Update htsjdk to 3.0.1

build.gradle

@@ -65,7 +65,7 @@ def ensureBuildPrerequisites(buildPrerequisitesMessage) {
 
 ensureBuildPrerequisites(buildPrerequisitesMessage)
 
-final htsjdkVersion = System.getProperty('htsjdk.version', '3.0.0')
+final htsjdkVersion = System.getProperty('htsjdk.version', '3.0.1')
 final googleNio = 'com.google.cloud:google-cloud-nio:0.123.25'
 
 // Get the jdk files we need to run javaDoc. We need to use these during compile, testCompile,

src/main/java/picard/util/SequenceDictionaryUtils.java

@@ -179,7 +179,7 @@ public static void encodeDictionary(final BufferedWriter writer, Iterator<SAMSeq
     }
 
     public static SortingCollection<String> makeSortingCollection() {
-        final File tmpDir = IOUtil.createTempDir("SamDictionaryNames", null);
+        final File tmpDir = IOUtil.createTempDir("SamDictionaryNames").toFile();
         tmpDir.deleteOnExit();
         // 256 byte for one name, and 1/10 part of all memory for this, rough estimate
         long maxNamesInRam = Runtime.getRuntime().maxMemory() / 256 / 10;

src/test/java/picard/analysis/artifacts/CollectSequencingArtifactMetricsTest.java

@@ -32,7 +32,7 @@ public String getCommandLineProgramName() {
 
     @BeforeTest
     public void setUp() throws IOException {
-        globalTempOutputDir = IOUtil.createTempDir("artifactMetrics.", ".tmp");
+        globalTempOutputDir = IOUtil.createTempDir("artifactMetrics.tmp").toFile();
     }
 
     @AfterTest

src/test/java/picard/analysis/directed/CollectHsMetricsTest.java

@@ -189,7 +189,7 @@ public void testHsMetricsHandlesIndelsAppropriately() throws IOException {
         }
 
         // Write things out to file
-        final File dir = IOUtil.createTempDir("hsmetrics.", ".test");
+        final File dir = IOUtil.createTempDir("hsmetrics.test").toFile();
         final File bs = new File(dir, "baits.interval_list").getAbsoluteFile();
         final File ts = new File(dir, "targets.interval_list").getAbsoluteFile();
         baits.write(bs);
@@ -235,7 +235,7 @@ public void testHsMetricsHighTargetCoverage() throws IOException {
         }
 
         // Write things out to file
-        final File dir = IOUtil.createTempDir("hsmetrics.", ".test");
+        final File dir = IOUtil.createTempDir("hsmetrics.test").toFile();
         final File bs = new File(dir, "baits.interval_list").getAbsoluteFile();
         final File ts = new File(dir, "targets.interval_list").getAbsoluteFile();
         baits.write(bs);

src/test/java/picard/analysis/replicates/CollectIndependentReplicatesMetricTest.java

@@ -30,7 +30,7 @@
  */
 public class CollectIndependentReplicatesMetricTest {
     private final static File testdir = new File("testdata/picard/independent_replicates");
-    private final static File bamOutDir = IOUtil.createTempDir("convertSamToBam", "dir");
+    private final static File bamOutDir = IOUtil.createTempDir("convertSamToBamDir").toFile();
 
     private final static Map<String, String> sams = new ImmutableMap.Builder<String, String>()
             .put("twoPairs", "twopairs.sam")

src/test/java/picard/fastq/BamToBfqTest.java

@@ -25,7 +25,7 @@ public static Object[][] inputs() throws IOException {
     @Test(dataProvider = "inputs")
     public void testBamToBfq(final File input, final boolean isPairedRun,
                      final String outputFilePrefix) throws IOException {
-        final File analysisDir = IOUtil.createTempDir("BamToBfqTest", ".dir");
+        final File analysisDir = IOUtil.createTempDir("BamToBfqTestDir").toFile();
         try {
             final String[] args = new String[] {
                     "INPUT=" + input.getAbsolutePath(),

src/test/java/picard/illumina/CheckIlluminaDirectoryTest.java

@@ -53,7 +53,7 @@ public String getCommandLineProgramName() {
 
     @BeforeMethod
     private void setUp() throws Exception {
-        illuminaDir = IOUtil.createTempDir("ift_test", "IlluminaDir");
+        illuminaDir = IOUtil.createTempDir("ift_test.IlluminaDir").toFile();
 
         interopDir = new File(illuminaDir, "InterOp");
         if (!interopDir.exists() && !interopDir.mkdir()) {

src/test/java/picard/illumina/IlluminaLaneMetricsCollectorTest.java

@@ -25,7 +25,7 @@ private static File buildOutputFile(final File directory, final String prefix, f
     public void testWriteLaneMetrics(final String testRun) {
         for (final boolean useReadStructure : Arrays.asList(true, false)) {
             final CollectIlluminaLaneMetrics clp = new CollectIlluminaLaneMetrics();
-            clp.OUTPUT_DIRECTORY = IOUtil.createTempDir("illuminaLaneMetricsCollectorTest", null);
+            clp.OUTPUT_DIRECTORY = IOUtil.createTempDir("illuminaLaneMetricsCollectorTest").toFile();
             clp.RUN_DIRECTORY = new File(TEST_DIRECTORY, testRun);
             clp.OUTPUT_PREFIX = "test";
             if (useReadStructure) clp.READ_STRUCTURE = new ReadStructure("101T8B101T");
@@ -54,7 +54,7 @@ public void testCollectIlluminaLaneMetrics(final String testRun, final ReadStruc
         for (final boolean useReadStructure : Arrays.asList(true, false)) {
             final File runDirectory = new File(TILE_RUN_DIRECTORY, testRun);
             final CollectIlluminaLaneMetrics clp = new CollectIlluminaLaneMetrics();
-            clp.OUTPUT_DIRECTORY = IOUtil.createTempDir("illuminaLaneMetricsCollectorTest", null);
+            clp.OUTPUT_DIRECTORY = IOUtil.createTempDir("illuminaLaneMetricsCollectorTest").toFile();
             clp.RUN_DIRECTORY = runDirectory;
             clp.OUTPUT_PREFIX = "test";
             if (useReadStructure) clp.READ_STRUCTURE = readStructure;
@@ -90,7 +90,7 @@ public void testMissingPhasingValuesStrict() {
         for (final boolean useReadStructure : Arrays.asList(true, false)) {
             final File runDirectory = TEST_MISSING_PHASING_DIRECTORY;
             final CollectIlluminaLaneMetrics clp = new CollectIlluminaLaneMetrics();
-            clp.OUTPUT_DIRECTORY = IOUtil.createTempDir("illuminaLaneMetricsCollectorTest", null);
+            clp.OUTPUT_DIRECTORY = IOUtil.createTempDir("illuminaLaneMetricsCollectorTest").toFile();
             clp.RUN_DIRECTORY = runDirectory;
             clp.OUTPUT_PREFIX = "test";
             clp.VALIDATION_STRINGENCY = ValidationStringency.STRICT;
@@ -115,7 +115,7 @@ public void testMissingPhasingValuesSilent() {
         for (final boolean useReadStructure : Arrays.asList(true, false)) {
             final File runDirectory = TEST_MISSING_PHASING_DIRECTORY;
             final CollectIlluminaLaneMetrics clp = new CollectIlluminaLaneMetrics();
-            clp.OUTPUT_DIRECTORY = IOUtil.createTempDir("illuminaLaneMetricsCollectorTest", null);
+            clp.OUTPUT_DIRECTORY = IOUtil.createTempDir("illuminaLaneMetricsCollectorTest").toFile();
             clp.RUN_DIRECTORY = runDirectory;
             clp.OUTPUT_PREFIX = "test";
             clp.VALIDATION_STRINGENCY = ValidationStringency.SILENT;
@@ -141,7 +141,7 @@ public void testMismatchedMetricsVersions() {
         final ReadStructure readStructure = new ReadStructure("151T8B8B151T");
         for (final boolean useReadStructure : Arrays.asList(true, false)) {
             final CollectIlluminaLaneMetrics clp = new CollectIlluminaLaneMetrics();
-            clp.OUTPUT_DIRECTORY = IOUtil.createTempDir("illuminaLaneMetricsCollectorTest", null);
+            clp.OUTPUT_DIRECTORY = IOUtil.createTempDir("illuminaLaneMetricsCollectorTest").toFile();
             clp.RUN_DIRECTORY = TEST_MISMATCHED_VERSIONS;
             clp.OUTPUT_PREFIX = "test";
             if (useReadStructure) clp.READ_STRUCTURE = readStructure;

src/test/java/picard/illumina/parser/BclParserTest.java

@@ -213,7 +213,7 @@ public void fullBclParserTestWBadDeletedSkips(final int[] tiles, final int size,
     }
 
     public void fullBclParserTestWDeletedSkipsImpl(final int[] tiles, final int size, final int seekAfter, final int newTileIndex, final int orderedTileIndex, final String readStructure) {
-        final File basecallDir = IOUtil.createTempDir("bclParserTest", "BaseCalls");
+        final File basecallDir = IOUtil.createTempDir("bclParserTest.BaseCalls").toFile();
 
         Exception exc = null;
         try {

src/test/java/picard/illumina/parser/IlluminaFileUtilTest.java

@@ -38,7 +38,7 @@ public class IlluminaFileUtilTest {
 
     @BeforeMethod
     private void setUp() throws Exception {
-        intensityDir = IOUtil.createTempDir("ift_test", "Intensities");
+        intensityDir = IOUtil.createTempDir("ift_test.Intensities").toFile();
         basecallDir = new File(intensityDir, "BaseCalls");
         if (!basecallDir.mkdir()) {
             throw new RuntimeException("Couldn't make basecalls dir " + basecallDir.getAbsolutePath());
@@ -517,7 +517,7 @@ public void testHasCbcls(final int lane,
                              final boolean createCbcl,
                              final boolean expectedResult) throws IOException {
 
-        final File basecallsDir = IOUtil.createTempDir("basecalls", "");
+        final File basecallsDir = IOUtil.createTempDir("basecalls").toFile();
         basecallsDir.deleteOnExit();
 
         if (0 < lane) {

src/test/java/picard/sam/CramCompatibilityTest.java

@@ -10,6 +10,8 @@
 import picard.cmdline.CommandLineProgram;
 
 import java.io.*;
+import java.nio.file.Files;
+import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
@@ -38,11 +40,11 @@ public class CramCompatibilityTest {
     public static final String MBA_UNMAPPED_CRAM = "testdata/picard/sam/MergeBamAlignment/cliptest.unmapped.cram";
     public static final String MBA_REFERENCE = "testdata/picard/sam/MergeBamAlignment/cliptest.fasta";
 
-    private static final File outputDir = IOUtil.createTempDir("testdata/picard/sam/CramCompatibilityTest", ".tmp");
+    private static final Path outputDir = IOUtil.createTempDir("CramCompatibilityTest.tmp");
 
     @AfterTest
     public void tearDown() {
-        IOUtil.recursiveDelete(outputDir.toPath());
+        IOUtil.recursiveDelete(outputDir);
     }
 
     @DataProvider(name = "programArgsForCRAMWithReference")
@@ -112,7 +114,7 @@ public void testShouldWriteCRAMWhenCRAMWithReference(String program,
             launchProgram(program, cramFile, outputFile.getAbsolutePath(), parameters, reference);
             assertCRAM(outputFile);
         } else {
-            final File tmpDir = IOUtil.createTempDir(outputDir.getAbsolutePath(), program);
+            final File tmpDir = Files.createTempDirectory(outputDir, program).toFile();
             launchProgram(program, cramFile, tmpDir.getAbsolutePath(), parameters, reference);
             assertCRAMs(tmpDir);
         }
@@ -164,7 +166,7 @@ public void testShouldFailWhenCRAMWithoutReference(String program,
             launchProgram(program, cramFile, outputFile.getAbsolutePath(), parameters, null);
             assertCRAM(outputFile);
         } else {
-            final File tmpDir = IOUtil.createTempDir(outputDir.getAbsolutePath(), program);
+            final File tmpDir = Files.createTempDirectory(outputDir, program).toFile();
             launchProgram(program, cramFile, tmpDir.getAbsolutePath(), parameters, null);
             assertCRAMs(tmpDir);
         }
@@ -214,7 +216,7 @@ public void testShouldWriteCRAMWhenUnmappedCRAMWithoutReference(String program,
             launchProgram(program, cramFile, outputFile.getAbsolutePath(), parameters, null);
             assertCRAM(outputFile);
         } else {
-            final File tmpDir = IOUtil.createTempDir(outputDir.getAbsolutePath(), program);
+            final File tmpDir = Files.createTempDirectory(outputDir, program).toFile();
             launchProgram(program, cramFile, tmpDir.getAbsolutePath(), parameters, null);
             assertCRAMs(tmpDir);
         }
@@ -227,7 +229,7 @@ private File createTempCram(String name) throws IOException {
     private static File createTempFile(String name, String extension) {
         File file = null;
         try {
-            file = File.createTempFile(name, extension, outputDir);
+            file = File.createTempFile(name, extension, outputDir.toFile());
             file.deleteOnExit();
         } catch (IOException e) {
             e.printStackTrace();

src/test/java/picard/sam/DownsampleSamTest.java

@@ -72,7 +72,7 @@ void setupBuilder() throws IOException {
             setBuilder.addPair(readName, 1, 1, 100);
         }
 
-        tempDir = IOUtil.createTempDir("ds_test", "Downsampling");
+        tempDir = IOUtil.createTempDir("ds_test_Downsampling").toFile();
         tempSamFile = File.createTempFile("DownsampleSam", ".bam", tempDir);
 
         BufferedLineReader bufferedLineReader = null;

src/test/java/picard/sam/PositionBasedDownsampleSamTest.java

@@ -75,7 +75,7 @@ void setupBuilder() throws IOException {
             setBuilder.addPair(readName, 1, 1, 100);
         }
 
-        tempDir = IOUtil.createTempDir("pds_test", "PositionalDownsampling");
+        tempDir = IOUtil.createTempDir("pds_test_PositionalDownsampling").toFile();
         tempSamFile = File.createTempFile("PositionalDownsampleSam", ".bam", tempDir);
 
         BufferedLineReader bufferedLineReader = null;

src/test/java/picard/sam/SamErrorMetric/CollectSamErrorMetricsTest.java

@@ -57,7 +57,7 @@ public void samMetricsProvider() {
             throw new PicardException("This should only be called once!");
         }
 
-        OUTPUT_DATA_PATH = IOUtil.createTempDir("CollectSamErrorMetricsTest", null);
+        OUTPUT_DATA_PATH = IOUtil.createTempDir("CollectSamErrorMetricsTest.tmp").toFile();
 
         for (final File file : files) {
             final File vcf = new File(TEST_DIR, "NIST.selected.vcf");

src/test/java/picard/sam/markduplicates/MarkDuplicatesTest.java

@@ -84,7 +84,7 @@ public void testTwoMappedPairsWithSoftClippingFirstOfPairOnly() {
     @Test(dataProvider = "pgRecordChainingTest")
     public void pgRecordChainingTest(final boolean suppressPg,
                                      final Map<String, List<ExpectedPnAndVn>> expectedPnVnByReadName) {
-        final File outputDir = IOUtil.createTempDir(TEST_BASE_NAME + ".", ".tmp");
+        final File outputDir = IOUtil.createTempDir(TEST_BASE_NAME + ".tmp").toFile();
         outputDir.deleteOnExit();
         try {
             // Run MarkDuplicates, merging the 3 input files, and either enabling or suppressing PG header
@@ -177,7 +177,7 @@ public Object[][] pgRecordChainingTestDataProvider() {
 
     @Test(dataProvider = "testOpticalDuplicateDetectionDataProvider")
     public void testOpticalDuplicateDetection(final File sam, final long expectedNumOpticalDuplicates) {
-        final File outputDir = IOUtil.createTempDir(TEST_BASE_NAME + ".", ".tmp");
+        final File outputDir = IOUtil.createTempDir(TEST_BASE_NAME + ".tmp").toFile();
         outputDir.deleteOnExit();
         final File outputSam = new File(outputDir, TEST_BASE_NAME + ".sam");
         outputSam.deleteOnExit();

src/test/java/picard/sam/testers/SamFileTester.java

@@ -95,7 +95,7 @@ public File getOutputDir() {
     }
 
     private void setOutputDir() {
-        this.outputDir = IOUtil.createTempDir(this.getClass().getSimpleName() + ".", ".tmp");
+        this.outputDir = IOUtil.createTempDir(this.getClass().getSimpleName() + ".tmp").toFile();
         if (deleteOnExit) {
             outputDir.deleteOnExit();
         }
@@ -387,7 +387,7 @@ private File createInputFile(final String extension) throws IOException {
         if (extension.equals(".cram")) {
             final Path fasta = fastaFiles.computeIfAbsent(samRecordSetBuilder.getHeader(), h -> {
 
-                final Path fastaDir = IOUtil.createTempDir("SamFileTester", "").toPath();
+                final Path fastaDir = IOUtil.createTempDir("SamFileTester");
                 IOUtil.deleteOnExit(fastaDir);
                 final Path newFasta = fastaDir.resolve("input.fasta");
                 IOUtil.deleteOnExit(newFasta);

src/test/java/picard/util/IntervalListToolsTest.java

@@ -356,7 +356,7 @@ public void testScatter(final IntervalListScattererTest.Testcase tc) throws IOEx
 
         args.add("SUBDIVISION_MODE=" + tc.mode);
 
-        final File ilOutDir = IOUtil.createTempDir("IntervalListTools", "lists");
+        final File ilOutDir = IOUtil.createTempDir("IntervalListTools_lists").toFile();
         dirsToDelete.add(ilOutDir);
 
         if (tc.scatterWidth == 1) {
@@ -397,7 +397,7 @@ public void testScatterByContent(final IntervalListScattererTest.Testcase tc) th
 
         args.add("SUBDIVISION_MODE=" + tc.mode);
 
-        final File ilOutDir = IOUtil.createTempDir("IntervalListTools", "lists");
+        final File ilOutDir = IOUtil.createTempDir("IntervalListTools_lists").toFile();
         dirsToDelete.add(ilOutDir);
 
         if (tc.scatterWidth == 1) {
@@ -432,7 +432,7 @@ public void testScatterByContent(final IntervalListScattererTest.Testcase tc) th
     @Test(timeOut = 40_000)
     public void testLargeScatters() throws IOException {
         final int scatterCount=1_000;
-        final File ilOutDir = IOUtil.createTempDir("IntervalListTools", "lists");
+        final File ilOutDir = IOUtil.createTempDir("IntervalListTools_lists").toFile();
         dirsToDelete.add(ilOutDir);
 
         //scatter

src/test/java/picard/util/LiftoverVcfTest.java

@@ -50,7 +50,7 @@ public class LiftoverVcfTest extends CommandLineProgramTest {
     private static final File REFERENCE_FILE = new File(TEST_DATA_PATH, "dummy.reference.fasta");
     private static final File TWO_INTERVALS_REFERENCE_FILE = new File(TEST_DATA_PATH, "dummy.two.block.reference.fasta");
 
-    private static final File OUTPUT_DATA_PATH = IOUtil.createTempDir("LiftoverVcfsTest", null);
+    private static final File OUTPUT_DATA_PATH = IOUtil.createTempDir("LiftoverVcfsTest.tmp").toFile();
 
     private final int CHAIN_SIZE = 540; // the length of the single chain in CHAIN_FILE
 

src/test/java/picard/vcf/GenotypeConcordanceTest.java

@@ -58,7 +58,7 @@
 
 public class GenotypeConcordanceTest {
 
-    private static final File OUTPUT_DATA_PATH = IOUtil.createTempDir("GenotypeConcordanceTest", null);
+    private static final File OUTPUT_DATA_PATH = IOUtil.createTempDir("GenotypeConcordanceTest.tmp").toFile();
     private static final Path TEST_DATA_PATH = new File("testdata/picard/vcf/").toPath();
     private static final String TEST_DATA_PATH_STRING = TEST_DATA_PATH.toString();
 

src/test/java/picard/vcf/SplitVcfsTest.java

@@ -14,7 +14,7 @@
 
 public class SplitVcfsTest extends CommandLineProgramTest {
 
-    private static final File OUTPUT_DATA_PATH = IOUtil.createTempDir("SplitVcfsTest", null);
+    private static final File OUTPUT_DATA_PATH = IOUtil.createTempDir("SplitVcfsTest.tmp").toFile();
     private static final File TEST_DATA_PATH = new File("testdata/picard/vcf/");
 
     public String getCommandLineProgramName() {

src/test/java/picard/vcf/UpdateVcfSequenceDictionaryTest.java

@@ -41,7 +41,7 @@ public class UpdateVcfSequenceDictionaryTest {
     // vcfFormatTest.bad_dict.vcf is a vcf with two (2) ##contig lines deleted
     private final File SAM_SEQUENCE_DICTIONARY_VCF = new File(TEST_DATA_PATH, "vcfFormatTest.bad_dict.vcf");
 
-    private static final File OUTPUT_DATA_PATH = IOUtil.createTempDir("UpdateVcfSequenceDictionaryTest", null);
+    private static final File OUTPUT_DATA_PATH = IOUtil.createTempDir("UpdateVcfSequenceDictionaryTest.tmp").toFile();
     private static final File STD_OUT_FILE = new File(OUTPUT_DATA_PATH, "stdout.vcf");
     private static final String STD_OUT_NAME = "/dev/stdout";
 

testdata/picard/sam/smallIntervals.interval_list

@@ -1,3 +1,3 @@
 @HD	VN:1.0
-@SQ	SN:chrM	LN:16903	UR:chrM.reference.fasta
+@SQ	SN:chrM	LN:16571	UR:chrM.reference.fasta
 chrM	1	1000	+	foo