/** * Checks to see if the two sets of coordinates have any overlap. */ public static boolean overlaps(final int start, final int end, final int start2, final int end2) { return (start2 >= start && start2 <= end) || (end2 >=start && end2 <= end) || encloses(start2, end2, start, end); }
/** * Checks to see if the two sets of coordinates have any overlap. */ public static boolean overlaps(final int start, final int end, final int start2, final int end2) { return (start2 >= start && start2 <= end) || (end2 >=start && end2 <= end) || encloses(start2, end2, start, end); }
/** * Checks to see if the two sets of coordinates have any overlap. */ public static boolean overlaps(final int start, final int end, final int start2, final int end2) { return (start2 >= start && start2 <= end) || (end2 >=start && end2 <= end) || encloses(start2, end2, start, end); }
/** * Determines whether this interval contains the entire region represented by other * (in other words, whether it covers it). * * * @param other interval to check * @return true if this interval contains all of the base positions spanned by other, otherwise false */ default boolean contains(Locatable other) { return contigsMatch(other) && CoordMath.encloses(getStart(), getEnd(), other.getStart(), other.getEnd()); }
/** * Determines whether this interval contains the entire region represented by other * (in other words, whether it covers it). * * * @param other interval to check * @return true if this interval contains all of the base positions spanned by other, otherwise false */ default boolean contains(Locatable other) { return contigsMatch(other) && CoordMath.encloses(getStart(), getEnd(), other.getStart(), other.getEnd()); }
public static IntervalComparison compareIntervalToRecord(final QueryInterval interval, final SAMRecord record) { // interval.end <= 0 implies the end of the reference sequence. final int intervalEnd = (interval.end <= 0? Integer.MAX_VALUE: interval.end); final int alignmentEnd; if (record.getReadUnmappedFlag() && record.getAlignmentStart() != SAMRecord.NO_ALIGNMENT_START) { // Unmapped read with coordinate of mate. alignmentEnd = record.getAlignmentStart(); } else { alignmentEnd = record.getAlignmentEnd(); } if (interval.referenceIndex < record.getReferenceIndex()) return IntervalComparison.BEFORE; else if (interval.referenceIndex > record.getReferenceIndex()) return IntervalComparison.AFTER; else if (intervalEnd < record.getAlignmentStart()) return IntervalComparison.BEFORE; else if (alignmentEnd < interval.start) return IntervalComparison.AFTER; else if (CoordMath.encloses(interval.start, intervalEnd, record.getAlignmentStart(), alignmentEnd)) { return IntervalComparison.CONTAINED; } else return IntervalComparison.OVERLAPPING; } }
private IntervalComparison compareIntervalToRecord(final QueryInterval interval, final SAMRecord record) { // interval.end <= 0 implies the end of the reference sequence. final int intervalEnd = (interval.end <= 0? Integer.MAX_VALUE: interval.end); final int alignmentEnd; if (record.getReadUnmappedFlag() && record.getAlignmentStart() != SAMRecord.NO_ALIGNMENT_START) { // Unmapped read with coordinate of mate. alignmentEnd = record.getAlignmentStart(); } else { alignmentEnd = record.getAlignmentEnd(); } if (interval.referenceIndex < record.getReferenceIndex()) return IntervalComparison.BEFORE; else if (interval.referenceIndex > record.getReferenceIndex()) return IntervalComparison.AFTER; else if (intervalEnd < record.getAlignmentStart()) return IntervalComparison.BEFORE; else if (alignmentEnd < interval.start) return IntervalComparison.AFTER; else if (CoordMath.encloses(interval.start, intervalEnd, record.getAlignmentStart(), alignmentEnd)) { return IntervalComparison.CONTAINED; } else return IntervalComparison.OVERLAPPING; } }
public static IntervalComparison compareIntervalToRecord(final QueryInterval interval, final SAMRecord record) { // interval.end <= 0 implies the end of the reference sequence. final int intervalEnd = (interval.end <= 0? Integer.MAX_VALUE: interval.end); final int alignmentEnd; if (record.getReadUnmappedFlag() && record.getAlignmentStart() != SAMRecord.NO_ALIGNMENT_START) { // Unmapped read with coordinate of mate. alignmentEnd = record.getAlignmentStart(); } else { alignmentEnd = record.getAlignmentEnd(); } if (interval.referenceIndex < record.getReferenceIndex()) return IntervalComparison.BEFORE; else if (interval.referenceIndex > record.getReferenceIndex()) return IntervalComparison.AFTER; else if (intervalEnd < record.getAlignmentStart()) return IntervalComparison.BEFORE; else if (alignmentEnd < interval.start) return IntervalComparison.AFTER; else if (CoordMath.encloses(interval.start, intervalEnd, record.getAlignmentStart(), alignmentEnd)) { return IntervalComparison.CONTAINED; } else return IntervalComparison.OVERLAPPING; } }
if (properOrientation && CoordMath.encloses(gene.getStart(), gene.getEnd(), leftMostAlignedBase, rightMostAlignedBase)) { if (negativeReadStrand == negativeTranscriptionStrand) { ++metrics.NUM_R1_TRANSCRIPT_STRAND_READS;
if (properOrientation && CoordMath.encloses(gene.getStart(), gene.getEnd(), leftMostAlignedBase, rightMostAlignedBase)) { if (negativeReadStrand == negativeTranscriptionStrand) { ++metrics.NUM_R1_TRANSCRIPT_STRAND_READS;