/** * Prepare to filter out SAMRecords that do not overlap the given list of intervals * @param intervals -- must be locus-ordered & non-overlapping */ public IntervalFilter(final List<Interval> intervals, final SAMFileHeader samHeader) { this.samHeader = samHeader; IntervalUtil.assertOrderedNonOverlapping(intervals.iterator(), samHeader.getSequenceDictionary()); this.intervals = intervals.iterator(); advanceInterval(); }
/** Return true if the sequence/position lie in the provided interval list. */ public static boolean contains(final IntervalList intervalList, final String sequenceName, final long position) { for (final Interval interval : intervalList.getUniqueIntervals()) { if (contains(interval, sequenceName, position)) return true; } return false; }
/** * Prepare to filter out SAMRecords that do not overlap the given list of intervals * @param intervals -- must be locus-ordered & non-overlapping */ public IntervalFilter(final List<Interval> intervals, final SAMFileHeader samHeader) { this.samHeader = samHeader; IntervalUtil.assertOrderedNonOverlapping(intervals.iterator(), samHeader.getSequenceDictionary()); this.intervals = intervals.iterator(); advanceInterval(); }
/** Return true if the sequence/position lie in the provided interval list. */ public static boolean contains(final IntervalList intervalList, final String sequenceName, final long position) { for (final Interval interval : intervalList.uniqued().getIntervals()) { if (contains(interval, sequenceName, position)) return true; } return false; }
/** * Prepare to filter out SAMRecords that do not overlap the given list of intervals * @param intervals -- must be locus-ordered & non-overlapping */ public IntervalFilter(final List<Interval> intervals, final SAMFileHeader samHeader) { this.samHeader = samHeader; IntervalUtil.assertOrderedNonOverlapping(intervals.iterator(), samHeader.getSequenceDictionary()); this.intervals = intervals.iterator(); advanceInterval(); }
/** Return true if the sequence/position lie in the provided interval list. */ public static boolean contains(final IntervalList intervalList, final String sequenceName, final long position) { for (final Interval interval : intervalList.uniqued().getIntervals()) { if (contains(interval, sequenceName, position)) return true; } return false; }