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 index a308297..dc56de7 100644 --- 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 getBaiParts(List 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 index 682437b..357833e 100644 --- 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 parts, String path) throws I static void concat(List 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 index 403c36e..c3cd1a7 100644 --- 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 fileStatuses, String outputFile) throws IOException { List 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 index 27eeedc..37c2863 100644 --- 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 parts = fileSystemWrapper.listDirectory(conf, tempPartsDirectory); List 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 index 93dd6c7..361d8d2 100644 --- 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 getTbiParts(List 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 index 14d9ff2..84ca6de 100644 --- 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 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 index eb519bd..008e835 100644 --- 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 bamParts = - fileSystemWrapper - .listDirectoryStatus(conf, tempPartsDirectory) - .stream() + fileSystemWrapper.listDirectoryStatus(conf, tempPartsDirectory).stream() .filter(fs -> new HiddenFileFilter().test(fs.getPath())) .collect(Collectors.toList()); List 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 index 807f6ec..889c630 100644 --- 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 getPathChunks( Map> pathToContainerOffsets = new LinkedHashMap<>(); if (fileSystemWrapper.isDirectory(conf, path)) { List 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 index a30e650..e87329a 100644 --- 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 vcfParts = - fileSystemWrapper - .listDirectoryStatus(jsc.hadoopConfiguration(), tempPartsDirectory) + fileSystemWrapper.listDirectoryStatus(jsc.hadoopConfiguration(), tempPartsDirectory) .stream() .filter(fs -> new HiddenFileFilter().test(fs.getPath())) .collect(Collectors.toList()); List partLengths = - vcfParts - .stream() + vcfParts.stream() .mapToLong(FileSystemWrapper.FileStatus::getLength) .boxed() .collect(Collectors.toList());