// Copyright (c) 2010 Aalto University // // 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. // File created: 2012-02-23 12:42:49 package org.seqdoop.hadoop_bam; import java.io.IOException; import java.io.OutputStream; import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMRecord; import htsjdk.samtools.SAMTextWriter; import org.apache.hadoop.fs.Path; import org.apache.hadoop.mapreduce.RecordWriter; import org.apache.hadoop.mapreduce.TaskAttemptContext; import org.seqdoop.hadoop_bam.util.SAMHeaderReader; /** A base {@link RecordWriter} for SAM records. * * <p>Handles the output stream, writing the header if requested, and provides * the {@link #writeAlignment} function for subclasses.</p> */ public abstract class SAMRecordWriter<K> extends RecordWriter<K,SAMRecordWritable> { private SAMTextWriter writer; private SAMFileHeader header; /** A SAMFileHeader is read from the input Path. */ public SAMRecordWriter( Path output, Path input, boolean writeHeader, TaskAttemptContext ctx) throws IOException { init( output, SAMHeaderReader.readSAMHeaderFrom(input, ctx.getConfiguration()), writeHeader, ctx); } public SAMRecordWriter( Path output, SAMFileHeader header, boolean writeHeader, TaskAttemptContext ctx) throws IOException { init( output.getFileSystem(ctx.getConfiguration()).create(output), header, writeHeader); } public SAMRecordWriter( OutputStream output, SAMFileHeader header, boolean writeHeader) throws IOException { init(output, header, writeHeader); } private void init( Path output, SAMFileHeader header, boolean writeHeader, TaskAttemptContext ctx) throws IOException { init( output.getFileSystem(ctx.getConfiguration()).create(output), header, writeHeader); } private void init( OutputStream output, SAMFileHeader header, boolean writeHeader) throws IOException { this.header = header; writer = new SAMTextWriter(output); writer.setSortOrder(header.getSortOrder(), false); if (writeHeader) writer.setHeader(header); } @Override public void close(TaskAttemptContext ctx) { writer.close(); } protected void writeAlignment(final SAMRecord rec) { rec.setHeader(header); writer.writeAlignment(rec); } }