Add Path options for SAMFileWriterFactory

Also: - use jimfs for most CRAM compliance tests - handle codec filenames starting with "file://" - add jimfs test for bam/cram writer - protect against null path
samtools · Aug 31, 2017 · a8a680f · a8a680f
1 parent e110f44
commit a8a680f
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Showing 11 changed files with 443 additions and 95 deletions.
diff --git a/src/main/java/htsjdk/samtools/BAMFileWriter.java b/src/main/java/htsjdk/samtools/BAMFileWriter.java
@@ -25,6 +25,7 @@
 
 import htsjdk.samtools.util.BinaryCodec;
 import htsjdk.samtools.util.BlockCompressedOutputStream;
+import htsjdk.samtools.util.IOUtil;
 import htsjdk.samtools.util.RuntimeIOException;
 import htsjdk.samtools.util.zip.DeflaterFactory;
 
@@ -34,6 +35,9 @@
 import java.io.OutputStream;
 import java.io.StringWriter;
 import java.io.Writer;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
 
 /**
  * Concrete implementation of SAMFileWriter for writing gzipped BAM files.
@@ -75,7 +79,13 @@ protected BAMFileWriter(final OutputStream os, final File file, final int compre
         outputBinaryCodec.setOutputFileName(getPathString(file));
     }
 
-    private void prepareToWriteAlignments() {
+    protected BAMFileWriter(final OutputStream os, final String absoluteFilename, final int compressionLevel, final DeflaterFactory deflaterFactory) {
+      blockCompressedOutputStream = new BlockCompressedOutputStream(os, null, compressionLevel, deflaterFactory);
+      outputBinaryCodec = new BinaryCodec(new DataOutputStream(blockCompressedOutputStream));
+      outputBinaryCodec.setOutputFileName(absoluteFilename);
+    }
+
+  private void prepareToWriteAlignments() {
         if (bamRecordCodec == null) {
             bamRecordCodec = new BAMRecordCodec(getFileHeader());
             bamRecordCodec.setOutputStream(outputBinaryCodec.getOutputStream(), getFilename());
@@ -99,17 +109,17 @@ void enableBamIndexConstruction () {
         bamIndexer = createBamIndex(getFilename());
     }
 
-    private BAMIndexer createBamIndex(final String path) {
+    private BAMIndexer createBamIndex(final String pathURI) {
         try {
-            final String indexFileBase = path.endsWith(BamFileIoUtils.BAM_FILE_EXTENSION) ?
-                    path.substring(0, path.lastIndexOf('.')) : path;
-            final File indexFile = new File(indexFileBase + BAMIndex.BAMIndexSuffix);
-            if (indexFile.exists()) {
-                if (!indexFile.canWrite()) {
-                    throw new SAMException("Not creating BAM index since unable to write index file " + indexFile);
+            final String indexFileBase = pathURI.endsWith(BamFileIoUtils.BAM_FILE_EXTENSION) ?
+                    pathURI.substring(0, pathURI.lastIndexOf('.')) : pathURI;
+            final Path indexPath = IOUtil.getPath(indexFileBase + BAMIndex.BAMIndexSuffix);
+            if (Files.exists(indexPath)) {
+                if (!Files.isWritable(indexPath)) {
+                    throw new SAMException("Not creating BAM index since unable to write index file " + indexPath.toUri());
                 }
             }
-            return new BAMIndexer(indexFile, getFileHeader());
+            return new BAMIndexer(indexPath, getFileHeader());
         } catch (Exception e) {
             throw new SAMException("Not creating BAM index", e);
         }
@@ -153,7 +163,8 @@ protected void finish() {
             }
     }
 
-    /** @return absolute path, or null if this writer does not correspond to a file.  */
+    /** @return absolute path in URI format, or null if this writer does not correspond to a file.
+     * To get a Path from this, use: IOUtil.getPath(getFilename()) */
     @Override
     protected String getFilename() {
         return outputBinaryCodec.getOutputFileName();

diff --git a/src/main/java/htsjdk/samtools/BAMIndexer.java b/src/main/java/htsjdk/samtools/BAMIndexer.java
@@ -27,6 +27,7 @@
 
 import java.io.File;
 import java.io.OutputStream;
+import java.nio.file.Path;
 import java.util.function.Function;
 
 /**
@@ -56,10 +57,18 @@ public class BAMIndexer {
      * @param output     binary BAM Index (.bai) file
      * @param fileHeader header for the corresponding bam file
      */
-    public BAMIndexer(final File output, final SAMFileHeader fileHeader) {
+    public BAMIndexer(final Path output, final SAMFileHeader fileHeader) {
         this(fileHeader, numRefs -> new BinaryBAMIndexWriter(numRefs, output));
     }
 
+    /**
+     * @param output     binary BAM Index (.bai) file
+     * @param fileHeader header for the corresponding bam file
+     */
+    public BAMIndexer(final File output, final SAMFileHeader fileHeader) {
+        this(output.toPath(), fileHeader);
+    }
+
     /**
      * Prepare to index a BAM.
      *
@@ -283,9 +292,9 @@ void startNewReference() {
      * Generates a BAM index file from an input BAM file
      *
      * @param reader SamReader for input BAM file
-     * @param output File for output index file
+     * @param output Path for output index file
      */
-    public static void createIndex(SamReader reader, File output) {
+    public static void createIndex(SamReader reader, Path output) {
         createIndex(reader, output, null);
     }
 
@@ -295,7 +304,17 @@ public static void createIndex(SamReader reader, File output) {
      * @param reader SamReader for input BAM file
      * @param output File for output index file
      */
-    public static void createIndex(SamReader reader, File output, Log log) {
+    public static void createIndex(SamReader reader, File output) {
+        createIndex(reader, output.toPath(), null);
+    }
+
+    /**
+     * Generates a BAM index file from an input BAM file
+     *
+     * @param reader SamReader for input BAM file
+     * @param output Path for output index file
+     */
+    public static void createIndex(SamReader reader, Path output, Log log) {
 
         BAMIndexer indexer = new BAMIndexer(output, reader.getFileHeader());
 
@@ -310,4 +329,14 @@ public static void createIndex(SamReader reader, File output, Log log) {
         }
         indexer.finish();
     }
+
+    /**
+     * Generates a BAM index file from an input BAM file
+     *
+     * @param reader SamReader for input BAM file
+     * @param output File for output index file
+     */
+    public static void createIndex(SamReader reader, File output, Log log) {
+        createIndex(reader, output.toPath(), log);
+    }
 }
diff --git a/src/main/java/htsjdk/samtools/BinaryBAMIndexWriter.java b/src/main/java/htsjdk/samtools/BinaryBAMIndexWriter.java
@@ -29,6 +29,7 @@
 import java.io.File;
 import java.io.IOException;
 import java.io.OutputStream;
+import java.nio.file.Path;
 import java.util.List;
 
 /**
@@ -41,12 +42,20 @@ class BinaryBAMIndexWriter implements BAMIndexWriter {
     private int count = 0;
 
     /**
-     * constructor
      *
      * @param nRef    Number of reference sequences
      * @param output  BAM Index output file
      */
     public BinaryBAMIndexWriter(final int nRef, final File output) {
+        this(nRef, null == output ? null : output.toPath());
+    }
+
+    /**
+     *
+     * @param nRef    Number of reference sequences
+     * @param output  BAM Index output file
+     */
+    public BinaryBAMIndexWriter(final int nRef, final Path output) {
 
         this.nRef = nRef;