Class CommonInfo

    • Method Detail

      • getName

        public String getName()
        Returns:
        the name
      • setName

        public void setName​(String name)
        Sets the name
        Parameters:
        name - the name associated with this information
      • getFiltersMaybeNull

        public Set<String> getFiltersMaybeNull()
      • getFilters

        public Set<String> getFilters()
      • filtersWereApplied

        public boolean filtersWereApplied()
      • isFiltered

        public boolean isFiltered()
      • isNotFiltered

        public boolean isNotFiltered()
      • addFilter

        public void addFilter​(String filter)
      • hasLog10PError

        public boolean hasLog10PError()
      • getLog10PError

        public double getLog10PError()
        Returns:
        the -1 * log10-based error estimate
      • getPhredScaledQual

        public double getPhredScaledQual()
        Floating-point arithmetic allows signed zeros such as +0.0 and -0.0. Adding the constant 0.0 to the result ensures that the returned value is never -0.0 since (-0.0) + 0.0 = 0.0. When this is set to '0.0', the resulting VCF would be 0 instead of -0.
        Returns:
        double - Phred scaled quality score
      • setLog10PError

        public void setLog10PError​(double log10PError)
      • clearAttributes

        public void clearAttributes()
      • getAttributes

        public Map<String,​Object> getAttributes()
        Returns:
        the attribute map
      • setAttributes

        public void setAttributes​(Map<String,​?> map)
      • putAttribute

        public void putAttribute​(String key,
                                 Object value)
      • putAttribute

        public void putAttribute​(String key,
                                 Object value,
                                 boolean allowOverwrites)
      • removeAttribute

        public void removeAttribute​(String key)
      • putAttributes

        public void putAttributes​(Map<String,​?> map)
      • hasAttribute

        public boolean hasAttribute​(String key)
      • getNumAttributes

        public int getNumAttributes()
      • getAttribute

        public Object getAttribute​(String key)
        Parameters:
        key - the attribute key
        Returns:
        the attribute value for the given key (or null if not set)
      • getAttributeAsList

        public List<Object> getAttributeAsList​(String key)
        Gets the attributes from a key as a list. Note: int[] and double[] arrays are boxed.
        Returns:
        empty list if the key was not found; Collections.singletonList(Object) if there is only one value; a list containing the values if the value is a List or array.
      • getAttributeAsStringList

        public List<String> getAttributeAsStringList​(String key,
                                                     String defaultValue)
      • getAttributeAsDoubleList

        public List<Double> getAttributeAsDoubleList​(String key,
                                                     Double defaultValue)
      • getAttributeAsString

        public String getAttributeAsString​(String key,
                                           String defaultValue)
      • getAttributeAsInt

        public int getAttributeAsInt​(String key,
                                     int defaultValue)
      • getAttributeAsDouble

        public double getAttributeAsDouble​(String key,
                                           double defaultValue)
      • getAttributeAsBoolean

        public boolean getAttributeAsBoolean​(String key,
                                             boolean defaultValue)