Fixup whitespace missed or caused by formatter.

HadoopGenomics · Sep 12, 2017 · 3deb8e1 · 3deb8e1
1 parent 4cc7b01
commit 3deb8e1
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Showing 12 changed files with 28 additions and 25 deletions.
diff --git a/src/main/java/org/seqdoop/hadoop_bam/BAMInputFormat.java b/src/main/java/org/seqdoop/hadoop_bam/BAMInputFormat.java
@@ -432,7 +432,9 @@ private int addBAISplits(final List<InputSplit> splits,
                 if (fSplit.getStart() == 0) {
                     final SeekableStream inFile =
                             WrapSeekable.openPath(path.getFileSystem(conf), path);
-                    SamReader open = SamReaderFactory.makeDefault().setUseAsyncIo(false)
+                    SamReader open = SamReaderFactory
+                            .makeDefault()
+                            .setUseAsyncIo(false)
                             .open(SamInputResource.of(inFile));
                     SAMFileSpan span = open.indexing().getFilePointerSpanningReads();
                     long bamStart = ((BAMFileSpan) span).getFirstOffset();
@@ -576,7 +578,8 @@ private List<InputSplit> filterByInterval(final List<InputSplit> splits,
             bamFiles.add(((FileVirtualSplit) split).getPath());
         }
         Map<Path, BAMFileSpan> fileToSpan = new LinkedHashMap<>();
-        SamReaderFactory readerFactory = SamReaderFactory.makeDefault()
+        SamReaderFactory readerFactory = SamReaderFactory
+                .makeDefault()
                 .setOption(SamReaderFactory.Option.CACHE_FILE_BASED_INDEXES, true)
                 .setOption(SamReaderFactory.Option.EAGERLY_DECODE, false)
                 .setUseAsyncIo(false);

diff --git a/src/main/java/org/seqdoop/hadoop_bam/BAMSplitGuesser.java b/src/main/java/org/seqdoop/hadoop_bam/BAMSplitGuesser.java
@@ -91,9 +91,9 @@ public BAMSplitGuesser(final SeekableStream ss,
             throws IOException {
         inFile = ss;
 
-        referenceSequenceCount =
-                SAMHeaderReader.readSAMHeaderFrom(headerStream, conf)
-                        .getSequenceDictionary().size();
+        referenceSequenceCount = SAMHeaderReader
+                .readSAMHeaderFrom(headerStream, conf)
+                .getSequenceDictionary().size();
 
         bamCodec = new BAMRecordCodec(null, new LazyBAMRecordFactory());
     }
@@ -110,7 +110,9 @@ public long guessNextBAMRecordStart(final long beg, final long end)
         // on subsequent calls to this method.
         if (beg == 0) {
             this.inFile.seek(beg);
-            SamReader open = SamReaderFactory.makeDefault().setUseAsyncIo(false)
+            SamReader open = SamReaderFactory
+                    .makeDefault()
+                    .setUseAsyncIo(false)
                     .open(SamInputResource.of(inFile));
             SAMFileSpan span = open.indexing().getFilePointerSpanningReads();
             if (span instanceof BAMFileSpan) {

diff --git a/src/main/java/org/seqdoop/hadoop_bam/BCFRecordWriter.java b/src/main/java/org/seqdoop/hadoop_bam/BCFRecordWriter.java
@@ -105,7 +105,8 @@ private void init(final OutputStream output,
         final BCFStoppableOutputStream stopOut =
                 new BCFStoppableOutputStream(!writeHeader, output);
 
-        writer = new VariantContextWriterBuilder().clearOptions()
+        writer = new VariantContextWriterBuilder()
+                .clearOptions()
                 .setOption(Options.FORCE_BCF)
                 .setOutputBCFStream(stopOut).build();
 

diff --git a/src/main/java/org/seqdoop/hadoop_bam/BaseSplitGuesser.java b/src/main/java/org/seqdoop/hadoop_bam/BaseSplitGuesser.java
@@ -34,8 +34,8 @@ public PosSize(final int p, final int s) {
     // anything.
     protected PosSize guessNextBGZFPos(int p, final int end) {
         try {
-            for (; ; ) {
-                for (; ; ) {
+            for (;;) {
+                for (;;) {
                     in.seek(p);
                     IOUtils.readFully(in, buf.array(), 0, 4);
                     int n = buf.getInt(0);

diff --git a/src/main/java/org/seqdoop/hadoop_bam/FastaInputFormat.java b/src/main/java/org/seqdoop/hadoop_bam/FastaInputFormat.java
@@ -190,8 +190,7 @@ public FastaRecordReader(final Configuration conf, final FileSplit split) throws
             CompressionCodecFactory codecFactory = new CompressionCodecFactory(conf);
             CompressionCodec codec = codecFactory.getCodec(file);
 
-            if (codec == null) // no codec.  Uncompressed file.
-            {
+            if (codec == null) { // no codec.  Uncompressed file.
                 positionAtFirstRecord(fileIn);
                 inputStream = fileIn;
             }

diff --git a/src/main/java/org/seqdoop/hadoop_bam/FastqInputFormat.java b/src/main/java/org/seqdoop/hadoop_bam/FastqInputFormat.java
@@ -109,8 +109,7 @@ public FastqRecordReader(final Configuration conf, final FileSplit split) throws
             CompressionCodecFactory codecFactory = new CompressionCodecFactory(conf);
             CompressionCodec codec = codecFactory.getCodec(file);
 
-            if (codec == null) // no codec.  Uncompressed file.
-            {
+            if (codec == null) { // no codec.  Uncompressed file.
                 positionAtFirstRecord(fileIn);
                 inputStream = fileIn;
             }

diff --git a/src/main/java/org/seqdoop/hadoop_bam/FormatConstants.java b/src/main/java/org/seqdoop/hadoop_bam/FormatConstants.java
@@ -53,8 +53,6 @@ public enum BaseQualityEncoding {
         Illumina, Sanger
     }
 
-    ;
-
     private FormatConstants() {
     } // no instantiation
 

diff --git a/src/main/java/org/seqdoop/hadoop_bam/QseqInputFormat.java b/src/main/java/org/seqdoop/hadoop_bam/QseqInputFormat.java
@@ -108,8 +108,7 @@ public QseqRecordReader(final Configuration conf, final FileSplit split) throws
             CompressionCodecFactory codecFactory = new CompressionCodecFactory(conf);
             CompressionCodec codec = codecFactory.getCodec(file);
 
-            if (codec == null) // no codec.  Uncompressed file.
-            {
+            if (codec == null) { // no codec.  Uncompressed file.
                 positionAtFirstRecord(fileIn);
                 inputStream = fileIn;
             }

diff --git a/src/main/java/org/seqdoop/hadoop_bam/QseqOutputFormat.java b/src/main/java/org/seqdoop/hadoop_bam/QseqOutputFormat.java
@@ -143,7 +143,6 @@ else if (baseQualityFormat == BaseQualityEncoding.Illumina) {
                 }
             }
             sBuilder.append(delim);
-            /////////
             sBuilder.append((seq.getFilterPassed() == null || seq.getFilterPassed()) ? 1 : 0);
 
             try {

diff --git a/src/main/java/org/seqdoop/hadoop_bam/util/BGZFSplitGuesser.java b/src/main/java/org/seqdoop/hadoop_bam/util/BGZFSplitGuesser.java
@@ -114,8 +114,8 @@ public long guessNextBGZFBlockStart(final long beg, final long end)
     // Returns a negative number if it doesn't find anything.
     private int guessNextBGZFPos(int p, final int end)
             throws IOException {
-        for (; ; ) {
-            for (; ; ) {
+        for (;;) {
+            for (;;) {
                 in.seek(p);
                 in.read(buf.array(), 0, 4);
                 int n = buf.getInt(0);

diff --git a/src/main/java/org/seqdoop/hadoop_bam/util/GetSortedBAMHeader.java b/src/main/java/org/seqdoop/hadoop_bam/util/GetSortedBAMHeader.java
@@ -43,10 +43,12 @@ public static void main(final String[] args) throws IOException {
             System.exit(1);
         }
 
-        final SAMFileHeader h =
-                SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT)
-                        .setUseAsyncIo(false)
-                        .open(new File(args[0])).getFileHeader();
+        final SAMFileHeader h = SamReaderFactory
+                .makeDefault()
+                .validationStringency(ValidationStringency.SILENT)
+                .setUseAsyncIo(false)
+                .open(new File(args[0]))
+                .getFileHeader();
         h.setSortOrder(SAMFileHeader.SortOrder.coordinate);
 
         new SAMOutputPreparer().prepareForRecords(

diff --git a/src/main/java/org/seqdoop/hadoop_bam/util/SAMHeaderReader.java b/src/main/java/org/seqdoop/hadoop_bam/util/SAMHeaderReader.java
@@ -57,7 +57,8 @@ public static SAMFileHeader readSAMHeaderFrom(
             final InputStream in, final Configuration conf) {
         final ValidationStringency
                 stringency = getValidationStringency(conf);
-        SamReaderFactory readerFactory = SamReaderFactory.makeDefault()
+        SamReaderFactory readerFactory = SamReaderFactory
+                .makeDefault()
                 .setOption(SamReaderFactory.Option.EAGERLY_DECODE, false)
                 .setUseAsyncIo(false);
         if (stringency != null) {
-Original file line number
+Diff line change
@@ Expand Up / @@ -53,8 +53,6 @@ public enum BaseQualityEncoding { @@
             Illumina, Sanger
         }
-        ;
         private FormatConstants() {
         } // no instantiation
@@ Expand Down @@