);
+ Assert.assertEquals(samFileValidator.getErrorsByType().get(errorType).getValue(), 1.0);
+ }
+
+ private Histogram<String> executeValidation(final SamReader samReader, final ReferenceSequenceFile reference,
+ final IndexValidationStringency stringency) throws IOException {
+ return executeValidationWithErrorIgnoring(samReader, reference, stringency, Collections.EMPTY_LIST);
+ }
+
+ private Histogram<String> executeValidationWithErrorIgnoring(final SamReader samReader, final ReferenceSequenceFile reference,
+ final IndexValidationStringency stringency, Collection<SAMValidationError.Type> ignoringError) throws IOException {
+ final File outFile = File.createTempFile("validation", ".txt");
+ outFile.deleteOnExit();
+
+ final PrintWriter out = new PrintWriter(outFile);
+ final SamFileValidator samFileValidator = new SamFileValidator(out, 8000);
+ samFileValidator.setIndexValidationStringency(stringency).setErrorsToIgnore(ignoringError);
+ samFileValidator.validateSamFileSummary(samReader, reference);
+
+ final LineNumberReader reader = new LineNumberReader(new FileReader(outFile));
+ if (reader.readLine().equals("No errors found")) {
+ return new Histogram<>();
+ }
+ final MetricsFile<MetricBase, String> outputFile = new MetricsFile<>();
+ outputFile.read(new FileReader(outFile));
+ Assert.assertNotNull(outputFile.getHistogram());
+ return outputFile.getHistogram();
+ }
+
+ private File getBrokenFile(int truncByte) throws IOException {
+ final FileChannel stream = FileChannel.open(new File(TEST_DATA_DIR + "/test_samfile_version_1pt5.bam").toPath());
+ final File breakingFile = File.createTempFile("trunc", ".bam");
+ breakingFile.deleteOnExit();
+ FileChannel.open(breakingFile.toPath(), StandardOpenOption.WRITE).transferFrom(stream, 0, stream.size() - truncByte);
+ return breakingFile;
+ }
}