Package htsjdk.samtools

Examples of htsjdk.samtools.SecondaryOrSupplementarySkippingIterator.advance()

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            }
            // Advance the right iterator until it is >= the left reads that have just been grabbed
            while (itRight.hasCurrent() && compareAlignmentCoordinates(left, itRight.getCurrent()) > 0) {
                final SAMRecord right = itRight.getCurrent();
                rightUnmatched.put(right.getReadName(), right);
                itRight.advance();
            }
            // For each right read that has the same coordinate as the current left reads,
            // see if there is a matching left read.  If so, process and discard.  If not,
            // save the right read for later.
            for (;itRight.hasCurrent() && compareAlignmentCoordinates(left, itRight.getCurrent()) == 0; itRight.advance()) {
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                itRight.advance();
            }
            // For each right read that has the same coordinate as the current left reads,
            // see if there is a matching left read.  If so, process and discard.  If not,
            // save the right read for later.
            for (;itRight.hasCurrent() && compareAlignmentCoordinates(left, itRight.getCurrent()) == 0; itRight.advance()) {
                final SAMRecord right = itRight.getCurrent();
                final SAMRecord matchingLeft = leftCurrentCoordinate.remove(right.getReadName());
                if (matchingLeft != null) {
                    ret = tallyAlignmentRecords(matchingLeft, right) && ret;
                } else {
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                leftUnmatched.put(samRecord.getReadName(), samRecord);
            }
        }
        // The left iterator has been exhausted.  See if any of the remaining right reads
        // match any of the saved left reads.
        for( ; itRight.hasCurrent(); itRight.advance()) {
            final SAMRecord right = itRight.getCurrent();
            final SAMRecord left = leftUnmatched.remove(right.getReadName());
            if (left != null) {
                tallyAlignmentRecords(left, right);
            } else {
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                ++missingRight;
                it1.advance();
                ret = false;
            } else if (cmp > 0) {
                ++missingLeft;
                it2.advance();
                ret = false;
            } else {
                if (!tallyAlignmentRecords(it1.getCurrent(), it2.getCurrent())) {
                    ret = false;
                }
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            } else {
                if (!tallyAlignmentRecords(it1.getCurrent(), it2.getCurrent())) {
                    ret = false;
                }
                it1.advance();
                it2.advance();
            }
        }
        if (it2.hasCurrent()) {
            missingLeft += countRemaining(it2);
            return false;
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    private boolean compareUnsortedAlignments() {
        final SecondaryOrSupplementarySkippingIterator it1 = new SecondaryOrSupplementarySkippingIterator(samReaders[0].iterator());
        final SecondaryOrSupplementarySkippingIterator it2 = new SecondaryOrSupplementarySkippingIterator(samReaders[1].iterator());
        boolean ret = true;
        for (; it1.hasCurrent(); it1.advance(), it2.advance()) {
            if (!it2.hasCurrent()) {
                missingRight += countRemaining(it1);
                return false;
            }
            final SAMRecord s1 = it1.getCurrent();
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