From e17d46c02050b980fa91b4f22766a2726b9a0b34 Mon Sep 17 00:00:00 2001
From: Chris Norman <cnorman@broadinstitute.org>
Date: Tue, 26 Feb 2019 17:49:45 -0500
Subject: [PATCH] Simplify CRAM sequence dictionary extractor to not require a
 fake reference.

---
 .../java/htsjdk/samtools/CRAMIterator.java    | 25 -------------------
 .../utils/SAMSequenceDictionaryExtractor.java | 23 ++++++++++++-----
 2 files changed, 17 insertions(+), 31 deletions(-)

diff --git a/src/main/java/htsjdk/samtools/CRAMIterator.java b/src/main/java/htsjdk/samtools/CRAMIterator.java
index 72b1082288..3e99e8e755 100644
--- a/src/main/java/htsjdk/samtools/CRAMIterator.java
+++ b/src/main/java/htsjdk/samtools/CRAMIterator.java
@@ -32,24 +32,13 @@
 
 import java.io.InputStream;
 import java.math.BigInteger;
-import java.nio.file.Files;
-import java.nio.file.Path;
 import java.util.*;
 
 import htsjdk.samtools.cram.CRAMException;
-import htsjdk.samtools.util.IOUtil;
 import htsjdk.samtools.util.RuntimeIOException;
 
 public class CRAMIterator implements SAMRecordIterator {
     
-    /** A CRAMReferenceSource that is never invoked . It's used in {@link #extractDictionary(Path)}*/
-    private static final CRAMReferenceSource NIL_CRAM_REFERENCE_SRC = new CRAMReferenceSource() {
-        @Override
-        public byte[] getReferenceBases(final SAMSequenceRecord sequenceRecord, boolean tryNameVariants) {
-            throw new IllegalStateException("CRAMReferenceSource.getReferenceBases shouldn't be called");
-            }
-    };
-    
     private final CountingInputStream countingInputStream;
     private final CramHeader cramHeader;
     private final ArrayList<SAMRecord> records;
@@ -315,18 +304,4 @@ public SAMFileHeader getSAMFileHeader() {
         return cramHeader.getSamFileHeader();
     }
 
-    /** extracts a {@link SAMSequenceDictionary} from a cram file.
-     * @return the dictionary of the cram file
-     * @throws SAMException if a dictionary cannot be extracted
-     */
-    public static SAMSequenceDictionary extractDictionary(final Path cramPath) {
-        IOUtil.assertFileIsReadable(cramPath);
-        try (final InputStream in = Files.newInputStream(cramPath)) {
-            try(final CRAMIterator iter= new CRAMIterator(in, NIL_CRAM_REFERENCE_SRC, ValidationStringency.SILENT)) {
-                return iter.getSAMFileHeader().getSequenceDictionary();
-            }
-        } catch (final Exception err) {
-           throw new SAMException("Cannot extract dictionary from "+cramPath, err);
-        }
-    }
 }
diff --git a/src/main/java/htsjdk/variant/utils/SAMSequenceDictionaryExtractor.java b/src/main/java/htsjdk/variant/utils/SAMSequenceDictionaryExtractor.java
index e236fc6303..46744efd7c 100644
--- a/src/main/java/htsjdk/variant/utils/SAMSequenceDictionaryExtractor.java
+++ b/src/main/java/htsjdk/variant/utils/SAMSequenceDictionaryExtractor.java
@@ -26,19 +26,20 @@
 
 import htsjdk.samtools.*;
 import htsjdk.samtools.cram.build.CramIO;
+import htsjdk.samtools.cram.structure.CramHeader;
 import htsjdk.samtools.reference.ReferenceSequenceFileFactory;
-import htsjdk.samtools.util.BufferedLineReader;
-import htsjdk.samtools.util.CollectionUtil;
-import htsjdk.samtools.util.IOUtil;
-import htsjdk.samtools.util.IntervalList;
+import htsjdk.samtools.util.*;
 import htsjdk.tribble.util.ParsingUtils;
 import htsjdk.variant.vcf.VCFFileReader;
 
 import java.io.File;
 import java.io.IOException;
+import java.io.InputStream;
+import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.Arrays;
 import java.util.Collection;
+import java.util.Optional;
 
 /**
  * Small class for loading a SAMSequenceDictionary from a file
@@ -74,8 +75,18 @@ SAMSequenceDictionary extractDictionary(final Path dictionary) {
         CRAM(CramIO.CRAM_FILE_EXTENSION) {
             
             @Override
-            SAMSequenceDictionary extractDictionary(final Path cram) {
-                    return CRAMIterator.extractDictionary(cram);
+            SAMSequenceDictionary extractDictionary(final Path cramPath) {
+                IOUtil.assertFileIsReadable(cramPath);
+                try (final InputStream in = Files.newInputStream(cramPath)) {
+                    final CramHeader cramHeader = CramIO.readCramHeader(in);
+                    final Optional<SAMFileHeader> samHeader = Optional.ofNullable(cramHeader.getSamFileHeader());
+                    if (samHeader.isPresent()) {
+                        return samHeader.get().getSequenceDictionary();
+                    }
+                } catch (IOException e) {
+                    throw new RuntimeIOException(e);
+                }
+                throw new SAMException(String.format("Can't retrieve sequence dictionary from %s", cramPath));
             }
         },
         SAM(IOUtil.SAM_FILE_EXTENSION, BamFileIoUtils.BAM_FILE_EXTENSION) {