From b24ac12ee50132643570511f908df0ebe0af1811 Mon Sep 17 00:00:00 2001
From: Joel Thibault <thibault@broadinstitute.org>
Date: Wed, 16 Jan 2019 11:30:29 -0500
Subject: [PATCH] more CRAMIterator cleanup

---
 .../java/htsjdk/samtools/CRAMIterator.java    | 38 +++++++++----------
 1 file changed, 18 insertions(+), 20 deletions(-)

diff --git a/src/main/java/htsjdk/samtools/CRAMIterator.java b/src/main/java/htsjdk/samtools/CRAMIterator.java
index a78cd6b571..51bb0ef023 100644
--- a/src/main/java/htsjdk/samtools/CRAMIterator.java
+++ b/src/main/java/htsjdk/samtools/CRAMIterator.java
@@ -29,7 +29,6 @@
 import htsjdk.samtools.cram.structure.CramHeader;
 import htsjdk.samtools.cram.structure.Slice;
 import htsjdk.samtools.seekablestream.SeekableStream;
-import htsjdk.samtools.util.Log;
 
 import java.io.IOException;
 import java.io.InputStream;
@@ -39,7 +38,6 @@
 import htsjdk.samtools.cram.CRAMException;
 
 public class CRAMIterator implements SAMRecordIterator {
-    private static final Log log = Log.getInstance(CRAMIterator.class);
     private final CountingInputStream countingInputStream;
     private final CramHeader cramHeader;
     private final ArrayList<SAMRecord> records;
@@ -63,8 +61,7 @@ public ValidationStringency getValidationStringency() {
         return validationStringency;
     }
 
-    public void setValidationStringency(
-            final ValidationStringency validationStringency) {
+    public void setValidationStringency(final ValidationStringency validationStringency) {
         this.validationStringency = validationStringency;
     }
 
@@ -75,11 +72,13 @@ public void setValidationStringency(
     private long samRecordIndex;
     private ArrayList<CramCompressionRecord> cramRecords;
 
-    public CRAMIterator(final InputStream inputStream, final CRAMReferenceSource referenceSource, final ValidationStringency validationStringency)
-            throws IOException {
+    public CRAMIterator(final InputStream inputStream,
+                        final CRAMReferenceSource referenceSource,
+                        final ValidationStringency validationStringency) {
         if (null == referenceSource) {
             throw new CRAMException("A reference source is required for CRAM files");
         }
+
         this.countingInputStream = new CountingInputStream(inputStream);
         this.referenceSource = referenceSource;
         this.validationStringency = validationStringency;
@@ -88,17 +87,20 @@ public CRAMIterator(final InputStream inputStream, final CRAMReferenceSource ref
         this.containerIterator = containerIterator;
 
         firstContainerOffset = this.countingInputStream.getCount();
-        records = new ArrayList<SAMRecord>(CRAMContainerStreamWriter.DEFAULT_RECORDS_PER_SLICE);
+        records = new ArrayList<>(CRAMContainerStreamWriter.DEFAULT_RECORDS_PER_SLICE);
         normalizer = new CramNormalizer(cramHeader.getSamFileHeader(),
                 referenceSource);
         parser = new ContainerParser(cramHeader.getSamFileHeader());
     }
 
-    public CRAMIterator(final SeekableStream seekableStream, final CRAMReferenceSource referenceSource, final long[] coordinates, final ValidationStringency validationStringency)
-            throws IOException {
+    public CRAMIterator(final SeekableStream seekableStream,
+                        final CRAMReferenceSource referenceSource,
+                        final long[] coordinates,
+                        final ValidationStringency validationStringency) {
         if (null == referenceSource) {
             throw new CRAMException("A reference source is required for CRAM files");
         }
+
         this.countingInputStream = new CountingInputStream(seekableStream);
         this.referenceSource = referenceSource;
         this.validationStringency = validationStringency;
@@ -107,15 +109,16 @@ public CRAMIterator(final SeekableStream seekableStream, final CRAMReferenceSour
         this.containerIterator = containerIterator;
 
         firstContainerOffset = containerIterator.getFirstContainerOffset();
-        records = new ArrayList<SAMRecord>(CRAMContainerStreamWriter.DEFAULT_RECORDS_PER_SLICE);
+        records = new ArrayList<>(CRAMContainerStreamWriter.DEFAULT_RECORDS_PER_SLICE);
         normalizer = new CramNormalizer(cramHeader.getSamFileHeader(),
                 referenceSource);
         parser = new ContainerParser(cramHeader.getSamFileHeader());
     }
 
     @Deprecated
-    public CRAMIterator(final SeekableStream seekableStream, final CRAMReferenceSource referenceSource, final long[] coordinates)
-            throws IOException {
+    public CRAMIterator(final SeekableStream seekableStream,
+                        final CRAMReferenceSource referenceSource,
+                        final long[] coordinates) {
         this(seekableStream, referenceSource, coordinates, ValidationStringency.DEFAULT_STRINGENCY);
     }
 
@@ -123,8 +126,7 @@ public CramHeader getCramHeader() {
         return cramHeader;
     }
 
-    void nextContainer() throws IOException, IllegalArgumentException,
-            IllegalAccessException, CRAMException {
+    void nextContainer() throws IllegalArgumentException, CRAMException {
 
         if (containerIterator != null) {
             if (!containerIterator.hasNext()) {
@@ -149,7 +151,7 @@ void nextContainer() throws IOException, IllegalArgumentException,
 
         records.clear();
         if (cramRecords == null)
-            cramRecords = new ArrayList<CramCompressionRecord>(container.nofRecords);
+            cramRecords = new ArrayList<>(container.nofRecords);
         else
             cramRecords.clear();
 
@@ -250,11 +252,7 @@ public boolean advanceToAlignmentInContainer(final int refIndex, final int pos)
     public boolean hasNext() {
         if (container != null && container.isEOF()) return false;
         if (!iterator.hasNext()) {
-            try {
-                nextContainer();
-            } catch (IOException | IllegalAccessException e) {
-                throw new SAMException(e);
-            }
+            nextContainer();
         }
 
         return !records.isEmpty();