AbstractSAMFilterModule.java

/*
 *                  Eoulsan development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public License version 2.1 or
 * later and CeCILL-C. This should be distributed with the code.
 * If you do not have a copy, see:
 *
 *      http://www.gnu.org/licenses/lgpl-2.1.txt
 *      http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.txt
 *
 * Copyright for this code is held jointly by the Genomic platform
 * of the Institut de Biologie de l'École normale supérieure and
 * the individual authors. These should be listed in @author doc
 * comments.
 *
 * For more information on the Eoulsan project and its aims,
 * or to join the Eoulsan Google group, visit the home page
 * at:
 *
 *      http://outils.genomique.biologie.ens.fr/eoulsan
 *
 */

package fr.ens.biologie.genomique.eoulsan.modules.mapping;

import static fr.ens.biologie.genomique.eoulsan.CommonHadoop.HADOOP_REDUCER_TASK_COUNT_PARAMETER_NAME;
import static fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder.singleInputPort;
import static fr.ens.biologie.genomique.eoulsan.core.OutputPortsBuilder.singleOutputPort;
import static fr.ens.biologie.genomique.eoulsan.data.DataFormats.MAPPER_RESULTS_SAM;

import java.util.Map;
import java.util.Set;

import fr.ens.biologie.genomique.eoulsan.EoulsanException;
import fr.ens.biologie.genomique.eoulsan.Globals;
import fr.ens.biologie.genomique.eoulsan.bio.alignmentsfilters.MultiReadAlignmentsFilter;
import fr.ens.biologie.genomique.eoulsan.bio.alignmentsfilters.MultiReadAlignmentsFilterBuilder;
import fr.ens.biologie.genomique.eoulsan.bio.alignmentsfilters.QualityReadAlignmentsFilter;
import fr.ens.biologie.genomique.eoulsan.core.InputPorts;
import fr.ens.biologie.genomique.eoulsan.core.Modules;
import fr.ens.biologie.genomique.eoulsan.core.OutputPorts;
import fr.ens.biologie.genomique.eoulsan.core.Parameter;
import fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext;
import fr.ens.biologie.genomique.eoulsan.core.Version;
import fr.ens.biologie.genomique.eoulsan.modules.AbstractModule;
import fr.ens.biologie.genomique.eoulsan.util.ReporterIncrementer;

/**
 * This class define an abstract module for alignments filtering.
 * @since 1.0
 * @author Laurent Jourdren
 * @author Claire Wallon
 */
public abstract class AbstractSAMFilterModule extends AbstractModule {

  private static final String MODULE_NAME = "filtersam";

  protected static final String COUNTER_GROUP = "sam_filtering";

  private Map<String, String> alignmentsFiltersParameters;
  private int reducerTaskCount = -1;

  /**
   * Get the parameters of the alignments filter.
   * @return a map with all the parameters of the filter
   */
  protected Map<String, String> getAlignmentsFilterParameters() {

    return this.alignmentsFiltersParameters;
  }

  /**
   * Get the reducer task count.
   * @return the reducer task count
   */
  protected int getReducerTaskCount() {

    return this.reducerTaskCount;
  }

  //
  // Module methods
  //

  @Override
  public String getName() {

    return MODULE_NAME;
  }

  @Override
  public String getDescription() {

    return "This module filters sam files.";
  }

  @Override
  public Version getVersion() {

    return Globals.APP_VERSION;
  }

  @Override
  public InputPorts getInputPorts() {

    return singleInputPort(MAPPER_RESULTS_SAM);
  }

  @Override
  public OutputPorts getOutputPorts() {
    return singleOutputPort(MAPPER_RESULTS_SAM);
  }

  @Override
  public void configure(final StepConfigurationContext context,
      final Set<Parameter> stepParameters) throws EoulsanException {

    final MultiReadAlignmentsFilterBuilder filterBuilder =
        new MultiReadAlignmentsFilterBuilder();

    for (Parameter p : stepParameters) {

      // Check if the parameter is deprecated
      checkDeprecatedParameter(context, p);

      switch (p.getName()) {

      case HADOOP_REDUCER_TASK_COUNT_PARAMETER_NAME:
        this.reducerTaskCount = p.getIntValueGreaterOrEqualsTo(1);
        break;

      default:

        filterBuilder.addParameter(p.getName(), p.getStringValue());
        break;
      }
    }

    // Force parameter checking
    filterBuilder.getAlignmentsFilter();

    this.alignmentsFiltersParameters = filterBuilder.getParameters();
  }

  //
  // Other methods
  //

  /**
   * Check deprecated parameters.
   * @param context configuration context
   * @param parameter the parameter to check
   * @throws EoulsanException if the parameter is no more supported
   */
  static void checkDeprecatedParameter(final StepConfigurationContext context,
      final Parameter parameter) throws EoulsanException {

    if (parameter == null) {
      return;
    }

    switch (parameter.getName()) {

    case "mappingqualitythreshold":
    case "mappingquality":
    case "mappingquality.threshold":
      Modules.renamedParameter(context, parameter,
          QualityReadAlignmentsFilter.FILTER_NAME + ".threshold", true);

    default:
      break;
    }
  }

  /**
   * Get the ReadAlignmentsFilter object.
   * @param incrementer incrementer to use
   * @param counterGroup counter group for the incrementer
   * @return a new ReadAlignmentsFilter object
   * @throws EoulsanException if an error occurs while initialize one of the
   *           filter
   */
  protected MultiReadAlignmentsFilter getAlignmentsFilter(
      final ReporterIncrementer incrementer, final String counterGroup)
      throws EoulsanException {

    // As filters are not thread safe, create a new
    // MultiReadAlignmentsFilterBuilder
    // with a new instance of each filter
    return new MultiReadAlignmentsFilterBuilder(
        this.alignmentsFiltersParameters).getAlignmentsFilter(incrementer,
            counterGroup);
  }

}