Java tutorial
// Copyright (C) 2011-2012 CRS4. // // This file is part of Seal. // // Seal is free software: you can redistribute it and/or modify it // under the terms of the GNU General Public License as published by the Free // Software Foundation, either version 3 of the License, or (at your option) // any later version. // // Seal is distributed in the hope that it will be useful, but // WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY // or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License // for more details. // // You should have received a copy of the GNU General Public License along // with Seal. If not, see <http://www.gnu.org/licenses/>. package it.crs4.seal.prq; import it.crs4.seal.common.SealToolParser; import it.crs4.seal.common.ClusterUtils; import it.crs4.seal.common.Utils; import java.util.ArrayList; import java.io.IOException; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.Path; import org.apache.commons.cli.*; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; public class PrqOptionParser extends SealToolParser { private static final Log LOG = LogFactory.getLog(PairReadsQSeq.class); public static final String ConfigSection = "Prq"; public static final String InputFormatDefault = "qseq"; public static final String OLD_INPUT_FORMAT_CONF = "seal.prq.input-format"; public static final int DefaultMinBasesThreshold = 30; public static final String MinBasesThresholdConfigName = "seal.prq.min-bases-per-read"; public static final String MinBasesThresholdConfigName_deprecated = "bl.prq.min-bases-per-read"; public static final boolean DropFailedFilterDefault = true; public static final String DropFailedFilterConfigName = "seal.prq.drop-failed-filter"; public static final String DropFailedFilterConfigName_deprecated = "bl.prq.drop-failed-filter"; public static final boolean WarningOnlyIfUnpairedDefault = false; public static final String WarningOnlyIfUnpairedConfigName = "seal.prq.warning-only-if-unpaired"; public static final String WarningOnlyIfUnpairedConfigName_deprecated = "bl.prq.warning-only-if-unpaired"; public static final int NumReadsExpectedDefault = 2; public static final String NumReadsExpectedConfigName = "seal.prq.num-reads"; private Option opt_traditionalIds; private boolean makeTraditionalIds = false; private Option opt_numReads; private int numReads = NumReadsExpectedDefault; @SuppressWarnings("static") // for OptionBuilder public PrqOptionParser() { super(ConfigSection, "seal_prq"); this.setMinReduceTasks(1); this.setAcceptedInputFormats(new String[] { "qseq", "fastq" }); this.setAcceptedOutputFormats(new String[] { "prq" }); opt_traditionalIds = OptionBuilder .withDescription("Create traditional read ids rather than new Illumina fastq-style read ids.") .withLongOpt("traditional-ids").create("t"); options.addOption(opt_traditionalIds); opt_numReads = OptionBuilder.withDescription("Number of reads expected per template.").hasArg() .withLongOpt("num-reads").create("nr"); options.addOption(opt_numReads); } @Override protected CommandLine parseOptions(Configuration conf, String[] args) throws IOException, ParseException { conf.setInt(MinBasesThresholdConfigName, DefaultMinBasesThreshold); conf.setBoolean(DropFailedFilterConfigName, DropFailedFilterDefault); conf.setBoolean(WarningOnlyIfUnpairedConfigName, WarningOnlyIfUnpairedDefault); conf.setInt(NumReadsExpectedConfigName, NumReadsExpectedDefault); CommandLine line = super.parseOptions(conf, args); /* **** handle deprected properties **** */ if (conf.get(PrqOptionParser.OLD_INPUT_FORMAT_CONF) != null) { throw new ParseException("The property " + PrqOptionParser.OLD_INPUT_FORMAT_CONF + " is no longer supported.\n" + "Please use the command line option --input-format instead."); } Utils.checkDeprecatedProp(conf, LOG, MinBasesThresholdConfigName_deprecated, MinBasesThresholdConfigName); Utils.checkDeprecatedProp(conf, LOG, DropFailedFilterConfigName_deprecated, DropFailedFilterConfigName); Utils.checkDeprecatedProp(conf, LOG, WarningOnlyIfUnpairedConfigName_deprecated, WarningOnlyIfUnpairedConfigName); // Let the deprecated properties override the new ones, unless the new ones have a non-default value. // If the new property has a non-default value, it must have been set by the user. // If, on the other hand, the deprecated property has a value, it must have been set by the user since // we're not setting them here. if (conf.get(MinBasesThresholdConfigName_deprecated) != null && conf.getInt(MinBasesThresholdConfigName, DefaultMinBasesThreshold) == DefaultMinBasesThreshold) { conf.setInt(MinBasesThresholdConfigName, conf.getInt(MinBasesThresholdConfigName_deprecated, DefaultMinBasesThreshold)); } if (conf.get(DropFailedFilterConfigName_deprecated) != null && conf.getBoolean(DropFailedFilterConfigName, DropFailedFilterDefault) == DropFailedFilterDefault) { conf.setBoolean(DropFailedFilterConfigName, conf.getBoolean(DropFailedFilterConfigName_deprecated, DropFailedFilterDefault)); } if (conf.get(WarningOnlyIfUnpairedConfigName_deprecated) != null && conf.getBoolean(WarningOnlyIfUnpairedConfigName, WarningOnlyIfUnpairedDefault) == WarningOnlyIfUnpairedDefault) { conf.setBoolean(WarningOnlyIfUnpairedConfigName, conf.getBoolean(WarningOnlyIfUnpairedConfigName_deprecated, WarningOnlyIfUnpairedDefault)); } /* **** end handle deprecated properties **** */ if (line.hasOption(opt_traditionalIds.getOpt())) conf.setBoolean(PairReadsQSeq.PRQ_CONF_TRADITIONAL_IDS, true); if (line.hasOption(opt_numReads.getOpt())) { int numReads; try { numReads = Integer.valueOf(line.getOptionValue(opt_numReads.getOpt())); if (numReads <= 0) throw new ParseException("Number of reads per fragment must be >= 0 (got " + numReads + ")"); if (numReads > 2) { throw new ParseException( "Working with more than two reads per template is not supported at the moment.\n" + "If you're interested in seeing this feature implemented contact the Seal developers."); } } catch (NumberFormatException e) { throw new ParseException(e.getMessage()); } conf.setInt(NumReadsExpectedConfigName, numReads); } // set number of reduce tasks to use conf.set(ClusterUtils.NUM_RED_TASKS_PROPERTY, String.valueOf(getNReduceTasks())); return line; } }