179 lines
7.7 KiB
Java
179 lines
7.7 KiB
Java
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package org.broadinstitute.sting.playground.indels;
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import net.sf.samtools.SAMRecord;
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import net.sf.samtools.Cigar;
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import net.sf.samtools.CigarElement;
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import edu.mit.broad.picard.reference.ReferenceSequence;
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import org.broadinstitute.sting.playground.utils.CountedObject;
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import java.util.*;
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/**
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* Created by IntelliJ IDEA.
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* User: asivache
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* Date: Mar 25, 2009
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* Time: 12:15:38 AM
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* To change this template use File | Settings | File Templates.
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*/
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public class AlignmentUtils {
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/** Computes number of mismatches in the read alignment to the refence <code>ref</code>
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* specified in the record <code>r</code>. Indels are completely <i>ignored</i> by this method:
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* only base mismatches in the alignment segments where both sequences are present are counted.
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* @param r
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* @param ref
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* @return
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*/
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public static int numMismatches(SAMRecord r, ReferenceSequence ref) {
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if ( r.getReadUnmappedFlag() ) return 1000000;
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int i_ref = r.getAlignmentStart()-1; // position on the ref
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int i_read = 0; // position on the read
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int mm_count = 0; // number of mismatches
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Cigar c = r.getCigar();
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for ( int k = 0 ; k < c.numCigarElements() ; k++ ) {
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CigarElement ce = c.getCigarElement(k);
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switch( ce.getOperator() ) {
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case M:
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for ( int l = 0 ; l < ce.getLength() ; l++, i_ref++, i_read++ ) {
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if ( Character.toUpperCase(r.getReadString().charAt(i_read) ) != 'N' ) continue; // do not count N's ?
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if ( Character.toUpperCase(r.getReadString().charAt(i_read) ) !=
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Character.toUpperCase((char)ref.getBases()[i_ref]) ) mm_count++;
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}
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break;
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case I: i_read += ce.getLength(); break;
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case D: i_ref += ce.getLength(); break;
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default: throw new RuntimeException("Unrecognized cigar element");
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}
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}
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return mm_count;
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}
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public static int numMismatches(SAMRecord r, String ref) {
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if ( r.getReadUnmappedFlag() ) return 1000000;
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int i_ref = r.getAlignmentStart()-1; // position on the ref
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int i_read = 0; // position on the read
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int mm_count = 0; // number of mismatches
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Cigar c = r.getCigar();
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for ( int k = 0 ; k < c.numCigarElements() ; k++ ) {
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CigarElement ce = c.getCigarElement(k);
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switch( ce.getOperator() ) {
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case M:
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for ( int l = 0 ; l < ce.getLength() ; l++, i_ref++, i_read++ ) {
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if ( Character.toUpperCase(r.getReadString().charAt(i_read) ) == 'N' ) continue; // do not count N's ?
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if ( Character.toUpperCase(r.getReadString().charAt(i_read) ) !=
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Character.toUpperCase(ref.charAt(i_ref)) ) mm_count++;
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}
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break;
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case I: i_read += ce.getLength(); break;
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case D: i_ref += ce.getLength(); break;
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default: throw new RuntimeException("Unrecognized cigar element");
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}
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}
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return mm_count;
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}
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/** Reads through the alignment cigar and returns all indels found in the alignment as a collection
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* of Indel objects.
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* @param c
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* @param start
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* @return
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*/
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public static Collection<Indel> extractIndels(final Cigar c, final int start) {
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//
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// firstpos,lastpos span of the indel will be interpreted as follows:
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// any alignment that ends strictly before firstpos or starts strictly after lastpos
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// on the *reference* (not inclusive!) does not overlap with an indel; in the case of
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// insertion it will result in firstpos > lastpos!
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// lastpos
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// | firstpos
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// | |
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// v v
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// ---------III----- Ref Insertion: bases I are not in the ref; any alignment that starts
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// after lastpos or ends before firstpos *on the reference*
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// is completely over the reference bases to the right or to
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// the left, respectively, of the insertion site
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//
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// firstpos
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// | lastpos
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// | |
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// v v
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//------------------ Ref Deletion: any alignment that ends before firstpos or starts after lastpos
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// -----DDD--- alignment on the reference does not overlap with the deletion
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int runninglength = start; // position on the original reference; start = alignment start position
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List<Indel> indels = new ArrayList<Indel>(4);
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if ( c.numCigarElements() <= 1 ) return indels; // most of the reads have no indels, save a few cycles by returning early
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for ( int i = 0 ; i < c.numCigarElements() ; i++ ) {
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final CigarElement ce = c.getCigarElement(i);
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Indel curr_indel = null;
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switch(ce.getOperator()) {
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case I: curr_indel = new Indel(runninglength, ce.getLength(), Indel.IndelType.I); break;
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case D: curr_indel = new Indel(runninglength, ce.getLength(), Indel.IndelType.D);
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runninglength += ce.getLength();
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break;
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case M: runninglength += ce.getLength(); break; // advance along the gapless block in the alignment
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default :
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throw new IllegalArgumentException("Unexpected operator in cigar string");
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}
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if ( curr_indel == null ) continue; // element was not an indel, go grab next element...
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indels.add(curr_indel); // this is a new indel. Add it.
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} // end for loop over all alignment cigar elements
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return indels;
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} // end extractIndels() method
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/** Reads through the alignment specified in the record and returns all indels found in the alignment as a collection
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* of Indel objects. If read is not mapped, silently returns an empty collection.
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* @param r
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* @return
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*/
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public static Collection<Indel> extractIndels(SAMRecord r) {
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if ( r.getReadUnmappedFlag() ) return new ArrayList<Indel>();
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return extractIndels(r.getCigar(), r.getAlignmentStart());
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}
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/** Extracts indels from the specified record (@see #extractIndels()) and updates the provided tree object.
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* Multiple occurences of the same indel (i.e. with support from multiple reads) will be grouped together
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* in one counted object held by the set.
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*
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* @param r
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* @param t
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*/
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public static void collectAndCountIndels(SAMRecord r, TreeSet<CountedObject<Indel> > t) {
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Collection<Indel> indels = AlignmentUtils.extractIndels(r);
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for ( Indel ind : indels ) {
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CountedObject<Indel> ci = new CountedObject<Indel>(ind);
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CountedObject<Indel> found = t.floor(ci);
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if ( ci.equals( found ) ) found.increment(); // we did find our indel, advance the counter
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else t.add(ci); // this is a new indel. Add it.
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}
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}
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public static String toString(Cigar cig) {
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StringBuilder b = new StringBuilder();
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for ( int i = 0 ; i < cig.numCigarElements() ; i++ ) {
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char c='?';
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switch ( cig.getCigarElement(i).getOperator() ) {
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case M : c = 'M'; break;
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case D : c = 'D'; break;
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case I : c = 'I'; break;
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}
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b.append(c);
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b.append(cig.getCigarElement(i).getLength());
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}
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return b.toString();
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}
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}
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