Package htsjdk.variant.variantcontext

Examples of htsjdk.variant.variantcontext.VariantContextComparator.compare()

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            final CloseableIterator<VariantContext> variantIterator = in.iterator();
            if (variantIterator.hasNext()) {
                final VariantContext currentContext = variantIterator.next();
                if (lastContext != null) {
                    if (comparator.compare(lastContext, currentContext) >= 0) {
                        throw new IllegalArgumentException("First record in file " + f.getAbsolutePath() + " is not after first record in " +
                                "previous file " + lastFile.getAbsolutePath());
                    }
                }
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                comparator = new VariantContextComparator(firstHeader.getContigLines());
            }

            if (lastContext != null && variantIterator.hasNext()) {
                final VariantContext vc = variantIterator.peek();
                if (comparator.compare(vc, lastContext) <= 0) {
                    throw new IllegalStateException("First variant in file " + f.getAbsolutePath() + " is at " + vc.getSource() +
                            " but last variant in earlier file " + lastFile.getAbsolutePath() + " is at " + lastContext.getSource());
                }
            }
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        final CloseableIterator<VariantContext> iterator = outputReader.iterator();
        while (iterator.hasNext()) {
            final VariantContext outputContext = iterator.next();
            if (outputContext.isIndel()) Assert.assertEquals(getContigPosition(outputContext), indelContigPositions.poll());
            if (outputContext.isSNP()) Assert.assertEquals(getContigPosition(outputContext), snpContigPositions.poll());
            if (last != null) Assert.assertTrue(outputComparator.compare(last, outputContext) <= 0);
            last = outputContext;
        }
        iterator.close();

        // We should have polled everything off the indel (snp) queues
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                if (position.equals(positionQueue.peek())) {
                    positionQueue.poll();
                    break;
                }
            }
            if (last != null) Assert.assertTrue(outputComparator.compare(last, outputContext) <= 0);
            last = outputContext;
        }
        iterator.close();

        for (final Queue<String> positionQueue : positionQueues) {
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        VariantContext last = null;
        int variantContextCount = 0;
        final CloseableIterator<VariantContext> iterator = outputReader.iterator();
        while (iterator.hasNext()) {
            final VariantContext outputContext = iterator.next();
            if (last != null) Assert.assertTrue(outputComparator.compare(last, outputContext) <= 0);
            last = outputContext;
            variantContextCount++;
        }
        iterator.close();
        Assert.assertEquals(variantContextCount, expectedVariantContextCount);
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