diff --git a/build.gradle b/build.gradle index a37de637ab..40ab6858b9 100644 --- a/build.gradle +++ b/build.gradle @@ -64,7 +64,7 @@ def ensureBuildPrerequisites(requiredJavaVersion, buildPrerequisitesMessage) { } ensureBuildPrerequisites(requiredJavaVersion, buildPrerequisitesMessage) -final htsjdkVersion = System.getProperty('htsjdk.version', '2.18.2') +final htsjdkVersion = System.getProperty('htsjdk.version', '2.19.0') // We use a custom shaded build of the NIO library to avoid a regression in the authentication layer. // GATK does the same, see https://github.com/broadinstitute/gatk/issues/3591 diff --git a/src/main/java/picard/sam/SamFormatConverter.java b/src/main/java/picard/sam/SamFormatConverter.java index 3a5eb4e65b..0e20184490 100644 --- a/src/main/java/picard/sam/SamFormatConverter.java +++ b/src/main/java/picard/sam/SamFormatConverter.java @@ -33,14 +33,13 @@ import htsjdk.samtools.util.IOUtil; import htsjdk.samtools.util.Log; import htsjdk.samtools.util.ProgressLogger; +import org.broadinstitute.barclay.argparser.Argument; +import org.broadinstitute.barclay.argparser.CommandLineProgramProperties; import org.broadinstitute.barclay.help.DocumentedFeature; import picard.PicardException; import picard.cmdline.CommandLineProgram; -import org.broadinstitute.barclay.argparser.CommandLineProgramProperties; -import org.broadinstitute.barclay.argparser.Argument; import picard.cmdline.StandardOptionDefinitions; import picard.cmdline.programgroups.ReadDataManipulationProgramGroup; -import picard.illumina.parser.ReadData; import java.io.File; @@ -55,15 +54,12 @@ oneLineSummary = "Convert a BAM file to a SAM file, or a SAM to a BAM", programGroup = ReadDataManipulationProgramGroup.class) @DocumentedFeature -public class - SamFormatConverter extends CommandLineProgram { - - private static final String PROGRAM_VERSION = "1.0"; +public class SamFormatConverter extends CommandLineProgram { // The following attributes define the command-line arguments - @Argument(doc = "The BAM or SAM file to parse.", shortName = StandardOptionDefinitions.INPUT_SHORT_NAME) public File INPUT; + @Argument(doc = "The BAM or SAM output file. ", shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME) public File OUTPUT; @@ -72,12 +68,24 @@ public static void main(final String[] argv) { } protected int doWork() { - IOUtil.assertFileIsReadable(INPUT); - IOUtil.assertFileIsWritable(OUTPUT); - final SamReader reader = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).open(INPUT); - final SAMFileWriter writer = new SAMFileWriterFactory().makeWriter(reader.getFileHeader(), true, OUTPUT, REFERENCE_SEQUENCE); + convert(INPUT, OUTPUT, REFERENCE_SEQUENCE, CREATE_INDEX); + return 0; + } - if (CREATE_INDEX && writer.getFileHeader().getSortOrder() != SAMFileHeader.SortOrder.coordinate) { + /** + * Convert a file from one of sam/bam/cram format to another based on the extension of output. + * + * @param input input file in one of sam/bam/cram format + * @param output output to write converted file to, the conversion is based on the extension of this filename + * @param referenceSequence the reference sequence to use, necessary when reading/writing cram + * @param createIndex whether or not an index should be written alongside the output file + */ + public static void convert(final File input, final File output, final File referenceSequence, final Boolean createIndex) { + IOUtil.assertFileIsReadable(input); + IOUtil.assertFileIsWritable(output); + final SamReader reader = SamReaderFactory.makeDefault().referenceSequence(referenceSequence).open(input); + final SAMFileWriter writer = new SAMFileWriterFactory().makeWriter(reader.getFileHeader(), true, output, referenceSequence); + if (createIndex && writer.getFileHeader().getSortOrder() != SAMFileHeader.SortOrder.coordinate) { throw new PicardException("Can't CREATE_INDEX unless sort order is coordinate"); } @@ -88,6 +96,5 @@ protected int doWork() { } CloserUtil.close(reader); writer.close(); - return 0; } } diff --git a/src/main/java/picard/vcf/RenameSampleInVcf.java b/src/main/java/picard/vcf/RenameSampleInVcf.java index 732de78c17..4a8af38a7f 100644 --- a/src/main/java/picard/vcf/RenameSampleInVcf.java +++ b/src/main/java/picard/vcf/RenameSampleInVcf.java @@ -115,7 +115,7 @@ protected int doWork() { IOUtil.assertFileIsReadable(INPUT); IOUtil.assertFileIsWritable(OUTPUT); - final VCFFileReader in = new VCFFileReader(INPUT); + final VCFFileReader in = new VCFFileReader(INPUT, false); final VCFHeader header = in.getFileHeader(); if (header.getGenotypeSamples().size() > 1) { diff --git a/src/test/java/picard/analysis/replicates/CollectIndependentReplicatesMetricTest.java b/src/test/java/picard/analysis/replicates/CollectIndependentReplicatesMetricTest.java index 94e201413d..0c6c5a15d8 100644 --- a/src/test/java/picard/analysis/replicates/CollectIndependentReplicatesMetricTest.java +++ b/src/test/java/picard/analysis/replicates/CollectIndependentReplicatesMetricTest.java @@ -60,7 +60,7 @@ public void prepareBams() throws IOException { @AfterTest public void tearDown() { - TestUtil.recursiveDelete(bamOutDir); + IOUtil.recursiveDelete(bamOutDir.toPath()); } @DataProvider(name = "simpleTests") diff --git a/src/test/java/picard/fastq/BamToBfqTest.java b/src/test/java/picard/fastq/BamToBfqTest.java index 5ea3f08d69..32d6538e88 100644 --- a/src/test/java/picard/fastq/BamToBfqTest.java +++ b/src/test/java/picard/fastq/BamToBfqTest.java @@ -42,7 +42,7 @@ public void testBamToBfq(final File input, final boolean isPairedRun, Assert.assertEquals(Files.readAllBytes(output.toPath()), Files.readAllBytes(expectedBFQ.toPath())); } finally { - TestUtil.recursiveDelete(analysisDir); + IOUtil.recursiveDelete(analysisDir.toPath()); } } } diff --git a/src/test/java/picard/illumina/IlluminaBasecallsToFastqTest.java b/src/test/java/picard/illumina/IlluminaBasecallsToFastqTest.java index 903b2fa8a7..704cd2013d 100644 --- a/src/test/java/picard/illumina/IlluminaBasecallsToFastqTest.java +++ b/src/test/java/picard/illumina/IlluminaBasecallsToFastqTest.java @@ -116,7 +116,7 @@ public void testMultiplexWithIlluminaReadNameHeaders() throws Exception { } } finally { - TestUtil.recursiveDelete(outputDir); + IOUtil.recursiveDelete(outputDir.toPath()); } } @@ -222,7 +222,7 @@ private void runStandardTest(final int lane, final String jobName, final String } } } finally { - TestUtil.recursiveDelete(outputDir); + IOUtil.recursiveDelete(outputDir.toPath()); } } diff --git a/src/test/java/picard/illumina/IlluminaBasecallsToSamTest.java b/src/test/java/picard/illumina/IlluminaBasecallsToSamTest.java index a8c6d757dc..9df2a46bee 100644 --- a/src/test/java/picard/illumina/IlluminaBasecallsToSamTest.java +++ b/src/test/java/picard/illumina/IlluminaBasecallsToSamTest.java @@ -260,8 +260,7 @@ private void runStandardTest(final int lane, final String jobName, final String IOUtil.assertFilesEqual(outputSam, new File(testDataDir, outputSam.getName())); } } finally { - TestUtil.recursiveDelete(outputDir.toFile()); - Files.delete(outputDir); + IOUtil.recursiveDelete(outputDir); } } } diff --git a/src/test/java/picard/sam/SamFileConverterTest.java b/src/test/java/picard/sam/SamFormatConverterTest.java similarity index 61% rename from src/test/java/picard/sam/SamFileConverterTest.java rename to src/test/java/picard/sam/SamFormatConverterTest.java index 7c567aa361..6a7e7b386c 100644 --- a/src/test/java/picard/sam/SamFileConverterTest.java +++ b/src/test/java/picard/sam/SamFormatConverterTest.java @@ -24,6 +24,8 @@ package picard.sam; +import htsjdk.samtools.Defaults; +import org.testng.annotations.DataProvider; import org.testng.annotations.Test; import java.io.File; @@ -34,63 +36,47 @@ import static org.testng.Assert.assertEquals; import static org.testng.Assert.assertTrue; -public class SamFileConverterTest { +public class SamFormatConverterTest { - private static final File TEST_DATA_DIR = new File("testdata/picard/sam/SamFileConverterTest"); + private static final File TEST_DATA_DIR = new File("testdata/picard/sam/SamFormatConverterTest"); private static final File unmappedSam = new File(TEST_DATA_DIR, "unmapped.sam"); private static final File unmappedBam = new File(TEST_DATA_DIR, "unmapped.bam"); private static final File unmappedCram = new File(TEST_DATA_DIR, "unmapped.cram"); - @Test - public void testSAMToBAM() { - convertFile(unmappedSam, unmappedBam, ".bam"); - } - - @Test - public void testSAMToCRAM() { - convertFile(unmappedSam, unmappedCram, ".cram"); - } + private static final File ESSENTIALLY_EMPTY_REFERENCE_TO_USE_WITH_UNMAPPED_CRAM = new File(TEST_DATA_DIR, "basicallyEmpty.fasta"); - @Test - public void testBAMToCRAM() { - convertFile(unmappedBam, unmappedCram, ".cram"); - } - - @Test - public void testBAMToSAM() { - convertFile(unmappedBam, unmappedSam, ".sam"); - } + @DataProvider + public Object[][] conversionCases() { + return new Object[][]{ + {unmappedSam, unmappedBam, ".bam"}, + {unmappedSam, unmappedCram, ".cram"}, + {unmappedBam, unmappedCram, ".cram"}, + {unmappedBam, unmappedSam, ".sam"}, + {unmappedCram, unmappedBam, ".bam"}, + {unmappedCram, unmappedSam, ".sam"}, - @Test - public void testCRAMToBAM() { - convertFile(unmappedCram, unmappedBam, ".bam"); + }; } - @Test - public void testCRAMToSAM() { - convertFile(unmappedCram, unmappedSam, ".sam"); + @Test(dataProvider = "conversionCases") + public void testConvert(File input, File expected, String extension) throws IOException { + convertFile(input, expected, extension); } - private void convertFile(final File inputFile, final File fileToCompare, final String extension) { - final SamFormatConverter samFormatConverter = new SamFormatConverter(); - final List samFiles = new ArrayList(); + private void convertFile(final File inputFile, final File fileToCompare, final String extension) throws IOException { + final List samFiles = new ArrayList<>(); final ValidateSamFile validateSamFile = new ValidateSamFile(); final CompareSAMs compareSAMs = new CompareSAMs(); - samFormatConverter.INPUT = inputFile; - try { - samFormatConverter.OUTPUT = File.createTempFile("SamFileConverterTest." + inputFile.getName(), extension); - samFormatConverter.OUTPUT.deleteOnExit(); - } catch (final IOException e) { - e.printStackTrace(); - } - samFormatConverter.doWork(); + final File output = File.createTempFile("SamFormatConverterTest." + inputFile.getName(), extension); + output.deleteOnExit(); + SamFormatConverter.convert(inputFile, output, ESSENTIALLY_EMPTY_REFERENCE_TO_USE_WITH_UNMAPPED_CRAM, Defaults.CREATE_INDEX); - validateSamFile.INPUT = samFormatConverter.OUTPUT; + validateSamFile.INPUT = output; assertEquals(validateSamFile.doWork(), 0); - samFiles.add(samFormatConverter.OUTPUT); + samFiles.add(output); samFiles.add(fileToCompare); compareSAMs.samFiles = samFiles; diff --git a/src/test/java/picard/sam/markduplicates/AbstractMarkDuplicatesCommandLineProgramTester.java b/src/test/java/picard/sam/markduplicates/AbstractMarkDuplicatesCommandLineProgramTester.java index cf6e4ba4af..46254929e1 100644 --- a/src/test/java/picard/sam/markduplicates/AbstractMarkDuplicatesCommandLineProgramTester.java +++ b/src/test/java/picard/sam/markduplicates/AbstractMarkDuplicatesCommandLineProgramTester.java @@ -33,6 +33,7 @@ import htsjdk.samtools.metrics.MetricsFile; import htsjdk.samtools.util.CloseableIterator; import htsjdk.samtools.util.FormatUtil; +import htsjdk.samtools.util.IOUtil; import htsjdk.samtools.util.TestUtil; import org.testng.Assert; import picard.cmdline.CommandLineProgram; @@ -202,7 +203,7 @@ public MetricsFile testMetrics() throws IOException } return metricsOutput; } finally { - TestUtil.recursiveDelete(getOutputDir()); + IOUtil.recursiveDelete(getOutputDir().toPath()); } } diff --git a/src/test/java/picard/sam/markduplicates/MarkDuplicatesSetSizeHistogramTester.java b/src/test/java/picard/sam/markduplicates/MarkDuplicatesSetSizeHistogramTester.java index ab126033cf..6b3c6767d5 100644 --- a/src/test/java/picard/sam/markduplicates/MarkDuplicatesSetSizeHistogramTester.java +++ b/src/test/java/picard/sam/markduplicates/MarkDuplicatesSetSizeHistogramTester.java @@ -26,14 +26,17 @@ import htsjdk.samtools.metrics.MetricsFile; import htsjdk.samtools.util.Histogram; -import htsjdk.samtools.util.TestUtil; +import htsjdk.samtools.util.IOUtil; import org.testng.Assert; import org.testng.annotations.AfterClass; import picard.cmdline.CommandLineProgram; import picard.sam.DuplicationMetrics; import java.io.IOException; -import java.util.*; +import java.util.Arrays; +import java.util.HashMap; +import java.util.List; +import java.util.Map; /** * This class is an extension of AbstractMarkDuplicatesCommandLineProgramTester used to test MarkDuplicatesWithMateCigar with SAM files generated on the fly. @@ -77,7 +80,7 @@ public void test() throws IOException { @AfterClass public void afterTest() { - TestUtil.recursiveDelete(getOutputDir()); + IOUtil.recursiveDelete(getOutputDir().toPath()); } } diff --git a/src/test/java/picard/sam/markduplicates/MarkDuplicatesTagRepresentativeReadIndexTester.java b/src/test/java/picard/sam/markduplicates/MarkDuplicatesTagRepresentativeReadIndexTester.java index 6926d1a574..5d38e9d168 100644 --- a/src/test/java/picard/sam/markduplicates/MarkDuplicatesTagRepresentativeReadIndexTester.java +++ b/src/test/java/picard/sam/markduplicates/MarkDuplicatesTagRepresentativeReadIndexTester.java @@ -29,6 +29,7 @@ import htsjdk.samtools.SamReaderFactory; import htsjdk.samtools.metrics.MetricsFile; import htsjdk.samtools.util.CloserUtil; +import htsjdk.samtools.util.IOUtil; import htsjdk.samtools.util.TestUtil; import org.testng.Assert; import picard.PicardException; @@ -118,7 +119,7 @@ public void test() { Assert.assertEquals(observedMetrics.ESTIMATED_LIBRARY_SIZE, expectedMetrics.ESTIMATED_LIBRARY_SIZE, "ESTIMATED_LIBRARY_SIZE does not match expected"); Assert.assertEquals(observedMetrics.SECONDARY_OR_SUPPLEMENTARY_RDS, expectedMetrics.SECONDARY_OR_SUPPLEMENTARY_RDS, "SECONDARY_OR_SUPPLEMENTARY_RDS does not match expected"); } finally { - TestUtil.recursiveDelete(getOutputDir()); + IOUtil.recursiveDelete(getOutputDir().toPath()); } } diff --git a/src/test/java/picard/sam/markduplicates/MarkDuplicatesTest.java b/src/test/java/picard/sam/markduplicates/MarkDuplicatesTest.java index fdc2f5d317..405e8b1a11 100644 --- a/src/test/java/picard/sam/markduplicates/MarkDuplicatesTest.java +++ b/src/test/java/picard/sam/markduplicates/MarkDuplicatesTest.java @@ -139,7 +139,7 @@ public void pgRecordChainingTest(final boolean suppressPg, } } finally { - TestUtil.recursiveDelete(outputDir); + IOUtil.recursiveDelete(outputDir.toPath()); } } @@ -195,7 +195,7 @@ public void testOpticalDuplicateDetection(final File sam, final long expectedNum markDuplicates.PROGRAM_RECORD_ID = null; Assert.assertEquals(markDuplicates.doWork(), 0); Assert.assertEquals(markDuplicates.numOpticalDuplicates(), expectedNumOpticalDuplicates); - TestUtil.recursiveDelete(outputDir); + IOUtil.recursiveDelete(outputDir.toPath()); } diff --git a/src/test/java/picard/sam/testers/CleanSamTester.java b/src/test/java/picard/sam/testers/CleanSamTester.java index 5522e1b0e4..a15c6df4cd 100644 --- a/src/test/java/picard/sam/testers/CleanSamTester.java +++ b/src/test/java/picard/sam/testers/CleanSamTester.java @@ -9,6 +9,7 @@ import htsjdk.samtools.SamReaderFactory; import htsjdk.samtools.ValidationStringency; import htsjdk.samtools.util.CloserUtil; +import htsjdk.samtools.util.IOUtil; import htsjdk.samtools.util.TestUtil; import org.testng.Assert; import picard.sam.CleanSam; @@ -58,7 +59,7 @@ protected void test() { Assert.assertTrue(validated, "ValidateSamFile failed"); } finally { - TestUtil.recursiveDelete(getOutputDir()); + IOUtil.recursiveDelete(getOutputDir().toPath()); } } } diff --git a/src/test/java/picard/util/IntervalListToolsTest.java b/src/test/java/picard/util/IntervalListToolsTest.java index 07c538b85c..5cafe0d507 100644 --- a/src/test/java/picard/util/IntervalListToolsTest.java +++ b/src/test/java/picard/util/IntervalListToolsTest.java @@ -172,7 +172,7 @@ public static Iterator testScatterTestcases() { @AfterTest void deleteTempDirs() { - dirsToDelete.forEach(TestUtil::recursiveDelete); + dirsToDelete.forEach(file -> IOUtil.recursiveDelete(file.toPath())); } @Test(dataProvider = "testScatterTestcases") diff --git a/src/test/java/picard/vcf/MendelianViolations/FindMendelianViolationsTest.java b/src/test/java/picard/vcf/MendelianViolations/FindMendelianViolationsTest.java index 05abf4a401..015e835e27 100644 --- a/src/test/java/picard/vcf/MendelianViolations/FindMendelianViolationsTest.java +++ b/src/test/java/picard/vcf/MendelianViolations/FindMendelianViolationsTest.java @@ -128,7 +128,7 @@ public void testFindMedelianViolations() throws IOException { Assert.assertEquals(grepMv(violationsFAKE, Haploid_Other.name()), mv.NUM_HAPLOID_OTHER); Assert.assertEquals(grepMv(violationsFAKE, Other.name()), mv.NUM_OTHER); - TestUtil.recursiveDelete(directoryForViolations); + IOUtil.recursiveDelete(directoryForViolations.toPath()); } /** returns the number of lines in the file that contain a regular expression (decorated with "MV=" and diff --git a/testdata/picard/sam/SamFormatConverterTest/basicallyEmpty.fasta b/testdata/picard/sam/SamFormatConverterTest/basicallyEmpty.fasta new file mode 100644 index 0000000000..ee6adf5f5d --- /dev/null +++ b/testdata/picard/sam/SamFormatConverterTest/basicallyEmpty.fasta @@ -0,0 +1,2 @@ +>chrNull +NNNNNNN \ No newline at end of file diff --git a/testdata/picard/sam/SamFileConverterTest/unmapped.bam b/testdata/picard/sam/SamFormatConverterTest/unmapped.bam similarity index 100% rename from testdata/picard/sam/SamFileConverterTest/unmapped.bam rename to testdata/picard/sam/SamFormatConverterTest/unmapped.bam diff --git a/testdata/picard/sam/SamFileConverterTest/unmapped.cram b/testdata/picard/sam/SamFormatConverterTest/unmapped.cram similarity index 100% rename from testdata/picard/sam/SamFileConverterTest/unmapped.cram rename to testdata/picard/sam/SamFormatConverterTest/unmapped.cram diff --git a/testdata/picard/sam/SamFileConverterTest/unmapped.sam b/testdata/picard/sam/SamFormatConverterTest/unmapped.sam similarity index 100% rename from testdata/picard/sam/SamFileConverterTest/unmapped.sam rename to testdata/picard/sam/SamFormatConverterTest/unmapped.sam