Class Marker

Method Details

• instance

  public static Marker instance(String rec, MarkerParser markerParser)

  Constructs a new Marker instance from the data. If the specified VCF record contains an INFO/END field, the INFO/END field will be stored.

  Parameters:

  rec - a VCF record

  markerParser - an object that filters and parses a VCF record's ID, QUAL, FILTER, and INFO subfields

  Returns:

  a new Marker instance

  Throws:

  IllegalArgumentException - if the specified VCF record does not contain at least 8 tab characters

  IllegalArgumentException - if the VCF CHROM field contains whitespace

  IllegalArgumentException - if the specified VCF record has more than 255 alleles

  IndexOutOfBoundsException - if the index of the VCF CHROM field exceeds Short.MAX_VALUE

  NullPointerException - if (vcfRecord == null) || (vcfFields==null)

  NumberFormatException - if the VCF record POS field is not a parsable integer

• chrom

  public String chrom()

  Returns the VCF CHROM field.

  Returns:

  the VCF CHROM field

• chromIndex

  public int chromIndex()

  Returns the chromosome index.

  Returns:

  the chromosome index

• pos

  public int pos()

  Returns the VCF POS field

  Returns:

  the VCF POS field

• hasIdData

  public boolean hasIdData()

  Returns true if the VCF ID field has non-missing data, and returns false otherwise.

  Returns:

  true if the VCF ID field has non-missing data, and returns false otherwise

• hasQualData

  public boolean hasQualData()

  Returns true if the VCF QUAL field has non-missing data, and returns false otherwise.

  Returns:

  true if the VCF QUAL field has non-missing data, and returns false otherwise

• hasFilterData

  public boolean hasFilterData()

  Returns true if the VCF FILTER field has non-missing data, and returns false otherwise.

  Returns:

  true if the VCF FILTER field has non-missing data, and returns false otherwise

• hasInfoData

  public boolean hasInfoData()

  Returns true if the VCF INFO field has non-missing data, and returns false otherwise.

  Returns:

  true if the VCF INFO field has non-missing data, and returns false otherwise

• hasEndValue

  public boolean hasEndValue()

  Returns true if the VCF INFO/END field is defined, and returns false otherwise.

  Returns:

  true if the VCF INFO/END field has is defined

• id

  public String id()

  Returns the VCF ID field.

  Returns:

  the VCF ID field

• alleles

  public String alleles()

  Returns the tab-separated VCF REF and ALT fields

  Returns:

  the tab-separated VCF REF and ALT fields

• nRefBases

  public int nRefBases()

  Returns the number of nucleotides in the reference allele.

  Returns:

  the number of nucleotides in the reference allele

• nAlleles

  public int nAlleles()

  Returns the number of alleles for the marker, including the REF allele.

  Returns:

  the number of alleles for the marker, including the REF allele

• bitsPerAllele

  public int bitsPerAllele()

  Returns the minimum number of bits required to store a non-missing allele.

  Returns:

  the minimum number of bits required to store a non-missing allele

• qual

  public String qual()

  Returns the VCF QUAL field.

  Returns:

  the VCF QUAL field

• filter

  public String filter()

  Returns the VCF FILTER field.

  Returns:

  the VCF FILTER field.

• info

  public String info()

  Returns the VCF INFO field.

  Returns:

  the VCF INFO field.

• endValue

  public String endValue()

  Returns the INFO/END value. Returns "" if the INFO/END value is not defined.

  Returns:

  the INFO/END value

• hashCode

  public int hashCode()

  Returns the hash code value for this object. The hash code is defined by the following calculation:

     int hash = 5;
     hash = 29 * hash + this.chromIndex();
     hash = 29 * hash + this.pos();
     hash = 29 * hash + this.alleles().hashCode();
     hash = 29 * hash + this.endValue().hashCode();
     

  Overrides:

  hashCode in class Object

  Returns:

  the hash code value for this marker

• equals

  public boolean equals(Object obj)

  Returns true if the specified object is a Marker with the same chromosome, position, alleles, and INFO/END value, and returns false otherwise.

  Overrides:

  equals in class Object

  Parameters:

  obj - object to be compared with this for equality

  Returns:

  true if the specified object is a Marker with the same chromosome, position, alleles, and INFO/END value

• compareTo

  public int compareTo(Marker other)

  Compares this marker with the specified marker for order, and returns a negative integer, 0, or a positive integer depending on whether this marker is less than, equal to, or greater than the specified marker. Markers are compared using the values returned by the chromIndex(), pos(), alleles(), and endValue() methods. The returned value is defined by the following calculation:

     if (this.chromIndex() != other.chromIndex()) {
         return (this.chromIndex < other.chromIndex()) ? -1 : 1;
     }
     if (this.pos() != other.pos()) {
         return (this.pos < other.pos()) ? -1 : 1;
     }
     int value = this.alleles().compareTo(other.alleles());
     if (value!=0) {
         return value;
     }
     return this.endValue().compareTo(other.endValue());
     

  Specified by:

  compareTo in interface Comparable<Marker>

  Parameters:

  other - the Marker to be compared

  Returns:

  a negative integer, 0, or a positive integer depending on whether this marker is less than, equal, or greater than the specified marker

• writeNonPosFields

  public void writeNonPosFields(DataOutput out) throws IOException

  Writes a representation of the VCF record ID, REF, ALT, QUAL, FILTER, and INFO fields to the specified output. The exact details of the representation are unspecified and subject to change. The written data can be read with the Marker.readNonPosFields() method.

  Parameters:

  out - the output destination

  Throws:

  IOException - if an I/O error occurs

  NullPointerException - if out == null

• readNonPosFields

  public static Marker readNonPosFields(short chromIndex, int pos, DataInput in) throws IOException

  Reads the VCF record ID, REF, ALT, QUAL, FILTER, and INFO fields and returns a marker with these fields and the specified CHROM and POS fields. The contract for this method is unspecified if chromIndex is not a valid chromosome index.

  Parameters:

  chromIndex - the chromosome index

  pos - the chromosome position

  in - the input source

  Returns:

  a Marker

  Throws:

  IOException - if an I/O error occurs

  NullPointerException - if in == null

• toString

  public String toString()

  Returns a string equal to the first five tab-delimited fields of a VCF record corresponding to this marker (the CHROM, POS, ID, REF, and ALT fields).

  Overrides:

  toString in class Object

  Returns:

  a string equal to the first five tab-delimited fields of a VCF record corresponding to this marker

• appendFirst8Fields

  public void appendFirst8Fields(StringBuilder sb)

  Appends the first eight tab-delimited fields of a VCF record for this marker (the CHROM, POS, ID, REF, ALT, QUAL, FILTER, and INFO fields) to the specified StringBuilder.

  Parameters:

  sb - the StringBuilder to be appended

  Throws:

  NullPointerException - if (sb == null)

• appendFirst8Fields

  public void appendFirst8Fields(StringBuilder sb, int an, int[] alleleCounts)

  Appends the first eight tab-delimited fields of a VCF record for this marker (the CHROM, POS, ID, REF, ALT, QUAL, FILTER, and INFO fields) and add the specified INFO/AN and INFO/AC fields. If the INFO/AN or iNFO/AC fields exist in this.info(), the fields will be replaced with the specified INFO/AN and INFO/AC fields.

  Parameters:

  sb - the StringBuilder to be appended

  an - the total number of alleles in called genotypes

  alleleCounts - an array of length this.nAlleles() whose k-th entry is the allele count in called genotypes for the k-th allele

  Throws:

  IllegalArgumentException - if (this.nAlleles() != alleleCounts.length)

  NullPointerException - if ((sb == null) || (alleleCounts == null))