Package htsjdk.variant.variantcontext

Examples of htsjdk.variant.variantcontext.VariantContextComparator

89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
     * (snp) queue is the same. Also make sure that the context is in the order
     * specified by the input files.
     */
    private void validateSnpAndIndelResults(final File output, final Queue<String> indelContigPositions, final Queue<String> snpContigPositions) {
        final VCFFileReader outputReader = new VCFFileReader(output, false);
        final VariantContextComparator outputComparator = outputReader.getFileHeader().getVCFRecordComparator();
        VariantContext last = null;
        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
View Full Code Here
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
        validateResultsForMultipleInputs(output, positionQueues);
  }

    private void validateResultsForMultipleInputs(final File output, final List<Queue<String>> positionQueues) {
        final VCFFileReader outputReader = new VCFFileReader(output, false);
        final VariantContextComparator outputComparator = outputReader.getFileHeader().getVCFRecordComparator();
        VariantContext last = null;
        final CloseableIterator<VariantContext> iterator = outputReader.iterator();
        while (iterator.hasNext()) {
            final VariantContext outputContext = iterator.next();
            final String position = getContigPosition(outputContext);
            for (final Queue<String> positionQueue : positionQueues) {
                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) {
View Full Code Here
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
     * @param output VCF file representing the output of SortVCF
     * @param expectedVariantContextCount the total number of variant context entries from all input files that were merged/sorted
     */
    private void validateSortingResults(final File output, final int expectedVariantContextCount) {
        final VCFFileReader outputReader = new VCFFileReader(output, false);
        final VariantContextComparator outputComparator = outputReader.getFileHeader().getVCFRecordComparator();
        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);
View Full Code Here
TOP

Related Classes of htsjdk.variant.variantcontext.VariantContextComparator

  • picard.vcf.AbstractVcfMergingClpTester
  • picard.vcf.GatherVcfs
  • picard.vcf.MergeVcfs
  • picard.vcf.PairedVariantSubContextIterator
  • picard.vcf.SortVcfsTest
  • picard.vcf.VariantContextComparatorTest
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.