Added ability to get a VariantContexts from an InputStream (#1245)

* new VCFIteratorBuilder allows you to convert an InputStream of a vcf/bcf into an iterator of VariantContexts
* new methods in IOUtils for identifying if a stream is gzipped or not
* deprecated SamStreams.isGzippedSAMFile and replaced it with IOUtil.isGZIPInputStream

src/main/java/htsjdk/samtools/SamReaderFactory.java

@@ -399,7 +399,7 @@ public SamReader open(final SamInputResource resource) {
                         }
                     } else if (BlockCompressedInputStream.isValidFile(bufferedStream)) {
                         primitiveSamReader = new SAMTextReader(new BlockCompressedInputStream(bufferedStream), validationStringency, this.samRecordFactory);
-                    } else if (SamStreams.isGzippedSAMFile(bufferedStream)) {
+                    } else if (IOUtil.isGZIPInputStream(bufferedStream)) {
                         primitiveSamReader = new SAMTextReader(new GZIPInputStream(bufferedStream), validationStringency, this.samRecordFactory);
                     } else if (SamStreams.isCRAMFile(bufferedStream)) {
                         if (referenceSource == null) {

src/main/java/htsjdk/samtools/SamStreams.java

@@ -4,14 +4,14 @@
 import htsjdk.samtools.seekablestream.SeekableStream;
 import htsjdk.samtools.util.BlockCompressedInputStream;
 import htsjdk.samtools.util.BlockCompressedStreamConstants;
+import htsjdk.samtools.util.IOUtil;
 
 import java.io.ByteArrayInputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.Arrays;
-import java.util.zip.GZIPInputStream;
 
 /**
  * Utilities related to processing of {@link java.io.InputStream}s encoding SAM data
@@ -66,26 +66,11 @@ public static boolean isBAMFile(final InputStream stream)
     /**
      * Checks whether the file is a gzipped sam file.  Returns true if it
      * is and false otherwise.
+     * @see @link IOUtil#isGZIPInputStream(InputStream)
      */
+    @Deprecated
     public static boolean isGzippedSAMFile(final InputStream stream) {
-        if (!stream.markSupported()) {
-            throw new IllegalArgumentException("Cannot test a stream that doesn't support marking.");
-        }
-        stream.mark(8000);
-
-        try {
-            final GZIPInputStream gunzip = new GZIPInputStream(stream);
-            final int ch = gunzip.read();
-            return true;
-        } catch (final IOException ioe) {
-            return false;
-        } finally {
-            try {
-                stream.reset();
-            } catch (final IOException ioe) {
-                throw new IllegalStateException("Could not reset stream.");
-            }
-        }
+        return IOUtil.isGZIPInputStream(stream);
     }
 
     // Its too expensive to examine the remote file to determine type.

src/main/java/htsjdk/samtools/util/IOUtil.java

@@ -26,6 +26,7 @@
 
 import htsjdk.samtools.Defaults;
 import htsjdk.samtools.SAMException;
+import htsjdk.samtools.SamStreams;
 import htsjdk.samtools.seekablestream.SeekableBufferedStream;
 import htsjdk.samtools.seekablestream.SeekableFileStream;
 import htsjdk.samtools.seekablestream.SeekableHTTPStream;
@@ -110,7 +111,6 @@ public class IOUtil {
     public static final Set<String> BLOCK_COMPRESSED_EXTENSIONS = Collections.unmodifiableSet(new HashSet<String>(Arrays.asList(".gz", ".gzip", ".bgz", ".bgzf")));
 
     private static int compressionLevel = Defaults.COMPRESSION_LEVEL;
-
     /**
      * Sets the GZip compression level for subsequent GZIPOutputStream object creation.
      * @param compressionLevel 0 <= compressionLevel <= 9
@@ -571,12 +571,13 @@ else if (!dir.canRead()) {
      * Checks that the two files are the same length, and have the same content, otherwise throws a runtime exception.
      */
     public static void assertFilesEqual(final File f1, final File f2) {
-        try {
-            if (f1.length() != f2.length()) {
-                throw new SAMException("File " + f1 + " is " + f1.length() + " bytes but file " + f2 + " is " + f2.length() + " bytes.");
-            }
+        if (f1.length() != f2.length()) {
+            throw new SAMException("File " + f1 + " is " + f1.length() + " bytes but file " + f2 + " is " + f2.length() + " bytes.");
+        }
+        try (
             final FileInputStream s1 = new FileInputStream(f1);
             final FileInputStream s2 = new FileInputStream(f2);
+            ) {
             final byte[] buf1 = new byte[1024 * 1024];
             final byte[] buf2 = new byte[1024 * 1024];
             int len1;
@@ -589,12 +590,9 @@ public static void assertFilesEqual(final File f1, final File f2) {
                     throw new SAMException("Files " + f1 + " and " + f2 + " differ.");
                 }
             }
-            s1.close();
-            s2.close();
-        } catch (IOException e) {
+        } catch (final IOException e) {
             throw new SAMException("Exception comparing files " + f1 + " and " + f2, e);
         }
-
     }
 
     /**
@@ -1157,6 +1155,38 @@ public static List<Path> filesToPaths(Collection<File> files){
         return files.stream().map(File::toPath).collect(Collectors.toList());
     }
 
+    /** number of bytes that will be read for the GZIP-header in the function {@link #isGZIPInputStream(InputStream)} */
+    public static final int GZIP_HEADER_READ_LENGTH = 8000;
+
+    /**
+     * Test whether a input stream looks like a GZIP input.
+     * @param stream the input stream.
+     * @return true if `stream` starts with a gzip signature
+     * @throws IllegalArgumentException if `stream` cannot mark or reset the stream
+     * @see SamStreams#isGzippedSAMFile(InputStream)
+     */
+    public static boolean isGZIPInputStream(final InputStream stream) {
+        /* this function was previously implemented in SamStreams.isGzippedSAMFile */
+        if (!stream.markSupported()) {
+            throw new IllegalArgumentException("isGZIPInputStream() : Cannot test a stream that doesn't support marking.");
+        }
+        stream.mark(GZIP_HEADER_READ_LENGTH);
+
+        try {
+            final GZIPInputStream gunzip = new GZIPInputStream(stream);
+            final int ch = gunzip.read();
+            return true;
+        } catch (final IOException ioe) {
+            return false;
+        } finally {
+            try {
+                stream.reset();
+            } catch (final IOException ioe) {
+                throw new IllegalStateException("isGZIPInputStream(): Could not reset stream.");
+            }
+        }
+    }
+
     /**
      * Adds the extension to the given path.
      *

src/main/java/htsjdk/variant/bcf2/BCF2Codec.java

@@ -59,6 +59,10 @@ public final class BCF2Codec extends BinaryFeatureCodec<VariantContext> {
     private final static int ALLOWED_MAJOR_VERSION = 2;
     private final static int MIN_MINOR_VERSION = 1;
 
+    /** sizeof a BCF header (+ min/max version). Used when trying to detect when a streams starts with a bcf header */
+    public static final int SIZEOF_BCF_HEADER =  BCFVersion.MAGIC_HEADER_START.length + 2*Byte.BYTES;
+
+
     private BCFVersion bcfVersion = null;
 
     private VCFHeader header = null;
@@ -477,4 +481,19 @@ protected BCF2GenotypeFieldDecoders.Decoder getGenotypeFieldDecoder(final String
     private void error(final String message) throws RuntimeException {
         throw new TribbleException(String.format("%s, at record %d with position %d:", message, recordNo, pos));
     }
+
+    /** try to read a BCFVersion from an uncompressed BufferedInputStream.
+     * The buffer must be large enough to contain {@link #SIZEOF_BCF_HEADER}
+     * 
+     * @param bufferedinput the uncompressed input stream
+     * @return the BCFVersion if it can be decoded, or null if not found.
+     * @throws IOException
+     */
+    public static BCFVersion tryReadBCFVersion(final BufferedInputStream uncompressedBufferedInput) throws IOException {
+        uncompressedBufferedInput.mark(SIZEOF_BCF_HEADER);
+        final BCFVersion bcfVersion = BCFVersion.readBCFVersion(uncompressedBufferedInput);
+        uncompressedBufferedInput.reset();
+        return bcfVersion;
+    }
+
 }

src/main/java/htsjdk/variant/vcf/VCFIterator.java

@@ -0,0 +1,56 @@
+/*
+*
+* 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 htsjdk.variant.vcf;
+
+import htsjdk.samtools.util.CloseableIterator;
+import htsjdk.variant.variantcontext.VariantContext;
+
+/**
+ * An iterator of `VariantContext`. This iterator can be used to
+ * decode VCF data on the fly .
+ *
+ * Example:
+ *
+ * <pre>
+ * VCFIterator r = new VCFIteratorBuilder().open(System.in);
+ * while (r.hasNext()) {
+ *     System.out.println(r.next());
+ * }
+ * r.close();
+ * </pre>
+ *
+ * @author Pierre Lindenbaum / @yokofakun
+ * @see htsjdk.variant.vcf.VCFIteratorBuilder
+ *
+ */
+public interface VCFIterator extends CloseableIterator<VariantContext> {
+    /** Returns the VCFHeader associated with this VCF/BCF file. */
+    public VCFHeader getHeader();
+
+    /**
+     * Returns the next object but does not advance the iterator. Subsequent
+     * calls to peek() and next() will return the same object.
+     */
+    public VariantContext peek();
+}