Fix calls to deprecated htsjdk APIs

disq-bio · Sep 30, 2019 · 202e1f0 · 202e1f0
1 parent 65cfd22
commit 202e1f0
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Showing 19 changed files with 46 additions and 43 deletions.
diff --git a/src/main/java/org/disq_bio/disq/BaiWriteOption.java b/src/main/java/org/disq_bio/disq/BaiWriteOption.java
@@ -25,7 +25,7 @@
  */
 package org.disq_bio.disq;
 
-import htsjdk.samtools.BAMIndex;
+import htsjdk.samtools.util.FileExtensions;
 
 /** An option for for enabling or disabling writing BAI files. Disabled by default. */
 public enum BaiWriteOption implements WriteOption {
@@ -44,6 +44,6 @@ public static BaiWriteOption fromBoolean(boolean writeBai) {
 
   /** @return the extension for BAI files. */
   public static String getIndexExtension() {
-    return BAMIndex.BAMIndexSuffix;
+    return FileExtensions.BAI_INDEX;
   }
 }
diff --git a/src/main/java/org/disq_bio/disq/CraiWriteOption.java b/src/main/java/org/disq_bio/disq/CraiWriteOption.java
@@ -25,7 +25,7 @@
  */
 package org.disq_bio.disq;
 
-import htsjdk.samtools.cram.CRAIIndex;
+import htsjdk.samtools.util.FileExtensions;
 
 /** An option for for enabling or disabling writing CRAI files. Disabled by default. */
 public enum CraiWriteOption implements WriteOption {
@@ -44,6 +44,6 @@ public static CraiWriteOption fromBoolean(boolean writeCrai) {
 
   /** @return the extension for CRAI files. */
   public static String getIndexExtension() {
-    return CRAIIndex.CRAI_INDEX_SUFFIX;
+    return FileExtensions.CRAM_INDEX;
   }
 }
diff --git a/src/main/java/org/disq_bio/disq/SbiWriteOption.java b/src/main/java/org/disq_bio/disq/SbiWriteOption.java
@@ -25,7 +25,7 @@
  */
 package org.disq_bio.disq;
 
-import htsjdk.samtools.SBIIndex;
+import htsjdk.samtools.util.FileExtensions;
 
 /** An option for for enabling or disabling writing SBI files. Disabled by default. */
 public enum SbiWriteOption implements WriteOption {
@@ -44,6 +44,6 @@ public static SbiWriteOption fromBoolean(boolean writeSbi) {
 
   /** @return the extension for SBI files. */
   public static String getIndexExtension() {
-    return SBIIndex.FILE_EXTENSION;
+    return FileExtensions.SBI;
   }
 }
diff --git a/src/main/java/org/disq_bio/disq/TabixIndexWriteOption.java b/src/main/java/org/disq_bio/disq/TabixIndexWriteOption.java
@@ -25,7 +25,7 @@
  */
 package org.disq_bio.disq;
 
-import htsjdk.tribble.util.TabixUtils;
+import htsjdk.samtools.util.FileExtensions;
 
 /** An option for for enabling or disabling writing tabix files. Disabled by default. */
 public enum TabixIndexWriteOption implements WriteOption {
@@ -44,6 +44,6 @@ public static TabixIndexWriteOption fromBoolean(boolean writeTabix) {
 
   /** @return the extension for tabix files. */
   public static String getIndexExtension() {
-    return TabixUtils.STANDARD_INDEX_EXTENSION;
+    return FileExtensions.TABIX_INDEX;
   }
 }
diff --git a/src/main/java/org/disq_bio/disq/impl/file/BaiMerger.java b/src/main/java/org/disq_bio/disq/impl/file/BaiMerger.java
@@ -26,7 +26,6 @@
 package org.disq_bio.disq.impl.file;
 
 import htsjdk.samtools.AbstractBAMFileIndex;
-import htsjdk.samtools.BAMIndex;
 import htsjdk.samtools.BAMIndexMerger;
 import htsjdk.samtools.IndexMerger;
 import htsjdk.samtools.SAMFileHeader;
@@ -36,6 +35,7 @@
 import java.io.IOException;
 import java.io.OutputStream;
 import org.apache.hadoop.conf.Configuration;
+import org.disq_bio.disq.BaiWriteOption;
 
 /** Merges BAM index files for (headerless) parts of a BAM file into a single index file. */
 public class BaiMerger extends IndexFileMerger<AbstractBAMFileIndex, SAMFileHeader> {
@@ -45,7 +45,7 @@ public BaiMerger(FileSystemWrapper fileSystemWrapper) {
 
   @Override
   protected String getIndexExtension() {
-    return BAMIndex.BAMIndexSuffix;
+    return BaiWriteOption.getIndexExtension();
   }
 
   @Override

diff --git a/src/main/java/org/disq_bio/disq/impl/file/CraiMerger.java b/src/main/java/org/disq_bio/disq/impl/file/CraiMerger.java
@@ -34,6 +34,7 @@
 import java.io.IOException;
 import java.io.OutputStream;
 import org.apache.hadoop.conf.Configuration;
+import org.disq_bio.disq.CraiWriteOption;
 
 /** Merges CRAM index files for (headerless) parts of a CRAM file into a single index file. */
 public class CraiMerger extends IndexFileMerger<CRAIIndex, SAMFileHeader> {
@@ -43,7 +44,7 @@ public CraiMerger(FileSystemWrapper fileSystemWrapper) {
 
   @Override
   protected String getIndexExtension() {
-    return CRAIIndex.CRAI_INDEX_SUFFIX;
+    return CraiWriteOption.getIndexExtension();
   }
 
   @Override

diff --git a/src/main/java/org/disq_bio/disq/impl/file/SbiMerger.java b/src/main/java/org/disq_bio/disq/impl/file/SbiMerger.java
@@ -33,6 +33,7 @@
 import java.io.IOException;
 import java.io.OutputStream;
 import org.apache.hadoop.conf.Configuration;
+import org.disq_bio.disq.SbiWriteOption;
 
 public class SbiMerger extends IndexFileMerger<SBIIndex, SAMFileHeader> {
 
@@ -42,7 +43,7 @@ public SbiMerger(FileSystemWrapper fileSystemWrapper) {
 
   @Override
   protected String getIndexExtension() {
-    return SBIIndex.FILE_EXTENSION;
+    return SbiWriteOption.getIndexExtension();
   }
 
   @Override

diff --git a/src/main/java/org/disq_bio/disq/impl/formats/bam/BamRecordGuesserChecker.java b/src/main/java/org/disq_bio/disq/impl/formats/bam/BamRecordGuesserChecker.java
@@ -30,6 +30,7 @@
 import htsjdk.samtools.SBIIndex;
 import htsjdk.samtools.seekablestream.SeekableStream;
 import htsjdk.samtools.util.BlockCompressedFilePointerUtil;
+import htsjdk.samtools.util.FileExtensions;
 import java.io.IOException;
 import java.io.OutputStream;
 import java.io.Serializable;
@@ -79,7 +80,7 @@ public BamRecordGuesserChecker(boolean useNio) {
   }
 
   SBIIndex getSBIIndex(Configuration conf, String bamFile) throws IOException {
-    String sbiFile = bamFile + SBIIndex.FILE_EXTENSION;
+    String sbiFile = bamFile + FileExtensions.SBI;
     if (!fileSystemWrapper.exists(conf, sbiFile)) {
       // create SBI file
       try (SeekableStream in = fileSystemWrapper.open(conf, bamFile);

diff --git a/src/main/java/org/disq_bio/disq/impl/formats/bam/BamSink.java b/src/main/java/org/disq_bio/disq/impl/formats/bam/BamSink.java
@@ -26,10 +26,8 @@
 package org.disq_bio.disq.impl.formats.bam;
 
 import htsjdk.samtools.BAMFileWriter;
-import htsjdk.samtools.BAMIndex;
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMRecord;
-import htsjdk.samtools.SBIIndex;
 import htsjdk.samtools.util.BlockCompressedStreamConstants;
 import java.io.IOException;
 import java.io.OutputStream;
@@ -122,7 +120,7 @@ public void save(
           .mergeParts(
               conf,
               tempPartsDirectory,
-              path + SBIIndex.FILE_EXTENSION,
+              path + SbiWriteOption.getIndexExtension(),
               header,
               partLengths,
               fileLength);
@@ -132,7 +130,7 @@ public void save(
           .mergeParts(
               conf,
               tempPartsDirectory,
-              path + BAMIndex.BAMIndexSuffix,
+              path + BaiWriteOption.getIndexExtension(),
               header,
               partLengths,
               fileLength);

diff --git a/src/main/java/org/disq_bio/disq/impl/formats/bam/BamSource.java b/src/main/java/org/disq_bio/disq/impl/formats/bam/BamSource.java
@@ -38,6 +38,7 @@
 import htsjdk.samtools.seekablestream.SeekableStream;
 import htsjdk.samtools.util.BlockCompressedFilePointerUtil;
 import htsjdk.samtools.util.CloseableIterator;
+import htsjdk.samtools.util.FileExtensions;
 import htsjdk.samtools.util.Locatable;
 import java.io.IOException;
 import java.io.Serializable;
@@ -95,7 +96,7 @@ protected JavaRDD<PathChunk> getPathChunks(
       String referenceSourcePath)
       throws IOException {
 
-    String sbiPath = path + SBIIndex.FILE_EXTENSION;
+    String sbiPath = path + FileExtensions.SBI;
     if (fileSystemWrapper.exists(jsc.hadoopConfiguration(), sbiPath)) {
       logger.debug("Using SBI file {} for finding splits", sbiPath);
       try (SeekableStream sbiStream = fileSystemWrapper.open(jsc.hadoopConfiguration(), sbiPath)) {

diff --git a/src/main/java/org/disq_bio/disq/impl/formats/bam/HeaderlessBamOutputFormat.java b/src/main/java/org/disq_bio/disq/impl/formats/bam/HeaderlessBamOutputFormat.java
@@ -26,15 +26,13 @@
 package org.disq_bio.disq.impl.formats.bam;
 
 import htsjdk.samtools.BAMFileSpan;
-import htsjdk.samtools.BAMIndex;
 import htsjdk.samtools.BAMIndexer2;
 import htsjdk.samtools.BAMRecordCodec;
 import htsjdk.samtools.Chunk;
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMFileSource;
 import htsjdk.samtools.SAMRecord;
 import htsjdk.samtools.SAMRecordHelper;
-import htsjdk.samtools.SBIIndex;
 import htsjdk.samtools.SBIIndexWriter;
 import htsjdk.samtools.util.BinaryCodec;
 import htsjdk.samtools.util.BlockCompressedOutputStream;
@@ -45,7 +43,9 @@
 import org.apache.hadoop.mapreduce.RecordWriter;
 import org.apache.hadoop.mapreduce.TaskAttemptContext;
 import org.apache.hadoop.mapreduce.lib.output.FileOutputFormat;
+import org.disq_bio.disq.BaiWriteOption;
 import org.disq_bio.disq.HtsjdkReadsRdd;
+import org.disq_bio.disq.SbiWriteOption;
 import org.disq_bio.disq.impl.formats.bgzf.TerminatorlessBlockCompressedOutputStream;
 
 /**
@@ -176,13 +176,15 @@ public RecordWriter<Void, SAMRecord> getRecordWriter(TaskAttemptContext taskAtte
     Path sbiFile;
     if (writeSbiFile) {
       // ensure sbi files are hidden so they don't interfere with merging of part files
-      sbiFile = new Path(file.getParent(), "." + file.getName() + SBIIndex.FILE_EXTENSION);
+      sbiFile =
+          new Path(file.getParent(), "." + file.getName() + SbiWriteOption.getIndexExtension());
     } else {
       sbiFile = null;
     }
     Path baiFile;
     if (writeBaiFile) {
-      baiFile = new Path(file.getParent(), "." + file.getName() + BAMIndex.BAMIndexSuffix);
+      baiFile =
+          new Path(file.getParent(), "." + file.getName() + BaiWriteOption.getIndexExtension());
     } else {
       baiFile = null;
     }

diff --git a/src/main/java/org/disq_bio/disq/impl/formats/cram/CramOutputFormat.java b/src/main/java/org/disq_bio/disq/impl/formats/cram/CramOutputFormat.java
@@ -29,7 +29,6 @@
 import htsjdk.samtools.CRAMContainerStreamWriter;
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMRecord;
-import htsjdk.samtools.cram.CRAIIndex;
 import htsjdk.samtools.cram.ref.CRAMReferenceSource;
 import java.io.IOException;
 import java.io.OutputStream;
@@ -38,6 +37,7 @@
 import org.apache.hadoop.mapreduce.RecordWriter;
 import org.apache.hadoop.mapreduce.TaskAttemptContext;
 import org.apache.hadoop.mapreduce.lib.output.FileOutputFormat;
+import org.disq_bio.disq.CraiWriteOption;
 import org.disq_bio.disq.HtsjdkReadsRdd;
 import org.disq_bio.disq.impl.file.FileSystemWrapper;
 import org.disq_bio.disq.impl.file.HadoopFileSystemWrapper;
@@ -73,7 +73,8 @@ public RecordWriter<Void, SAMRecord> getRecordWriter(TaskAttemptContext taskAtte
     Path craiFile;
     if (writeCraiFile) {
       // ensure CRAI files are hidden so they don't interfere with merging of part files
-      craiFile = new Path(file.getParent(), "." + file.getName() + CRAIIndex.CRAI_INDEX_SUFFIX);
+      craiFile =
+          new Path(file.getParent(), "." + file.getName() + CraiWriteOption.getIndexExtension());
     } else {
       craiFile = null;
     }

diff --git a/src/main/java/org/disq_bio/disq/impl/formats/cram/CramReferenceSourceBuilder.java b/src/main/java/org/disq_bio/disq/impl/formats/cram/CramReferenceSourceBuilder.java
@@ -32,6 +32,7 @@
 import htsjdk.samtools.reference.ReferenceSequenceFile;
 import htsjdk.samtools.reference.ReferenceSequenceFileFactory;
 import htsjdk.samtools.seekablestream.SeekableStream;
+import htsjdk.samtools.util.FileExtensions;
 import htsjdk.samtools.util.GZIIndex;
 import htsjdk.samtools.util.IOUtil;
 import java.io.IOException;
@@ -40,16 +41,14 @@
 
 /** A utility class for creating a {@link CRAMReferenceSource}. */
 public class CramReferenceSourceBuilder {
-  private static final String FASTA_INDEX_EXTENSION = ".fai";
-
   public static CRAMReferenceSource build(
       FileSystemWrapper fileSystemWrapper, Configuration conf, String referenceSourcePath)
       throws IOException {
     SeekableStream refIn = fileSystemWrapper.open(conf, referenceSourcePath);
-    String indexPath = referenceSourcePath + FASTA_INDEX_EXTENSION;
+    String indexPath = referenceSourcePath + FileExtensions.FASTA_INDEX;
     ReferenceSequenceFile refSeqFile;
     if (IOUtil.hasBlockCompressedExtension(referenceSourcePath)) {
-      String gziIndexPath = referenceSourcePath + GZIIndex.DEFAULT_EXTENSION;
+      String gziIndexPath = referenceSourcePath + FileExtensions.GZI;
       try (SeekableStream indexIn = fileSystemWrapper.open(conf, indexPath);
           SeekableStream gziIndexIn = fileSystemWrapper.open(conf, gziIndexPath)) {
         FastaSequenceIndex index = new FastaSequenceIndex(indexIn);

diff --git a/src/main/java/org/disq_bio/disq/impl/formats/cram/CramSink.java b/src/main/java/org/disq_bio/disq/impl/formats/cram/CramSink.java
@@ -28,7 +28,6 @@
 import htsjdk.samtools.CRAMContainerStreamWriter;
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMRecord;
-import htsjdk.samtools.cram.CRAIIndex;
 import htsjdk.samtools.cram.build.CramIO;
 import htsjdk.samtools.cram.common.CramVersions;
 import htsjdk.samtools.cram.ref.CRAMReferenceSource;
@@ -121,7 +120,7 @@ public void save(
           .mergeParts(
               conf,
               tempPartsDirectory,
-              path + CRAIIndex.CRAI_INDEX_SUFFIX,
+              path + CraiWriteOption.getIndexExtension(),
               header,
               partLengths,
               fileLength);

diff --git a/src/main/java/org/disq_bio/disq/impl/formats/vcf/VcfSource.java b/src/main/java/org/disq_bio/disq/impl/formats/vcf/VcfSource.java
@@ -25,9 +25,9 @@
  */
 package org.disq_bio.disq.impl.formats.vcf;
 
-import htsjdk.samtools.SamStreams;
 import htsjdk.samtools.seekablestream.SeekableStream;
 import htsjdk.samtools.util.BlockCompressedInputStream;
+import htsjdk.samtools.util.IOUtil;
 import htsjdk.samtools.util.Locatable;
 import htsjdk.samtools.util.OverlapDetector;
 import htsjdk.tribble.FeatureCodecHeader;
@@ -108,7 +108,7 @@ private static InputStream bufferAndDecompressIfNecessary(final InputStream in)
     BufferedInputStream bis = new BufferedInputStream(in);
     // despite the name, SamStreams.isGzippedSAMFile looks for any gzipped stream (including block
     // compressed)
-    return SamStreams.isGzippedSAMFile(bis) ? new GZIPInputStream(bis) : bis;
+    return IOUtil.isGZIPInputStream(bis) ? new GZIPInputStream(bis) : bis;
   }
 
   public <T extends Locatable> JavaRDD<VariantContext> getVariants(

diff --git a/src/test/java/org/disq_bio/disq/BaseTest.java b/src/test/java/org/disq_bio/disq/BaseTest.java
@@ -25,7 +25,7 @@
  */
 package org.disq_bio.disq;
 
-import htsjdk.samtools.SBIIndex;
+import htsjdk.samtools.util.FileExtensions;
 import java.io.IOException;
 import java.net.URI;
 import java.net.URISyntaxException;
@@ -143,7 +143,7 @@ protected List<String> listPartFiles(String dir) throws IOException {
 
   protected List<String> listSBIIndexFiles(String dir) throws IOException {
     return Files.list(Paths.get(URI.create(dir)))
-        .filter(path -> path.getFileName().toString().endsWith(SBIIndex.FILE_EXTENSION))
+        .filter(path -> path.getFileName().toString().endsWith(FileExtensions.SBI))
         .map(path -> path.toUri().toString())
         .collect(Collectors.toList());
   }

diff --git a/src/test/java/org/disq_bio/disq/HtsjdkReadsRddTest.java b/src/test/java/org/disq_bio/disq/HtsjdkReadsRddTest.java
@@ -31,6 +31,7 @@
 import htsjdk.samtools.SBIIndex;
 import htsjdk.samtools.seekablestream.SeekablePathStream;
 import htsjdk.samtools.seekablestream.SeekableStream;
+import htsjdk.samtools.util.FileExtensions;
 import htsjdk.samtools.util.Interval;
 import htsjdk.samtools.util.Locatable;
 import java.io.ByteArrayInputStream;
@@ -180,7 +181,7 @@ public void testWriteSBIIndex(String inputFile, int splitSize, boolean useNio) t
         createTempPath(SamFormat.fromFormatWriteOption(ReadsFormatWriteOption.BAM).getExtension());
     htsjdkReadsRddStorage.write(htsjdkReadsRdd, outputPath, SbiWriteOption.ENABLE);
 
-    Path sbiFile = Paths.get(URI.create(outputPath + SBIIndex.FILE_EXTENSION));
+    Path sbiFile = Paths.get(URI.create(outputPath + FileExtensions.SBI));
     Assert.assertTrue(Files.exists(sbiFile));
     SBIIndex actualSbiIndex = SBIIndex.load(sbiFile);
 
@@ -501,7 +502,7 @@ public void testSBIIndexWrittenWhenNotCoordinateSorted() throws Exception {
         createTempPath(SamFormat.fromFormatWriteOption(ReadsFormatWriteOption.BAM).getExtension());
     htsjdkReadsRddStorage.write(htsjdkReadsRdd, outputPath, SbiWriteOption.ENABLE);
 
-    Assert.assertTrue(Files.exists(Paths.get(URI.create(outputPath + SBIIndex.FILE_EXTENSION))));
+    Assert.assertTrue(Files.exists(Paths.get(URI.create(outputPath + FileExtensions.SBI))));
   }
 
   @Test

diff --git a/src/test/java/org/disq_bio/disq/TbiMergingTest.java b/src/test/java/org/disq_bio/disq/TbiMergingTest.java
@@ -26,10 +26,10 @@
 package org.disq_bio.disq;
 
 import htsjdk.samtools.TbiEqualityChecker;
+import htsjdk.samtools.util.FileExtensions;
 import htsjdk.samtools.util.RuntimeIOException;
 import htsjdk.tribble.index.IndexFactory;
 import htsjdk.tribble.index.tabix.TabixIndex;
-import htsjdk.tribble.util.TabixUtils;
 import htsjdk.variant.vcf.VCFCodec;
 import java.io.File;
 import java.io.IOException;
@@ -84,8 +84,8 @@ public void test(String inputFile) throws Exception {
 
     File outputVcf = new File(URI.create(outputPath));
     File outputTbi =
-        new File(outputVcf.getParent(), outputVcf.getName() + TabixUtils.STANDARD_INDEX_EXTENSION);
-    String outputTbiHtsjdkPath = createTempPath(TabixUtils.STANDARD_INDEX_EXTENSION);
+        new File(outputVcf.getParent(), outputVcf.getName() + FileExtensions.TABIX_INDEX);
+    String outputTbiHtsjdkPath = createTempPath(FileExtensions.TABIX_INDEX);
     File outputTbiHtsjdk = indexVcf(outputVcf, new File(URI.create(outputTbiHtsjdkPath)));
 
     // Don't check for strict equality (byte identical), since the TBI files