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disq-bio · Mar 8, 2019 · 3eca79a · 3eca79a
1 parent 9a98cb2
commit 3eca79a
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Showing 9 changed files with 11 additions and 24 deletions.
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
@@ -81,8 +81,7 @@ public void mergeParts(
   }
 
   private List<String> getBaiParts(List<String> parts) {
-    return parts
-        .stream()
+    return parts.stream()
         .filter(f -> f.endsWith(BAMIndex.BAMIndexSuffix))
         .collect(Collectors.toList());
   }

diff --git a/src/main/java/org/disq_bio/disq/impl/file/HadoopFileSystemWrapper.java b/src/main/java/org/disq_bio/disq/impl/file/HadoopFileSystemWrapper.java
@@ -152,8 +152,7 @@ public void concat(Configuration conf, List<String> parts, String path) throws I
   static void concat(List<String> parts, Path outputPath, FileSystem filesystem)
       throws IOException {
     org.apache.hadoop.fs.Path[] fsParts =
-        parts
-            .stream()
+        parts.stream()
             .map(Path::new)
             .collect(Collectors.toList())
             .toArray(new org.apache.hadoop.fs.Path[parts.size()]);

diff --git a/src/main/java/org/disq_bio/disq/impl/file/Merger.java b/src/main/java/org/disq_bio/disq/impl/file/Merger.java
@@ -42,8 +42,7 @@ public void mergeParts(
       Configuration conf, List<FileSystemWrapper.FileStatus> fileStatuses, String outputFile)
       throws IOException {
     List<String> parts =
-        fileStatuses
-            .stream()
+        fileStatuses.stream()
             .map(FileSystemWrapper.FileStatus::getPath)
             .collect(Collectors.toList());
     fileSystemWrapper.concat(conf, parts, outputFile);

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
@@ -56,8 +56,7 @@ public void mergeParts(
     logger.info("Merging .sbi files in temp directory {} to {}", tempPartsDirectory, outputFile);
     List<String> parts = fileSystemWrapper.listDirectory(conf, tempPartsDirectory);
     List<String> filteredParts =
-        parts
-            .stream()
+        parts.stream()
             .filter(f -> f.endsWith(SBIIndex.FILE_EXTENSION))
             .collect(Collectors.toList());
     try (OutputStream out = fileSystemWrapper.create(conf, outputFile)) {

diff --git a/src/main/java/org/disq_bio/disq/impl/file/TbiMerger.java b/src/main/java/org/disq_bio/disq/impl/file/TbiMerger.java
@@ -75,8 +75,7 @@ public void mergeParts(
   }
 
   private List<String> getTbiParts(List<String> parts) {
-    return parts
-        .stream()
+    return parts.stream()
         .filter(f -> f.endsWith(TabixIndexWriteOption.getIndexExtension()))
         .collect(Collectors.toList());
   }

diff --git a/src/main/java/org/disq_bio/disq/impl/formats/BoundedTraversalUtil.java b/src/main/java/org/disq_bio/disq/impl/formats/BoundedTraversalUtil.java
@@ -40,8 +40,7 @@ public static <T extends Locatable> QueryInterval[] prepareQueryIntervals(
 
     // Convert each SimpleInterval to a QueryInterval
     final QueryInterval[] convertedIntervals =
-        rawIntervals
-            .stream()
+        rawIntervals.stream()
             .map(
                 rawInterval ->
                     convertSimpleIntervalToQueryInterval(rawInterval, sequenceDictionary))

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
@@ -107,14 +107,11 @@ public void save(
     }
 
     List<FileSystemWrapper.FileStatus> bamParts =
-        fileSystemWrapper
-            .listDirectoryStatus(conf, tempPartsDirectory)
-            .stream()
+        fileSystemWrapper.listDirectoryStatus(conf, tempPartsDirectory).stream()
             .filter(fs -> new HiddenFileFilter().test(fs.getPath()))
             .collect(Collectors.toList());
     List<Long> partLengths =
-        bamParts
-            .stream()
+        bamParts.stream()
             .mapToLong(FileSystemWrapper.FileStatus::getLength)
             .boxed()
             .collect(Collectors.toList());

diff --git a/src/main/java/org/disq_bio/disq/impl/formats/cram/CramSource.java b/src/main/java/org/disq_bio/disq/impl/formats/cram/CramSource.java
@@ -93,9 +93,7 @@ protected JavaRDD<PathChunk> getPathChunks(
     Map<String, NavigableSet<Long>> pathToContainerOffsets = new LinkedHashMap<>();
     if (fileSystemWrapper.isDirectory(conf, path)) {
       List<FileSystemWrapper.FileStatus> statuses =
-          fileSystemWrapper
-              .listDirectoryStatus(conf, path)
-              .stream()
+          fileSystemWrapper.listDirectoryStatus(conf, path).stream()
               .filter(fs -> SamFormat.CRAM.fileMatches(fs.getPath()))
               .collect(Collectors.toList());
       for (FileSystemWrapper.FileStatus status : statuses) {

diff --git a/src/main/java/org/disq_bio/disq/impl/formats/vcf/VcfSink.java b/src/main/java/org/disq_bio/disq/impl/formats/vcf/VcfSink.java
@@ -103,14 +103,12 @@ public void save(
     }
 
     List<FileSystemWrapper.FileStatus> vcfParts =
-        fileSystemWrapper
-            .listDirectoryStatus(jsc.hadoopConfiguration(), tempPartsDirectory)
+        fileSystemWrapper.listDirectoryStatus(jsc.hadoopConfiguration(), tempPartsDirectory)
             .stream()
             .filter(fs -> new HiddenFileFilter().test(fs.getPath()))
             .collect(Collectors.toList());
     List<Long> partLengths =
-        vcfParts
-            .stream()
+        vcfParts.stream()
             .mapToLong(FileSystemWrapper.FileStatus::getLength)
             .boxed()
             .collect(Collectors.toList());