Package htsjdk.beta.plugin.interval

Class HtsQueryInterval

java.lang.Object
htsjdk.beta.plugin.interval.HtsQueryInterval
All Implemented Interfaces:
HtsInterval
public class HtsQueryInterval extends Object implements HtsInterval
An concrete query interval implementation of HtsInterval used for random access queries on file formats represented by HtsDecoders that support random access.

  • Constructor Details

    • HtsQueryInterval

      public HtsQueryInterval(String queryName, long start, long end)
      Create an HtsQueryInterval from query components
      Parameters:
      queryName - the string query nae
      start - the integer start position
      end - the end position

    • HtsQueryInterval

      public HtsQueryInterval(QueryInterval queryInterval, SAMSequenceDictionary dictionary)
      Convenience method for creating a query interval from an old-style QueryInterval.
      Parameters:
      queryInterval - the query interval to convert
      dictionary - the sequence dictionary to use to do the conversion

  • Method Details

    • getQueryName

      public String getQueryName()
      Description copied from interface: HtsInterval
      Get the name part of this interval query.
      Specified by:
      getQueryName in interface HtsInterval
      Returns:
      the name part of this interval query

    • getStart

      public long getStart()
      Description copied from interface: HtsInterval
      Get the 1-based inclusive start coordinate for this interval.
      Specified by:
      getStart in interface HtsInterval
      Returns:
      the 1-based inclusive start coordinate for this interval

    • getEnd

      public long getEnd()
      Description copied from interface: HtsInterval
      Get the inclusive end coordinate for this interval.
      Specified by:
      getEnd in interface HtsInterval
      Returns:
      the inclusive end coordinate for this interval