Class VcfEntry

Method Details

• cleanUnderscores

  public static String cleanUnderscores(String s)

  Return a string without leading, trailing and duplicated underscores

• isEmpty

  public static boolean isEmpty(String value)

  Does 'value' represent an EMPTY / MISSING value in a VCF field? (or multiple MISSING comma-separated values)

• isValidInfoKey

  public static boolean isValidInfoKey(String key)

  Make sure the INFO key matches the regular expression (as specified in VCF spec 4.3)

• isValidInfoValue

  public static boolean isValidInfoValue(String value)

  Check that this value can be added to an INFO field

  Returns:

  true if OK, false if invalid value

• vcfInfoDecode

  public static String vcfInfoDecode(String str)

  Decode INFO value

• vcfInfoEncode

  public static String vcfInfoEncode(String str)

  Encode a string to be used in an 'INFO' field value From the VCF 4.3 specification Characters with special meaning (such as field delimiters ';' in INFO or ':' FORMAT fields) must be represented using the capitalized percent encoding: %3A : (colon) %3B ; (semicolon) %3D = (equal sign) %25 % (percent sign) %2C , (comma) %0D CR %0A LF %09 TAB

• vcfInfoKeySafe

  public static String vcfInfoKeySafe(String str)

  Return a string safe to be used in an 'INFO' field key

• vcfInfoValueSafe

  public static String vcfInfoValueSafe(String str)

  Return a string safe to be used in an 'INFO' field value

• addFilter

  public void addFilter(String filterStr)

  Add string to FILTER field

• addFormat

  public void addFormat(String formatName)

  Add a 'FORMAT' field

• addGenotype

  public void addGenotype(String vcfGenotypeStr)

  Add a genotype as a string

• addInfo

  public void addInfo(String key, String value)

  Add a "key=value" tuple the info field

  Parameters:

  key - : INFO key name

  value - : Can be null if it is a boolean field.

• alleleFrequencyType

  public VcfEntry.AlleleFrequencyType alleleFrequencyType()

  Categorization by allele frequency

• calcHetero

  public Boolean calcHetero()

  Is this entry heterozygous? Infer Hom/Her if there is only one sample in the file. Ohtherwise the field is null.

• check

  public String check()

  Perform several simple checks and report problems (if any).

• cloneShallow

  public Cds cloneShallow()

  Description copied from class: Marker

  Perform a shallow clone

  Overrides:

  cloneShallow in class Marker

• compressGenotypes

  public boolean compressGenotypes()

  Compress genotypes into "HO/HE/NA" INFO fields

• delFilter

  public boolean delFilter(String filterStr)

  Remove a string from FILTER field

• getAltIndex

  public int getAltIndex(String alt)

  Get index of matching ALT entry

  Returns:

  -1 if not found

• getAlts

  public String[] getAlts()

• getAltsStr

  public String getAltsStr()

  Create a comma separated ALTS string

• getChromosomeNameOri

  public String getChromosomeNameOri()

  Original chromosome name (as it appeared in the VCF file)

  Overrides:

  getChromosomeNameOri in class Interval

• getFilter

  public String getFilter()

• getFormat

  public String getFormat()

• getFormatFields

  public String[] getFormatFields()

• getGenotypesScores

  public byte[] getGenotypesScores()

  Return genotypes parsed as an array of codes

• getInfo

  public String getInfo(String key)

  Get info string

• getInfo

  public String getInfo(String key, String allele)

  Get info string for a specific allele

• getInfo

  public String getInfo(String key, Variant var)

  Get an INFO field matching a variant

• getInfoFlag

  public boolean getInfoFlag(String key)

  Does the entry exists?

• getInfoFloat

  public double getInfoFloat(String key)

  Get info field as a 'double' number The norm specifies data type as 'FLOAT', that is why the name of this method might be not intuitive

• getInfoInt

  public long getInfoInt(String key)

  Get info field as an long number The norm specifies data type as 'INT', that is why the name of this method might be not intuitive

• getInfoKeys

  public Set<String> getInfoKeys()

  Get all keys available in the info field

• getInfoStr

  public String getInfoStr()

  Get the full (unparsed) INFO field

• getLine

  public String getLine()

  Original VCF line (from file)

• getLineNum

  public int getLineNum()

• getNumberOfSamples

  public int getNumberOfSamples()

  number of samples in this VCF file

• getQuality

  public double getQuality()

• getRef

  public String getRef()

• getStr

  public String getStr()

• getVcfEffects

  public List<VcfEffect> getVcfEffects()

• getVcfEffects

  public List<VcfEffect> getVcfEffects(EffFormatVersion formatVersion)

  Parse 'EFF' info field and get a list of effects

• getVcfFileIterator

  public VcfFileIterator getVcfFileIterator()

• getVcfGenotype

  public VcfGenotype getVcfGenotype(int index)

• getVcfGenotypes

  public List<VcfGenotype> getVcfGenotypes()

• getVcfInfo

  public VcfHeaderInfo getVcfInfo(String id)

  Get VcfInfo type for a given ID

• getVcfInfoNumber

  public VcfInfoType getVcfInfoNumber(String id)

  Get Info number for a given ID

• hasField

  public boolean hasField(String filedName)

• hasGenotypes

  public boolean hasGenotypes()

• hasInfo

  public boolean hasInfo(String infoFieldName)

• hasQuality

  public boolean hasQuality()

• isBiAllelic

  public boolean isBiAllelic()

  Is this bi-allelic (based ONLY on the number of ALTs) WARINIG: You should use 'calcHetero()' method for a more precise calculation.

• isCompressedGenotypes

  public boolean isCompressedGenotypes()

  Do we have compressed genotypes in "HO,HE,NA" INFO fields?

• isFilterPass

  public boolean isFilterPass()

• isMultiallelic

  public boolean isMultiallelic()

  Is this multi-allelic (based ONLY on the number of ALTs) WARINIG: You should use 'calcHetero()' method for a more precise calculation.

• isShowWarningIfParentDoesNotInclude

  protected boolean isShowWarningIfParentDoesNotInclude()

  Description copied from class: Marker

  Show an error if parent does not include child?

  Overrides:

  isShowWarningIfParentDoesNotInclude in class Marker

• isSingleSnp

  public boolean isSingleSnp()

  Is thins a VCF entry with a single SNP?

• isSingleton

  public boolean isSingleton()

  Is this variant a singleton (appears only in one genotype)

• isVariant

  public boolean isVariant()

  Is this a change or are the ALTs actually the same as the reference

• isVariant

  public boolean isVariant(String alt)

  Is this ALT string a variant?

• iterator

  public Iterator<VcfGenotype> iterator()

  Specified by:

  iterator in interface Iterable<VcfGenotype>

• mac

  public int mac()

  Calculate Minor allele count

• maf

  public double maf()

  Calculate Minor allele frequency

• parse

  public void parse()

  Parse a 'line' from a 'vcfFileIterator'

• parseLof

  public List<VcfLof> parseLof()

  Parse LOF from VcfEntry

• parseNmd

  public List<VcfNmd> parseNmd()

  Parse NMD from VcfEntry

• removeInfo

  public void removeInfo(String key)

  Remove INFO field

• rmInfo

  public boolean rmInfo(String info)

  Parse INFO fields

• setFilter

  public void setFilter(String filter)

• setFormat

  public void setFormat(String format)

• setGenotypeStr

  public void setGenotypeStr(String genotypeFieldsStr)

• setLineNum

  public void setLineNum(int lineNum)

• toStr

  public String toStr()

  To string as a simple "CHR:START_REF/ALTs" format

  Overrides:

  toStr in class Interval

• toString

  public String toString()

  Overrides:

  toString in class Marker

• toStringNoGt

  public String toStringNoGt()

  Show only first eight fields (no genotype entries)

• uncompressGenotypes

  public VcfEntry uncompressGenotypes()

  Uncompress VCF entry having genotypes in "HO,HE,NA" fields

• variants

  public List<Variant> variants()

  Create a list of variants from this VcfEntry