Add LiftOver constructor that takes an input stream

src/main/java/htsjdk/samtools/liftover/Chain.java

@@ -36,6 +36,7 @@
 import java.util.List;
 import java.util.regex.Pattern;
 
+
 /**
  * Holds a single chain from a UCSC chain file.  Chain file format is described here: http://genome.ucsc.edu/goldenPath/help/chain.html
  *
@@ -309,26 +310,36 @@ public int hashCode() {
     /**
      * Read all the chains and load into an OverlapDetector.
      * @param chainFile File in UCSC chain format.
-     * @return OverlapDetector will all Chains from reader loaded into it.
+     * @return OverlapDetector with all Chains from reader loaded into it.
      */
     static OverlapDetector<Chain> loadChains(final File chainFile) {
-        final BufferedLineReader reader = new BufferedLineReader(IOUtil.openFileForReading(chainFile));
+        IOUtil.assertFileIsReadable(chainFile);
+        try(final BufferedLineReader reader = new BufferedLineReader(IOUtil.openFileForReading(chainFile))){
+            return loadChains(reader, chainFile.toString());
+        }
+    }
+
+    /**
+     * Read all the chains and load into an OverlapDetector.
+     * @param reader reader of file in UCSC chain format.
+     * @return OverlapDetector with all Chains from reader loaded into it.
+     */
+    static OverlapDetector<Chain> loadChains(final BufferedLineReader reader, String sourceName) {
         final OverlapDetector<Chain> ret = new OverlapDetector<Chain>(0, 0);
         Chain chain;
-        while ((chain = Chain.loadChain(reader, chainFile.toString())) != null) {
+        while ((chain = Chain.loadChain(reader, sourceName)) != null) {
             ret.addLhs(chain, chain.interval);
         }
-        reader.close();
         return ret;
     }
 
     /**
      * Read a single Chain from reader.
      * @param reader Text representation of chains.
-     * @param chainFile For error messages only.
+     * @param sourceName For error messages only.
      * @return New Chain with associated ContinuousBlocks.
      */
-    private static Chain loadChain(final BufferedLineReader reader, final String chainFile) {
+    private static Chain loadChain(final BufferedLineReader reader, final String sourceName) {
         String line;
         while (true) {
             line = reader.readLine();
@@ -342,10 +353,10 @@ private static Chain loadChain(final BufferedLineReader reader, final String cha
         }
         final String[] chainFields = SPLITTER.split(line);
         if (chainFields.length != 13) {
-            throwChainFileParseException("chain line has wrong number of fields", chainFile, reader.getLineNumber());
+            throwChainFileParseException("chain line has wrong number of fields", sourceName, reader.getLineNumber());
         }
         if (!"chain".equals(chainFields[0])) {
-            throwChainFileParseException("chain line does not start with 'chain'", chainFile, reader.getLineNumber());
+            throwChainFileParseException("chain line does not start with 'chain'", sourceName, reader.getLineNumber());
         }
         double score = 0;
         String fromSequenceName = null;
@@ -372,7 +383,7 @@ private static Chain loadChain(final BufferedLineReader reader, final String cha
             toChainEnd = Integer.parseInt(chainFields[11]);
             id = Integer.parseInt(chainFields[12]);
         } catch (NumberFormatException e) {
-            throwChainFileParseException("Invalid field", chainFile, reader.getLineNumber());
+            throwChainFileParseException("Invalid field", sourceName, reader.getLineNumber());
         }
         final Chain chain = new Chain(score, fromSequenceName, fromSequenceSize, fromChainStart, fromChainEnd, toSequenceName, toSequenceSize, toNegativeStrand, toChainStart,
                 toChainEnd, id);
@@ -383,18 +394,18 @@ private static Chain loadChain(final BufferedLineReader reader, final String cha
             line = reader.readLine();
             if (line == null || line.equals("")) {
                 if (!sawLastLine) {
-                    throwChainFileParseException("Reached end of chain without seeing terminal block", chainFile, reader.getLineNumber());
+                    throwChainFileParseException("Reached end of chain without seeing terminal block", sourceName, reader.getLineNumber());
                 }
                 break;
             }
             if (sawLastLine) {
-                throwChainFileParseException("Terminal block seen before end of chain", chainFile, reader.getLineNumber());
+                throwChainFileParseException("Terminal block seen before end of chain", sourceName, reader.getLineNumber());
             }
             String[] blockFields = SPLITTER.split(line);
             if (blockFields.length == 1) {
                 sawLastLine = true;
             } else if (blockFields.length != 3) {
-                throwChainFileParseException("Block line has unexpected number of fields", chainFile, reader.getLineNumber());
+                throwChainFileParseException("Block line has unexpected number of fields", sourceName, reader.getLineNumber());
             }
             int size = Integer.parseInt(blockFields[0]);
             chain.addBlock(fromBlockStart, toBlockStart, size);
@@ -408,7 +419,7 @@ private static Chain loadChain(final BufferedLineReader reader, final String cha
         return chain;
     }
 
-    private static void throwChainFileParseException(final String message, final String chainFile, final int lineNumber) {
-        throw new SAMException(message + " in chain file " + chainFile + " at line " + lineNumber);
+    private static void throwChainFileParseException(final String message, final String sourceName, final int lineNumber) {
+        throw new SAMException(message + " in chain file " + sourceName + " at line " + lineNumber);
     }
 }

src/main/java/htsjdk/samtools/liftover/LiftOver.java

@@ -25,12 +25,10 @@
 
 import htsjdk.samtools.SAMException;
 import htsjdk.samtools.SAMSequenceDictionary;
-import htsjdk.samtools.util.IOUtil;
-import htsjdk.samtools.util.Interval;
-import htsjdk.samtools.util.Log;
-import htsjdk.samtools.util.OverlapDetector;
+import htsjdk.samtools.util.*;
 
 import java.io.File;
+import java.io.InputStream;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashMap;
@@ -39,6 +37,7 @@
 import java.util.Map;
 import java.util.Set;
 
+
 /**
  * Java port of UCSC liftOver.  Only the most basic liftOver functionality is implemented.
  * Internally coordinates are 0-based, half-open. The API is standard Picard 1-based, inclusive.
@@ -84,10 +83,19 @@ public long getFailedIntervalsBelowThreshold() {
     /**
      * Load UCSC chain file in order to lift over Intervals.
      */
-    public LiftOver(File chainFile) {
-        IOUtil.assertFileIsReadable(chainFile);
-        chains = Chain.loadChains(chainFile);
+    public LiftOver(File chainFile){
+        this(Chain.loadChains(chainFile));
+    }
+
+    /**
+     * Load UCSC chain file in order to lift over Intervals.
+     */
+    public LiftOver(InputStream chainFileInputStream, String sourceName) {
+        this(Chain.loadChains(new BufferedLineReader(chainFileInputStream), sourceName));
+    }
 
+    private LiftOver(OverlapDetector<Chain> chains) {
+        this.chains = chains;
         for (final Chain chain : this.chains.getAll()) {
             final String from = chain.fromSequenceName;
             final String to   = chain.toSequenceName;

src/test/java/htsjdk/samtools/liftover/LiftOverTest.java

@@ -31,8 +31,7 @@
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
-import java.io.File;
-import java.io.PrintWriter;
+import java.io.*;
 import java.util.*;
 import java.util.stream.Stream;
 
@@ -44,14 +43,21 @@ public class LiftOverTest extends HtsjdkTest {
     private static final File CHAIN_FILE = new File(TEST_DATA_DIR, "hg18ToHg19.over.chain");
 
     private LiftOver liftOver;
-    Map<String, Set<String>> contigMap;
+    private Map<String, Set<String>> contigMap;
+    private LiftOver liftOverFromInputStream;
 
     @BeforeClass
     public void initLiftOver() {
         liftOver = new LiftOver(CHAIN_FILE);
         contigMap = liftOver.getContigMap();
     }
 
+    @BeforeClass
+    public void initLiftOverFromInputStream() throws FileNotFoundException {
+        InputStream chainFileInputStream = new FileInputStream(CHAIN_FILE);
+        liftOverFromInputStream = new LiftOver(chainFileInputStream, CHAIN_FILE.toString());
+    }
+
     @Test(dataProvider = "testIntervals")
     public void testBasic(final Interval in, final Interval expected) {
         Assert.assertEquals(liftOver.liftOver(in), expected);
@@ -461,21 +467,26 @@ public void testWriteChain() throws Exception {
         File outFile = File.createTempFile("test.", ".chain");
         outFile.deleteOnExit();
         PrintWriter pw = new PrintWriter(outFile);
-        final Map<Integer, Chain> originalChainMap = new TreeMap<Integer, Chain>();
+        final Map<Integer, Chain> originalChainMap = new TreeMap<>();
         for (final Chain chain : chains.getAll()) {
             chain.write(pw);
             originalChainMap.put(chain.id, chain);
         }
         pw.close();
 
         final OverlapDetector<Chain> newChains = Chain.loadChains(outFile);
-        final Map<Integer, Chain> newChainMap = new TreeMap<Integer, Chain>();
+        final Map<Integer, Chain> newChainMap = new TreeMap<>();
         for (final Chain chain : newChains.getAll()) {
             newChainMap.put(chain.id, chain);
         }
         Assert.assertEquals(newChainMap, originalChainMap);
     }
 
+    @Test(dataProvider = "testIntervals")
+    public void loadLiftOverFromInputStream(final Interval in, final Interval expected) {
+        Assert.assertEquals(liftOverFromInputStream.liftOver(in), expected);
+    }
+
     @Test(dataProvider = "testIntervals")
     public void testGetContigMap(final Interval in, final Interval expected) {
         if (expected != null) {