IndexedFastaSequenceFile is now in Picard; transitioning to that implementation.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3701 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -23,15 +23,17 @@
  * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.fasta;
+package net.sf.picard.reference;
 
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceDataSourceProgressListener;
 import org.broadinstitute.sting.utils.StingException;
-import static org.broadinstitute.sting.utils.fasta.FastaSequenceIndexBuilder.Status.*;
+import static net.sf.picard.reference.FastaSequenceIndexBuilder.Status.*;
 
 import java.io.*;
 import java.util.Iterator;
 
+import net.sf.picard.reference.FastaSequenceIndex;
+
 /**
  * Builds FastaSequenceIndex from fasta file.
  * Produces fai file with same output as samtools faidx
@@ -46,6 +48,7 @@ public class FastaSequenceIndexBuilder {
     // vars that store information about the contig that is currently being read
     String contig;
     long location, size, bytesPerLine, basesPerLine, basesThisLine;
+    int thisSequenceIndex = 0;
 
     // vars that keep loop state
     byte lastByte = 0, currentByte = 0, nextByte = 0;
@@ -241,7 +244,7 @@ public class FastaSequenceIndexBuilder {
      * Reset iterators and add contig to sequence index
      */
     private void finishReadingContig(FastaSequenceIndex sequenceIndex) {
-        sequenceIndex.addIndexEntry(contig, location, size, (int) basesPerLine, (int) bytesPerLine);
+        sequenceIndex.add(new FastaSequenceIndexEntry(contig, location, size, (int) basesPerLine, (int) bytesPerLine, thisSequenceIndex++));
         status = Status.NONE;
         contig = "";
         size = 0;
@@ -271,11 +274,9 @@ public class FastaSequenceIndexBuilder {
                     faiFile.getAbsolutePath()), e);
         }
 
-        Iterator<FastaSequenceIndexEntry> iter = sequenceIndex.iterator();
-
         try {
-            while (iter.hasNext()) {
+            for(FastaSequenceIndexEntry entry: sequenceIndex) {
-                out.write(iter.next().toIndexFileLine());
+                out.write(toIndexFileLine(entry));
                 out.newLine();
             }
             out.close();
@@ -284,4 +285,13 @@ public class FastaSequenceIndexBuilder {
             throw new StingException(String.format("An error occurred while writing file %s", e));
         }
     }
+
+    /**
+     * Print string in format of fai file line
+     * @return Contig as one line in a fai file
+     */
+    private static String toIndexFileLine(FastaSequenceIndexEntry entry) {
+        return String.format("%s\t%d\t%d\t%d\t%d", entry.getContig(), entry.getSize(), entry.getLocation(), entry.getBasesPerLine(), entry.getBytesPerLine());
+    }
+
 }

java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java

@@ -4,12 +4,12 @@ import org.broadinstitute.sting.alignment.Aligner;
 import org.broadinstitute.sting.alignment.Alignment;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 
 import java.io.File;
 import java.io.FileNotFoundException;
 
 import net.sf.samtools.*;
+import net.sf.picard.reference.IndexedFastaSequenceFile;
 
 /**
  * A test harness to ensure that the perfect aligner works.

java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusShardDataProvider.java

@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.gatk.datasources.providers;
 
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 import org.broadinstitute.sting.gatk.datasources.shards.Shard;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.iterators.LocusIterator;
@@ -9,6 +8,8 @@ import org.broadinstitute.sting.gatk.Reads;
 
 import java.util.Collection;
 
+import net.sf.picard.reference.IndexedFastaSequenceFile;
+
 /**
  * Presents data sharded by locus to the traversal engine.
  *

java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadShardDataProvider.java

@@ -4,10 +4,11 @@ import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
 import org.broadinstitute.sting.gatk.datasources.shards.Shard;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 
 import java.util.Collection;
 
+import net.sf.picard.reference.IndexedFastaSequenceFile;
+
 /**
  * Present data sharded by read to a traversal engine.
  *

java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java

@@ -1,6 +1,5 @@
 package org.broadinstitute.sting.gatk.datasources.providers;
 
-import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.StingException;
@@ -14,6 +13,7 @@ import net.sf.samtools.SAMSequenceRecord;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.util.StringUtil;
 import net.sf.picard.reference.ReferenceSequence;
+import net.sf.picard.reference.IndexedFastaSequenceFile;
 /**
  * User: hanna
  * Date: May 22, 2009

java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java

@@ -2,12 +2,13 @@ package org.broadinstitute.sting.gatk.datasources.providers;
 
 import org.broadinstitute.sting.gatk.datasources.shards.Shard;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
-import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Collection;
+
+import net.sf.picard.reference.IndexedFastaSequenceFile;
 /**
  * User: hanna
  * Date: May 8, 2009

java/src/org/broadinstitute/sting/gatk/datasources/shards/LocusShardStrategy.java

@@ -27,7 +27,6 @@ package org.broadinstitute.sting.gatk.datasources.shards;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMReaderID;
 
@@ -36,6 +35,7 @@ import java.util.*;
 import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMSequenceRecord;
 import net.sf.samtools.SAMFileSpan;
+import net.sf.picard.reference.IndexedFastaSequenceFile;
 
 /**
  * A sharding strategy for loci based on reading of the index.

java/src/org/broadinstitute/sting/gatk/datasources/shards/ShardStrategyFactory.java

@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.gatk.datasources.shards;
 
 import net.sf.samtools.SAMSequenceDictionary;
+import net.sf.picard.reference.IndexedFastaSequenceFile;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
-import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource;
 
 /**

java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceDataSource.java

@@ -25,17 +25,13 @@
 
 package org.broadinstitute.sting.gatk.datasources.simpleDataSources;
 
-import net.sf.samtools.SAMSequenceDictionary;
-import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.fasta.FastaSequenceIndex;
+import net.sf.picard.reference.FastaSequenceIndexBuilder;
-import org.broadinstitute.sting.utils.fasta.FastaSequenceIndexBuilder;
-import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 import net.sf.picard.sam.CreateSequenceDictionary;
-import org.broadinstitute.sting.utils.file.FSLock;
+import net.sf.picard.reference.IndexedFastaSequenceFile;
+import net.sf.picard.reference.FastaSequenceIndex;
 
 import java.io.File;
-import java.io.IOException;
 import java.io.RandomAccessFile;
 import java.nio.channels.FileChannel;
 import java.nio.channels.FileLock;

java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java

@@ -9,7 +9,6 @@ import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrde
 import org.broadinstitute.sting.gatk.io.*;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 import org.broadinstitute.sting.utils.threading.ThreadPoolMonitor;
 
 import javax.management.MBeanServer;
@@ -24,6 +23,8 @@ import java.util.concurrent.Future;
 import java.util.concurrent.FutureTask;
 import java.lang.management.ManagementFactory;
 
+import net.sf.picard.reference.IndexedFastaSequenceFile;
+
 /**
  * A microscheduler that schedules shards according to a tree-like structure.
  * Requires a special walker tagged with a 'TreeReducible' interface.

java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java

@@ -13,12 +13,12 @@ import org.broadinstitute.sting.gatk.io.DirectOutputTracker;
 import org.broadinstitute.sting.gatk.io.OutputTracker;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.traversals.TraversalEngine;
-import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 
 import java.util.Collection;
 
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.util.CloseableIterator;
+import net.sf.picard.reference.IndexedFastaSequenceFile;
 
 
 /** A micro-scheduling manager for single-threaded execution of a traversal. */

java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java

@@ -38,12 +38,13 @@ import org.broadinstitute.sting.gatk.iterators.NullSAMIterator;
 import org.broadinstitute.sting.gatk.Reads;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.WalkerManager;
-import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.util.*;
 import java.io.File;
 
+import net.sf.picard.reference.IndexedFastaSequenceFile;
+
 
 /**
  * Created by IntelliJ IDEA.

java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestReadFishingWalker.java

@@ -36,10 +36,10 @@ import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.util.StringUtil;
 import net.sf.picard.reference.ReferenceSequence;
+import net.sf.picard.reference.IndexedFastaSequenceFile;
 
 import java.io.File;
 import java.io.FileInputStream;

java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/HybSelPerformanceWalker.java

@@ -26,6 +26,7 @@
 package org.broadinstitute.sting.playground.gatk.walkers.hybridselection;
 
 import net.sf.picard.reference.ReferenceSequence;
+import net.sf.picard.reference.IndexedFastaSequenceFile;
 import net.sf.picard.util.Interval;
 import net.sf.picard.util.IntervalList;
 import net.sf.picard.util.OverlapDetector;
@@ -49,7 +50,6 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 
 import java.io.File;
 import java.io.IOException;
@@ -300,7 +300,6 @@ public class HybSelPerformanceWalker extends LocusWalker<Integer, HybSelPerforma
     IndexedFastaSequenceFile seqFile = null;
 
     private double calculateGC(GenomeLoc target) {
-        try {
             if (seqFile == null) {
                 seqFile = new IndexedFastaSequenceFile(getToolkit().getArguments().referenceFile);
             }
@@ -313,9 +312,5 @@ public class HybSelPerformanceWalker extends LocusWalker<Integer, HybSelPerforma
             }
             return ( (double) gcCount ) / ((double) refSeq.getBases().length);
 
-        } catch (IOException ioe) {
-            throw new RuntimeException(ioe);
-        }
-
     }
 }

java/src/org/broadinstitute/sting/utils/fasta/FastaSequenceIndex.java

@@ -1,268 +0,0 @@
-/*
- * Copyright (c) 2010 The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
- */
-
-package org.broadinstitute.sting.utils.fasta;
-
-import net.sf.picard.PicardException;
-import net.sf.picard.io.IoUtil;
-
-import java.util.Scanner;
-import java.util.Map;
-import java.util.LinkedHashMap;
-import java.util.Iterator;
-import java.util.regex.MatchResult;
-import java.io.File;
-import java.io.FileNotFoundException;
-
-/**
- * Reads a fasta index file (.fai), as generated by `samtools faidx`.
- */
-public class FastaSequenceIndex implements Iterable {
-    /**
-     * Store the entries.  Use a LinkedHashMap for consistent iteration in insertion order.
-     */
-    private final Map<String,FastaSequenceIndexEntry> sequenceEntries = new LinkedHashMap<String,FastaSequenceIndexEntry>();
-
-    /**
-     * Build a sequence index from the specified file.
-     * @param indexFile File to open.
-     * @throws FileNotFoundException if the index file cannot be found.
-     */
-    protected FastaSequenceIndex( File indexFile ) throws FileNotFoundException {
-        if(!indexFile.exists())
-            throw new FileNotFoundException(String.format("Fasta index file is missing: %s",indexFile.getAbsolutePath()));
-
-        IoUtil.assertFileIsReadable(indexFile);
-        parseIndexFile(indexFile);
-    }
-
-     /**
-     * Build an empty sequence index. Entries can be added later.
-     */
-    protected FastaSequenceIndex() {
-
-    }
-
-    /**
-     * Parse the contents of an index file, caching the results internally.
-     * @param indexFile File to parse.
-     * @throws FileNotFoundException Thrown if file could not be opened.
-     */
-    private void parseIndexFile(File indexFile) throws FileNotFoundException {
-        Scanner scanner = new Scanner(indexFile);
-
-        while( scanner.hasNext() ) {
-            // Tokenize and validate the index line.                     
-            String result = scanner.findInLine("(.+)\\t+(\\d+)\\s+(\\d+)\\s+(\\d+)\\s+(\\d+)");
-            if( result == null )
-                throw new PicardException("Found invalid line in index file:" + scanner.nextLine());
-            MatchResult tokens = scanner.match();
-            if( tokens.groupCount() != 5 )
-                throw new PicardException("Found invalid line in index file:" + scanner.nextLine());
-
-            // Skip past the line separator
-            scanner.nextLine();
-
-            // Parse the index line.
-            String contig = tokens.group(1);
-            long size = Long.valueOf(tokens.group(2));
-            long location = Long.valueOf(tokens.group(3));
-            int basesPerLine = Integer.valueOf(tokens.group(4));
-            int bytesPerLine = Integer.valueOf(tokens.group(5));
-
-            // Build sequence structure
-            sequenceEntries.put( contig,new FastaSequenceIndexEntry(contig,location,size,basesPerLine,bytesPerLine) );
-        }
-    }
-
-    /**
-     * Does the given contig name have a corresponding entry?
-     * @param contigName The contig name for which to search.
-     * @return True if contig name is present; false otherwise.
-     */
-    public boolean hasIndexEntry( String contigName ) {
-        return sequenceEntries.containsKey(contigName);
-    }
-
-    /**
-     * Retrieve the index entry associated with the given contig.
-     * @param contigName Name of the contig for which to search.
-     * @return Index entry associated with the given contig.
-     * @throws PicardException if the associated index entry can't be found.
-     */
-    public FastaSequenceIndexEntry getIndexEntry( String contigName ) {
-        if( !hasIndexEntry(contigName) )
-            throw new PicardException("Unable to find entry for contig: " + contigName);
-
-        return sequenceEntries.get(contigName);
-    }
-
-    /**
-     * Creates an iterator which can iterate through all entries in a fasta index.
-     * @return iterator over all fasta index entries.
-     */
-    public Iterator<FastaSequenceIndexEntry> iterator() {
-        return sequenceEntries.values().iterator();
-    }
-
-    /**
-     * Returns the number of elements in the index.
-     * @return Number of elements in the index.
-     */
-    public int size() {
-        return sequenceEntries.size();
-    }
-
-    /**
-     * Adds entry to index. Used by Fai file generator to create index entry on the fly.
-     * @param contig The name of the contig
-     * @param location Byte-referenced location of contig in file
-     * @param size Number of bases in contig
-     * @param basesPerLine Number of bases in each line. Must be uniform.
-     * @param bytesPerLine Number of bytes in each line. Must be uniform.
-     */
-    public void addIndexEntry(String contig, long location, long size, int basesPerLine, int bytesPerLine) {
-        sequenceEntries.put( contig,new FastaSequenceIndexEntry(contig,location,size,basesPerLine,bytesPerLine) );
-    }
-
-    /**
-     * Compare two FastaSequenceIndex objects. Built for use in testing. No hash function has been created.
-     * @param other Another FastaSequenceIndex to compare
-     * @return True if index has the same entries as other instance, in the same order
-     */
-    public boolean equals(FastaSequenceIndex other) {
-        Iterator<FastaSequenceIndexEntry> iter = this.iterator();
-        Iterator<FastaSequenceIndexEntry> otherIter = other.iterator();
-        while (iter.hasNext()) {
-            if (!otherIter.hasNext())
-                return false;
-            if (!iter.next().equals(otherIter.next()))
-                return false;
-        }
-        return true;
-    }
-}
-
-/**
- * Hold an individual entry in a fasta sequence index file.
- */
-class FastaSequenceIndexEntry {
-    private final String contig;
-    private final long location;
-    private final long size;
-    private final int basesPerLine;
-    private final int bytesPerLine;
-
-    /**
-     * Create a new entry with the given parameters.
-     * @param contig Contig this entry represents.
-     * @param location Location (byte coordinate) in the fasta file.
-     * @param size The number of bases in the contig.
-     * @param basesPerLine How many bases are on each line.
-     * @param bytesPerLine How many bytes are on each line (includes newline characters).
-     */
-    public FastaSequenceIndexEntry( String contig,
-                                    long location,
-                                    long size,
-                                    int basesPerLine,
-                                    int bytesPerLine ) {
-        this.contig = contig;
-        this.location = location;
-        this.size = size;
-        this.basesPerLine = basesPerLine;
-        this.bytesPerLine = bytesPerLine;
-    }
-
-    /**
-     * Gets the contig associated with this entry.
-     * @return String representation of the contig.
-     */
-    public String getContig() {
-        return contig;
-    }
-
-    /**
-     * Gets the location of this contig within the fasta.
-     * @return seek position within the fasta.
-     */
-    public long getLocation() {
-        return location;
-    }
-
-    /**
-     * Gets the size, in bytes, of the data in the contig.
-     * @return size of the contig bases in bytes.
-     */
-    public long getSize() {
-        return size;
-    }
-
-    /**
-     * Gets the number of bases in a given line.
-     * @return Number of bases in the fasta line.
-     */
-    public int getBasesPerLine() {
-        return basesPerLine;
-    }
-
-    /**
-     * How many bytes (bases + whitespace) are consumed by the
-     * given line?
-     * @return Number of bytes in a line.
-     */
-    public int getBytesPerLine() {
-        return bytesPerLine;
-    }
-
-    /**
-     * For debugging.  Emit the contents of each contig line.
-     * @return A string representation of the contig line.
-     */
-    public String toString() {
-        return String.format("contig %s; location %d; size %d; basesPerLine %d; bytesPerLine %d", contig,
-                                                                                                  location,
-                                                                                                  size,
-                                                                                                  basesPerLine,
-                                                                                                  bytesPerLine );
-    }
-
-    /**
-     * Print string in format of fai file line
-     * @return Contig as one line in a fai file
-     */
-    public String toIndexFileLine() {
-        return String.format("%s\t%d\t%d\t%d\t%d", contig, size, location, basesPerLine, bytesPerLine);
-    }
-
-    /**
-     * Compare entry to another instance
-     * @param other another FastaSequenceIndexEntry
-     * @return True if each has the same name, location, size, basesPerLine and bytesPerLine
-     */
-    public boolean equals(FastaSequenceIndexEntry other) {
-        return (contig.equals(other.contig) && size == other.size && location == other.location
-        && basesPerLine == other.basesPerLine && bytesPerLine == other.bytesPerLine);
-    }
-}

java/src/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFile.java

@@ -1,285 +0,0 @@
-package org.broadinstitute.sting.utils.fasta;
-
-import net.sf.picard.PicardException;
-import net.sf.picard.io.IoUtil;
-import net.sf.picard.reference.ReferenceSequence;
-import net.sf.picard.reference.ReferenceSequenceFile;
-import net.sf.samtools.SAMFileHeader;
-import net.sf.samtools.SAMSequenceDictionary;
-import net.sf.samtools.SAMSequenceRecord;
-import net.sf.samtools.SAMTextHeaderCodec;
-import net.sf.samtools.util.AsciiLineReader;
-import org.broadinstitute.sting.utils.StingException;
-
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.nio.ByteBuffer;
-import java.nio.channels.FileChannel;
-import java.util.Iterator;
-
-/**
- * A fasta file driven by an index for fast, concurrent lookups.  Supports two interfaces:
- * the ReferenceSequenceFile for old-style, stateful lookups and a direct getter.
- */
-public class IndexedFastaSequenceFile implements ReferenceSequenceFile {
-    /**
-     * Size of the read buffer.
-     */
-    private static final int BUFFER_SIZE = 128 * 1024;
-
-    /**
-     * Stores the main fasta file.
-     */
-    private final File file;
-
-    /**
-     * The interface facilitating direct access to the fasta.
-     */
-    private FileChannel channel;
-
-    /**
-     * A representation of the sequence dictionary, stored alongside the fasta in a .dict file.
-     */
-    private SAMSequenceDictionary sequenceDictionary = null;
-
-    /**
-     * A representation of the sequence index, stored alongside the fasta in a .fasta.fai file.
-     */
-    private FastaSequenceIndex index;
-
-    /**
-     * An iterator into the fasta index, for traversing iteratively across the fasta.
-     */
-    private Iterator<FastaSequenceIndexEntry> indexIterator;
-
-    /**
-     * Open the given indexed fasta sequence file.  Throw an exception if the file cannot be opened.
-     * @param file The file to open.
-     * @throws FileNotFoundException If the fasta or any of its supporting files cannot be found.
-     */
-    public IndexedFastaSequenceFile(File file) throws FileNotFoundException {
-        this.file = file;
-        FileInputStream in = new FileInputStream(file);
-        channel = in.getChannel();
-
-        loadDictionary(file);
-        loadIndex(file);
-        sanityCheckDictionaryAgainstIndex();
-    }
-
-
-    /**
-     * Open the given indexed fasta sequence file.  Throw an exception if the file cannot be opened.
-     * @param file The file to open.
-     * @param sequenceIndex FastaSequenceIndex that was previously created
-     * @throws FileNotFoundException If the fasta or any of its supporting files cannot be found.
-     */
-    public IndexedFastaSequenceFile(File file, FastaSequenceIndex sequenceIndex) throws FileNotFoundException {
-        this.file = file;
-        FileInputStream in = new FileInputStream(file);
-        channel = in.getChannel();
-
-        loadDictionary(file);
-        // Temporary change: sequenceIndex is passed in directly. See comments in ReferenceDataSource. 
-        index = sequenceIndex;
-        sanityCheckDictionaryAgainstIndex();
-    }
-
-    /**
-     * Always returns true for this implementation.
-     * @return True.
-     */
-    public boolean isIndexed() {
-        return true;
-    }
-
-    /**
-     * Loads a dictionary, if available.
-     * @param fastaFile File to check for a match.
-     */
-    private void loadDictionary( File fastaFile ) {
-        // Try and locate the dictionary
-        String dictionaryName = fastaFile.getAbsolutePath();
-        dictionaryName = dictionaryName.substring(0, getFastaFileExtensionStart(dictionaryName));
-        dictionaryName += ".dict";
-        final File dictionary = new File(dictionaryName);
-        if (!dictionary.exists())
-            throw new PicardException("Unable to load .dict file.  Dictionary is required for the indexed fasta reader.");
-
-        IoUtil.assertFileIsReadable(dictionary);
-
-        try {
-            final SAMTextHeaderCodec codec = new SAMTextHeaderCodec();
-            final SAMFileHeader header = codec.decode(new AsciiLineReader(new FileInputStream(dictionary)),
-                                                      dictionary.toString());
-            if (header.getSequenceDictionary() != null && header.getSequenceDictionary().size() > 0) {
-                this.sequenceDictionary = header.getSequenceDictionary();
-            }
-        }
-        catch (Exception e) {
-            throw new PicardException("Could not open sequence dictionary file: " + dictionaryName, e);
-        }
-
-    }
-
-    /**
-     * Gets the index of the first character in the fasta file's extension.
-     * @param filename The filename of the fasta.  Must not be null, and must end with either '.fasta' or '.fa'.
-     * @return The index of the start of the extension within the filename.  If neither '.fasta' nor '.fa' are
-     *         present in the filename, a StingException will be thrown.
-     */
-    private int getFastaFileExtensionStart( String filename ) {
-        if( filename.endsWith(".fasta") )
-            return filename.lastIndexOf(".fasta");
-        else if( filename.endsWith(".fa") )
-            return filename.lastIndexOf(".fa");
-        else
-            throw new StingException("Invalid fasta filename; fasta filename must end with '.fasta' or '.fa'.");
-    }
-
-    /**
-     * Loads the index for the fasta, if present.  Throws an exception if now present.
-     * @param fastaFile FASTA file to load.
-     * @throws FileNotFoundException if FASTA file cannot be found.
-     */
-    private void loadIndex( File fastaFile ) throws FileNotFoundException {
-        File indexFile = new File(fastaFile.getAbsolutePath() + ".fai");
-        if (!indexFile.exists())
-            throw new PicardException(String.format("Unable to load fasta index file %s.  "+
-                                                    "Please create it using 'samtools faidx'.",indexFile.getAbsolutePath()));
-        index = new FastaSequenceIndex(indexFile);
-        reset();
-    }
-
-    /**
-     * Do some basic checking to make sure the dictionary and the index match.
-     */
-    private void sanityCheckDictionaryAgainstIndex() {
-        // Make sure dictionary and index are the same size.
-        if( sequenceDictionary.getSequences().size() != index.size() )
-            throw new PicardException("Sequence dictionary and index contain different numbers of contigs");
-
-        for( SAMSequenceRecord sequenceRecord: sequenceDictionary.getSequences() ) {
-            // Make sure sequence name is present in the index.
-            String sequenceName = sequenceRecord.getSequenceName();
-            if( !index.hasIndexEntry(sequenceName) )
-                throw new PicardException("Index does not contain dictionary entry: " + sequenceName );
-
-            // Make sure sequence length matches index length.
-            if( sequenceRecord.getSequenceLength() != index.getIndexEntry(sequenceName).getSize())
-                throw new PicardException("Index length does not match dictionary length for contig: " + sequenceName );
-        }
-    }
-
-    /**
-     * Retrieves the sequence dictionary for the fasta file.
-     * @return sequence dictionary of the fasta.
-     */
-    public SAMSequenceDictionary getSequenceDictionary() {
-        return sequenceDictionary;
-    }
-
-    /**
-     * Retrieves the complete sequence described by this contig.
-     * @param contig contig whose data should be returned.
-     * @return The full sequence associated with this contig.
-     */
-    public ReferenceSequence getSequence( String contig ) {
-        return getSubsequenceAt( contig, 1, (int)index.getIndexEntry(contig).getSize() );
-    }
-
-    /**
-     * Gets the subsequence of the contig in the range [start,stop]
-     * @param contig Contig whose subsequence to retrieve.
-     * @param start inclusive, 1-based start of region.
-     * @param stop inclusive, 1-based stop of region.
-     * @return The partial reference sequence associated with this range.
-     */
-    public ReferenceSequence getSubsequenceAt( String contig, long start, long stop ) {
-        if(start > stop)
-            throw new PicardException(String.format("Malformed query; start point %d lies after end point %d",start,stop));
-
-        FastaSequenceIndexEntry indexEntry = index.getIndexEntry(contig);
-
-        if(stop > indexEntry.getSize())
-            throw new PicardException("Query asks for data past end of contig");
-
-        int length = (int)(stop - start + 1);
-
-        byte[] target = new byte[length];
-        ByteBuffer targetBuffer = ByteBuffer.wrap(target);
-
-        final int basesPerLine = indexEntry.getBasesPerLine();
-        final int bytesPerLine = indexEntry.getBytesPerLine();
-        final int terminatorLength = bytesPerLine - basesPerLine;
-
-        long startOffset = ((start-1)/basesPerLine)*bytesPerLine + (start-1)%basesPerLine;
-
-        // Allocate a 128K buffer for reading in sequence data.
-        ByteBuffer channelBuffer = ByteBuffer.allocate(BUFFER_SIZE);
-
-        while(targetBuffer.position() < length) {
-            // If the bufferOffset is currently within the eol characters in the string, push the bufferOffset forward to the next printable character.
-            startOffset += Math.max((int)(startOffset%bytesPerLine - basesPerLine + 1),0);
-
-            try {
-                 startOffset += channel.read(channelBuffer,indexEntry.getLocation()+startOffset);
-            }
-            catch(IOException ex) {
-                throw new PicardException("Unable to map FASTA file into memory.");
-            }
-
-            // Reset the buffer for outbound transfers.
-            channelBuffer.flip();
-
-            // Calculate the size of the next run of bases based on the contents we've already retrieved.
-            final int positionInContig = (int)start-1+targetBuffer.position();
-            final int nextBaseSpan = Math.min(basesPerLine-positionInContig%basesPerLine,length-targetBuffer.position());
-            // Cap the bytes to transfer by limiting the nextBaseSpan to the size of the channel buffer.
-            int bytesToTransfer = Math.min(nextBaseSpan,channelBuffer.capacity());
-
-            channelBuffer.limit(channelBuffer.position()+bytesToTransfer);
-
-            while(channelBuffer.hasRemaining()) {
-                targetBuffer.put(channelBuffer);
-
-                bytesToTransfer = Math.min(basesPerLine,length-targetBuffer.position());
-                channelBuffer.limit(Math.min(channelBuffer.position()+bytesToTransfer+terminatorLength,channelBuffer.capacity()));
-                channelBuffer.position(Math.min(channelBuffer.position()+terminatorLength,channelBuffer.capacity()));
-            }
-
-            // Reset the buffer for inbound transfers.
-            channelBuffer.flip();
-        }
-
-        return new ReferenceSequence( contig, sequenceDictionary.getSequenceIndex(contig), target );
-    }
-
-    /**
-     * Gets the next sequence if available, or null if not present.
-     * @return next sequence if available, or null if not present.
-     */
-    public ReferenceSequence nextSequence() {
-        if( !indexIterator.hasNext() )
-            return null;
-        return getSequence( indexIterator.next().getContig() );
-    }
-
-    /**
-     * Reset the iterator over the index.
-     */
-    @Override
-    public void reset() {
-        indexIterator = index.iterator();
-    }
-
-    /**
-     * A simple toString implementation for debugging.
-     * @return String representation of the file.
-     */
-    public String toString() {
-        return this.file.getAbsolutePath();
-    }
-}

java/test/net/sf/picard/reference/FastaSequenceIndexBuilderUnitTest.java

@@ -23,9 +23,8 @@
  * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.fasta;
+package net.sf.picard.reference;
 
-import net.sf.picard.PicardException;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceDataSourceProgressListener;
 import org.junit.Assert;
@@ -61,7 +60,7 @@ public class FastaSequenceIndexBuilderUnitTest extends BaseTest {
         fastaFile = new File(validationDataLocation + "exampleFASTA.fasta");
         builder = new FastaSequenceIndexBuilder(fastaFile, progress);
         FastaSequenceIndex index = builder.createIndex();
-        controlIndex.addIndexEntry("chr1", 6, 100000, 60, 61);
+        controlIndex.add(new FastaSequenceIndexEntry("chr1", 6, 100000, 60, 61,0));
 
         Assert.assertTrue(index.equals(controlIndex));
     }
@@ -78,7 +77,7 @@ public class FastaSequenceIndexBuilderUnitTest extends BaseTest {
         fastaFile = new File(validationDataLocation + "exampleFASTA-windows.fasta");
         builder = new FastaSequenceIndexBuilder(fastaFile, progress);
         FastaSequenceIndex index = builder.createIndex();
-        controlIndex.addIndexEntry("chr2", 7, 29, 7, 9);
+        controlIndex.add(new FastaSequenceIndexEntry("chr2", 7, 29, 7, 9,0));
 
         Assert.assertTrue(index.equals(controlIndex));
     }
@@ -94,8 +93,8 @@ public class FastaSequenceIndexBuilderUnitTest extends BaseTest {
         fastaFile = new File(validationDataLocation + "exampleFASTA-combined.fasta");
         builder = new FastaSequenceIndexBuilder(fastaFile, progress);
         FastaSequenceIndex index = builder.createIndex();
-        controlIndex.addIndexEntry("chr1", 6, 100000, 60, 61);
+        controlIndex.add(new FastaSequenceIndexEntry("chr1", 6, 100000, 60, 61,0));
-        controlIndex.addIndexEntry("chr2", 101680, 29, 7, 9);
+        controlIndex.add(new FastaSequenceIndexEntry("chr2", 101680, 29, 7, 9,1));
 
         Assert.assertTrue(index.equals(controlIndex));
     }
@@ -111,9 +110,9 @@ public class FastaSequenceIndexBuilderUnitTest extends BaseTest {
         fastaFile = new File(validationDataLocation + "exampleFASTA-3contigs.fasta");
         builder = new FastaSequenceIndexBuilder(fastaFile, progress);
         FastaSequenceIndex index = builder.createIndex();
-        controlIndex.addIndexEntry("chr1", 6, 17, 5, 6);
+        controlIndex.add(new FastaSequenceIndexEntry("chr1", 6, 17, 5, 6,0));
-        controlIndex.addIndexEntry("chr2", 35, 21, 7, 8);
+        controlIndex.add(new FastaSequenceIndexEntry("chr2", 35, 21, 7, 8,1));
-        controlIndex.addIndexEntry("chr3", 66, 100, 10, 11);
+        controlIndex.add(new FastaSequenceIndexEntry("chr3", 66, 100, 10, 11,2));
 
         Assert.assertTrue(index.equals(controlIndex));
     }

java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUnitTest.java

@@ -7,7 +7,6 @@ package org.broadinstitute.sting.gatk.contexts.variantcontext;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 import org.junit.Assert;
 import org.junit.Before;
 import org.junit.Test;
@@ -19,6 +18,7 @@ import java.io.FileNotFoundException;
 import java.io.File;
 
 import net.sf.picard.reference.ReferenceSequenceFile;
+import net.sf.picard.reference.IndexedFastaSequenceFile;
 
 /**
  * Basic unit test for RecalData

java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java

@@ -10,7 +10,6 @@ import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
 import org.broadinstitute.sting.gatk.refdata.TabularROD;
 import org.broadinstitute.sting.gatk.refdata.tracks.RODRMDTrack;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 import org.junit.Assert;
 import org.junit.BeforeClass;
 import org.junit.Test;
@@ -19,6 +18,8 @@ import java.io.File;
 import java.io.FileNotFoundException;
 import java.util.Arrays;
 import java.util.Collections;
+
+import net.sf.picard.reference.IndexedFastaSequenceFile;
 /**
  * User: hanna
  * Date: May 27, 2009

java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceViewTemplate.java

@@ -1,10 +1,10 @@
 package org.broadinstitute.sting.gatk.datasources.providers;
 
 import net.sf.samtools.SAMSequenceRecord;
+import net.sf.picard.reference.IndexedFastaSequenceFile;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 import org.junit.BeforeClass;
 import org.junit.Test;
 

java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataPoolUnitTest.java

@@ -8,7 +8,6 @@ import org.broadinstitute.sting.gatk.refdata.tracks.RODRMDTrack;
 import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 import org.junit.Assert;
 import org.junit.Before;
 import org.junit.BeforeClass;
@@ -18,6 +17,7 @@ import java.io.File;
 import java.io.FileNotFoundException;
 
 import static org.junit.Assert.assertTrue;
+import net.sf.picard.reference.IndexedFastaSequenceFile;
 /**
  * User: hanna
  * Date: May 21, 2009

java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMBAMDataSourceUnitTest.java

@@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.datasources.simpleDataSources;
 
 import static junit.framework.Assert.fail;
 import net.sf.picard.reference.ReferenceSequenceFile;
+import net.sf.picard.reference.IndexedFastaSequenceFile;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.gatk.datasources.shards.Shard;
@@ -11,7 +12,6 @@ import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
 import org.broadinstitute.sting.gatk.Reads;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;

java/test/org/broadinstitute/sting/gatk/iterators/BoundedReadIteratorUnitTest.java

@@ -5,10 +5,10 @@ import static junit.framework.Assert.fail;
 import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMRecord;
 import net.sf.picard.reference.ReferenceSequenceFile;
+import net.sf.picard.reference.IndexedFastaSequenceFile;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.gatk.Reads;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 
 import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
 import org.junit.Assert;

java/test/org/broadinstitute/sting/gatk/refdata/TabularRODUnitTest.java

@@ -5,12 +5,12 @@ package org.broadinstitute.sting.gatk.refdata;
 // the imports for unit testing.
 
 import net.sf.picard.reference.ReferenceSequenceFile;
+import net.sf.picard.reference.IndexedFastaSequenceFile;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeatureIterator;
 import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 import org.junit.Before;
 import org.junit.BeforeClass;
 import org.junit.Test;

java/test/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptorsUnitTest.java

@@ -4,13 +4,13 @@ import edu.mit.broad.picard.genotype.geli.GeliFileReader;
 import edu.mit.broad.picard.genotype.geli.GenotypeLikelihoods;
 import net.sf.samtools.SAMFileReader;
 import net.sf.samtools.util.CloseableIterator;
+import net.sf.picard.reference.IndexedFastaSequenceFile;
 import org.broad.tribble.gelitext.GeliTextCodec;
 import org.broad.tribble.gelitext.GeliTextFeature;
 import org.broad.tribble.util.AsciiLineReader;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 import org.broadinstitute.sting.utils.genotype.GenotypeWriter;
 import org.broadinstitute.sting.utils.genotype.GenotypeWriterFactory;
 import org.broadinstitute.sting.utils.genotype.geli.GeliGenotypeWriter;
@@ -43,11 +43,7 @@ public class VariantContextAdaptorsUnitTest extends BaseTest {
 
     @BeforeClass
     public static void beforeClass() {
-        try {
         seq = new IndexedFastaSequenceFile(new File(oneKGLocation + "/reference/human_b36_both.fasta")); // TODO: make human reference use BaseTest
-        } catch (FileNotFoundException e) {
-            Assert.fail("Unable to load reference " + oneKGLocation + "/reference/human_b36_both.fasta");
-        }
         GenomeLocParser.setupRefContigOrdering(seq);
     }
 

java/test/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4UnitTest.java

@@ -10,7 +10,6 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
 import org.junit.Assert;
 import org.junit.BeforeClass;
@@ -25,6 +24,8 @@ import java.util.List;
 import java.util.Map;
 import java.util.Set;
 
+import net.sf.picard.reference.IndexedFastaSequenceFile;
+
 /**
  * test out pieces of the VCF 4 codec.
  */
@@ -36,11 +37,7 @@ public class VCF4UnitTest extends BaseTest {
     @BeforeClass
     public static void setupContig() {
         IndexedFastaSequenceFile seq;
-        try {
         seq = new IndexedFastaSequenceFile(new File(oneKGLocation + "reference/human_b36_both.fasta"));
-        } catch (FileNotFoundException e) {
-            throw new StingException("unable to load the sequence dictionary");
-        }
         GenomeLocParser.setupRefContigOrdering(seq.getSequenceDictionary());
     }
 

java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackManagerUnitTest.java

@@ -24,11 +24,11 @@
 package org.broadinstitute.sting.gatk.refdata.tracks;
 
 import net.sf.samtools.SAMSequenceRecord;
+import net.sf.picard.reference.IndexedFastaSequenceFile;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 import org.junit.Assert;
 import org.junit.Before;
 import org.junit.Test;
@@ -100,11 +100,7 @@ public class RMDTrackManagerUnitTest extends BaseTest {
     // @Test used only to determine how fast queries are, don't uncomment! (unless you know what you're doing).
     public void testSpeedOfRealQuery() {
         IndexedFastaSequenceFile file = null;
-        try {
         file = new IndexedFastaSequenceFile(new File("/broad/1KG/reference/human_b36_both.fasta"));
-        } catch (FileNotFoundException e) {
-            Assert.assertTrue(false);
-        }
         final int intervalSize = 10000000;
         GenomeLocParser.setupRefContigOrdering(file.getSequenceDictionary());
         RMDTrackManager manager = new RMDTrackManager();

java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsUnitTest.java

@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.gatk.traversals;
 
 import net.sf.picard.reference.ReferenceSequenceFile;
+import net.sf.picard.reference.IndexedFastaSequenceFile;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.gatk.Reads;
 import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
@@ -12,7 +13,6 @@ import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource
 import org.broadinstitute.sting.gatk.walkers.qc.CountReadsWalker;
 import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 import static org.junit.Assert.fail;
 import org.junit.Before;
 import org.junit.Test;
@@ -106,12 +106,7 @@ public class TraverseReadsUnitTest extends BaseTest {
     @Test
     public void testUnmappedReadCount() {
         IndexedFastaSequenceFile ref = null;
-        try {
         ref = new IndexedFastaSequenceFile(refFile);
-        }
-        catch (FileNotFoundException ex) {
-            throw new RuntimeException("File not found opening fasta file; please do this check before MicroManaging", ex);
-        }
         GenomeLocParser.setupRefContigOrdering(ref);
 
         SAMDataSource dataSource = new SAMDataSource(new Reads(bamList));

java/test/org/broadinstitute/sting/utils/GenomeLocUnitTest.java

@@ -8,12 +8,12 @@ import org.junit.Assert;
 import org.junit.BeforeClass;
 import org.junit.Test;
 import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 
 import java.io.File;
 import java.io.FileNotFoundException;
 
 import net.sf.picard.reference.ReferenceSequenceFile;
+import net.sf.picard.reference.IndexedFastaSequenceFile;
 
 /**
  * Basic unit test for GenomeLoc

java/test/org/broadinstitute/sting/utils/bed/BedParserUnitTest.java

@@ -2,7 +2,6 @@ package org.broadinstitute.sting.utils.bed;
 
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
-import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.GenomeLoc;
@@ -14,6 +13,8 @@ import java.io.File;
 import java.io.FileNotFoundException;
 import java.util.List;
 
+import net.sf.picard.reference.IndexedFastaSequenceFile;
+
 
 public class BedParserUnitTest extends BaseTest {
 
@@ -22,11 +23,7 @@ public class BedParserUnitTest extends BaseTest {
 
     @BeforeClass
     public static void beforeTests() {
-        try {
         seq = new IndexedFastaSequenceFile(new File(oneKGLocation + "reference/human_b36_both.fasta"));
-        } catch (FileNotFoundException e) {
-            throw new StingException("unable to load the sequence dictionary");
-        }
         GenomeLocParser.setupRefContigOrdering(seq);
     }
 

java/test/org/broadinstitute/sting/utils/fasta/FastaSequenceIndexUnitTest.java

@@ -1,250 +0,0 @@
-package org.broadinstitute.sting.utils.fasta;
-
-import net.sf.picard.PicardException;
-import org.broadinstitute.sting.BaseTest;
-import org.junit.Assert;
-import org.junit.Before;
-import org.junit.BeforeClass;
-import org.junit.Test;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.util.Iterator;
-
-/**
- * Test the fasta sequence index reader.
- */
-public class FastaSequenceIndexUnitTest extends BaseTest {
-    // our basic human 18 fai
-    private static String sequenceIndexName = null;
-    private FastaSequenceIndex sequenceIndex = null;
-
-    // a custom index that tests the colon, and semi-colon, and other random characters
-    private static String sequenceIndexColonSemiColonTestName = null;
-    private FastaSequenceIndex sequenceIndexColonSemiColonTest = null;
-
-
-    @BeforeClass
-    public static void initialize() {
-        sequenceIndexName = seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta.fai";
-        sequenceIndexColonSemiColonTestName = validationDataLocation + "testing.fai";
-    }
-
-    @Before
-    public void doForEachTest() throws FileNotFoundException {
-        sequenceIndex = new FastaSequenceIndex( new File(sequenceIndexName) );
-        sequenceIndexColonSemiColonTest = new FastaSequenceIndex( new File(sequenceIndexColonSemiColonTestName) );
-    }
-
-    @Test
-    public void testInitialContig() {
-        logger.warn("Executing testInitialContig");
-
-        Assert.assertTrue("Contig chrM is not present", sequenceIndex.hasIndexEntry("chrM"));
-        FastaSequenceIndexEntry entry = sequenceIndex.getIndexEntry("chrM");
-        Assert.assertEquals("Contig chrM name is incorrect",entry.getContig(),"chrM");
-        Assert.assertEquals("Contig chrM location is incorrect",entry.getLocation(),6L);
-        Assert.assertEquals("Contig chrM size is incorrect",entry.getSize(),16571L);
-        Assert.assertEquals("Contig chrM bases per line is incorrect",entry.getBasesPerLine(),50);
-        Assert.assertEquals("Contig chrM bytes per line is incorrect",entry.getBytesPerLine(),51);
-    }
-
-    @Test
-    public void testMiddleContig() {
-        logger.warn("Executing testMiddleContig");
-
-        Assert.assertTrue("Contig chr8 is not present", sequenceIndex.hasIndexEntry("chr8"));
-        FastaSequenceIndexEntry entry = sequenceIndex.getIndexEntry("chr8");
-        Assert.assertEquals("Contig chr8 name is incorrect",entry.getContig(),"chr8");
-        Assert.assertEquals("Contig chr8 location is incorrect",entry.getLocation(),1419403101L);
-        Assert.assertEquals("Contig chr8 size is incorrect",entry.getSize(),146274826L);
-        Assert.assertEquals("Contig chr8 bases per line is incorrect",entry.getBasesPerLine(),50);
-        Assert.assertEquals("Contig chr8 bytes per line is incorrect",entry.getBytesPerLine(),51);
-    }
-
-    @Test
-    public void testLastContig() {
-        logger.warn("Executing testLastContig");
-
-        Assert.assertTrue("Contig chrX_random is not present", sequenceIndex.hasIndexEntry("chrX_random"));
-        FastaSequenceIndexEntry entry = sequenceIndex.getIndexEntry("chrX_random");
-        Assert.assertEquals("Contig chrX_random name is incorrect",entry.getContig(),"chrX_random");
-        Assert.assertEquals("Contig chrX_random location is incorrect",entry.getLocation(),3156698441L);
-        Assert.assertEquals("Contig chrX_random size is incorrect",entry.getSize(),1719168L);
-        Assert.assertEquals("Contig chrX_random bases per line is incorrect",entry.getBasesPerLine(),50);
-        Assert.assertEquals("Contig chrX_random bytes per line is incorrect",entry.getBytesPerLine(),51);
-    }
-
-    @Test
-    public void testAllContigsPresent() {
-        logger.warn("Executing testAllContigsPresent");
-
-        Assert.assertTrue("Contig chrM is not present", sequenceIndex.hasIndexEntry("chrM"));
-        Assert.assertTrue("Contig chr1 is not present", sequenceIndex.hasIndexEntry("chr1"));
-        Assert.assertTrue("Contig chr2 is not present", sequenceIndex.hasIndexEntry("chr2"));
-        Assert.assertTrue("Contig chr3 is not present", sequenceIndex.hasIndexEntry("chr3"));
-        Assert.assertTrue("Contig chr4 is not present", sequenceIndex.hasIndexEntry("chr4"));
-        Assert.assertTrue("Contig chr5 is not present", sequenceIndex.hasIndexEntry("chr5"));
-        Assert.assertTrue("Contig chr6 is not present", sequenceIndex.hasIndexEntry("chr6"));
-        Assert.assertTrue("Contig chr7 is not present", sequenceIndex.hasIndexEntry("chr7"));
-        Assert.assertTrue("Contig chr8 is not present", sequenceIndex.hasIndexEntry("chr8"));
-        Assert.assertTrue("Contig chr9 is not present", sequenceIndex.hasIndexEntry("chr9"));
-        Assert.assertTrue("Contig chr10 is not present", sequenceIndex.hasIndexEntry("chr10"));
-        Assert.assertTrue("Contig chr11 is not present", sequenceIndex.hasIndexEntry("chr11"));
-        Assert.assertTrue("Contig chr12 is not present", sequenceIndex.hasIndexEntry("chr12"));
-        Assert.assertTrue("Contig chr13 is not present", sequenceIndex.hasIndexEntry("chr13"));
-        Assert.assertTrue("Contig chr14 is not present", sequenceIndex.hasIndexEntry("chr14"));
-        Assert.assertTrue("Contig chr15 is not present", sequenceIndex.hasIndexEntry("chr15"));
-        Assert.assertTrue("Contig chr16 is not present", sequenceIndex.hasIndexEntry("chr16"));
-        Assert.assertTrue("Contig chr17 is not present", sequenceIndex.hasIndexEntry("chr17"));
-        Assert.assertTrue("Contig chr18 is not present", sequenceIndex.hasIndexEntry("chr18"));
-        Assert.assertTrue("Contig chr19 is not present", sequenceIndex.hasIndexEntry("chr19"));
-        Assert.assertTrue("Contig chr20 is not present", sequenceIndex.hasIndexEntry("chr20"));
-        Assert.assertTrue("Contig chr21 is not present", sequenceIndex.hasIndexEntry("chr21"));
-        Assert.assertTrue("Contig chr22 is not present", sequenceIndex.hasIndexEntry("chr22"));
-        Assert.assertTrue("Contig chrX is not present", sequenceIndex.hasIndexEntry("chrX"));
-        Assert.assertTrue("Contig chrY is not present", sequenceIndex.hasIndexEntry("chrY"));
-        Assert.assertTrue("Contig chr1_random is not present", sequenceIndex.hasIndexEntry("chr1_random"));
-        Assert.assertTrue("Contig chr2_random is not present", sequenceIndex.hasIndexEntry("chr2_random"));
-        Assert.assertTrue("Contig chr3_random is not present", sequenceIndex.hasIndexEntry("chr3_random"));
-        Assert.assertTrue("Contig chr4_random is not present", sequenceIndex.hasIndexEntry("chr4_random"));
-        Assert.assertTrue("Contig chr5_random is not present", sequenceIndex.hasIndexEntry("chr5_random"));
-        Assert.assertTrue("Contig chr6_random is not present", sequenceIndex.hasIndexEntry("chr6_random"));
-        Assert.assertTrue("Contig chr7_random is not present", sequenceIndex.hasIndexEntry("chr7_random"));
-        Assert.assertTrue("Contig chr8_random is not present", sequenceIndex.hasIndexEntry("chr8_random"));
-        Assert.assertTrue("Contig chr9_random is not present", sequenceIndex.hasIndexEntry("chr9_random"));
-        Assert.assertTrue("Contig chr10_random is not present", sequenceIndex.hasIndexEntry("chr10_random"));
-        Assert.assertTrue("Contig chr11_random is not present", sequenceIndex.hasIndexEntry("chr11_random"));
-        Assert.assertTrue("Contig chr13_random is not present", sequenceIndex.hasIndexEntry("chr13_random"));
-        Assert.assertTrue("Contig chr15_random is not present", sequenceIndex.hasIndexEntry("chr15_random"));
-        Assert.assertTrue("Contig chr16_random is not present", sequenceIndex.hasIndexEntry("chr16_random"));
-        Assert.assertTrue("Contig chr17_random is not present", sequenceIndex.hasIndexEntry("chr17_random"));
-        Assert.assertTrue("Contig chr18_random is not present", sequenceIndex.hasIndexEntry("chr18_random"));
-        Assert.assertTrue("Contig chr19_random is not present", sequenceIndex.hasIndexEntry("chr19_random"));
-        Assert.assertTrue("Contig chr21_random is not present", sequenceIndex.hasIndexEntry("chr21_random"));
-        Assert.assertTrue("Contig chr22_random is not present", sequenceIndex.hasIndexEntry("chr22_random"));
-        Assert.assertTrue("Contig chrX_random is not present", sequenceIndex.hasIndexEntry("chrX_random"));
-    }
-
-    @Test
-    public void testHasInvalidEntry() {
-        logger.warn("Executing testHasInvalidEntry");
-
-        Assert.assertFalse("Found an invalid entry", sequenceIndex.hasIndexEntry("invalid"));
-    }
-
-    @Test(expected= PicardException.class)
-    public void testGetInvalidEntry() {
-        logger.warn("Executing testGetInvalidEntry");
-
-        sequenceIndex.getIndexEntry("invalid");
-    }
-
-    @Test
-    public void testIteration() {
-        logger.warn("Executing testIteration");        
-
-        Iterator<FastaSequenceIndexEntry> sequenceIndexEntries = sequenceIndex.iterator();
-
-        Assert.assertEquals("Contig chrM is not present", "chrM", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr1 is not present", "chr1", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr2 is not present", "chr2", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr3 is not present", "chr3", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr4 is not present", "chr4", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr5 is not present", "chr5", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr6 is not present", "chr6", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr7 is not present", "chr7", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr8 is not present", "chr8", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr9 is not present", "chr9", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr10 is not present", "chr10", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr11 is not present", "chr11", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr12 is not present", "chr12", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr13 is not present", "chr13", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr14 is not present", "chr14", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr15 is not present", "chr15", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr16 is not present", "chr16", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr17 is not present", "chr17", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr18 is not present", "chr18", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr19 is not present", "chr19", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr20 is not present", "chr20", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr21 is not present", "chr21", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr22 is not present", "chr22", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chrX is not present", "chrX", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chrY is not present", "chrY", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr1_random is not present", "chr1_random", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr2_random is not present", "chr2_random", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr3_random is not present", "chr3_random", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr4_random is not present", "chr4_random", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr5_random is not present", "chr5_random", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr6_random is not present", "chr6_random", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr7_random is not present", "chr7_random", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr8_random is not present", "chr8_random", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr9_random is not present", "chr9_random", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr10_random is not present", "chr10_random", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr11_random is not present", "chr11_random", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr13_random is not present", "chr13_random", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr15_random is not present", "chr15_random", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr16_random is not present", "chr16_random", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr17_random is not present", "chr17_random", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr18_random is not present", "chr18_random", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr19_random is not present", "chr19_random", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr21_random is not present", "chr21_random", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chr22_random is not present", "chr22_random", sequenceIndexEntries.next().getContig());
-        Assert.assertEquals("Contig chrX_random is not present", "chrX_random", sequenceIndexEntries.next().getContig());
-        Assert.assertFalse("Iterator still has more entries", sequenceIndexEntries.hasNext());
-    }
-
-    @Test
-    public void testSpecialCharacters() {
-        /* file contents:
-        chrM	16571	6	50	51
-        chr1;boat	247249719	16915	50	51
-        chr2:money	242951149	252211635	50	51
-        chr3::;	199501827	500021813	50	51
-        ;;;;;;  1234            1234            1234    1234
-        file:gi|17981852|ref|NC_001807.4|    16571   2911876801      70      71
-        */
-        Iterator<FastaSequenceIndexEntry> sequenceIndexEntries = sequenceIndexColonSemiColonTest.iterator();
-        FastaSequenceIndexEntry ent = sequenceIndexEntries.next();
-        Assert.assertEquals("Contig chrM is not present","chrM",ent.getContig());
-        Assert.assertEquals("Contig chrM size is not correct",16571,ent.getSize());
-        Assert.assertEquals("Contig chrM location is not correct",6,ent.getLocation());
-        Assert.assertEquals("Contig chrM bases per line is not correct",50,ent.getBasesPerLine());
-        Assert.assertEquals("Contig chrM bytes per line is not correct",51,ent.getBytesPerLine());
-
-        ent = sequenceIndexEntries.next();
-        Assert.assertEquals("Contig chr1;boat is not present","chr1;boat",ent.getContig());
-        Assert.assertEquals("Contig chr1;boat size is not correct",247249719,ent.getSize());
-        Assert.assertEquals("Contig chr1;boat location is not correct",16915,ent.getLocation());
-        Assert.assertEquals("Contig chr1;boat bases per line is not correct",50,ent.getBasesPerLine());
-        Assert.assertEquals("Contig chr1;boat bytes per line is not correct",51,ent.getBytesPerLine());
-
-        ent = sequenceIndexEntries.next();
-        Assert.assertEquals("Contig chr2:money is not present","chr2:money",ent.getContig());
-        Assert.assertEquals("Contig chr2:money size is not correct",242951149,ent.getSize());
-        Assert.assertEquals("Contig chr2:money location is not correct",252211635,ent.getLocation());
-        Assert.assertEquals("Contig chr2:money bases per line is not correct",50,ent.getBasesPerLine());
-        Assert.assertEquals("Contig chr2:money bytes per line is not correct",51,ent.getBytesPerLine());
-
-        ent = sequenceIndexEntries.next();
-        Assert.assertEquals("Contig chr3::; is not present","chr3::;",ent.getContig());
-        Assert.assertEquals("Contig chr3::; size is not correct",199501827,ent.getSize());
-        Assert.assertEquals("Contig chrM location is not correct",500021813,ent.getLocation());
-        Assert.assertEquals("Contig chr3::; bases per line is not correct",50,ent.getBasesPerLine());
-        Assert.assertEquals("Contig chr3::; bytes per line is not correct",51,ent.getBytesPerLine());
-
-        ent = sequenceIndexEntries.next();
-        Assert.assertEquals("Contig ;;;;;;;; is not present",";;;;;;;;",ent.getContig());
-        Assert.assertEquals("Contig ;;;;;;;; size is not correct",123,ent.getSize());
-        Assert.assertEquals("Contig ;;;;;;;; location is not correct",234,ent.getLocation());
-        Assert.assertEquals("Contig ;;;;;;;; bases per line is not correct",456,ent.getBasesPerLine());
-        Assert.assertEquals("Contig ;;;;;;;; bytes per line is not correct",789,ent.getBytesPerLine());
-
-        ent = sequenceIndexEntries.next();
-        Assert.assertEquals("Contig file:gi|17981852|ref|NC_001807.4| is not present","file:gi|17981852|ref|NC_001807.4|",ent.getContig());
-        Assert.assertEquals("Contig file:gi|17981852|ref|NC_001807.4| size is not correct",16571,ent.getSize());
-        Assert.assertEquals("Contig file:gi|17981852|ref|NC_001807.4| location is not correct",2911876801L,ent.getLocation());
-        Assert.assertEquals("Contig file:gi|17981852|ref|NC_001807.4| bases per line is not correct",70,ent.getBasesPerLine());
-        Assert.assertEquals("Contig file:gi|17981852|ref|NC_001807.4| bytes per line is not correct",71,ent.getBytesPerLine());
-    }
-}

java/test/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFileUnitTest.java

@@ -1,272 +0,0 @@
-package org.broadinstitute.sting.utils.fasta;
-
-import org.junit.BeforeClass;
-import org.junit.Before;
-import org.junit.Test;
-import org.junit.Assert;
-import org.broadinstitute.sting.BaseTest;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-
-import net.sf.picard.reference.ReferenceSequence;
-import net.sf.picard.reference.ReferenceSequenceFile;
-import net.sf.picard.reference.ReferenceSequenceFileFactory;
-import net.sf.picard.PicardException;
-import net.sf.samtools.util.StringUtil;
-
-/**
- * Test the indexed fasta sequence file reader.
- */
-public class IndexedFastaSequenceFileUnitTest extends BaseTest {
-    private static String sequenceFileName;
-    private IndexedFastaSequenceFile sequenceFile = null;
-
-    private final String firstBasesOfChrM = "GATCACAGGTCTATCACCCT";
-    private final String extendedBasesOfChrM = "GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCAT" +
-                                               "TTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTG" +
-                                               "GAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATT";    
-    private final String firstBasesOfChr1 = "taaccctaaccctaacccta";
-    private final String firstBasesOfChr8 = "GCAATTATGACACAAAAAAT";
-
-    @BeforeClass
-    public static void initialize() {
-         sequenceFileName = seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta";
-    }
-
-    @Before
-    public void doForEachTest() throws FileNotFoundException {
-        sequenceFile = new IndexedFastaSequenceFile( new File(sequenceFileName) );
-    }
-
-    @Test
-    public void testOpenFile() {
-        long startTime = System.currentTimeMillis();
-        Assert.assertNotNull( sequenceFile );
-        long endTime = System.currentTimeMillis();
-
-        System.err.printf("testOpenFile runtime: %dms%n", (endTime - startTime)) ;
-    }
-
-    @Test
-    public void testFirstSequence() {
-        long startTime = System.currentTimeMillis();
-        ReferenceSequence sequence = sequenceFile.getSubsequenceAt("chrM",1,firstBasesOfChrM.length());
-        long endTime = System.currentTimeMillis();
-
-        Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chrM");
-        Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 0);
-        Assert.assertArrayEquals( "First n bases of chrM are incorrect",StringUtil.stringToBytes(firstBasesOfChrM),sequence.getBases());
-
-        System.err.printf("testFirstSequence runtime: %dms%n", (endTime - startTime)) ;
-    }
-
-    @Test
-    public void testFirstSequenceExtended() {
-        long startTime = System.currentTimeMillis();
-        ReferenceSequence sequence = sequenceFile.getSubsequenceAt("chrM",1,extendedBasesOfChrM.length());
-        long endTime = System.currentTimeMillis();
-
-        Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chrM");
-        Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 0);
-        Assert.assertArrayEquals( "First n bases of chrM are incorrect",StringUtil.stringToBytes(extendedBasesOfChrM),sequence.getBases());
-
-        System.err.printf("testFirstSequenceExtended runtime: %dms%n", (endTime - startTime)) ;
-    }
-
-    @Test
-    public void testReadStartingInCenterOfFirstLine() {
-        final int bytesToChopOff = 5;
-        String truncated = extendedBasesOfChrM.substring(bytesToChopOff);
-
-        long startTime = System.currentTimeMillis();
-        ReferenceSequence sequence = sequenceFile.getSubsequenceAt("chrM",
-                                                                   bytesToChopOff + 1,
-                                                                   bytesToChopOff + truncated.length());
-        long endTime = System.currentTimeMillis();
-
-        Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chrM");
-        Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 0);
-        Assert.assertArrayEquals( "First n bases of chrM are incorrect",StringUtil.stringToBytes(truncated),sequence.getBases());
-
-        System.err.printf("testReadStartingInCenterOfFirstLine runtime: %dms%n", (endTime - startTime)) ;
-    }
-
-    @Test
-    public void testReadStartingInCenterOfMiddleLine() {
-        final int bytesToChopOff = 120;
-        String truncated = extendedBasesOfChrM.substring(bytesToChopOff);
-
-        long startTime = System.currentTimeMillis();
-        ReferenceSequence sequence = sequenceFile.getSubsequenceAt("chrM",
-                                                                   bytesToChopOff + 1,
-                                                                   bytesToChopOff + truncated.length());
-        long endTime = System.currentTimeMillis();
-
-        Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chrM");
-        Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 0);
-        Assert.assertArrayEquals( "First n bases of chrM are incorrect",StringUtil.stringToBytes(truncated),sequence.getBases());
-
-        System.err.printf("testReadStartingInCenterOfMiddleLine runtime: %dms%n", (endTime - startTime)) ;
-    }
-
-    @Test
-    public void testFirstCompleteContigRead() {
-        ReferenceSequenceFile originalSequenceFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(new File(sequenceFileName));
-        ReferenceSequence expectedSequence = originalSequenceFile.nextSequence();
-
-        long startTime = System.currentTimeMillis();
-        ReferenceSequence sequence = sequenceFile.getSequence("chrM");
-        long endTime = System.currentTimeMillis();
-
-        Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chrM");
-        Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 0);
-        Assert.assertArrayEquals("chrM is incorrect",expectedSequence.getBases(),sequence.getBases());
-
-        System.err.printf("testFirstCompleteContigRead runtime: %dms%n", (endTime - startTime)) ;
-    }
-
-    @Test(expected= PicardException.class)
-    public void testReadThroughEndOfContig() {
-        long startTime = System.currentTimeMillis();
-        try {
-            ReferenceSequence sequence = sequenceFile.getSubsequenceAt("chrM",16500,16600);
-        }
-        finally {
-            long endTime = System.currentTimeMillis();
-            System.err.printf("testReadThroughEndOfContig runtime: %dms%n", (endTime - startTime)) ;
-        }
-    }
-
-    @Test(expected= PicardException.class)
-    public void testReadPastEndOfContig() {
-         long startTime = System.currentTimeMillis();
-         try {
-             ReferenceSequence sequence = sequenceFile.getSubsequenceAt("chrM",16800,16900);
-         }
-         finally {
-             long endTime = System.currentTimeMillis();
-             System.err.printf("testReadPastEndOfContig runtime: %dms%n", (endTime - startTime)) ;
-         }
-     }
-
-    @Test
-    public void testMiddleCompleteContigRead() {
-        ReferenceSequenceFile originalSequenceFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(new File(sequenceFileName));
-        ReferenceSequence expectedSequence = originalSequenceFile.nextSequence();
-        while( !expectedSequence.getName().equals("chrY") )
-            expectedSequence = originalSequenceFile.nextSequence();
-
-        long startTime = System.currentTimeMillis();
-        ReferenceSequence sequence = sequenceFile.getSequence("chrY");
-        long endTime = System.currentTimeMillis();
-
-        Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chrY");
-        Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 24);
-        Assert.assertArrayEquals("chrY is incorrect",expectedSequence.getBases(),sequence.getBases());
-
-        System.err.printf("testMiddleCompleteContigRead runtime: %dms%n", (endTime - startTime)) ;
-    }
-
-    @Test
-    public void testLastCompleteContigRead() {
-        ReferenceSequenceFile originalSequenceFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(new File(sequenceFileName));
-        ReferenceSequence expectedSequence = originalSequenceFile.nextSequence();
-        while( !expectedSequence.getName().equals("chrX_random") )
-            expectedSequence = originalSequenceFile.nextSequence();
-
-        long startTime = System.currentTimeMillis();
-        ReferenceSequence sequence = sequenceFile.getSequence("chrX_random");
-        long endTime = System.currentTimeMillis();
-
-        Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chrX_random");
-        Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 44);
-        Assert.assertArrayEquals("chrX_random is incorrect",expectedSequence.getBases(),sequence.getBases());
-
-        System.err.printf("testLastCompleteContigRead runtime: %dms%n", (endTime - startTime)) ;
-    }
-
-
-    @Test
-    public void testFirstOfChr1() {
-        long startTime = System.currentTimeMillis();
-        ReferenceSequence sequence = sequenceFile.getSubsequenceAt("chr1",1,firstBasesOfChr1.length());
-        long endTime = System.currentTimeMillis();
-
-        Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chr1");
-        Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 1);
-        Assert.assertArrayEquals( "First n bases of chr1 are incorrect",StringUtil.stringToBytes(firstBasesOfChr1),sequence.getBases());
-
-        System.err.printf("testFirstOfChr1 runtime: %dms%n", (endTime - startTime)) ;
-    }
-
-    @Test
-    public void testFirstOfChr8() {
-        long startTime = System.currentTimeMillis();
-        ReferenceSequence sequence = sequenceFile.getSubsequenceAt("chr8",1,firstBasesOfChr8.length());
-        long endTime = System.currentTimeMillis();
-
-        Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chr8");
-        Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 8);
-        Assert.assertArrayEquals( "First n bases of chr8 are incorrect",StringUtil.stringToBytes(firstBasesOfChr8),sequence.getBases());
-
-        System.err.printf("testFirstOfChr8 runtime: %dms%n", (endTime - startTime)) ;
-    }
-
-    @Test
-    public void testFirstElementOfIterator() {
-        ReferenceSequenceFile originalSequenceFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(new File(sequenceFileName));
-        ReferenceSequence expectedSequence = originalSequenceFile.nextSequence();
-
-        long startTime = System.currentTimeMillis();
-        ReferenceSequence sequence = sequenceFile.nextSequence();
-        long endTime = System.currentTimeMillis();
-
-        Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chrM");
-        Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 0);
-        Assert.assertArrayEquals("chrM is incorrect",expectedSequence.getBases(),sequence.getBases());
-
-        System.err.printf("testFirstElementOfIterator runtime: %dms%n", (endTime - startTime)) ;
-    }
-
-    @Test
-    public void testNextElementOfIterator() {
-        ReferenceSequenceFile originalSequenceFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(new File(sequenceFileName));
-        // Skip past the first one and load the second one.
-        originalSequenceFile.nextSequence();
-        ReferenceSequence expectedSequence = originalSequenceFile.nextSequence();
-
-        long startTime = System.currentTimeMillis();
-        sequenceFile.nextSequence();
-        ReferenceSequence sequence = sequenceFile.nextSequence();
-        long endTime = System.currentTimeMillis();
-
-        Assert.assertEquals("Sequence contig is not correct", "chr1", sequence.getName());
-        Assert.assertEquals("Sequence contig index is not correct", 1, sequence.getContigIndex());
-        Assert.assertEquals("Sequence size is not correct", expectedSequence.length(), sequence.length());
-        Assert.assertArrayEquals("chr1 is incorrect",expectedSequence.getBases(),sequence.getBases());
-
-        System.err.printf("testNextElementOfIterator runtime: %dms%n", (endTime - startTime)) ;
-    }
-
-    @Test
-    public void testReset() {
-        ReferenceSequenceFile originalSequenceFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(new File(sequenceFileName));
-        // Skip past the first one and load the second one.
-        ReferenceSequence expectedSequence = originalSequenceFile.nextSequence();
-
-        long startTime = System.currentTimeMillis();
-        sequenceFile.nextSequence();
-        sequenceFile.nextSequence();
-        sequenceFile.reset();
-        ReferenceSequence sequence = sequenceFile.nextSequence();
-        long endTime = System.currentTimeMillis();
-
-        Assert.assertEquals("Sequence contig is not correct", "chrM", sequence.getName());
-        Assert.assertEquals("Sequence contig index is not correct", 0, sequence.getContigIndex());
-        Assert.assertEquals("Sequence size is not correct", expectedSequence.length(), sequence.length());
-        Assert.assertArrayEquals("chrM is incorrect", expectedSequence.getBases(),sequence.getBases());
-
-        System.err.printf("testReset runtime: %dms%n", (endTime - startTime)) ;
-    }
-}

java/test/org/broadinstitute/sting/utils/genotype/glf/GLFWriterUnitTest.java

@@ -4,7 +4,6 @@ import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 import org.broadinstitute.sting.utils.genotype.LikelihoodObject;
 import org.junit.Assert;
 import org.junit.Before;
@@ -15,6 +14,7 @@ import java.io.File;
 import java.io.FileNotFoundException;
 
 import net.sf.samtools.SAMSequenceRecord;
+import net.sf.picard.reference.IndexedFastaSequenceFile;
 
 
 /*
@@ -66,11 +66,7 @@ public class GLFWriterUnitTest extends BaseTest {
     @BeforeClass
     public static void beforeTests() {
         IndexedFastaSequenceFile seq;
-        try {
         seq = new IndexedFastaSequenceFile(new File(oneKGLocation + "reference/human_b36_both.fasta"));
-        } catch (FileNotFoundException e) {
-            throw new StingException("unable to load the sequence dictionary");
-        }
         GenomeLocParser.setupRefContigOrdering(seq);
 
     }

java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java

@@ -3,7 +3,6 @@ package org.broadinstitute.sting.utils.genotype.vcf;
 import org.broad.tribble.vcf.*;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.gatk.refdata.tracks.builders.TribbleRMDTrackBuilder;
-import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.junit.Assert;
@@ -14,6 +13,8 @@ import java.io.File;
 import java.io.FileNotFoundException;
 import java.util.*;
 
+import net.sf.picard.reference.IndexedFastaSequenceFile;
+
 
 /**
  * @author aaron
@@ -29,12 +30,8 @@ public class VCFWriterUnitTest extends BaseTest {
 
     @BeforeClass
     public static void beforeTests() {
-        try {
         IndexedFastaSequenceFile seq = new IndexedFastaSequenceFile(new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"));
         GenomeLocParser.setupRefContigOrdering(seq);
-        } catch (FileNotFoundException e) {
-            throw new StingException("unable to load the sequence dictionary");
-        }
     }
 
     /** test, using the writer and reader, that we can output and input a VCF file without problems */