FindBugs 'Maintainability' fixes

public/java/src/net/sf/picard/reference/FastaSequenceIndexBuilder.java

@@ -208,6 +208,7 @@ public class FastaSequenceIndexBuilder {
                         break;
                 }
             }
+            in.close();
             return sequenceIndex;
         }
         catch (IOException e) {

public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/SampleStatistics.java

@@ -264,7 +264,7 @@ class SampleStatistics {
             return false;
 
         // different contigs
-        if (read.getMateReferenceIndex() != read.getReferenceIndex())
+        if (!read.getMateReferenceIndex().equals(read.getReferenceIndex()))
             return false;
 
         // unmapped

public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java

@@ -104,7 +104,9 @@ public class BAMDiffableReader implements DiffableReader {
             InputStream fstream = new BufferedInputStream(new FileInputStream(file));
             if ( !BlockCompressedInputStream.isValidFile(fstream) )
                 return false;
-            new BlockCompressedInputStream(fstream).read(buffer, 0, BAM_MAGIC.length);
+            final BlockCompressedInputStream BCIS = new BlockCompressedInputStream(fstream);
+            BCIS.read(buffer, 0, BAM_MAGIC.length);
+            BCIS.close();
             return Arrays.equals(buffer, BAM_MAGIC);
         } catch ( IOException e ) {
             return false;

public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java

@@ -90,8 +90,10 @@ public class GATKReportDiffableReader implements DiffableReader {
     public boolean canRead(File file) {
         try {
             final String HEADER = GATKReport.GATKREPORT_HEADER_PREFIX;
-            char[] buff = new char[HEADER.length()];
+            final char[] buff = new char[HEADER.length()];
-            new FileReader(file).read(buff, 0, HEADER.length());
+            final FileReader FR = new FileReader(file);
+            FR.read(buff, 0, HEADER.length());
+            FR.close();
             String firstLine = new String(buff);
             return firstLine.startsWith(HEADER);
         } catch (IOException e) {

public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java

@@ -305,7 +305,7 @@ public class ConstrainedMateFixingManager {
     }
 
     public static boolean iSizeTooBigToMove(SAMRecord read, int maxInsertSizeForMovingReadPairs) {
-        return ( read.getReadPairedFlag() && ! read.getMateUnmappedFlag() && read.getReferenceName() != read.getMateReferenceName() ) // maps to different chromosomes
+        return ( read.getReadPairedFlag() && ! read.getMateUnmappedFlag() && !read.getReferenceName().equals(read.getMateReferenceName()) ) // maps to different chromosomes
                 || Math.abs(read.getInferredInsertSize()) > maxInsertSizeForMovingReadPairs;     // we won't try to move such a read
     }
 

public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java

@@ -177,6 +177,7 @@ public class TrancheManager {
                 double runningValue = metric.getRunningMetric(i);
                 out.printf("%.4f %d %.4f%n", d.lod, score, runningValue);
             }
+            out.close();
         } catch (FileNotFoundException e) {
             throw new UserException.CouldNotCreateOutputFile(f, e);
         }

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java

@@ -270,6 +270,7 @@ public class VariantsToBinaryPed extends RodWalker<Integer,Integer> {
                     inStream.read(readGenotypes);
                     outBed.write(readGenotypes);
                 }
+                inStream.close();
             } catch (IOException e) {
                 throw new ReviewedStingException("Error reading form temp file for input.",e);
             }

public/java/src/org/broadinstitute/sting/utils/help/ForumAPIUtils.java

@@ -135,6 +135,7 @@ public class ForumAPIUtils {
                 System.out.println(line);
             }
 
+            br.close();
             httpClient.getConnectionManager().shutdown();
             return output;