Reformat source code for consistent use of whitespace.

etc/IntelliJ IDEA Code Style.xml

@@ -0,0 +1,32 @@
+<code_scheme name="Default (1)">
+    <option name="CLASS_COUNT_TO_USE_IMPORT_ON_DEMAND" value="99"/>
+    <option name="NAMES_COUNT_TO_USE_IMPORT_ON_DEMAND" value="99"/>
+    <option name="IMPORT_LAYOUT_TABLE">
+        <value>
+            <package name="java" withSubpackages="true" static="false"/>
+            <package name="javax" withSubpackages="true" static="false"/>
+            <package name="" withSubpackages="true" static="false"/>
+            <emptyLine/>
+            <emptyLine/>
+            <package name="" withSubpackages="true" static="true"/>
+        </value>
+    </option>
+    <option name="JD_ALIGN_PARAM_COMMENTS" value="false"/>
+    <option name="JD_ALIGN_EXCEPTION_COMMENTS" value="false"/>
+    <ScalaCodeStyleSettings>
+        <option name="USE_SCALADOC2_FORMATTING" value="false"/>
+        <option name="ENABLE_SCALADOC_FORMATTING" value="false"/>
+    </ScalaCodeStyleSettings>
+    <codeStyleSettings language="JAVA">
+        <option name="ELSE_ON_NEW_LINE" value="true"/>
+        <option name="WHILE_ON_NEW_LINE" value="true"/>
+        <option name="CATCH_ON_NEW_LINE" value="true"/>
+        <option name="FINALLY_ON_NEW_LINE" value="true"/>
+        <option name="SPACE_WITHIN_ARRAY_INITIALIZER_BRACES" value="true"/>
+        <option name="SPACE_BEFORE_ARRAY_INITIALIZER_LBRACE" value="true"/>
+        <option name="IF_BRACE_FORCE" value="3"/>
+        <option name="DOWHILE_BRACE_FORCE" value="3"/>
+        <option name="WHILE_BRACE_FORCE" value="3"/>
+        <option name="FOR_BRACE_FORCE" value="3"/>
+    </codeStyleSettings>
+</code_scheme>

examples/pom.xml

@@ -21,8 +21,9 @@
   ~ IN THE SOFTWARE.
   -->
 
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
-
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+
     <modelVersion>4.0.0</modelVersion>
     <groupId>org.seqdoop</groupId>
     <artifactId>hadoop-bam-examples</artifactId>

examples/src/main/java/org/seqdoop/hadoop_bam/examples/TestBAM.java

@@ -22,7 +22,7 @@
 
 import java.io.IOException;
 import java.util.Iterator;
-
+import htsjdk.samtools.SAMRecord;
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.conf.Configured;
 import org.apache.hadoop.fs.Path;
@@ -34,94 +34,90 @@
 import org.apache.hadoop.mapreduce.TaskAttemptContext;
 import org.apache.hadoop.util.Tool;
 import org.apache.hadoop.util.ToolRunner;
-
-import htsjdk.samtools.SAMRecord;
-
 import org.seqdoop.hadoop_bam.AnySAMInputFormat;
 import org.seqdoop.hadoop_bam.KeyIgnoringBAMOutputFormat;
 import org.seqdoop.hadoop_bam.SAMRecordWritable;
 
 /**
  * Simple example that reads a BAM (or SAM) file, groups reads by their name and writes the
  * output again as BAM file. Note that both the file and its index must be present.
- *
+ * <p>
  * Usage: hadoop jar target/*-jar-with-dependencies.jar org.seqdoop.hadoop_bam.examples.TestBAM \
- *     <input.bam> <output_directory>
+ * <input.bam> <output_directory>
  */
 public class TestBAM extends Configured implements Tool {
 
-  static class MyOutputFormat extends KeyIgnoringBAMOutputFormat<NullWritable> {
-      public final static String HEADER_FROM_FILE = "TestBAM.header";
+    static class MyOutputFormat extends KeyIgnoringBAMOutputFormat<NullWritable> {
+        public final static String HEADER_FROM_FILE = "TestBAM.header";
 
-      @Override
-      public RecordWriter<NullWritable, SAMRecordWritable> getRecordWriter(TaskAttemptContext ctx) throws IOException {
-          final Configuration conf = ctx.getConfiguration();
-          readSAMHeaderFrom(new Path(conf.get(HEADER_FROM_FILE)), conf);
-          return super.getRecordWriter(ctx);
-      }
-  }
+        @Override
+        public RecordWriter<NullWritable, SAMRecordWritable> getRecordWriter(TaskAttemptContext ctx) throws IOException {
+            final Configuration conf = ctx.getConfiguration();
+            readSAMHeaderFrom(new Path(conf.get(HEADER_FROM_FILE)), conf);
+            return super.getRecordWriter(ctx);
+        }
+    }
 
-  public int run(String[] args) throws Exception {
-      final Configuration conf = getConf();
+    public int run(String[] args) throws Exception {
+        final Configuration conf = getConf();
 
-      conf.set(MyOutputFormat.HEADER_FROM_FILE, args[0]);
+        conf.set(MyOutputFormat.HEADER_FROM_FILE, args[0]);
 
-      final Job job = new Job(conf);
+        final Job job = new Job(conf);
 
-      job.setJarByClass(TestBAM.class);
-      job.setMapperClass (TestBAMMapper.class);
-      job.setReducerClass(TestBAMReducer.class);
+        job.setJarByClass(TestBAM.class);
+        job.setMapperClass(TestBAMMapper.class);
+        job.setReducerClass(TestBAMReducer.class);
 
-      job.setMapOutputKeyClass(Text.class);
-      job.setMapOutputValueClass(SAMRecordWritable.class);
-      job.setOutputKeyClass(Text.class);
-      job.setOutputValueClass (SAMRecordWritable.class);
+        job.setMapOutputKeyClass(Text.class);
+        job.setMapOutputValueClass(SAMRecordWritable.class);
+        job.setOutputKeyClass(Text.class);
+        job.setOutputValueClass(SAMRecordWritable.class);
 
-      job.setInputFormatClass(AnySAMInputFormat.class);
-      job.setOutputFormatClass(TestBAM.MyOutputFormat.class);
+        job.setInputFormatClass(AnySAMInputFormat.class);
+        job.setOutputFormatClass(TestBAM.MyOutputFormat.class);
 
-      org.apache.hadoop.mapreduce.lib.input.FileInputFormat.addInputPath(job, new Path(args[0]));
+        org.apache.hadoop.mapreduce.lib.input.FileInputFormat.addInputPath(job, new Path(args[0]));
 
-      org.apache.hadoop.mapreduce.lib.output.FileOutputFormat.setOutputPath(job, new Path(args[1]));
-      job.submit();
+        org.apache.hadoop.mapreduce.lib.output.FileOutputFormat.setOutputPath(job, new Path(args[1]));
+        job.submit();
 
-      if (!job.waitForCompletion(true)) {
-          System.err.println("sort :: Job failed.");
-          return 1;
-      }
+        if (!job.waitForCompletion(true)) {
+            System.err.println("sort :: Job failed.");
+            return 1;
+        }
 
-    return 0;
-  }
-
-
-  public static void main(String[] args) throws Exception {
-    if (args.length != 2) {
-        System.out.printf("Usage: hadoop jar <name.jar> %s <input.bam> <output_directory>\n", TestBAM.class.getCanonicalName());
-        System.exit(0);
+        return 0;
     }
 
-    int res = ToolRunner.run(new Configuration(), new TestBAM(), args);
-    System.exit(res);
-  }
+
+    public static void main(String[] args) throws Exception {
+        if (args.length != 2) {
+            System.out.printf("Usage: hadoop jar <name.jar> %s <input.bam> <output_directory>\n", TestBAM.class.getCanonicalName());
+            System.exit(0);
+        }
+
+        int res = ToolRunner.run(new Configuration(), new TestBAM(), args);
+        System.exit(res);
+    }
 }
 
 final class TestBAMMapper
-        extends org.apache.hadoop.mapreduce.Mapper<LongWritable,SAMRecordWritable, Text,SAMRecordWritable>
-{
-    @Override protected void map(
+        extends org.apache.hadoop.mapreduce.Mapper<LongWritable, SAMRecordWritable, Text, SAMRecordWritable> {
+    @Override
+    protected void map(
             LongWritable ignored, SAMRecordWritable wrec,
-            org.apache.hadoop.mapreduce.Mapper<LongWritable,SAMRecordWritable, Text,SAMRecordWritable>.Context
+            org.apache.hadoop.mapreduce.Mapper<LongWritable, SAMRecordWritable, Text, SAMRecordWritable>.Context
                     ctx)
-            throws InterruptedException, IOException
-    {
+            throws InterruptedException, IOException {
         final SAMRecord record = wrec.get();
         System.out.println(record.toString());
         ctx.write(new Text(wrec.get().getReadName()), wrec);
     }
 }
 
 final class TestBAMReducer
-        extends org.apache.hadoop.mapreduce.Reducer<Text,SAMRecordWritable, Text,SAMRecordWritable> {
+        extends org.apache.hadoop.mapreduce.Reducer<Text, SAMRecordWritable, Text, SAMRecordWritable> {
 
     @Override
     protected void reduce(

examples/src/main/java/org/seqdoop/hadoop_bam/examples/TestVCF.java

@@ -22,7 +22,7 @@
 
 import java.io.IOException;
 import java.util.Iterator;
-
+import htsjdk.variant.variantcontext.VariantContext;
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.conf.Configured;
 import org.apache.hadoop.fs.Path;
@@ -34,9 +34,6 @@
 import org.apache.hadoop.mapreduce.lib.output.FileOutputFormat;
 import org.apache.hadoop.util.Tool;
 import org.apache.hadoop.util.ToolRunner;
-
-import htsjdk.variant.variantcontext.VariantContext;
-
 import org.seqdoop.hadoop_bam.KeyIgnoringVCFOutputFormat;
 import org.seqdoop.hadoop_bam.VCFInputFormat;
 import org.seqdoop.hadoop_bam.VCFOutputFormat;
@@ -45,9 +42,9 @@
 /**
  * Simple example that reads a VCF file, groups variants by their ID and writes the
  * output again as VCF file.
- *
+ * <p>
  * Usage: hadoop jar target/*-jar-with-dependencies.jar org.seqdoop.hadoop_bam.examples.TestVCF \
- *     <input.vcf> <output_directory>
+ * <input.vcf> <output_directory>
  */
 public class TestVCF extends Configured implements Tool {
 
@@ -58,8 +55,9 @@ static class MyVCFOutputFormat
         private KeyIgnoringVCFOutputFormat<Text> baseOF;
 
         private void initBaseOF(Configuration conf) {
-            if (baseOF == null)
+            if (baseOF == null) {
                 baseOF = new KeyIgnoringVCFOutputFormat<Text>(conf);
+            }
         }
 
         @Override
@@ -87,7 +85,7 @@ public int run(String[] args) throws Exception {
         final Job job = new Job(conf);
 
         job.setJarByClass(TestVCF.class);
-        job.setMapperClass (TestVCFMapper.class);
+        job.setMapperClass(TestVCFMapper.class);
         job.setReducerClass(TestVCFReducer.class);
 
         job.setMapOutputKeyClass(Text.class);
@@ -123,22 +121,21 @@ public static void main(String[] args) throws Exception {
 }
 
 final class TestVCFMapper
-        extends org.apache.hadoop.mapreduce.Mapper<LongWritable,VariantContextWritable, Text, VariantContextWritable>
-{
-    @Override protected void map(
+        extends org.apache.hadoop.mapreduce.Mapper<LongWritable, VariantContextWritable, Text, VariantContextWritable> {
+    @Override
+    protected void map(
             LongWritable ignored, VariantContextWritable wrec,
             org.apache.hadoop.mapreduce.Mapper<LongWritable, VariantContextWritable, Text, VariantContextWritable>.Context
                     ctx)
-            throws InterruptedException, IOException
-    {
+            throws InterruptedException, IOException {
         final VariantContext context = wrec.get();
         System.out.println(context.toString());
-        ctx.write(new Text(context.getChr()+":" + context.getID()), wrec);
+        ctx.write(new Text(context.getChr() + ":" + context.getID()), wrec);
     }
 }
 
 final class TestVCFReducer
-        extends org.apache.hadoop.mapreduce.Reducer<Text,VariantContextWritable, Text, VariantContextWritable> {
+        extends org.apache.hadoop.mapreduce.Reducer<Text, VariantContextWritable, Text, VariantContextWritable> {
 
     @Override
     protected void reduce(

findbugs-exclude.xml

@@ -1,11 +1,11 @@
 <FindBugsFilter>
-  <Match>
-    <Bug pattern="EI_EXPOSE_REP" />
-  </Match>
-  <Match>
-    <Bug pattern="EI_EXPOSE_REP2" />
-  </Match>
-  <Match>
-    <Bug pattern="VA_FORMAT_STRING_USES_NEWLINE" />
-  </Match>
+    <Match>
+        <Bug pattern="EI_EXPOSE_REP"/>
+    </Match>
+    <Match>
+        <Bug pattern="EI_EXPOSE_REP2"/>
+    </Match>
+    <Match>
+        <Bug pattern="VA_FORMAT_STRING_USES_NEWLINE"/>
+    </Match>
 </FindBugsFilter>

pom.xml

@@ -21,12 +21,13 @@
   ~ IN THE SOFTWARE.
   -->
 
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
     <parent>
         <groupId>org.sonatype.oss</groupId>
         <artifactId>oss-parent</artifactId>
         <version>7</version>
-        <relativePath />
+        <relativePath/>
     </parent>
 
     <modelVersion>4.0.0</modelVersion>
@@ -35,7 +36,9 @@
     <version>7.9.2-SNAPSHOT</version>
     <packaging>jar</packaging>
     <name>Hadoop-BAM</name>
-    <description>A Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework.</description>
+    <description>A Java library for the manipulation of files in common bioinformatics formats using the Hadoop
+        MapReduce framework.
+    </description>
     <url>http://sourceforge.net/projects/hadoop-bam/</url>
 
     <properties>
@@ -215,7 +218,7 @@
                 <artifactId>maven-surefire-plugin</artifactId>
                 <version>2.19.1</version>
                 <configuration>
-                  <argLine>-Xms1g -Xmx4g</argLine>
+                    <argLine>-Xms1g -Xmx4g</argLine>
                 </configuration>
             </plugin>
             <plugin>

src/main/java/htsjdk/samtools/LinearBAMIndex.java

@@ -19,21 +19,18 @@
 // IN THE SOFTWARE.
 package htsjdk.samtools;
 
-import htsjdk.samtools.CachingBAMFileIndex;
-import htsjdk.samtools.LinearIndex;
-import htsjdk.samtools.SAMSequenceDictionary;
 import htsjdk.samtools.seekablestream.SeekableStream;
 
 /**
  * The htsjdk APIs for accessing the linear BAM index are private...
  */
 public class LinearBAMIndex extends CachingBAMFileIndex {
 
-        public LinearBAMIndex(SeekableStream stream, SAMSequenceDictionary dict) {
-                super(stream, dict);
-        }
-        
-        public LinearIndex getLinearIndex(int idx) {
-                return getQueryResults(idx).getLinearIndex();
-        }
+    public LinearBAMIndex(SeekableStream stream, SAMSequenceDictionary dict) {
+        super(stream, dict);
+    }
+
+    public LinearIndex getLinearIndex(int idx) {
+        return getQueryResults(idx).getLinearIndex();
+    }
 }

src/main/java/htsjdk/samtools/SAMRecordHelper.java

@@ -5,7 +5,7 @@
  * {@link SAMRecord#eagerDecode()} method in HTSJDK.
  */
 public class SAMRecordHelper {
-  public static void eagerDecode(SAMRecord record) {
-    record.eagerDecode();
-  }
+    public static void eagerDecode(SAMRecord record) {
+        record.eagerDecode();
+    }
 }