Class VcfHeader

Method Details

• isFormatLine

  public static boolean isFormatLine(String line)

• isInfoLine

  public static boolean isInfoLine(String line)

• add

  public void add(VcfHeader newVcfHeader)

  Add all missing lines from 'vcfHeader'

• add

  public void add(VcfHeaderEntry vcfHeader)

  Add header line

• addFormat

  public void addFormat(VcfHeaderFormat vcfFormat)

  Add a 'FORMAT' meta info

• addInfo

  public void addInfo(VcfHeaderInfo vcfInfo)

  Add a VCF INFO header definition

• addLine

  public void addLine(String newHeaderLine)

  Add line to header (can add many lines)

• getLines

  public String[] getLines()

• getNumberOfSamples

  public int getNumberOfSamples()

  Number of samples

• getPedigree

  public List<PedigreeEntry> getPedigree()

  Get pedigree (if any)

• getSampleNames

  public List<String> getSampleNames()

  Get sample names

• getSampleNum

  public int getSampleNum(String sameplName)

  Sample number (position in "#CHROM" line)

  Returns:

  -1 if not found

• getVcfHeaderFormat

  public Collection<VcfHeaderFormat> getVcfHeaderFormat()

• getVcfHeaderFormat

  public VcfHeaderFormat getVcfHeaderFormat(String id)

• getVcfHeaderInfo

  public Collection<VcfHeaderInfo> getVcfHeaderInfo()

  Get all VcfInfo entries

• getVcfHeaderInfo

  public VcfHeaderInfo getVcfHeaderInfo(String id)

  Get Info type for a given ID

• hasFormat

  public boolean hasFormat(VcfHeaderFormat vcfFormat)

  Do we already have this 'format' entry?

• hasInfo

  public boolean hasInfo(VcfHeaderInfo vcfInfo)

  Do we already have this 'info' header?

• parse

  public void parse()

  Parse header lines

• parseSampleNames

  protected List<String> parseSampleNames()

• parseSampleNum

  protected void parseSampleNum()

• remove

  public void remove(String linePrefix)

  Remove header line starting with a prefix

• removeInfo

  public void removeInfo(String infoId)

  Remove header line matching an INFO field

• toString

  public String toString()

  Get header information

  Overrides:

  toString in class Object