Convert FastqToSam and RevertSam to use PicardHtsPath

src/main/java/picard/cmdline/CommandLineProgram.java

@@ -40,7 +40,6 @@
 import htsjdk.samtools.util.BlockGunzipper;
 import htsjdk.samtools.util.IOUtil;
 import htsjdk.samtools.util.Log;
-import htsjdk.samtools.util.zip.DeflaterFactory;
 import htsjdk.variant.variantcontext.writer.Options;
 import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder;
 import org.broadinstitute.barclay.argparser.Argument;
@@ -51,7 +50,6 @@
 import org.broadinstitute.barclay.argparser.CommandLineParserOptions;
 import org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParser;
 import org.broadinstitute.barclay.argparser.SpecialArgumentsCollection;
-import picard.PicardException;
 import picard.cmdline.argumentcollections.OptionalReferenceArgumentCollection;
 import picard.cmdline.argumentcollections.ReferenceArgumentCollection;
 import picard.cmdline.argumentcollections.RequiredReferenceArgumentCollection;

src/main/java/picard/sam/FastqToSam.java

@@ -51,9 +51,15 @@
 import picard.cmdline.CommandLineProgram;
 import picard.cmdline.StandardOptionDefinitions;
 import picard.cmdline.programgroups.ReadDataManipulationProgramGroup;
+import picard.nio.PicardHtsPath;
 
 import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
 
 /**
@@ -150,10 +156,10 @@ public class FastqToSam extends CommandLineProgram {
     private static final Log LOG = Log.getInstance(FastqToSam.class);
 
     @Argument(shortName="F1", doc="Input fastq file (optionally gzipped) for single end data, or first read in paired end data.")
-    public File FASTQ;
+    public PicardHtsPath FASTQ;
 
     @Argument(shortName="F2", doc="Input fastq file (optionally gzipped) for the second read of paired end data.", optional=true)
-    public File FASTQ2;
+    public PicardHtsPath FASTQ2;
 
     @Argument(doc="Use sequential fastq files with the suffix <prefix>_###.fastq or <prefix>_###.fastq.gz." +
             "The files should be named:\n" +
@@ -274,53 +280,53 @@ public static FastqQualityFormat determineQualityFormat(final FastqReader reader
      *   RUNNAME_S8_L005_R1_004.fastq
      * where `baseFastq` is the first in that list.
      */
-    protected static List<File> getSequentialFileList(final File baseFastq) {
-        final List<File> files = new ArrayList<>();
+    protected static List<Path> getSequentialFileList(final Path baseFastq) {
+        final List<Path> files = new ArrayList<>();
         files.add(baseFastq);
 
         // Find the correct extension used in the base FASTQ
         FastqExtensions fastqExtensions = null;
         String suffix = null; // store the suffix including the extension
         for (final FastqExtensions ext : FastqExtensions.values()) {
             suffix = "_001" + ext.getExtension();
-            if (baseFastq.getAbsolutePath().endsWith(suffix)) {
+            if (baseFastq.toString().endsWith(suffix)) {
                 fastqExtensions = ext;
                 break;
             }
         }
         if (null == fastqExtensions) {
-            throw new PicardException(String.format("Could not parse the FASTQ extension (expected '_001' + '%s'): %s", FastqExtensions.values().toString(), baseFastq));
+            throw new PicardException(String.format("Could not parse the FASTQ extension (expected '_001' + '%s'): %s", Arrays.toString(FastqExtensions.values()), baseFastq));
         }
 
         // Find all the files
         for (int idx = 2; true; idx++) {
-            String fastq = baseFastq.getAbsolutePath();
+            String fastq = baseFastq.toAbsolutePath().toString();
             fastq = String.format("%s_%03d%s", fastq.substring(0, fastq.length() - suffix.length()), idx, fastqExtensions.getExtension());
             try {
-                IOUtil.assertFileIsReadable(new File(fastq));
+                IOUtil.assertFileIsReadable(Paths.get(fastq));
             } catch (final SAMException e) { // the file is not readable, so do not continue
                 break;
             }
-            files.add(new File(fastq));
+            files.add(Paths.get(fastq));
         }
 
         return files;
     }
 
     /* Simply invokes the right method for unpaired or paired data. */
     protected int doWork() {
-        IOUtil.assertFileIsReadable(FASTQ);
+        IOUtil.assertFileIsReadable(FASTQ.toPath());
         if (FASTQ2 != null) {
-            IOUtil.assertFileIsReadable(FASTQ2);
+            IOUtil.assertFileIsReadable(FASTQ2.toPath());
         }
         IOUtil.assertFileIsWritable(OUTPUT);
 
         final SAMFileHeader header = createSamFileHeader();
         final SAMFileWriter writer = new SAMFileWriterFactory().makeWriter(header, false, OUTPUT, REFERENCE_SEQUENCE);
 
         // Set the quality format
-        QUALITY_FORMAT = FastqToSam.determineQualityFormat(fileToFastqReader(FASTQ),
-                (FASTQ2 == null) ? null : fileToFastqReader(FASTQ2),
+        QUALITY_FORMAT = FastqToSam.determineQualityFormat(fileToFastqReader(FASTQ.toPath()),
+                (FASTQ2 == null) ? null : fileToFastqReader(FASTQ2.toPath()),
                 QUALITY_FORMAT);
 
         // Lists for sequential files, but also used when not sequential
@@ -329,11 +335,11 @@ protected int doWork() {
 
         if (USE_SEQUENTIAL_FASTQS) {
             // Get all the files
-            for (final File fastq : getSequentialFileList(FASTQ)) {
+            for (final Path fastq : getSequentialFileList(FASTQ.toPath())) {
                 readers1.add(fileToFastqReader(fastq));
             }
             if (null != FASTQ2) {
-                for (final File fastq : getSequentialFileList(FASTQ2)) {
+                for (final Path fastq : getSequentialFileList(FASTQ2.toPath())) {
                     readers2.add(fileToFastqReader(fastq));
                 }
                 if (readers1.size() != readers2.size()) {
@@ -342,9 +348,9 @@ protected int doWork() {
             }
         }
         else {
-            readers1.add(fileToFastqReader(FASTQ));
+            readers1.add(fileToFastqReader(FASTQ.toPath()));
             if (FASTQ2 != null) {
-                readers2.add(fileToFastqReader(FASTQ2));
+                readers2.add(fileToFastqReader(FASTQ2.toPath()));
             }
         }
 
@@ -428,8 +434,12 @@ protected int doPaired(final FastqReader freader1, final FastqReader freader2, f
         return readCount;
     }
 
-    private FastqReader fileToFastqReader(final File file) {
-        return new FastqReader(file, ALLOW_AND_IGNORE_EMPTY_LINES);
+    private FastqReader fileToFastqReader(final Path path) throws PicardException {
+        try {
+            return new FastqReader(null, Files.newBufferedReader(path), ALLOW_AND_IGNORE_EMPTY_LINES);
+        } catch (IOException e){
+            throw new PicardException("cannot create a reader for " + path, e);
+        }
     }
 
     private SAMRecord createSamRecord(final SAMFileHeader header, final String baseName, final FastqRecord frec, final boolean paired) {

src/main/java/picard/sam/RevertSam.java

@@ -57,6 +57,7 @@
 import picard.cmdline.CommandLineProgram;
 import picard.cmdline.StandardOptionDefinitions;
 import picard.cmdline.programgroups.ReadDataManipulationProgramGroup;
+import picard.nio.PicardHtsPath;
 import picard.util.TabbedTextFileWithHeaderParser;
 
 import java.io.File;
@@ -144,7 +145,7 @@ public class RevertSam extends CommandLineProgram {
             "(e.g. invalid alignment information will be obviated when the REMOVE_ALIGNMENT_INFORMATION option is used).\n" +
             "";
     @Argument(shortName = StandardOptionDefinitions.INPUT_SHORT_NAME, doc = "The input SAM/BAM/CRAM file to revert the state of.")
-    public File INPUT;
+    public PicardHtsPath INPUT;
 
     @Argument(mutex = {"OUTPUT_MAP"}, shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME, doc = "The output SAM/BAM/CRAM file to create, or an output directory if OUTPUT_BY_READGROUP is true.")
     public File OUTPUT;
@@ -249,11 +250,11 @@ protected String[] customCommandLineValidation() {
     }
 
     protected int doWork() {
-        IOUtil.assertFileIsReadable(INPUT);
+        IOUtil.assertFileIsReadable(INPUT.toPath());
         ValidationUtil.assertWritable(OUTPUT, OUTPUT_BY_READGROUP);
 
         final boolean sanitizing = SANITIZE;
-        final SamReader in = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).validationStringency(VALIDATION_STRINGENCY).open(INPUT);
+        final SamReader in = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).validationStringency(VALIDATION_STRINGENCY).open(INPUT.toPath());
         final SAMFileHeader inHeader = in.getFileHeader();
         ValidationUtil.validateHeaderOverrides(inHeader, SAMPLE_ALIAS, LIBRARY_NAME);
 
@@ -326,8 +327,14 @@ protected int doWork() {
             out.close();
         } else {
             final Map<SAMReadGroupRecord, FastqQualityFormat> readGroupToFormat;
+            final Path referenceSequencePath;
             try {
-                readGroupToFormat = createReadGroupFormatMap(inHeader, REFERENCE_SEQUENCE, VALIDATION_STRINGENCY, INPUT, RESTORE_ORIGINAL_QUALITIES);
+                if (REFERENCE_SEQUENCE != null) {
+                    referenceSequencePath = REFERENCE_SEQUENCE.toPath();
+                } else {
+                    referenceSequencePath = null;
+                }
+                readGroupToFormat = createReadGroupFormatMap(inHeader, referenceSequencePath, VALIDATION_STRINGENCY, INPUT.toPath(), RESTORE_ORIGINAL_QUALITIES);
             } catch (final PicardException e) {
                 log.error(e.getMessage());
                 return -1;
@@ -613,9 +620,9 @@ private SAMFileHeader createOutHeader(
 
     private Map<SAMReadGroupRecord, FastqQualityFormat> createReadGroupFormatMap(
             final SAMFileHeader inHeader,
-            final File referenceSequence,
+            final Path referenceSequence,
             final ValidationStringency validationStringency,
-            final File input,
+            final Path input,
             final boolean restoreOriginalQualities) {
 
         final Map<SAMReadGroupRecord, FastqQualityFormat> readGroupToFormat = new HashMap<>();

src/test/java/picard/sam/AbstractAlignmentMergerTest.java

@@ -15,9 +15,11 @@
 import org.testng.annotations.Test;
 import picard.cmdline.CommandLineProgramTest;
 import picard.cmdline.argumentcollections.RequiredReferenceArgumentCollection;
+import picard.nio.PicardHtsPath;
 
 import java.io.File;
 import java.io.IOException;
+import java.nio.file.Path;
 import java.util.Collections;
 import java.util.Iterator;
 import java.util.LinkedList;
@@ -675,9 +677,9 @@ public void testUnmapBacterialContamination() throws IOException {
 //        builder.addFrag("frag3",1,500,false,false,"20S20M60S",null, 45);
 //        builder.addFrag("frag4",1,500,true,false,"20S20M60S",null, 45);
 
-        final File file = newTempSamFile("aligned");
+        final PicardHtsPath file = PicardHtsPath.fromPath(newTempSamFile("aligned").toPath());
 
-        try (SAMFileWriter writer = new SAMFileWriterFactory().makeWriter(builder.getHeader(), true, file, null)) {
+        try (SAMFileWriter writer = new SAMFileWriterFactory().makeWriter(builder.getHeader(), true, file.toPath(), (Path) null)) {
             builder.getRecords().forEach(writer::addAlignment);
         }
 
@@ -697,7 +699,7 @@ public void testUnmapBacterialContamination() throws IOException {
 
         MergeBamAlignment mergeBamAlignment = new MergeBamAlignment();
 
-        mergeBamAlignment.ALIGNED_BAM = Collections.singletonList(file);
+        mergeBamAlignment.ALIGNED_BAM = Collections.singletonList(file.toPath().toFile()); // TODO update to use Path when MergeBamAlignment is updated to use Path
         mergeBamAlignment.UNMAPPED_BAM = fileUnaligned;
         mergeBamAlignment.UNMAP_CONTAMINANT_READS = true;
 

src/test/java/picard/sam/FastqToSamTest.java

@@ -38,6 +38,7 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -185,7 +186,7 @@ private File convertFile(final String fastqFilename1,
         final File fastq2 = (fastqFilename2 != null) ? new File(TEST_DATA_DIR, fastqFilename2) : null;
         final File samFile = newTempSamFile(fastq1.getName());
 
-        final List<String> args =new ArrayList<String>();
+        final List<String> args = new ArrayList<>();
 
         args.add("FASTQ=" + fastq1.getAbsolutePath());
         args.add("OUTPUT=" + samFile.getAbsolutePath());
@@ -296,9 +297,9 @@ public void testSequentialFiles() throws IOException {
         final String pairedEnd1 = "sequential-files/paired_end_R1_001.fastq";
         final String pairedEnd2 = "sequential-files/paired_end_R2_001.fastq";
 
-        Assert.assertEquals(FastqToSam.getSequentialFileList(new File(TEST_DATA_DIR, "/" + singleEnd)).size(), 2);
-        Assert.assertEquals(FastqToSam.getSequentialFileList(new File(TEST_DATA_DIR, "/" + pairedEnd1)).size(), 2);
-        Assert.assertEquals(FastqToSam.getSequentialFileList(new File(TEST_DATA_DIR, "/" + pairedEnd2)).size(), 2);
+        Assert.assertEquals(FastqToSam.getSequentialFileList(Paths.get(TEST_DATA_DIR.getPath(), singleEnd)).size(), 2);
+        Assert.assertEquals(FastqToSam.getSequentialFileList(Paths.get(TEST_DATA_DIR.getPath(),  pairedEnd1)).size(), 2);
+        Assert.assertEquals(FastqToSam.getSequentialFileList(Paths.get(TEST_DATA_DIR.getPath(), pairedEnd2)).size(), 2);
 
         convertFileAndVerifyRecordCount(1, singleEnd, null, FastqQualityFormat.Illumina, true, false);
         convertFileAndVerifyRecordCount(2, singleEnd, null, FastqQualityFormat.Illumina, true, true);