/htsjdk

Removed deprecated VariantContextWriterFactory #756

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1 src/main/java/htsjdk/variant/variantcontext/writer/VariantContextWriterBuilder.java
@@ -53,7 +53,6 @@
*
* <p>
* Provides methods for creating <code>VariantContextWriter</code>s using the Builder pattern.
- * Replaces <code>VariantContextWriterFactory</code>.
* </p>
* <p>
* The caller must choose an output file or an output stream for the <code>VariantContextWriter</code> to write to.
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282 src/main/java/htsjdk/variant/variantcontext/writer/VariantContextWriterFactory.java
@@ -1,282 +0,0 @@
-/*
-* Copyright (c) 2012 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 htsjdk.variant.variantcontext.writer;
-
-import htsjdk.samtools.Defaults;
-import htsjdk.samtools.SAMSequenceDictionary;
-import htsjdk.samtools.util.BlockCompressedOutputStream;
-import htsjdk.samtools.util.IOUtil;
-import htsjdk.samtools.util.RuntimeIOException;
-import htsjdk.tribble.AbstractFeatureReader;
-import htsjdk.tribble.index.IndexCreator;
-import htsjdk.tribble.index.tabix.TabixFormat;
-import htsjdk.tribble.index.tabix.TabixIndexCreator;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.OutputStream;
-import java.util.EnumSet;
-
-/**
- * Factory methods to create VariantContext writers
- *
- * @author depristo
- * @since 5/12
- *
- * @deprecated Replaced by {@link VariantContextWriterBuilder}
- */
-@Deprecated
-public class VariantContextWriterFactory {
-
- public static final EnumSet<Options> DEFAULT_OPTIONS = EnumSet.of(Options.INDEX_ON_THE_FLY);
- public static final EnumSet<Options> NO_OPTIONS = EnumSet.noneOf(Options.class);
-
- static {
- if (Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE) {
- DEFAULT_OPTIONS.add(Options.USE_ASYNC_IO);
- }
- }
-
- private VariantContextWriterFactory() {}
-
- public static VariantContextWriter create(final File location, final SAMSequenceDictionary refDict) {
- return create(location, openOutputStream(location), refDict, DEFAULT_OPTIONS);
- }
-
- public static VariantContextWriter create(final File location, final SAMSequenceDictionary refDict, final EnumSet<Options> options) {
- return create(location, openOutputStream(location), refDict, options);
- }
-
- /**
- * @param output If buffered writing is desired, caller must provide some kind of buffered OutputStream.
- */
- public static VariantContextWriter create(final File location,
- final OutputStream output,
- final SAMSequenceDictionary refDict) {
- return create(location, output, refDict, DEFAULT_OPTIONS);
- }
-
- /**
- * @param output If buffered writing is desired, caller must provide some kind of buffered OutputStream.
- */
- public static VariantContextWriter create(final OutputStream output,
- final SAMSequenceDictionary refDict,
- final EnumSet<Options> options) {
- return create(null, output, refDict, options);
- }
-
- /**
- * @param location Note that this parameter is used to producing intelligent log messages, and for naming the index,
- * but does not control where the file is written
- * @param output This is where the BCF is actually written. If buffered writing is desired, caller must provide
- * some kind of buffered OutputStream.
- */
- public static VariantContextWriter createBcf2(final File location,
- final OutputStream output,
- final SAMSequenceDictionary refDict,
- final EnumSet<Options> options) {
- return maybeWrapWithAsyncWriter(new BCF2Writer(location, output, refDict,
- options.contains(Options.INDEX_ON_THE_FLY),
- options.contains(Options.DO_NOT_WRITE_GENOTYPES)), options);
- }
-
- /**
- * @param location Note that this parameter is used to producing intelligent log messages, and for naming the index,
- * but does not control where the file is written
- * @param output This is where the BCF is actually written. If buffered writing is desired, caller must provide
- * some kind of buffered OutputStream.
- */
- public static VariantContextWriter createBcf2(final File location,
- final OutputStream output,
- final SAMSequenceDictionary refDict,
- final IndexCreator indexCreator,
- final EnumSet<Options> options) {
- return maybeWrapWithAsyncWriter(new BCF2Writer(location, output, refDict, indexCreator,
- options.contains(Options.INDEX_ON_THE_FLY),
- options.contains(Options.DO_NOT_WRITE_GENOTYPES)), options);
- }
-
- /**
- * @param location Note that this parameter is used to producing intelligent log messages, and for naming the index,
- * but does not control where the file is written
- * @param output This is where the VCF is actually written. If buffered writing is desired, caller must provide
- * some kind of buffered OutputStream.
- */
- public static VariantContextWriter createVcf(final File location,
- final OutputStream output,
- final SAMSequenceDictionary refDict,
- final EnumSet<Options> options) {
- return maybeWrapWithAsyncWriter(new VCFWriter(location, output, refDict,
- options.contains(Options.INDEX_ON_THE_FLY),
- options.contains(Options.DO_NOT_WRITE_GENOTYPES),
- options.contains(Options.ALLOW_MISSING_FIELDS_IN_HEADER),
- options.contains(Options.WRITE_FULL_FORMAT_FIELD)), options);
- }
-
- /**
- * @param location Note that this parameter is used to producing intelligent log messages, and for naming the index,
- * but does not control where the file is written
- * @param output This is where the VCF is actually written. If buffered writing is desired, caller must provide
- * some kind of buffered OutputStream.
- */
- public static VariantContextWriter createVcf(final File location,
- final OutputStream output,
- final SAMSequenceDictionary refDict,
- final IndexCreator indexCreator,
- final EnumSet<Options> options) {
- return maybeWrapWithAsyncWriter(new VCFWriter(location, output, refDict, indexCreator,
- options.contains(Options.INDEX_ON_THE_FLY),
- options.contains(Options.DO_NOT_WRITE_GENOTYPES),
- options.contains(Options.ALLOW_MISSING_FIELDS_IN_HEADER),
- options.contains(Options.WRITE_FULL_FORMAT_FIELD)), options);
- }
-
- /**
- * @param location Note that this parameter is used to producing intelligent log messages,
- * but does not control where the file is written
- * @param output This is where the VCF is actually written. If buffered writing is desired, caller must provide
- * some kind of buffered OutputStream.
- */
- public static VariantContextWriter createBlockCompressedVcf(final File location,
- final OutputStream output,
- final SAMSequenceDictionary refDict,
- final EnumSet<Options> options) {
- final TabixIndexCreator indexCreator;
- if (options.contains(Options.INDEX_ON_THE_FLY)) {
- indexCreator = new TabixIndexCreator(refDict, TabixFormat.VCF);
- } else {
- indexCreator = null;
- }
- return maybeWrapWithAsyncWriter(new VCFWriter(location, BlockCompressedOutputStream.maybeBgzfWrapOutputStream(location, output),
- refDict, indexCreator,
- options.contains(Options.INDEX_ON_THE_FLY),
- options.contains(Options.DO_NOT_WRITE_GENOTYPES),
- options.contains(Options.ALLOW_MISSING_FIELDS_IN_HEADER),
- options.contains(Options.WRITE_FULL_FORMAT_FIELD)), options);
- }
-
- /**
- * @param location Note that this parameter is used to producing intelligent log messages,
- * but does not control where the file is written
- * @param output This is where the VCF is actually written. If buffered writing is desired, caller must provide
- * some kind of buffered OutputStream.
- */
- public static VariantContextWriter createBlockCompressedVcf(final File location,
- final OutputStream output,
- final SAMSequenceDictionary refDict,
- final IndexCreator indexCreator,
- final EnumSet<Options> options) {
- return maybeWrapWithAsyncWriter(new VCFWriter(location, BlockCompressedOutputStream.maybeBgzfWrapOutputStream(location, output),
- refDict, indexCreator,
- options.contains(Options.INDEX_ON_THE_FLY),
- options.contains(Options.DO_NOT_WRITE_GENOTYPES),
- options.contains(Options.ALLOW_MISSING_FIELDS_IN_HEADER),
- options.contains(Options.WRITE_FULL_FORMAT_FIELD)), options);
- }
-
- public static VariantContextWriter create(final File location,
- final OutputStream output,
- final SAMSequenceDictionary refDict,
- final EnumSet<Options> options) {
-
- if (isBCFOutput(location, options)) {
- return createBcf2(location, output, refDict, options);
- } else if (isCompressedVcf(location)) {
- return createBlockCompressedVcf(location, output, refDict, options);
- } else {
- return createVcf(location, output, refDict, options);
- }
- }
-
- /**
- * @param output If buffered writing is desired, caller must provide some kind of buffered OutputStream.
- */
- public static VariantContextWriter create(final File location,
- final OutputStream output,
- final SAMSequenceDictionary refDict,
- final IndexCreator indexCreator,
- final EnumSet<Options> options) {
-
- if (isBCFOutput(location, options)) {
- return createBcf2(location, output, refDict, indexCreator, options);
- } else if (isCompressedVcf(location)) {
- return createBlockCompressedVcf(location, output, refDict, indexCreator, options);
- } else {
- return createVcf(location, output, refDict, indexCreator, options);
- }
- }
-
- private static VariantContextWriter maybeWrapWithAsyncWriter(final VariantContextWriter writer,
- final EnumSet<Options> options) {
- if (options.contains(Options.USE_ASYNC_IO)) {
- return new AsyncVariantContextWriter(writer, AsyncVariantContextWriter.DEFAULT_QUEUE_SIZE);
- }
- else return writer;
- }
-
- /**
- * Should we output a BCF file based solely on the name of the file at location?
- *
- * @param location
- * @return
- */
- public static boolean isBCFOutput(final File location) {
- return isBCFOutput(location, EnumSet.noneOf(Options.class));
- }
-
- public static boolean isBCFOutput(final File location, final EnumSet<Options> options) {
- return options.contains(Options.FORCE_BCF) || (location != null && location.getName().contains(".bcf"));
- }
-
- public static boolean isCompressedVcf(final File location) {
- if (location == null)
- return false;
-
- return AbstractFeatureReader.hasBlockCompressedExtension(location);
- }
-
- public static VariantContextWriter sortOnTheFly(final VariantContextWriter innerWriter, final int maxCachingStartDistance) {
@ronlevine

ronlevine Nov 29, 2016

Contributor

Does sortOnTheFly need to be added to VariantContextWriterBuilder ?

@magicDGS

magicDGS Nov 29, 2016

Contributor

I can add these two static method, but they are just syntactic sugar for the SortingVariantContextWriter constructors. This only requires two change appearances of the following lines of code:

final VariantContextWriter sortingWriter = VariantContextWriterFactory.sortOnTheFly(writer, 1000);
...
final VariantContextWriter sortingWriter = VariantContextWriterFactory.sortOnTheFly(writer, 1000, true);

for these:

final VariantContextWriter sortingWriter = new SortingVariantContextWriter(writer, 1000);
...
final VariantContextWriter sortingWriter = new SortingVariantContextWriter(writer, 1000, true);

I don't think that it is necessary, because code that is using these methods should be refactored anyway. But of course, I could include it.

@ronlevine

ronlevine Nov 29, 2016

Contributor

@magicDGS I agree with you, no need to add it. The builder pattern should not have any static methods plus it the a VERY thin wrapper around SortingVariantContextWriter.
- return sortOnTheFly(innerWriter, maxCachingStartDistance, false);
- }
-
- public static VariantContextWriter sortOnTheFly(final VariantContextWriter innerWriter, final int maxCachingStartDistance, final boolean takeOwnershipOfInner) {
- return new SortingVariantContextWriter(innerWriter, maxCachingStartDistance, takeOwnershipOfInner);
- }
-
- /**
- * Returns a output stream writing to location, or throws an exception if this fails
- * @param location
- * @return
- */
- protected static OutputStream openOutputStream(final File location) {
- try {
- return IOUtil.maybeBufferOutputStream(new FileOutputStream(location));
- } catch (final FileNotFoundException e) {
- throw new RuntimeIOException(location + ": Unable to create VCF writer", e);
- }
- }
-}