Class HtsIntervalUtils

Method Details

• toQueryInterval

  @InternalAPI public static QueryInterval toQueryInterval(HtsInterval interval, SAMSequenceDictionary dictionary)

  Convert an HtsInterval to a QueryInterval

  Parameters:

  interval - HtsInterval to convert

  dictionary - sequence dictionary to use to convert string query names to contig index

  Returns:

  a QueryInterval equivalent to interval

• toLocatable

  @InternalAPI public static Locatable toLocatable(HtsInterval interval)

  Convert an HtsInterval to a Locatable

  Parameters:

  interval - HtsInterval to convert

  Returns:

  a Locatable equivalent to interval

• toLocatableList

  @InternalAPI public static List<Locatable> toLocatableList(List<HtsInterval> intervals)

  Convert a List of HtsInterval to a list of Locatable.

  Parameters:

  intervals - list of HtsIntervals to convert

  Returns:

  a list of Locatable

• toQueryIntervalArray

  @InternalAPI public static QueryInterval[] toQueryIntervalArray(List<HtsInterval> intervals, SAMSequenceDictionary dictionary)

  Convert a list of HtsInterval to an array of QueryInterval

  Parameters:

  intervals - list of HtsIntervals to convert

  dictionary - sequence dictionary to use

  Returns:

  array of QueryInterval

• fromQueryIntervalArray

  @InternalAPI public static List<HtsInterval> fromQueryIntervalArray(QueryInterval[] queryIntervals, SAMSequenceDictionary dictionary)

  Parameters:

  queryIntervals - list of QueryInterval to convert

  dictionary - sequence dictionary to use for the conversion

  Returns:

  list of HtsInterval

• toIntegerSafe

  @InternalAPI public static int toIntegerSafe(long coord)

  Convert a long coordinate to an integer, for use with interconverting between old style integer coordinates and new style long coordinates. Throws on overflow.

  Parameters:

  coord - long coordinate to convert

  Returns:

  an integer representation of coord if the conversion is safe

  Throws:

  IllegalArgumentException - if converting results in overflow