New upstream version 2.14.3+dfsg (26feb9cc) · Commits · Debian Med / htsjdk

.gitignore

+1 −0

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		@@ -10,6 +10,7 @@ src/htsjdk.iml
		*.iml
		*.ipr
		*.iws
		out/

src/main/java/htsjdk/samtools/BAMFileWriter.java

+7 −9

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		@@ -29,7 +29,6 @@ import htsjdk.samtools.util.IOUtil;
		import htsjdk.samtools.util.RuntimeIOException;
		import htsjdk.samtools.util.zip.DeflaterFactory;

		import java.io.DataOutputStream;
		import java.io.File;
		import java.io.IOException;
		import java.io.OutputStream;
		@@ -37,7 +36,6 @@ import java.io.StringWriter;
		import java.io.Writer;
		import java.nio.file.Files;
		import java.nio.file.Path;
		import java.nio.file.Paths;

		/**
		* Concrete implementation of SAMFileWriter for writing gzipped BAM files.
		@@ -51,37 +49,37 @@ class BAMFileWriter extends SAMFileWriterImpl {

		protected BAMFileWriter(final File path) {
		blockCompressedOutputStream = new BlockCompressedOutputStream(path);
		outputBinaryCodec = new BinaryCodec(new DataOutputStream(blockCompressedOutputStream));
		outputBinaryCodec = new BinaryCodec(blockCompressedOutputStream);
		outputBinaryCodec.setOutputFileName(path.getAbsolutePath());
		}

		protected BAMFileWriter(final File path, final int compressionLevel) {
		blockCompressedOutputStream = new BlockCompressedOutputStream(path, compressionLevel);
		outputBinaryCodec = new BinaryCodec(new DataOutputStream(blockCompressedOutputStream));
		outputBinaryCodec = new BinaryCodec(blockCompressedOutputStream);
		outputBinaryCodec.setOutputFileName(path.getAbsolutePath());
		}

		protected BAMFileWriter(final OutputStream os, final File file) {
		blockCompressedOutputStream = new BlockCompressedOutputStream(os, file);
		outputBinaryCodec = new BinaryCodec(new DataOutputStream(blockCompressedOutputStream));
		outputBinaryCodec = new BinaryCodec(blockCompressedOutputStream);
		outputBinaryCodec.setOutputFileName(getPathString(file));
		}

		protected BAMFileWriter(final OutputStream os, final File file, final int compressionLevel) {
		blockCompressedOutputStream = new BlockCompressedOutputStream(os, file, compressionLevel);
		outputBinaryCodec = new BinaryCodec(new DataOutputStream(blockCompressedOutputStream));
		outputBinaryCodec = new BinaryCodec(blockCompressedOutputStream);
		outputBinaryCodec.setOutputFileName(getPathString(file));
		}

		protected BAMFileWriter(final OutputStream os, final File file, final int compressionLevel, final DeflaterFactory deflaterFactory) {
		blockCompressedOutputStream = new BlockCompressedOutputStream(os, file, compressionLevel, deflaterFactory);
		outputBinaryCodec = new BinaryCodec(new DataOutputStream(blockCompressedOutputStream));
		outputBinaryCodec = new BinaryCodec(blockCompressedOutputStream);
		outputBinaryCodec.setOutputFileName(getPathString(file));
		}

		protected BAMFileWriter(final OutputStream os, final String absoluteFilename, final int compressionLevel, final DeflaterFactory deflaterFactory) {
		blockCompressedOutputStream = new BlockCompressedOutputStream(os, null, compressionLevel, deflaterFactory);
		outputBinaryCodec = new BinaryCodec(new DataOutputStream(blockCompressedOutputStream));
		outputBinaryCodec = new BinaryCodec(blockCompressedOutputStream);
		outputBinaryCodec.setOutputFileName(absoluteFilename);
		}

		@@ -204,7 +202,7 @@ class BAMFileWriter extends SAMFileWriterImpl {

		protected static void writeHeader(final OutputStream outputStream, final SAMFileHeader samFileHeader) {
		final BlockCompressedOutputStream blockCompressedOutputStream = new BlockCompressedOutputStream(outputStream, null);
		final BinaryCodec outputBinaryCodec = new BinaryCodec(new DataOutputStream(blockCompressedOutputStream));
		final BinaryCodec outputBinaryCodec = new BinaryCodec(blockCompressedOutputStream);
		writeHeader(outputBinaryCodec, samFileHeader);
		try {
		blockCompressedOutputStream.flush();

src/main/java/htsjdk/samtools/Defaults.java

+1 −1

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		@@ -110,7 +110,7 @@ public class Defaults {
		}
		REFERENCE_FASTA = getFileProperty("reference_fasta", null);
		USE_CRAM_REF_DOWNLOAD = getBooleanProperty("use_cram_ref_download", false);
		EBI_REFERENCE_SERVICE_URL_MASK = "http://www.ebi.ac.uk/ena/cram/md5/%s";
		EBI_REFERENCE_SERVICE_URL_MASK = "https://www.ebi.ac.uk/ena/cram/md5/%s";
		CUSTOM_READER_FACTORY = getStringProperty("custom_reader", "");
		SAM_FLAG_FIELD_FORMAT = SamFlagField.valueOf(getStringProperty("sam_flag_field_format", SamFlagField.DECIMAL.name()));
		SRA_LIBRARIES_DOWNLOAD = getBooleanProperty("sra_libraries_download", false);

src/main/java/htsjdk/samtools/DownsamplingIteratorFactory.java

+1 −1

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		@@ -53,7 +53,7 @@ public class DownsamplingIteratorFactory {
		"strategy to finish. Works in a single pass, and will provide accuracy close to (but often not as good as) HighAccuracy while requiring " +
		"memory proportional to the set of reads emitted from the ConstantMemory strategy to the HighAccuracy strategy. Works well when downsampling " +
		"large inputs to small proportions (e.g. downsampling hundreds of millions of reads and retaining only 2%. Should be accurate 99.9% of the time " +
		"when the input contains >= 50,000 templates (read names). For smaller inputs, HighAccuracy is recommended instead.";
		"when the input contains more than 50,000 templates (read names). For smaller inputs, HighAccuracy is recommended instead.";

		/** Describes the available downsampling strategies. */
		public enum Strategy {

src/main/java/htsjdk/samtools/NotPrimarySkippingIterator.java

+5 −27

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		@@ -24,39 +24,17 @@
		package htsjdk.samtools;

		import htsjdk.samtools.util.CloseableIterator;
		import htsjdk.samtools.util.PeekIterator;

		/**
		* Wrapper around SAMRecord iterator that skips over non-primary elements.
		* This iterator conflates a filtering iterator and a peekable iterator. It would be cleaner to
		* handle those concerns separately.
		* @deprecated use {@link SecondaryAlignmentSkippingIterator} instead.
		*/
		public class NotPrimarySkippingIterator {
		private final PeekIterator<SAMRecord> it;
		@Deprecated
		public class NotPrimarySkippingIterator extends SecondaryAlignmentSkippingIterator {

		public NotPrimarySkippingIterator(final CloseableIterator<SAMRecord> underlyingIt) {
		it = new PeekIterator<SAMRecord>(underlyingIt);
		skipAnyNotprimary();
		}

		public boolean hasCurrent() {
		return it.hasNext();
		}

		public SAMRecord getCurrent() {
		assert(hasCurrent());
		return it.peek();
		}

		public boolean advance() {
		it.next();
		skipAnyNotprimary();
		return hasCurrent();
		}

		private void skipAnyNotprimary() {
		while (it.hasNext() && it.peek().getNotPrimaryAlignmentFlag()) {
		it.next();
		}
		public NotPrimarySkippingIterator(CloseableIterator<SAMRecord> underlyingIt) {
		super(underlyingIt);
		}
		}