53 lines
1.5 KiB
Java
53 lines
1.5 KiB
Java
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package org.broadinstitute.sting.alignment;
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import net.sf.samtools.SAMRecord;
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import net.sf.samtools.SAMFileHeader;
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import java.util.List;
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import java.util.Iterator;
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/**
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* Create perfect alignments from the read to the genome represented by the given BWT / suffix array.
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*
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* @author mhanna
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* @version 0.1
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*/
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public interface Aligner {
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/**
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* Close this instance of the BWA pointer and delete its resources.
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*/
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public void close();
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/**
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* Allow the aligner to choose one alignment randomly from the pile of best alignments.
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* @param bases Bases to align.
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* @return An align
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*/
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public Alignment getBestAlignment(final byte[] bases);
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/**
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* Align the read to the reference.
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* @param read Read to align.
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* @param header Optional header to drop in place.
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* @return A list of the alignments.
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*/
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public SAMRecord align(final SAMRecord read, final SAMFileHeader header);
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/**
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* Get a iterator of alignments, batched by mapping quality.
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* @param bases List of bases.
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* @return Iterator to alignments.
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*/
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public Iterable<Alignment[]> getAllAlignments(final byte[] bases);
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/**
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* Get a iterator of aligned reads, batched by mapping quality.
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* @param read Read to align.
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* @param newHeader Optional new header to use when aligning the read. If present, it must be null.
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* @return Iterator to alignments.
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*/
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public Iterable<SAMRecord[]> alignAll(final SAMRecord read, final SAMFileHeader newHeader);
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}
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