Java tutorial
// Copyright (c) 2013 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: 2013-06-18 10:26:55 package org.seqdoop.hadoop_bam.cli.plugins; import hbparquet.hadoop.util.ContextUtil; import java.io.IOException; import java.util.ArrayList; import java.util.Iterator; import java.util.List; import htsjdk.samtools.SamPairUtil; import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMFileReader; import htsjdk.samtools.ValidationStringency; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.Path; import org.apache.hadoop.io.LongWritable; import org.apache.hadoop.io.Text; import org.apache.hadoop.mapreduce.Job; import org.apache.hadoop.mapreduce.Mapper; import org.apache.hadoop.mapreduce.Reducer; import org.apache.hadoop.mapreduce.lib.input.FileInputFormat; import org.apache.hadoop.mapreduce.lib.output.FileOutputFormat; import org.apache.hadoop.mapreduce.lib.partition.InputSampler; import org.apache.hadoop.mapreduce.lib.partition.TotalOrderPartitioner; import org.seqdoop.hadoop_bam.AnySAMInputFormat; import org.seqdoop.hadoop_bam.SAMRecordWritable; import org.seqdoop.hadoop_bam.cli.CLIMRBAMPlugin; import org.seqdoop.hadoop_bam.cli.CLIMergingAnySAMOutputFormat; import org.seqdoop.hadoop_bam.cli.Utils; import org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser; import org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.Option.BooleanOption; import org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.Option.StringOption; import org.seqdoop.hadoop_bam.util.Pair; import org.seqdoop.hadoop_bam.util.SAMHeaderReader; import org.seqdoop.hadoop_bam.util.Timer; public final class FixMate extends CLIMRBAMPlugin { private static final List<Pair<CmdLineParser.Option, String>> optionDescs = new ArrayList<Pair<CmdLineParser.Option, String>>(); private static final CmdLineParser.Option sortOpt = new BooleanOption('s', "sort"), noCombinerOpt = new BooleanOption('C', "no-combine"), stringencyOpt = new StringOption("validation-stringency=S"); public FixMate() { super("fixmate", "BAM and SAM mate information fixing", "1.1", "WORKDIR INPATH [INPATH...]", optionDescs, "Merges together the BAM and SAM files (the INPATHs), while filling " + "in mate information, all distributed with Hadoop MapReduce. Output " + "parts are placed in WORKDIR in, by default, headerless and " + "unterminated BAM format." + "\n\n" + "When more than two primary reads with the same name exist in the " + "inputs, the result is unpredictable. Without using the -C option, " + "it is possible that multiple reads are mated to the same read."); } static { optionDescs.add( new Pair<CmdLineParser.Option, String>(sortOpt, "also globally sort the result by query name")); optionDescs.add( new Pair<CmdLineParser.Option, String>(noCombinerOpt, "don't use a combiner; less efficient, but " + "guarantees validity of results when there are " + "multiple possible pairings")); optionDescs.add(new Pair<CmdLineParser.Option, String>(stringencyOpt, Utils.getStringencyOptHelp())); } @Override protected int run(CmdLineParser parser) { final List<String> args = parser.getRemainingArgs(); if (args.isEmpty()) { System.err.println("fixmate :: WORKDIR not given."); return 3; } if (args.size() == 1) { System.err.println("fixmate :: INPATH not given."); return 3; } if (!cacheAndSetProperties(parser)) return 3; final ValidationStringency stringency = Utils.toStringency( parser.getOptionValue(stringencyOpt, ValidationStringency.DEFAULT_STRINGENCY.toString()), "fixmate"); if (stringency == null) return 3; Path wrkDir = new Path(args.get(0)); final List<String> strInputs = args.subList(1, args.size()); final List<Path> inputs = new ArrayList<Path>(strInputs.size()); for (final String in : strInputs) inputs.add(new Path(in)); final Configuration conf = getConf(); // Used by Utils.getMergeableWorkFile() to name the output files. final String intermediateOutName = (outPath == null ? inputs.get(0) : outPath).getName(); conf.set(Utils.WORK_FILENAME_PROPERTY, intermediateOutName); if (stringency != null) conf.set(SAMHeaderReader.VALIDATION_STRINGENCY_PROPERTY, stringency.toString()); final boolean globalSort = parser.getBoolean(sortOpt); if (globalSort) Utils.setHeaderMergerSortOrder(conf, SAMFileHeader.SortOrder.queryname); conf.setStrings(Utils.HEADERMERGER_INPUTS_PROPERTY, strInputs.toArray(new String[0])); final Timer t = new Timer(); try { // Required for path ".", for example. wrkDir = wrkDir.getFileSystem(conf).makeQualified(wrkDir); if (globalSort) Utils.configureSampling(wrkDir, intermediateOutName, conf); final Job job = new Job(conf); job.setJarByClass(FixMate.class); job.setMapperClass(FixMateMapper.class); job.setReducerClass(FixMateReducer.class); if (!parser.getBoolean(noCombinerOpt)) job.setCombinerClass(FixMateReducer.class); job.setOutputKeyClass(Text.class); job.setOutputValueClass(SAMRecordWritable.class); job.setInputFormatClass(AnySAMInputFormat.class); job.setOutputFormatClass(CLIMergingAnySAMOutputFormat.class); for (final Path in : inputs) FileInputFormat.addInputPath(job, in); FileOutputFormat.setOutputPath(job, wrkDir); if (globalSort) { job.setPartitionerClass(TotalOrderPartitioner.class); System.out.println("fixmate :: Sampling..."); t.start(); InputSampler.<LongWritable, SAMRecordWritable>writePartitionFile(job, new InputSampler.RandomSampler<LongWritable, SAMRecordWritable>(0.01, 10000, Math.max(100, reduceTasks))); System.out.printf("fixmate :: Sampling complete in %d.%03d s.\n", t.stopS(), t.fms()); } job.submit(); System.out.println("fixmate :: Waiting for job completion..."); t.start(); if (!job.waitForCompletion(verbose)) { System.err.println("fixmate :: Job failed."); return 4; } System.out.printf("fixmate :: Job complete in %d.%03d s.\n", t.stopS(), t.fms()); } catch (IOException e) { System.err.printf("fixmate :: Hadoop error: %s\n", e); return 4; } catch (ClassNotFoundException e) { throw new RuntimeException(e); } catch (InterruptedException e) { throw new RuntimeException(e); } if (outPath != null) try { Utils.mergeSAMInto(outPath, wrkDir, "", "", samFormat, conf, "fixmate"); } catch (IOException e) { System.err.printf("fixmate :: Output merging failed: %s\n", e); return 5; } return 0; } } final class FixMateMapper extends Mapper<LongWritable, SAMRecordWritable, Text, SAMRecordWritable> { @Override protected void map(LongWritable ignored, SAMRecordWritable wrec, Mapper<LongWritable, SAMRecordWritable, Text, SAMRecordWritable>.Context ctx) throws InterruptedException, IOException { Utils.correctSAMRecordForMerging(wrec.get(), ContextUtil.getConfiguration(ctx)); ctx.write(new Text(wrec.get().getReadName()), wrec); } } // Because this can be used as a combiner, we output the key instead of a // NullWritable. final class FixMateReducer extends Reducer<Text, SAMRecordWritable, Text, SAMRecordWritable> { private final SAMRecordWritable wrec = new SAMRecordWritable(); @Override protected void reduce(Text key, Iterable<SAMRecordWritable> records, Reducer<Text, SAMRecordWritable, Text, SAMRecordWritable>.Context ctx) throws IOException, InterruptedException { // Non-primary records are simply written out, but as long as we can find // two primaries, pair them up. final SAMFileHeader header = Utils.getSAMHeaderMerger(ContextUtil.getConfiguration(ctx)).getMergedHeader(); final Iterator<SAMRecordWritable> it = records.iterator(); while (it.hasNext()) { SAMRecordWritable a = it.next(); if (a.get().getNotPrimaryAlignmentFlag()) { ctx.write(key, a); continue; } // Cache the record since the iterator does its own caching, meaning // that after another it.next() we would have a == b. wrec.set(a.get()); a = wrec; SAMRecordWritable b = null; while (it.hasNext()) { b = it.next(); if (!b.get().getNotPrimaryAlignmentFlag()) break; ctx.write(key, b); } if (b == null) { // No more primaries, so just write the unpaired one as-is. ctx.write(key, a); break; } a.get().setHeader(header); b.get().setHeader(header); SamPairUtil.setMateInfo(a.get(), b.get(), header); ctx.write(key, a); ctx.write(key, b); } } }