Reformat in line with the Google Java Style Guide

.travis.yml

@@ -13,7 +13,7 @@ before_install:
   - sed -e "s/^\\(127\\.0\\.0\\.1.*\\)/\\1 $(hostname | cut -c1-63)/" /etc/hosts | sudo tee /etc/hosts
   - cat /etc/hosts # optionally check the content *after*
 
-script: mvn clean test jacoco:report
+script: mvn clean fmt:check test jacoco:report
 
 after_success:
   - python scripts/deploy/addServerToM2Settings.py

pom.xml

@@ -121,6 +121,18 @@
             </plugins>
         </pluginManagement>
         <plugins>
+            <plugin>
+                <groupId>com.coveo</groupId>
+                <artifactId>fmt-maven-plugin</artifactId>
+                <version>2.2.0</version>
+                <executions>
+                    <execution>
+                        <goals>
+                            <goal>check</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-release-plugin</artifactId>

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

@@ -19,21 +19,16 @@
 // 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...
- */
+/** 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

@@ -1,10 +1,11 @@
 package htsjdk.samtools;
 
 /**
- * This class is required in order to access the protected
- * {@link SAMRecord#eagerDecode()} method in HTSJDK.
+ * This class is required in order to access the protected {@link SAMRecord#eagerDecode()} method in
+ * HTSJDK.
  */
 public class SAMRecordHelper {
+
   public static void eagerDecode(SAMRecord record) {
     record.eagerDecode();
   }