From 77b3b8ff94a47f5601684beead2d2b499863c840 Mon Sep 17 00:00:00 2001
From: Tom White <tom.e.white@gmail.com>
Date: Mon, 11 Feb 2019 19:23:47 +0000
Subject: [PATCH] Fix fields that should be final, as reported by SpotBugs
 (#1268)

---
 src/main/java/htsjdk/samtools/SAMRecord.java           |  4 ++--
 src/main/java/htsjdk/samtools/SamReaderFactory.java    |  2 +-
 src/main/java/htsjdk/samtools/cram/CRAIEntry.java      |  2 +-
 .../reference/ReferenceSequenceFileFactory.java        |  5 +++--
 src/main/java/htsjdk/samtools/util/TestUtil.java       |  2 +-
 src/main/java/htsjdk/samtools/util/ftp/FTPClient.java  |  3 ++-
 .../tribble/index/interval/IntervalIndexCreator.java   |  2 +-
 .../tribble/index/linear/LinearIndexCreator.java       |  2 +-
 .../java/htsjdk/tribble/index/tabix/TabixFormat.java   | 10 +++++-----
 src/main/java/htsjdk/tribble/util/ParsingUtils.java    |  2 +-
 src/test/java/htsjdk/tribble/TestUtils.java            |  2 +-
 .../java/htsjdk/variant/vcf/VCFHeaderUnitTest.java     |  6 +++---
 12 files changed, 22 insertions(+), 20 deletions(-)

diff --git a/src/main/java/htsjdk/samtools/SAMRecord.java b/src/main/java/htsjdk/samtools/SAMRecord.java
index 732faf4722..b8e2185756 100644
--- a/src/main/java/htsjdk/samtools/SAMRecord.java
+++ b/src/main/java/htsjdk/samtools/SAMRecord.java
@@ -164,12 +164,12 @@ public class SAMRecord implements Cloneable, Locatable, Serializable {
      * Tags that are known to need the reverse complement if the read is reverse complemented.
      */
     @SuppressWarnings("deprecated")
-    public static List<String> TAGS_TO_REVERSE_COMPLEMENT = Arrays.asList(SAMTag.E2.name(), SAMTag.SQ.name());
+    public static final List<String> TAGS_TO_REVERSE_COMPLEMENT = Arrays.asList(SAMTag.E2.name(), SAMTag.SQ.name());
 
     /**
      * Tags that are known to need the reverse if the read is reverse complemented.
      */
-    public static List<String> TAGS_TO_REVERSE = Arrays.asList(SAMTag.OQ.name(), SAMTag.U2.name());
+    public static final List<String> TAGS_TO_REVERSE = Arrays.asList(SAMTag.OQ.name(), SAMTag.U2.name());
 
     private String mReadName = null;
     private byte[] mReadBases = NULL_SEQUENCE;
diff --git a/src/main/java/htsjdk/samtools/SamReaderFactory.java b/src/main/java/htsjdk/samtools/SamReaderFactory.java
index 506bd79305..5838eb63af 100644
--- a/src/main/java/htsjdk/samtools/SamReaderFactory.java
+++ b/src/main/java/htsjdk/samtools/SamReaderFactory.java
@@ -607,7 +607,7 @@ void applyTo(final SRAFileReader underlyingReader, final SamReader reader) {
 
         };
 
-        public static EnumSet<Option> DEFAULTS = EnumSet.noneOf(Option.class);
+        public static final EnumSet<Option> DEFAULTS = EnumSet.noneOf(Option.class);
 
         /** Applies this option to the provided reader, if applicable. */
         void applyTo(final SamReader.PrimitiveSamReaderToSamReaderAdapter reader) {
diff --git a/src/main/java/htsjdk/samtools/cram/CRAIEntry.java b/src/main/java/htsjdk/samtools/cram/CRAIEntry.java
index c6878050f9..6176aa48dd 100644
--- a/src/main/java/htsjdk/samtools/cram/CRAIEntry.java
+++ b/src/main/java/htsjdk/samtools/cram/CRAIEntry.java
@@ -137,7 +137,7 @@ public int compare(final CRAIEntry o1, final CRAIEntry o2) {
         }
     };
 
-    public static Comparator<CRAIEntry> byStartDesc = new Comparator<CRAIEntry>() {
+    public static final Comparator<CRAIEntry> byStartDesc = new Comparator<CRAIEntry>() {
 
         @Override
         public int compare(CRAIEntry o1, CRAIEntry o2) {
diff --git a/src/main/java/htsjdk/samtools/reference/ReferenceSequenceFileFactory.java b/src/main/java/htsjdk/samtools/reference/ReferenceSequenceFileFactory.java
index a3a6edf7ac..09789b3318 100644
--- a/src/main/java/htsjdk/samtools/reference/ReferenceSequenceFileFactory.java
+++ b/src/main/java/htsjdk/samtools/reference/ReferenceSequenceFileFactory.java
@@ -41,6 +41,7 @@
 import java.io.InputStream;
 import java.nio.file.Files;
 import java.nio.file.Path;
+import java.util.Collections;
 import java.util.HashSet;
 import java.util.Set;
 
@@ -51,7 +52,7 @@
  * @author Tim Fennell
  */
 public class ReferenceSequenceFileFactory {
-    public static final Set<String> FASTA_EXTENSIONS = new HashSet<String>() {{
+    public static final Set<String> FASTA_EXTENSIONS = Collections.unmodifiableSet(new HashSet<String>() {{
         add(".fasta");
         add(".fasta.gz");
         add(".fa");
@@ -60,7 +61,7 @@ public class ReferenceSequenceFileFactory {
         add(".fna.gz");
         add(".txt");
         add(".txt.gz");
-    }};
+    }});
 
     public static final String FASTA_INDEX_EXTENSION = ".fai";
 
diff --git a/src/main/java/htsjdk/samtools/util/TestUtil.java b/src/main/java/htsjdk/samtools/util/TestUtil.java
index 196a9cfa96..e2fafadc8b 100644
--- a/src/main/java/htsjdk/samtools/util/TestUtil.java
+++ b/src/main/java/htsjdk/samtools/util/TestUtil.java
@@ -29,7 +29,7 @@
 
 public class TestUtil {
 
-    public static int RANDOM_SEED = 42;
+    public static final int RANDOM_SEED = 42;
 
 
     /**
diff --git a/src/main/java/htsjdk/samtools/util/ftp/FTPClient.java b/src/main/java/htsjdk/samtools/util/ftp/FTPClient.java
index c26bb6023e..dc15915813 100644
--- a/src/main/java/htsjdk/samtools/util/ftp/FTPClient.java
+++ b/src/main/java/htsjdk/samtools/util/ftp/FTPClient.java
@@ -1,3 +1,4 @@
+
 /*
  * Copyright (c) 2007-2011 by The Broad Institute of MIT and Harvard.  All Rights Reserved.
  *
@@ -38,7 +39,7 @@ public class FTPClient {
 
     private Socket commandSocket = null;
 
-    public static int READ_TIMEOUT = 5 * 60 * 1000;
+    public static final int READ_TIMEOUT = 5 * 60 * 1000;
 
     /**
      * Stream to write commands.
diff --git a/src/main/java/htsjdk/tribble/index/interval/IntervalIndexCreator.java b/src/main/java/htsjdk/tribble/index/interval/IntervalIndexCreator.java
index dc8825396c..5910466345 100644
--- a/src/main/java/htsjdk/tribble/index/interval/IntervalIndexCreator.java
+++ b/src/main/java/htsjdk/tribble/index/interval/IntervalIndexCreator.java
@@ -36,7 +36,7 @@
  */
 public class IntervalIndexCreator extends TribbleIndexCreator {
 
-    public static int DEFAULT_FEATURE_COUNT = 600;
+    public static final int DEFAULT_FEATURE_COUNT = 600;
 
     /**
      * Maximum number of features stored per interval.
diff --git a/src/main/java/htsjdk/tribble/index/linear/LinearIndexCreator.java b/src/main/java/htsjdk/tribble/index/linear/LinearIndexCreator.java
index c4ff04da36..acbe3b8d77 100644
--- a/src/main/java/htsjdk/tribble/index/linear/LinearIndexCreator.java
+++ b/src/main/java/htsjdk/tribble/index/linear/LinearIndexCreator.java
@@ -40,7 +40,7 @@
  * @author jrobinso
  */
 public class LinearIndexCreator  extends TribbleIndexCreator {
-    public static int DEFAULT_BIN_WIDTH = 8000;
+    public static final int DEFAULT_BIN_WIDTH = 8000;
     // the set bin width
     private int binWidth = DEFAULT_BIN_WIDTH;
 
diff --git a/src/main/java/htsjdk/tribble/index/tabix/TabixFormat.java b/src/main/java/htsjdk/tribble/index/tabix/TabixFormat.java
index e9fe2923cb..ef8d40dac9 100644
--- a/src/main/java/htsjdk/tribble/index/tabix/TabixFormat.java
+++ b/src/main/java/htsjdk/tribble/index/tabix/TabixFormat.java
@@ -36,11 +36,11 @@ public class TabixFormat implements Cloneable {
     public static final int UCSC_FLAGS    = GENERIC_FLAGS | ZERO_BASED;
 
     /** Predefined headers for known formats */
-    public static TabixFormat GFF = new TabixFormat(GENERIC_FLAGS, 1, 4, 5, '#', 0);
-    public static TabixFormat BED = new TabixFormat(UCSC_FLAGS, 1, 2, 3, '#', 0);
-    public static TabixFormat PSLTBL = new TabixFormat(UCSC_FLAGS, 15, 17, 18, '#', 0);
-    public static TabixFormat SAM = new TabixFormat(SAM_FLAGS, 3, 4, 0, '@', 0);
-    public static TabixFormat VCF = new TabixFormat(VCF_FLAGS, 1, 2, 0, '#', 0);
+    public static final TabixFormat GFF = new TabixFormat(GENERIC_FLAGS, 1, 4, 5, '#', 0);
+    public static final TabixFormat BED = new TabixFormat(UCSC_FLAGS, 1, 2, 3, '#', 0);
+    public static final TabixFormat PSLTBL = new TabixFormat(UCSC_FLAGS, 15, 17, 18, '#', 0);
+    public static final TabixFormat SAM = new TabixFormat(SAM_FLAGS, 3, 4, 0, '@', 0);
+    public static final TabixFormat VCF = new TabixFormat(VCF_FLAGS, 1, 2, 0, '#', 0);
 
     /** Describes interpretation of file being indexed.  See FLAGS constants above. */
     public int flags;
diff --git a/src/main/java/htsjdk/tribble/util/ParsingUtils.java b/src/main/java/htsjdk/tribble/util/ParsingUtils.java
index 79f5361c47..0ed9ff2eb9 100644
--- a/src/main/java/htsjdk/tribble/util/ParsingUtils.java
+++ b/src/main/java/htsjdk/tribble/util/ParsingUtils.java
@@ -44,7 +44,7 @@
  */
 public class ParsingUtils {
 
-    public static Map<Object, Color> colorCache = new WeakHashMap<>(100);
+    public static final Map<Object, Color> colorCache = new WeakHashMap<>(100);
 
     // HTML 4.1 color table,  + orange and magenta
     static Map<String, String> colorSymbols = new HashMap();
diff --git a/src/test/java/htsjdk/tribble/TestUtils.java b/src/test/java/htsjdk/tribble/TestUtils.java
index c77f58a68e..e5b2f90644 100644
--- a/src/test/java/htsjdk/tribble/TestUtils.java
+++ b/src/test/java/htsjdk/tribble/TestUtils.java
@@ -37,7 +37,7 @@
  * Date: 2012-Dec-13
  */
 public class TestUtils {
-    public static String DATA_DIR = "src/test/resources/htsjdk/tribble/";
+    public static final String DATA_DIR = "src/test/resources/htsjdk/tribble/";
 
     /**
      * A utility method for copying a tribble file (and possibly its index) into a Jimfs-like FileSystem
diff --git a/src/test/java/htsjdk/variant/vcf/VCFHeaderUnitTest.java b/src/test/java/htsjdk/variant/vcf/VCFHeaderUnitTest.java
index 2e534d1197..5fd0bbc7b8 100644
--- a/src/test/java/htsjdk/variant/vcf/VCFHeaderUnitTest.java
+++ b/src/test/java/htsjdk/variant/vcf/VCFHeaderUnitTest.java
@@ -596,9 +596,9 @@ private void checkMD5ofHeaderFile(VCFHeader header, String md5sum) {
         Assert.assertEquals(md5SumFile(myTempFile), md5sum);
     }
 
-    public static int VCF4headerStringCount = 16;
+    public static final int VCF4headerStringCount = 16;
 
-    public static String VCF4headerStrings =
+    public static final String VCF4headerStrings =
             "##fileformat=VCFv4.2\n" +
                     "##filedate=2010-06-21\n" +
                     "##reference=NCBI36\n" +
@@ -618,7 +618,7 @@ private void checkMD5ofHeaderFile(VCFHeader header, String md5sum) {
                     "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n";
 
 
-    public static String VCF4headerStrings_with_negativeOne =
+    public static final String VCF4headerStrings_with_negativeOne =
             "##fileformat=VCFv4.2\n" +
                     "##filedate=2010-06-21\n" +
                     "##reference=NCBI36\n" +