Package htsjdk.variant.variantcontext

Class CommonInfo

java.lang.Object
htsjdk.variant.variantcontext.CommonInfo
All Implemented Interfaces:
Serializable
public final class CommonInfo extends Object implements Serializable
Common utility routines for VariantContext and Genotype
See Also:

  • Field Details

  • Constructor Details

  • Method Details

    • 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)

    • addFilters

      public void addFilters(Collection<String> filters)

    • 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)

    • getAttribute

      public Object getAttribute(String key, Object defaultValue)

    • 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)

    • getAttributeAsIntList

      public List<Integer> getAttributeAsIntList(String key, Integer 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)