gatk-3.8/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java

/*
 * Copyright (c) 2010, The Broad Institute
 *
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
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 * copies of the Software, and to permit persons to whom the
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 *
 * 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,
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 * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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package org.broadinstitute.sting.utils.pileup;

import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.gatk.iterators.IterableIterator;
import net.sf.samtools.SAMRecord;

import java.util.List;
import java.util.Collection;

/**
 * A data retrieval interface for accessing parts of the pileup.
 *
 * @author mhanna
 * @version 0.1
 */
public interface ReadBackedPileup extends Iterable<PileupElement> {
    /**
     * Returns a new ReadBackedPileup that is free of deletion spanning reads in this pileup.  Note that this
     * does not copy the data, so both ReadBackedPileups should not be changed.  Doesn't make an unnecessary copy
     * of the pileup (just returns this) if there are no deletions in the pileup.
     *
     * @return
     */
    public ReadBackedPileup getPileupWithoutDeletions();

    /**
     * Returns a new ReadBackedPileup where only one read from an overlapping read
     * pair is retained.  If the two reads in question disagree to their basecall,
     * neither read is retained.  If they agree on the base, the read with the higher
     * quality observation is retained
     *
     * @return the newly filtered pileup
     */
    public ReadBackedPileup getOverlappingFragmentFilteredPileup();

    /**
     * Returns a new ReadBackedPileup that is free of mapping quality zero reads in this pileup.  Note that this
     * does not copy the data, so both ReadBackedPileups should not be changed.  Doesn't make an unnecessary copy
     * of the pileup (just returns this) if there are no MQ0 reads in the pileup.
     *
     * @return
     */
    public ReadBackedPileup getPileupWithoutMappingQualityZeroReads();

    /** Returns subset of this pileup that contains only bases with quality >= minBaseQ, coming from
     * reads with mapping qualities >= minMapQ. This method allocates and returns a new instance of ReadBackedPileup.
     * @param minBaseQ
     * @param minMapQ
     * @return
     */
    public ReadBackedPileup getBaseAndMappingFilteredPileup( int minBaseQ, int minMapQ );

    /** Returns subset of this pileup that contains only bases with quality >= minBaseQ.
     * This method allocates and returns a new instance of ReadBackedPileup.
     * @param minBaseQ
     * @return
     */
    public ReadBackedPileup getBaseFilteredPileup( int minBaseQ );

    /** Returns subset of this pileup that contains only bases coming from reads with mapping quality >= minMapQ.
     * This method allocates and returns a new instance of ReadBackedPileup.
     * @param minMapQ
     * @return
     */
    public ReadBackedPileup getMappingFilteredPileup( int minMapQ );

    /**
     * Returns a pileup randomly downsampled to the desiredCoverage.
     *
     * @param desiredCoverage
     * @return
     */
    public ReadBackedPileup getDownsampledPileup(int desiredCoverage);

    /**
     * Returns true if any reads have been filtered out of the pileup due to excess DoC.
     * @return True if reads have been filtered out.  False otherwise.
     */
    public boolean hasPileupBeenDownsampled();

    /**
     * Gets a collection of all the samples stored in this pileup.
     * @return Collection of samples in this pileup.
     */
    public Collection<String> getSamples();

    /**
     * Gets the particular subset of this pileup with the given sample name.
     * @param sampleName Name of the sample to use.
     * @return A subset of this pileup containing only reads with the given sample.
     */
    public ReadBackedPileup getPileupForSample(String sampleName);
    
    // todo -- delete or make private
    public IterableIterator<ExtendedPileupElement> extendedForeachIterator();    

    /**
     * Simple useful routine to count the number of deletion bases in this pileup
     *
     * @return
     */
    public int getNumberOfDeletions();

    public int getNumberOfMappingQualityZeroReads();

    /**
     * @return the number of elements in this pileup
     */
    public int size();

    /**
     * @return the location of this pileup
     */
    public GenomeLoc getLocation();

    /**
     * Get counts of A, C, G, T in order, which returns a int[4] vector with counts according
     * to BaseUtils.simpleBaseToBaseIndex for each base.
     *
     * @return
     */
    public int[] getBaseCounts();

    /**
     * Somewhat expensive routine that returns true if any base in the pileup has secondary bases annotated
     * @return
     */
    public boolean hasSecondaryBases();

    public String getPileupString(Character ref);

    /**
     * Returns a list of the reads in this pileup. Note this call costs O(n) and allocates fresh lists each time
     * @return
     */
    public List<SAMRecord> getReads();

    /**
     * Returns a list of the offsets in this pileup. Note this call costs O(n) and allocates fresh lists each time
     * @return
     */
    public List<Integer> getOffsets();

    /**
     * Returns an array of the bases in this pileup. Note this call costs O(n) and allocates fresh array each time
     * @return
     */
    public byte[] getBases();

    /**
     * Returns an array of the secondary bases in this pileup. Note this call costs O(n) and allocates fresh array each time
     * @return
     */
    public byte[] getSecondaryBases();

    /**
    * Returns an array of the quals in this pileup. Note this call costs O(n) and allocates fresh array each time
    * @return
    */
    public byte[] getQuals();

    /**
     * Get an array of the mapping qualities
     * @return
     */
    public byte[] getMappingQuals();
}