/** * Converts a List of SimpleIntervals into the format required by the SamReader query API * @param rawIntervals SimpleIntervals to be converted * @return A sorted, merged list of QueryIntervals suitable for passing to the SamReader query API */ 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 * @param rawIntervals SimpleIntervals to be converted * @return A sorted, merged list of QueryIntervals suitable for passing to the SamReader query API */ 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 * @param rawIntervals SimpleIntervals to be converted * @return A sorted, merged list of QueryIntervals suitable for passing to the SamReader query API */ 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); } /**