Package org.bdgenomics.formats.avro

Class Alignment

  • All Implemented Interfaces:
    Externalizable, Serializable, Comparable<org.apache.avro.specific.SpecificRecord>, org.apache.avro.generic.GenericContainer, org.apache.avro.generic.GenericRecord, org.apache.avro.generic.IndexedRecord, org.apache.avro.specific.SpecificRecord
    public class Alignment
extends org.apache.avro.specific.SpecificRecordBase
implements org.apache.avro.specific.SpecificRecord
    Alignment.
    See Also:
    Serialized Form

    • Field Detail

      • SCHEMA$

        public static final org.apache.avro.Schema SCHEMA$

    • Constructor Detail

      • Alignment

        public Alignment()
        Default constructor. Note that this does not initialize fields to their default values from the schema. If that is desired then one should use newBuilder().

      • Alignment

        public Alignment​(String referenceName,
                 Long start,
                 Long originalStart,
                 Long end,
                 Integer mappingQuality,
                 String readName,
                 String sequence,
                 String qualityScores,
                 String cigar,
                 String originalCigar,
                 Integer basesTrimmedFromStart,
                 Integer basesTrimmedFromEnd,
                 Boolean readPaired,
                 Boolean properPair,
                 Boolean readMapped,
                 Boolean mateMapped,
                 Boolean failedVendorQualityChecks,
                 Boolean duplicateRead,
                 Boolean readNegativeStrand,
                 Boolean mateNegativeStrand,
                 Boolean primaryAlignment,
                 Boolean secondaryAlignment,
                 Boolean supplementaryAlignment,
                 String mismatchingPositions,
                 String originalQualityScores,
                 String readGroupId,
                 String readGroupSampleId,
                 Long mateAlignmentStart,
                 String mateReferenceName,
                 Long insertSize,
                 Integer readInFragment,
                 String attributes)
        All-args constructor.
        Parameters:
        referenceName - The reference for this alignment. If the read is unaligned, this field should be null. SAM column 3 field RNAME.
        start - Start position for this alignment, in zero-based coordinate system with closed-open intervals. Should be null if the read is unaligned. SAM column 4 field POS converted to zero-based coordinate system, closed-open intervals.
        originalStart - Original start position for this alignment, before local realignment, in zero-based coordinate system with closed-open intervals. Should be null if the read is unaligned. SAM optional field reserved tag OP converted to zero-based coordinate system, closed-open intervals.
        end - End position for this alignment, in zero-based coordinate system with closed-open intervals. Should be null if the read is unaligned.
        mappingQuality - Global mapping quality for this alignment. SAM column 5 field MAPQ.
        readName - Name of the read for this alignment. This should be unique within the read group that the read is from, and can be used to identify other reads that are derived from a single fragment. SAM column 5 field QNAME.
        sequence - Sequence of the read for this alignment. If the read has been hard clipped, this may not represent all the bases in the original read. SAM column 10 field SEQ.
        qualityScores - Per-base quality scores of the read for this alignment. If the read has been hard clipped, this may not represent all the bases in the original read. Additionally, if the error scores have been recalibrated, this field will not contain the original base quality scores. SAM column 11 field QUAL.
        cigar - Compact Ideosyncratic Gapped Alignment Report (CIGAR) string that describes the local alignment of the read for this alignment. SAM column 6 field CIGAR. Contains {length, operator} pairs for all contiguous alignment operations. The operators include: M, ALIGNMENT_MATCH: An alignment match indicates that a sequence can be aligned to the reference without evidence of an INDEL. Unlike the SEQUENCE_MATCH and SEQUENCE_MISMATCH operators, the ALIGNMENT_MATCH operator does not indicate whether the reference and read sequences are an exact match. I, INSERT: The insert operator indicates that the read contains evidence of bases being inserted into the reference. D, DELETE: The delete operator indicates that the read contains evidence of bases being deleted from the reference. N, SKIP: The skip operator indicates that this read skips a long segment of the reference, but the bases have not been deleted. This operator is commonly used when working with RNA-seq data, where reads may skip long segments of the reference between exons. S, CLIP_SOFT: The soft clip operator indicates that bases at the start/end of a read have not been considered during alignment. This may occur if the majority of a read maps, except for low quality bases at the start/end of a read. Bases that are soft clipped will still be stored in the read. H, CLIP_HARD: The hard clip operator indicates that bases at the start/end of a read have been omitted from this alignment. This may occur if this linear alignment is part of a chimeric alignment, or if the read has been trimmed (e.g., during error correction, or to trim poly-A tails for RNA-seq). P, PAD: The pad operator indicates that there is padding in an alignment. =, SEQUENCE_MATCH: This operator indicates that this portion of the aligned sequence exactly matches the reference (e.g., all bases are equal to the reference bases). X, SEQUENCE_MISMATCH: This operator indicates that this portion of the aligned sequence is an alignment match to the reference, but a sequence mismatch (e.g., the bases are not equal to the reference). This can indicate a SNP or a read error.
        originalCigar - Original CIGAR string that describes the local alignment of the read for this alignment, before local realignment. SAM optional field reserved tag OC.
        basesTrimmedFromStart - Number of bases in the read for this alignment that have been trimmed from the start of the read. By default, this is equal to 0. If the value is non-zero, that means that the start of the read has been hard-clipped.
        basesTrimmedFromEnd - Number of bases in the read for this alignment that have been trimmed from the end of the read. By default, this is equal to 0. If the value is non-zero, that means that the end of the read has been hard-clipped.
        readPaired - True if the read for this alignment has a mate. Defaults to false.
        properPair - True if the read for this alignment and its mate are a proper pair. Defaults to false.
        readMapped - True if the read for this alignment has been mapped. Defaults to false.
        mateMapped - True if the mate of the read for this alignment has been mapped. Defaults to false.
        failedVendorQualityChecks - True if the read for this alignent failed vendor quality checks. Defaults to false.
        duplicateRead - True if the read for this alignment has been marked as duplicate. Defaults to false.
        readNegativeStrand - True if this alignment is mapped as a reverse compliment. Defaults to false.
        mateNegativeStrand - True if the mate pair for this alignment is mapped as a reverse compliment. Defaults to false.
        primaryAlignment - True if this alignment is either the best linear alignment, or the first linear alignment in a chimeric alignment. Defaults to false.
        secondaryAlignment - True if this alignment is a lower quality linear alignment for a multiply-mapped read. Defaults to false.
        supplementaryAlignment - True if this alignment is a non-primary linear alignment in a chimeric alignment. Defaults to false.
        mismatchingPositions - Mismatching positions for this alignment. SAM optional field reserved tag MD. Format (not enforced here): [0-9]+(([A-Z]|\^[A-Z]+)[0-9]+)*
        originalQualityScores - Original per-base quality scores of the read for this alignment, before recalibration. SAM optional field reserved tag OQ.
        readGroupId - Read group identifier for the read for this alignment. Join with ReadGroup.id for read group metadata.
        readGroupSampleId - Read group sample identifier for the read for this alignment. Join with ReadGroup.sampleId for read group metadata or Sample.id for sample metadata.
        mateAlignmentStart - Start position of the mate of the read for this alignment, in zero-based coordinate system with closed-open intervals. Should be set to null if the mate is unaligned, or if the mate does not exist. SAM column 8 field PNEXT converted to zero-based coordinate system, closed-open intervals.
        mateReferenceName - Reference for the mate of the read for this alignment. Should be set to null if the mate is unaligned, or if the mate does not exist. SAM column 7 field RNEXT.
        insertSize - Insert size between the read for this alignment and its mate, derived from alignment, if the reads have been aligned. Should be set to null if the mate is unaligned, or if the mate does not exist.
        readInFragment - Index of the read for this alignment within an array of fragments. Defaults to zero.
        attributes - Additional alignment attributes that do not fit into the standard fields above, flattened into a string.

    • Method Detail

      • getClassSchema

        public static org.apache.avro.Schema getClassSchema()

      • getEncoder

        public static org.apache.avro.message.BinaryMessageEncoder<Alignment> getEncoder()
        Return the BinaryMessageEncoder instance used by this class.
        Returns:
        the message encoder used by this class

      • getDecoder

        public static org.apache.avro.message.BinaryMessageDecoder<Alignment> getDecoder()
        Return the BinaryMessageDecoder instance used by this class.
        Returns:
        the message decoder used by this class

      • createDecoder

        public static org.apache.avro.message.BinaryMessageDecoder<Alignment> createDecoder​(org.apache.avro.message.SchemaStore resolver)
        Create a new BinaryMessageDecoder instance for this class that uses the specified SchemaStore.
        Parameters:
        resolver - a SchemaStore used to find schemas by fingerprint
        Returns:
        a BinaryMessageDecoder instance for this class backed by the given SchemaStore

      • toByteBuffer

        public ByteBuffer toByteBuffer()
                        throws IOException
        Serializes this Alignment to a ByteBuffer.
        Returns:
        a buffer holding the serialized data for this instance
        Throws:
        IOException - if this instance could not be serialized

      • fromByteBuffer

        public static Alignment fromByteBuffer​(ByteBuffer b)
                                throws IOException
        Deserializes a Alignment from a ByteBuffer.
        Parameters:
        b - a byte buffer holding serialized data for an instance of this class
        Returns:
        a Alignment instance decoded from the given buffer
        Throws:
        IOException - if the given bytes could not be deserialized into an instance of this class

      • getSpecificData

        public org.apache.avro.specific.SpecificData getSpecificData()
        Overrides:
        getSpecificData in class org.apache.avro.specific.SpecificRecordBase

      • getSchema

        public org.apache.avro.Schema getSchema()
        Specified by:
        getSchema in interface org.apache.avro.generic.GenericContainer
        Specified by:
        getSchema in class org.apache.avro.specific.SpecificRecordBase

      • get

        public Object get​(int field$)
        Specified by:
        get in interface org.apache.avro.generic.IndexedRecord
        Specified by:
        get in class org.apache.avro.specific.SpecificRecordBase

      • put

        public void put​(int field$,
                Object value$)
        Specified by:
        put in interface org.apache.avro.generic.IndexedRecord
        Specified by:
        put in class org.apache.avro.specific.SpecificRecordBase

      • getReferenceName

        public String getReferenceName()
        Gets the value of the 'referenceName' field.
        Returns:
        The reference for this alignment. If the read is unaligned, this field should be null. SAM column 3 field RNAME.

      • setReferenceName

        public void setReferenceName​(String value)
        Sets the value of the 'referenceName' field. The reference for this alignment. If the read is unaligned, this field should be null. SAM column 3 field RNAME.
        Parameters:
        value - the value to set.

      • getStart

        public Long getStart()
        Gets the value of the 'start' field.
        Returns:
        Start position for this alignment, in zero-based coordinate system with closed-open intervals. Should be null if the read is unaligned. SAM column 4 field POS converted to zero-based coordinate system, closed-open intervals.

      • setStart

        public void setStart​(Long value)
        Sets the value of the 'start' field. Start position for this alignment, in zero-based coordinate system with closed-open intervals. Should be null if the read is unaligned. SAM column 4 field POS converted to zero-based coordinate system, closed-open intervals.
        Parameters:
        value - the value to set.

      • getOriginalStart

        public Long getOriginalStart()
        Gets the value of the 'originalStart' field.
        Returns:
        Original start position for this alignment, before local realignment, in zero-based coordinate system with closed-open intervals. Should be null if the read is unaligned. SAM optional field reserved tag OP converted to zero-based coordinate system, closed-open intervals.

      • setOriginalStart

        public void setOriginalStart​(Long value)
        Sets the value of the 'originalStart' field. Original start position for this alignment, before local realignment, in zero-based coordinate system with closed-open intervals. Should be null if the read is unaligned. SAM optional field reserved tag OP converted to zero-based coordinate system, closed-open intervals.
        Parameters:
        value - the value to set.

      • getEnd

        public Long getEnd()
        Gets the value of the 'end' field.
        Returns:
        End position for this alignment, in zero-based coordinate system with closed-open intervals. Should be null if the read is unaligned.

      • setEnd

        public void setEnd​(Long value)
        Sets the value of the 'end' field. End position for this alignment, in zero-based coordinate system with closed-open intervals. Should be null if the read is unaligned.
        Parameters:
        value - the value to set.

      • getMappingQuality

        public Integer getMappingQuality()
        Gets the value of the 'mappingQuality' field.
        Returns:
        Global mapping quality for this alignment. SAM column 5 field MAPQ.

      • setMappingQuality

        public void setMappingQuality​(Integer value)
        Sets the value of the 'mappingQuality' field. Global mapping quality for this alignment. SAM column 5 field MAPQ.
        Parameters:
        value - the value to set.

      • getReadName

        public String getReadName()
        Gets the value of the 'readName' field.
        Returns:
        Name of the read for this alignment. This should be unique within the read group that the read is from, and can be used to identify other reads that are derived from a single fragment. SAM column 5 field QNAME.

      • setReadName

        public void setReadName​(String value)
        Sets the value of the 'readName' field. Name of the read for this alignment. This should be unique within the read group that the read is from, and can be used to identify other reads that are derived from a single fragment. SAM column 5 field QNAME.
        Parameters:
        value - the value to set.

      • getSequence

        public String getSequence()
        Gets the value of the 'sequence' field.
        Returns:
        Sequence of the read for this alignment. If the read has been hard clipped, this may not represent all the bases in the original read. SAM column 10 field SEQ.

      • setSequence

        public void setSequence​(String value)
        Sets the value of the 'sequence' field. Sequence of the read for this alignment. If the read has been hard clipped, this may not represent all the bases in the original read. SAM column 10 field SEQ.
        Parameters:
        value - the value to set.

      • getQualityScores

        public String getQualityScores()
        Gets the value of the 'qualityScores' field.
        Returns:
        Per-base quality scores of the read for this alignment. If the read has been hard clipped, this may not represent all the bases in the original read. Additionally, if the error scores have been recalibrated, this field will not contain the original base quality scores. SAM column 11 field QUAL.

      • setQualityScores

        public void setQualityScores​(String value)
        Sets the value of the 'qualityScores' field. Per-base quality scores of the read for this alignment. If the read has been hard clipped, this may not represent all the bases in the original read. Additionally, if the error scores have been recalibrated, this field will not contain the original base quality scores. SAM column 11 field QUAL.
        Parameters:
        value - the value to set.

      • getCigar

        public String getCigar()
        Gets the value of the 'cigar' field.
        Returns:
        Compact Ideosyncratic Gapped Alignment Report (CIGAR) string that describes the local alignment of the read for this alignment. SAM column 6 field CIGAR. Contains {length, operator} pairs for all contiguous alignment operations. The operators include: M, ALIGNMENT_MATCH: An alignment match indicates that a sequence can be aligned to the reference without evidence of an INDEL. Unlike the SEQUENCE_MATCH and SEQUENCE_MISMATCH operators, the ALIGNMENT_MATCH operator does not indicate whether the reference and read sequences are an exact match. I, INSERT: The insert operator indicates that the read contains evidence of bases being inserted into the reference. D, DELETE: The delete operator indicates that the read contains evidence of bases being deleted from the reference. N, SKIP: The skip operator indicates that this read skips a long segment of the reference, but the bases have not been deleted. This operator is commonly used when working with RNA-seq data, where reads may skip long segments of the reference between exons. S, CLIP_SOFT: The soft clip operator indicates that bases at the start/end of a read have not been considered during alignment. This may occur if the majority of a read maps, except for low quality bases at the start/end of a read. Bases that are soft clipped will still be stored in the read. H, CLIP_HARD: The hard clip operator indicates that bases at the start/end of a read have been omitted from this alignment. This may occur if this linear alignment is part of a chimeric alignment, or if the read has been trimmed (e.g., during error correction, or to trim poly-A tails for RNA-seq). P, PAD: The pad operator indicates that there is padding in an alignment. =, SEQUENCE_MATCH: This operator indicates that this portion of the aligned sequence exactly matches the reference (e.g., all bases are equal to the reference bases). X, SEQUENCE_MISMATCH: This operator indicates that this portion of the aligned sequence is an alignment match to the reference, but a sequence mismatch (e.g., the bases are not equal to the reference). This can indicate a SNP or a read error.

      • setCigar

        public void setCigar​(String value)
        Sets the value of the 'cigar' field. Compact Ideosyncratic Gapped Alignment Report (CIGAR) string that describes the local alignment of the read for this alignment. SAM column 6 field CIGAR. Contains {length, operator} pairs for all contiguous alignment operations. The operators include: M, ALIGNMENT_MATCH: An alignment match indicates that a sequence can be aligned to the reference without evidence of an INDEL. Unlike the SEQUENCE_MATCH and SEQUENCE_MISMATCH operators, the ALIGNMENT_MATCH operator does not indicate whether the reference and read sequences are an exact match. I, INSERT: The insert operator indicates that the read contains evidence of bases being inserted into the reference. D, DELETE: The delete operator indicates that the read contains evidence of bases being deleted from the reference. N, SKIP: The skip operator indicates that this read skips a long segment of the reference, but the bases have not been deleted. This operator is commonly used when working with RNA-seq data, where reads may skip long segments of the reference between exons. S, CLIP_SOFT: The soft clip operator indicates that bases at the start/end of a read have not been considered during alignment. This may occur if the majority of a read maps, except for low quality bases at the start/end of a read. Bases that are soft clipped will still be stored in the read. H, CLIP_HARD: The hard clip operator indicates that bases at the start/end of a read have been omitted from this alignment. This may occur if this linear alignment is part of a chimeric alignment, or if the read has been trimmed (e.g., during error correction, or to trim poly-A tails for RNA-seq). P, PAD: The pad operator indicates that there is padding in an alignment. =, SEQUENCE_MATCH: This operator indicates that this portion of the aligned sequence exactly matches the reference (e.g., all bases are equal to the reference bases). X, SEQUENCE_MISMATCH: This operator indicates that this portion of the aligned sequence is an alignment match to the reference, but a sequence mismatch (e.g., the bases are not equal to the reference). This can indicate a SNP or a read error.
        Parameters:
        value - the value to set.

      • getOriginalCigar

        public String getOriginalCigar()
        Gets the value of the 'originalCigar' field.
        Returns:
        Original CIGAR string that describes the local alignment of the read for this alignment, before local realignment. SAM optional field reserved tag OC.

      • setOriginalCigar

        public void setOriginalCigar​(String value)
        Sets the value of the 'originalCigar' field. Original CIGAR string that describes the local alignment of the read for this alignment, before local realignment. SAM optional field reserved tag OC.
        Parameters:
        value - the value to set.

      • getBasesTrimmedFromStart

        public Integer getBasesTrimmedFromStart()
        Gets the value of the 'basesTrimmedFromStart' field.
        Returns:
        Number of bases in the read for this alignment that have been trimmed from the start of the read. By default, this is equal to 0. If the value is non-zero, that means that the start of the read has been hard-clipped.

      • setBasesTrimmedFromStart

        public void setBasesTrimmedFromStart​(Integer value)
        Sets the value of the 'basesTrimmedFromStart' field. Number of bases in the read for this alignment that have been trimmed from the start of the read. By default, this is equal to 0. If the value is non-zero, that means that the start of the read has been hard-clipped.
        Parameters:
        value - the value to set.

      • getBasesTrimmedFromEnd

        public Integer getBasesTrimmedFromEnd()
        Gets the value of the 'basesTrimmedFromEnd' field.
        Returns:
        Number of bases in the read for this alignment that have been trimmed from the end of the read. By default, this is equal to 0. If the value is non-zero, that means that the end of the read has been hard-clipped.

      • setBasesTrimmedFromEnd

        public void setBasesTrimmedFromEnd​(Integer value)
        Sets the value of the 'basesTrimmedFromEnd' field. Number of bases in the read for this alignment that have been trimmed from the end of the read. By default, this is equal to 0. If the value is non-zero, that means that the end of the read has been hard-clipped.
        Parameters:
        value - the value to set.

      • getReadPaired

        public Boolean getReadPaired()
        Gets the value of the 'readPaired' field.
        Returns:
        True if the read for this alignment has a mate. Defaults to false.

      • setReadPaired

        public void setReadPaired​(Boolean value)
        Sets the value of the 'readPaired' field. True if the read for this alignment has a mate. Defaults to false.
        Parameters:
        value - the value to set.

      • getProperPair

        public Boolean getProperPair()
        Gets the value of the 'properPair' field.
        Returns:
        True if the read for this alignment and its mate are a proper pair. Defaults to false.

      • setProperPair

        public void setProperPair​(Boolean value)
        Sets the value of the 'properPair' field. True if the read for this alignment and its mate are a proper pair. Defaults to false.
        Parameters:
        value - the value to set.

      • getReadMapped

        public Boolean getReadMapped()
        Gets the value of the 'readMapped' field.
        Returns:
        True if the read for this alignment has been mapped. Defaults to false.

      • setReadMapped

        public void setReadMapped​(Boolean value)
        Sets the value of the 'readMapped' field. True if the read for this alignment has been mapped. Defaults to false.
        Parameters:
        value - the value to set.

      • getMateMapped

        public Boolean getMateMapped()
        Gets the value of the 'mateMapped' field.
        Returns:
        True if the mate of the read for this alignment has been mapped. Defaults to false.

      • setMateMapped

        public void setMateMapped​(Boolean value)
        Sets the value of the 'mateMapped' field. True if the mate of the read for this alignment has been mapped. Defaults to false.
        Parameters:
        value - the value to set.

      • getFailedVendorQualityChecks

        public Boolean getFailedVendorQualityChecks()
        Gets the value of the 'failedVendorQualityChecks' field.
        Returns:
        True if the read for this alignent failed vendor quality checks. Defaults to false.

      • setFailedVendorQualityChecks

        public void setFailedVendorQualityChecks​(Boolean value)
        Sets the value of the 'failedVendorQualityChecks' field. True if the read for this alignent failed vendor quality checks. Defaults to false.
        Parameters:
        value - the value to set.

      • getDuplicateRead

        public Boolean getDuplicateRead()
        Gets the value of the 'duplicateRead' field.
        Returns:
        True if the read for this alignment has been marked as duplicate. Defaults to false.

      • setDuplicateRead

        public void setDuplicateRead​(Boolean value)
        Sets the value of the 'duplicateRead' field. True if the read for this alignment has been marked as duplicate. Defaults to false.
        Parameters:
        value - the value to set.

      • getReadNegativeStrand

        public Boolean getReadNegativeStrand()
        Gets the value of the 'readNegativeStrand' field.
        Returns:
        True if this alignment is mapped as a reverse compliment. Defaults to false.

      • setReadNegativeStrand

        public void setReadNegativeStrand​(Boolean value)
        Sets the value of the 'readNegativeStrand' field. True if this alignment is mapped as a reverse compliment. Defaults to false.
        Parameters:
        value - the value to set.

      • getMateNegativeStrand

        public Boolean getMateNegativeStrand()
        Gets the value of the 'mateNegativeStrand' field.
        Returns:
        True if the mate pair for this alignment is mapped as a reverse compliment. Defaults to false.

      • setMateNegativeStrand

        public void setMateNegativeStrand​(Boolean value)
        Sets the value of the 'mateNegativeStrand' field. True if the mate pair for this alignment is mapped as a reverse compliment. Defaults to false.
        Parameters:
        value - the value to set.

      • getPrimaryAlignment

        public Boolean getPrimaryAlignment()
        Gets the value of the 'primaryAlignment' field.
        Returns:
        True if this alignment is either the best linear alignment, or the first linear alignment in a chimeric alignment. Defaults to false.

      • setPrimaryAlignment

        public void setPrimaryAlignment​(Boolean value)
        Sets the value of the 'primaryAlignment' field. True if this alignment is either the best linear alignment, or the first linear alignment in a chimeric alignment. Defaults to false.
        Parameters:
        value - the value to set.

      • getSecondaryAlignment

        public Boolean getSecondaryAlignment()
        Gets the value of the 'secondaryAlignment' field.
        Returns:
        True if this alignment is a lower quality linear alignment for a multiply-mapped read. Defaults to false.

      • setSecondaryAlignment

        public void setSecondaryAlignment​(Boolean value)
        Sets the value of the 'secondaryAlignment' field. True if this alignment is a lower quality linear alignment for a multiply-mapped read. Defaults to false.
        Parameters:
        value - the value to set.

      • getSupplementaryAlignment

        public Boolean getSupplementaryAlignment()
        Gets the value of the 'supplementaryAlignment' field.
        Returns:
        True if this alignment is a non-primary linear alignment in a chimeric alignment. Defaults to false.

      • setSupplementaryAlignment

        public void setSupplementaryAlignment​(Boolean value)
        Sets the value of the 'supplementaryAlignment' field. True if this alignment is a non-primary linear alignment in a chimeric alignment. Defaults to false.
        Parameters:
        value - the value to set.

      • getMismatchingPositions

        public String getMismatchingPositions()
        Gets the value of the 'mismatchingPositions' field.
        Returns:
        Mismatching positions for this alignment. SAM optional field reserved tag MD. Format (not enforced here): [0-9]+(([A-Z]|\^[A-Z]+)[0-9]+)*

      • setMismatchingPositions

        public void setMismatchingPositions​(String value)
        Sets the value of the 'mismatchingPositions' field. Mismatching positions for this alignment. SAM optional field reserved tag MD. Format (not enforced here): [0-9]+(([A-Z]|\^[A-Z]+)[0-9]+)*
        Parameters:
        value - the value to set.

      • getOriginalQualityScores

        public String getOriginalQualityScores()
        Gets the value of the 'originalQualityScores' field.
        Returns:
        Original per-base quality scores of the read for this alignment, before recalibration. SAM optional field reserved tag OQ.

      • setOriginalQualityScores

        public void setOriginalQualityScores​(String value)
        Sets the value of the 'originalQualityScores' field. Original per-base quality scores of the read for this alignment, before recalibration. SAM optional field reserved tag OQ.
        Parameters:
        value - the value to set.

      • getReadGroupId

        public String getReadGroupId()
        Gets the value of the 'readGroupId' field.
        Returns:
        Read group identifier for the read for this alignment. Join with ReadGroup.id for read group metadata.

      • setReadGroupId

        public void setReadGroupId​(String value)
        Sets the value of the 'readGroupId' field. Read group identifier for the read for this alignment. Join with ReadGroup.id for read group metadata.
        Parameters:
        value - the value to set.

      • getReadGroupSampleId

        public String getReadGroupSampleId()
        Gets the value of the 'readGroupSampleId' field.
        Returns:
        Read group sample identifier for the read for this alignment. Join with ReadGroup.sampleId for read group metadata or Sample.id for sample metadata.

      • setReadGroupSampleId

        public void setReadGroupSampleId​(String value)
        Sets the value of the 'readGroupSampleId' field. Read group sample identifier for the read for this alignment. Join with ReadGroup.sampleId for read group metadata or Sample.id for sample metadata.
        Parameters:
        value - the value to set.

      • getMateAlignmentStart

        public Long getMateAlignmentStart()
        Gets the value of the 'mateAlignmentStart' field.
        Returns:
        Start position of the mate of the read for this alignment, in zero-based coordinate system with closed-open intervals. Should be set to null if the mate is unaligned, or if the mate does not exist. SAM column 8 field PNEXT converted to zero-based coordinate system, closed-open intervals.

      • setMateAlignmentStart

        public void setMateAlignmentStart​(Long value)
        Sets the value of the 'mateAlignmentStart' field. Start position of the mate of the read for this alignment, in zero-based coordinate system with closed-open intervals. Should be set to null if the mate is unaligned, or if the mate does not exist. SAM column 8 field PNEXT converted to zero-based coordinate system, closed-open intervals.
        Parameters:
        value - the value to set.

      • getMateReferenceName

        public String getMateReferenceName()
        Gets the value of the 'mateReferenceName' field.
        Returns:
        Reference for the mate of the read for this alignment. Should be set to null if the mate is unaligned, or if the mate does not exist. SAM column 7 field RNEXT.

      • setMateReferenceName

        public void setMateReferenceName​(String value)
        Sets the value of the 'mateReferenceName' field. Reference for the mate of the read for this alignment. Should be set to null if the mate is unaligned, or if the mate does not exist. SAM column 7 field RNEXT.
        Parameters:
        value - the value to set.

      • getInsertSize

        public Long getInsertSize()
        Gets the value of the 'insertSize' field.
        Returns:
        Insert size between the read for this alignment and its mate, derived from alignment, if the reads have been aligned. Should be set to null if the mate is unaligned, or if the mate does not exist.

      • setInsertSize

        public void setInsertSize​(Long value)
        Sets the value of the 'insertSize' field. Insert size between the read for this alignment and its mate, derived from alignment, if the reads have been aligned. Should be set to null if the mate is unaligned, or if the mate does not exist.
        Parameters:
        value - the value to set.

      • getReadInFragment

        public Integer getReadInFragment()
        Gets the value of the 'readInFragment' field.
        Returns:
        Index of the read for this alignment within an array of fragments. Defaults to zero.

      • setReadInFragment

        public void setReadInFragment​(Integer value)
        Sets the value of the 'readInFragment' field. Index of the read for this alignment within an array of fragments. Defaults to zero.
        Parameters:
        value - the value to set.

      • getAttributes

        public String getAttributes()
        Gets the value of the 'attributes' field.
        Returns:
        Additional alignment attributes that do not fit into the standard fields above, flattened into a string.

      • setAttributes

        public void setAttributes​(String value)
        Sets the value of the 'attributes' field. Additional alignment attributes that do not fit into the standard fields above, flattened into a string.
        Parameters:
        value - the value to set.

      • newBuilder

        public static Alignment.Builder newBuilder()
        Creates a new Alignment RecordBuilder.
        Returns:
        A new Alignment RecordBuilder

      • newBuilder

        public static Alignment.Builder newBuilder​(Alignment.Builder other)
        Creates a new Alignment RecordBuilder by copying an existing Builder.
        Parameters:
        other - The existing builder to copy.
        Returns:
        A new Alignment RecordBuilder

      • newBuilder

        public static Alignment.Builder newBuilder​(Alignment other)
        Creates a new Alignment RecordBuilder by copying an existing Alignment instance.
        Parameters:
        other - The existing instance to copy.
        Returns:
        A new Alignment RecordBuilder

      • hasCustomCoders

        protected boolean hasCustomCoders()
        Overrides:
        hasCustomCoders in class org.apache.avro.specific.SpecificRecordBase

      • customEncode

        public void customEncode​(org.apache.avro.io.Encoder out)
                  throws IOException
        Overrides:
        customEncode in class org.apache.avro.specific.SpecificRecordBase
        Throws:
        IOException

      • customDecode

        public void customDecode​(org.apache.avro.io.ResolvingDecoder in)
                  throws IOException
        Overrides:
        customDecode in class org.apache.avro.specific.SpecificRecordBase
        Throws:
        IOException