static QueryInterval [ ] prepareQueryIntervals ( final List < Interval > rawIntervals , final SAMSequenceDictionary sequenceDictionary ) { if ( rawIntervals == null || rawIntervals . isEmpty ( ) ) { return null ; } // Convert each SimpleInterval to a QueryInterval final QueryInterval [ ] convertedIntervals = rawIntervals . stream ( ) . map ( rawInterval -> convertSimpleIntervalToQueryInterval ( rawInterval , sequenceDictionary ) ) . toArray ( QueryInterval [ ] :: new ) ; // Intervals must be optimized (sorted and merged) in order to use the htsjdk query API return QueryInterval . optimizeIntervals ( convertedIntervals ) ; }
Converts a List of SimpleIntervals into the format required by the SamReader query API