org.nmdp.ngs.variant.vcf.VcfReader Maven / Gradle / Ivy
/*
ngs-variant Variants.
Copyright (c) 2014-2015 National Marrow Donor Program (NMDP)
This library is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation; either version 3 of the License, or (at
your option) any later version.
This library is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; with out even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
License for more details.
You should have received a copy of the GNU Lesser General Public License
along with this library; if not, write to the Free Software Foundation,
Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
> http://www.gnu.org/licenses/lgpl.html
*/
package org.nmdp.ngs.variant.vcf;
import static com.google.common.base.Preconditions.checkNotNull;
import java.net.URL;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.IOException;
import com.google.common.base.Charsets;
import com.google.common.io.Resources;
/**
* VCF reader.
*/
public final class VcfReader {
/**
* Private no-arg constructor.
*/
private VcfReader() {
// empty
}
// todo: think about Strictness; none vs. research vs. clinical
// callback methods
/**
* Parse the specified readable.
*
* @param readable readable to parse, must not be null
* @param listener low-level event based parser callback, must not be null
* @throws IOException if an I/O error occurs
*/
public static void parse(final Readable readable, final VcfParseListener listener) throws IOException {
VcfParser.parse(readable, listener);
}
/**
* Stream the specified readable.
*
* @param readable readable to stream, must not be null
* @param listener event based reader callback, must not be null
* @throws IOException if an I/O error occurs
*/
public static void stream(final Readable readable, final VcfStreamListener listener) throws IOException {
StreamingVcfParser.stream(readable, listener);
}
// collect methods
/**
* Read the VCF header from the specified readable.
*
* @param readable readable to read from, must not be null
* @return the VCF header read from the specified readable
* @throws IOException if an I/O error occurs
*/
public static VcfHeader header(final Readable readable) throws IOException {
return VcfHeaderParser.header(readable);
}
/**
* Read zero or more VCF samples from the specified readable.
*
* @param readable readable to read from, must not be null
* @return zero or more VCF samples read from the specified readable
* @throws IOException if an I/O error occurs
*/
public static Iterable samples(final Readable readable) throws IOException {
return VcfSampleParser.samples(readable);
}
/**
* Read zero or more VCF records from the specified readable.
*
* @param readable readable to read from, must not be null
* @return zero or more VCF records read from the specified readable
* @throws IOException if an I/O error occurs
*/
public static Iterable records(final Readable readable) throws IOException {
return VcfRecordParser.records(readable);
}
// convenience methods
/**
* Read the VCF header from the specified file.
*
* @param file file to read from, must not be null
* @return the VCF header read from the specified file
* @throws IOException if an I/O error occurs
*/
public static VcfHeader header(final File file) throws IOException {
checkNotNull(file);
// could also use Files.asCharSource(file, Charsets.UTF_8).openBufferedStream()
try (BufferedReader reader = new BufferedReader(new FileReader(file))) {
return header(reader);
}
}
/**
* Read the VCF header from the specified URL.
*
* @param url URL to read from, must not be null
* @return the VCF header read from the specified URL
* @throws IOException if an I/O error occurs
*/
public static VcfHeader header(final URL url) throws IOException {
checkNotNull(url);
try (BufferedReader reader = Resources.asCharSource(url, Charsets.UTF_8).openBufferedStream()) {
return header(reader);
}
}
/**
* Read the VCF header from the specified input stream.
*
* @param inputStream input stream to read from, must not be null
* @return the VCF header read from the specified input stream
* @throws IOException if an I/O error occurs
*/
public static VcfHeader header(final InputStream inputStream) throws IOException {
checkNotNull(inputStream);
try (BufferedReader reader = new BufferedReader(new InputStreamReader(inputStream))) {
return header(reader);
}
}
/**
* Read zero or more VCF samples from the specified file.
*
* @param file file to read from, must not be null
* @return zero or more VCF samples read from the specified file
* @throws IOException if an I/O error occurs
*/
public static Iterable samples(final File file) throws IOException {
checkNotNull(file);
try (BufferedReader reader = new BufferedReader(new FileReader(file))) {
return samples(reader);
}
}
/**
* Read zero or more VCF samples from the specified URL.
*
* @param url URL to read from, must not be null
* @return zero or more VCF samples read from the specified URL
* @throws IOException if an I/O error occurs
*/
public static Iterable samples(final URL url) throws IOException {
checkNotNull(url);
try (BufferedReader reader = Resources.asCharSource(url, Charsets.UTF_8).openBufferedStream()) {
return samples(reader);
}
}
/**
* Read zero or more VCF samples from the specified input stream.
*
* @param inputStream input stream to read from, must not be null
* @return zero or more VCF samples read from the specified input stream
* @throws IOException if an I/O error occurs
*/
public static Iterable samples(final InputStream inputStream) throws IOException {
checkNotNull(inputStream);
try (BufferedReader reader = new BufferedReader(new InputStreamReader(inputStream))) {
return samples(reader);
}
}
/**
* Read zero or more VCF records from the specified file.
*
* @param file file to read from, must not be null
* @return zero or more VCF records read from the specified file
* @throws IOException if an I/O error occurs
*/
public static Iterable records(final File file) throws IOException {
checkNotNull(file);
try (BufferedReader reader = new BufferedReader(new FileReader(file))) {
return records(reader);
}
}
/**
* Read zero or more VCF records from the specified URL.
*
* @param url URL to read from, must not be null
* @return zero or more VCF records read from the specified URL
* @throws IOException if an I/O error occurs
*/
public static Iterable records(final URL url) throws IOException {
checkNotNull(url);
try (BufferedReader reader = Resources.asCharSource(url, Charsets.UTF_8).openBufferedStream()) {
return records(reader);
}
}
/**
* Read zero or more VCF records from the specified input stream.
*
* @param inputStream input stream to read from, must not be null
* @return zero or more VCF records read from the specified input stream
* @throws IOException if an I/O error occurs
*/
public static Iterable records(final InputStream inputStream) throws IOException {
checkNotNull(inputStream);
try (BufferedReader reader = new BufferedReader(new InputStreamReader(inputStream))) {
return records(reader);
}
}
}
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