/*
* The MIT License
*
* Copyright (c) 2009 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package picard.analysis;
import htsjdk.samtools.metrics.MetricsFile;
import org.testng.Assert;
import org.testng.annotations.Test;
import picard.cmdline.CommandLineProgramTest;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.text.NumberFormat;
/**
* Tests CollectAlignmentSummaryStatistics
*
* @author Doug Voet (dvoet at broadinstitute dot org)
*/
public class CollectAlignmentSummaryMetricsTest extends CommandLineProgramTest {
private static final File TEST_DATA_DIR = new File("testdata/picard/sam");
public String getCommandLineProgramName() {
return CollectAlignmentSummaryMetrics.class.getSimpleName();
}
@Test
public void test() throws IOException {
final File input = new File(TEST_DATA_DIR, "summary_alignment_stats_test.sam");
final File reference = new File(TEST_DATA_DIR, "summary_alignment_stats_test.fasta");
final File outfile = File.createTempFile("alignmentMetrics", ".txt");
outfile.deleteOnExit();
final String[] args = new String[] {
"INPUT=" + input.getAbsolutePath(),
"OUTPUT=" + outfile.getAbsolutePath(),
"REFERENCE_SEQUENCE=" + reference.getAbsolutePath(),
};
Assert.assertEquals(runPicardCommandLine(args), 0);
final MetricsFile<AlignmentSummaryMetrics, Comparable<?>> output = new MetricsFile<AlignmentSummaryMetrics, Comparable<?>>();
output.read(new FileReader(outfile));
for (final AlignmentSummaryMetrics metrics : output.getMetrics()) {
Assert.assertEquals(metrics.MEAN_READ_LENGTH, 101.0);
switch (metrics.CATEGORY) {
case FIRST_OF_PAIR:
Assert.assertEquals(metrics.TOTAL_READS, 9);
Assert.assertEquals(metrics.PF_READS, 7);
Assert.assertEquals(metrics.PF_NOISE_READS, 1);
Assert.assertEquals(metrics.PF_HQ_ALIGNED_READS, 3);
Assert.assertEquals(metrics.PF_HQ_ALIGNED_Q20_BASES, 59);
Assert.assertEquals(metrics.PF_HQ_MEDIAN_MISMATCHES, 19.0);
Assert.assertEquals(metrics.PF_ALIGNED_BASES, 303);
Assert.assertEquals(metrics.PF_MISMATCH_RATE, /*58D/303D*/0.191419);
Assert.assertEquals(metrics.BAD_CYCLES, 19);
break;
case SECOND_OF_PAIR:
Assert.assertEquals(metrics.TOTAL_READS, 9);
Assert.assertEquals(metrics.PF_READS, 9);
Assert.assertEquals(metrics.PF_NOISE_READS, 1);
Assert.assertEquals(metrics.PF_HQ_ALIGNED_READS, 7);
Assert.assertEquals(metrics.PF_HQ_ALIGNED_Q20_BASES, 239);
Assert.assertEquals(metrics.PF_HQ_MEDIAN_MISMATCHES, 3.0);
Assert.assertEquals(metrics.PF_ALIGNED_BASES, 707);
Assert.assertEquals(metrics.PF_MISMATCH_RATE, /*19D/707D*/0.026874);
Assert.assertEquals(metrics.BAD_CYCLES, 3);
break;
case PAIR:
Assert.assertEquals(metrics.TOTAL_READS, 18);
Assert.assertEquals(metrics.PF_READS, 16);
Assert.assertEquals(metrics.PF_NOISE_READS, 2);
Assert.assertEquals(metrics.PF_HQ_ALIGNED_READS, 10);
Assert.assertEquals(metrics.PF_HQ_ALIGNED_Q20_BASES, 298);
Assert.assertEquals(metrics.PF_HQ_MEDIAN_MISMATCHES, 3.0);
Assert.assertEquals(metrics.PF_ALIGNED_BASES, 1010);
Assert.assertEquals(metrics.PF_MISMATCH_RATE, /*77D/1010D*/0.076238);
Assert.assertEquals(metrics.BAD_CYCLES, 22);
break;
case UNPAIRED:
default:
Assert.fail("Data does not contain this category: " + metrics.CATEGORY);
}
}
}
@Test
public void testBisulfite() throws IOException {
final File input = new File(TEST_DATA_DIR, "summary_alignment_bisulfite_test.sam");
final File reference = new File(TEST_DATA_DIR, "summary_alignment_stats_test.fasta");
final File outfile = File.createTempFile("alignmentMetrics", ".txt");
outfile.deleteOnExit();
final String[] args = new String[] {
"INPUT=" + input.getAbsolutePath(),
"OUTPUT=" + outfile.getAbsolutePath(),
"REFERENCE_SEQUENCE=" + reference.getAbsolutePath(),
"IS_BISULFITE_SEQUENCED=true"
};
Assert.assertEquals(runPicardCommandLine(args), 0);
final NumberFormat format = NumberFormat.getInstance();
format.setMaximumFractionDigits(4);
final MetricsFile<AlignmentSummaryMetrics, Comparable<?>> output = new MetricsFile<AlignmentSummaryMetrics, Comparable<?>>();
output.read(new FileReader(outfile));
for (final AlignmentSummaryMetrics metrics : output.getMetrics()) {
Assert.assertEquals(metrics.MEAN_READ_LENGTH, 101.0);
switch (metrics.CATEGORY) {
case FIRST_OF_PAIR:
// 19 no-calls, one potentially methylated base, one mismatch at a potentially methylated base
Assert.assertEquals(metrics.TOTAL_READS, 1);
Assert.assertEquals(metrics.PF_READS, 1);
Assert.assertEquals(metrics.PF_HQ_ALIGNED_BASES, 101);
Assert.assertEquals(metrics.PF_HQ_MEDIAN_MISMATCHES, 20.0);
Assert.assertEquals(metrics.PF_ALIGNED_BASES, 101);
Assert.assertEquals(metrics.PF_MISMATCH_RATE, 20D/100D);
Assert.assertEquals(metrics.BAD_CYCLES, 20);
Assert.assertEquals(format.format(metrics.PF_HQ_ERROR_RATE), format.format(20/(double)100));
break;
case SECOND_OF_PAIR:
// Three no-calls, two potentially methylated bases
Assert.assertEquals(metrics.TOTAL_READS, 1);
Assert.assertEquals(metrics.PF_READS, 1);
Assert.assertEquals(metrics.PF_HQ_ALIGNED_BASES, 101);
Assert.assertEquals(metrics.PF_HQ_MEDIAN_MISMATCHES, 3.0);
Assert.assertEquals(metrics.PF_ALIGNED_BASES, 101);
Assert.assertEquals(metrics.PF_MISMATCH_RATE, /*3D/99D*/0.030303);
Assert.assertEquals(metrics.BAD_CYCLES, 3);
Assert.assertEquals(format.format(metrics.PF_HQ_ERROR_RATE), format.format(3/(double)99));
break;
case PAIR:
Assert.assertEquals(metrics.TOTAL_READS, 2);
Assert.assertEquals(metrics.PF_READS, 2);
Assert.assertEquals(metrics.PF_HQ_ALIGNED_BASES, 202);
Assert.assertEquals(metrics.PF_HQ_MEDIAN_MISMATCHES, 11.5);
Assert.assertEquals(metrics.PF_ALIGNED_BASES, 202);
Assert.assertEquals(metrics.PF_MISMATCH_RATE, /*23D/199D*/0.115578);
Assert.assertEquals(metrics.BAD_CYCLES, 23);
Assert.assertEquals(format.format(metrics.PF_HQ_ERROR_RATE), format.format(23/(double)199));
break;
case UNPAIRED:
default:
Assert.fail("Data does not contain this category: " + metrics.CATEGORY);
}
}
}
@Test
public void testNoReference() throws IOException {
final File input = new File(TEST_DATA_DIR, "summary_alignment_stats_test.sam");
final File outfile = File.createTempFile("alignmentMetrics", ".txt");
outfile.deleteOnExit();
final String[] args = new String[] {
"INPUT=" + input.getAbsolutePath(),
"OUTPUT=" + outfile.getAbsolutePath(),
};
Assert.assertEquals(runPicardCommandLine(args), 0);
final MetricsFile<AlignmentSummaryMetrics, Comparable<?>> output = new MetricsFile<AlignmentSummaryMetrics, Comparable<?>>();
output.read(new FileReader(outfile));
for (final AlignmentSummaryMetrics metrics : output.getMetrics()) {
Assert.assertEquals(metrics.MEAN_READ_LENGTH, 101.0);
switch (metrics.CATEGORY) {
case FIRST_OF_PAIR:
Assert.assertEquals(metrics.TOTAL_READS, 9);
Assert.assertEquals(metrics.PF_READS, 7);
Assert.assertEquals(metrics.PF_NOISE_READS, 1);
Assert.assertEquals(metrics.PF_HQ_ALIGNED_READS, 0);
Assert.assertEquals(metrics.PF_HQ_ALIGNED_Q20_BASES, 0);
Assert.assertEquals(metrics.PF_HQ_MEDIAN_MISMATCHES, 0.0);
Assert.assertEquals(metrics.PF_ALIGNED_BASES, 0);
Assert.assertEquals(metrics.PF_MISMATCH_RATE, 0.0);
Assert.assertEquals(metrics.BAD_CYCLES, 19);
break;
case SECOND_OF_PAIR:
Assert.assertEquals(metrics.TOTAL_READS, 9);
Assert.assertEquals(metrics.PF_READS, 9);
Assert.assertEquals(metrics.PF_NOISE_READS, 1);
Assert.assertEquals(metrics.PF_HQ_ALIGNED_READS, 0);
Assert.assertEquals(metrics.PF_HQ_ALIGNED_Q20_BASES, 0);
Assert.assertEquals(metrics.PF_HQ_MEDIAN_MISMATCHES, 0.0);
Assert.assertEquals(metrics.PF_ALIGNED_BASES, 0);
Assert.assertEquals(metrics.PF_MISMATCH_RATE, 0.0);
Assert.assertEquals(metrics.BAD_CYCLES, 3);
break;
case PAIR:
Assert.assertEquals(metrics.TOTAL_READS, 18);
Assert.assertEquals(metrics.PF_READS, 16);
Assert.assertEquals(metrics.PF_NOISE_READS, 2);
Assert.assertEquals(metrics.PF_HQ_ALIGNED_READS, 0);
Assert.assertEquals(metrics.PF_HQ_ALIGNED_Q20_BASES, 0);
Assert.assertEquals(metrics.PF_HQ_MEDIAN_MISMATCHES, 0.0);
Assert.assertEquals(metrics.PF_ALIGNED_BASES, 0);
Assert.assertEquals(metrics.PF_MISMATCH_RATE, 0.0);
Assert.assertEquals(metrics.BAD_CYCLES, 22);
break;
case UNPAIRED:
default:
Assert.fail("Data does not contain this category: " + metrics.CATEGORY);
}
}
}
@Test
public void testZeroLengthReads() throws IOException {
final File input = new File(TEST_DATA_DIR, "summary_alignment_stats_test2.sam");
final File outfile = File.createTempFile("alignmentMetrics", ".txt");
outfile.deleteOnExit();
final String[] args = new String[] {
"INPUT=" + input.getAbsolutePath(),
"OUTPUT=" + outfile.getAbsolutePath(),
};
Assert.assertEquals(runPicardCommandLine(args), 0);
final MetricsFile<AlignmentSummaryMetrics, Comparable<?>> output = new MetricsFile<AlignmentSummaryMetrics, Comparable<?>>();
output.read(new FileReader(outfile));
for (final AlignmentSummaryMetrics metrics : output.getMetrics()) {
// test that it doesn't blow up
}
}
@Test
public void testMultipleLevelsOfMetrics() throws IOException {
final File input = new File(TEST_DATA_DIR, "summary_alignment_stats_test_multiple.sam");
final File outfile = File.createTempFile("alignmentMetrics", ".txt");
outfile.deleteOnExit();
final String[] args = new String[] {
"INPUT=" + input.getAbsolutePath(),
"OUTPUT=" + outfile.getAbsolutePath(),
"METRIC_ACCUMULATION_LEVEL=ALL_READS",
"METRIC_ACCUMULATION_LEVEL=SAMPLE",
"METRIC_ACCUMULATION_LEVEL=LIBRARY",
"METRIC_ACCUMULATION_LEVEL=READ_GROUP",
};
Assert.assertEquals(runPicardCommandLine(args), 0);
final MetricsFile<AlignmentSummaryMetrics, Comparable<?>> output = new MetricsFile<AlignmentSummaryMetrics, Comparable<?>>();
output.read(new FileReader(outfile));
for (final AlignmentSummaryMetrics metrics : output.getMetrics()) {
Assert.assertEquals(metrics.MEAN_READ_LENGTH, 101.0);
if (metrics.SAMPLE == null) {
switch (metrics.CATEGORY) {
case FIRST_OF_PAIR:
Assert.assertEquals(metrics.TOTAL_READS, 9);
Assert.assertEquals(metrics.PF_READS, 7);
Assert.assertEquals(metrics.PF_NOISE_READS, 1);
Assert.assertEquals(metrics.PF_HQ_ALIGNED_READS, 0);
Assert.assertEquals(metrics.PF_HQ_ALIGNED_Q20_BASES, 0);
Assert.assertEquals(metrics.PF_HQ_MEDIAN_MISMATCHES, 0.0);
Assert.assertEquals(metrics.PF_ALIGNED_BASES, 0);
Assert.assertEquals(metrics.PF_MISMATCH_RATE, 0.0);
Assert.assertEquals(metrics.BAD_CYCLES, 19);
break;
case SECOND_OF_PAIR:
Assert.assertEquals(metrics.TOTAL_READS, 9);
Assert.assertEquals(metrics.PF_READS, 9);
Assert.assertEquals(metrics.PF_NOISE_READS, 1);
Assert.assertEquals(metrics.PF_HQ_ALIGNED_READS, 0);
Assert.assertEquals(metrics.PF_HQ_ALIGNED_Q20_BASES, 0);
Assert.assertEquals(metrics.PF_HQ_MEDIAN_MISMATCHES, 0.0);
Assert.assertEquals(metrics.PF_ALIGNED_BASES, 0);
Assert.assertEquals(metrics.PF_MISMATCH_RATE, 0.0);
Assert.assertEquals(metrics.BAD_CYCLES, 3);
break;
case PAIR:
Assert.assertEquals(metrics.TOTAL_READS, 18);
Assert.assertEquals(metrics.PF_READS, 16);
Assert.assertEquals(metrics.PF_NOISE_READS, 2);
Assert.assertEquals(metrics.PF_HQ_ALIGNED_READS, 0);
Assert.assertEquals(metrics.PF_HQ_ALIGNED_Q20_BASES, 0);
Assert.assertEquals(metrics.PF_HQ_MEDIAN_MISMATCHES, 0.0);
Assert.assertEquals(metrics.PF_ALIGNED_BASES, 0);
Assert.assertEquals(metrics.PF_MISMATCH_RATE, 0.0);
Assert.assertEquals(metrics.BAD_CYCLES, 22);
break;
case UNPAIRED:
default:
Assert.fail("Data does not contain this category: " + metrics.CATEGORY);
}
}
else if (metrics.SAMPLE.equals("Ma")) {
// There's only one library and one read group for this sample so the metrics for
// every level should be identical
switch (metrics.CATEGORY) {
case FIRST_OF_PAIR:
Assert.assertEquals(metrics.TOTAL_READS, 5);
Assert.assertEquals(metrics.PF_READS, 3);
Assert.assertEquals(metrics.PF_NOISE_READS, 1);
Assert.assertEquals(metrics.PF_HQ_ALIGNED_READS, 0);
Assert.assertEquals(metrics.PF_HQ_ALIGNED_Q20_BASES, 0);
Assert.assertEquals(metrics.PF_HQ_MEDIAN_MISMATCHES, 0.0);
Assert.assertEquals(metrics.PF_ALIGNED_BASES, 0);
Assert.assertEquals(metrics.PF_MISMATCH_RATE, 0.0);
Assert.assertEquals(metrics.BAD_CYCLES, 24);
break;
case SECOND_OF_PAIR:
Assert.assertEquals(metrics.TOTAL_READS, 5);
Assert.assertEquals(metrics.PF_READS, 5);
Assert.assertEquals(metrics.PF_NOISE_READS, 0);
Assert.assertEquals(metrics.PF_HQ_ALIGNED_READS, 0);
Assert.assertEquals(metrics.PF_HQ_ALIGNED_Q20_BASES, 0);
Assert.assertEquals(metrics.PF_HQ_MEDIAN_MISMATCHES, 0.0);
Assert.assertEquals(metrics.PF_ALIGNED_BASES, 0);
Assert.assertEquals(metrics.PF_MISMATCH_RATE, 0.0);
Assert.assertEquals(metrics.BAD_CYCLES, 3);
break;
case PAIR:
Assert.assertEquals(metrics.TOTAL_READS, 10);
Assert.assertEquals(metrics.PF_READS, 8);
Assert.assertEquals(metrics.PF_NOISE_READS, 1);
Assert.assertEquals(metrics.PF_HQ_ALIGNED_READS, 0);
Assert.assertEquals(metrics.PF_HQ_ALIGNED_Q20_BASES, 0);
Assert.assertEquals(metrics.PF_HQ_MEDIAN_MISMATCHES, 0.0);
Assert.assertEquals(metrics.PF_ALIGNED_BASES, 0);
Assert.assertEquals(metrics.PF_MISMATCH_RATE, 0.0);
Assert.assertEquals(metrics.BAD_CYCLES, 27);
break;
case UNPAIRED:
default:
Assert.fail("Data does not contain this category: " + metrics.CATEGORY);
}
}
else if (metrics.SAMPLE.equals("Pa")) {
// Two libraries and three read groups for this sample
if (metrics.LIBRARY == null) {
switch (metrics.CATEGORY) {
case FIRST_OF_PAIR:
Assert.assertEquals(metrics.TOTAL_READS, 4);
Assert.assertEquals(metrics.PF_READS, 4);
Assert.assertEquals(metrics.PF_NOISE_READS, 0);
Assert.assertEquals(metrics.PF_HQ_ALIGNED_READS, 0);
Assert.assertEquals(metrics.PF_HQ_ALIGNED_Q20_BASES, 0);
Assert.assertEquals(metrics.PF_HQ_MEDIAN_MISMATCHES, 0.0);
Assert.assertEquals(metrics.PF_ALIGNED_BASES, 0);
Assert.assertEquals(metrics.PF_MISMATCH_RATE, 0.0);
Assert.assertEquals(metrics.BAD_CYCLES, 19);
break;
case SECOND_OF_PAIR:
Assert.assertEquals(metrics.TOTAL_READS, 4);
Assert.assertEquals(metrics.PF_READS, 4);
Assert.assertEquals(metrics.PF_NOISE_READS, 1);
Assert.assertEquals(metrics.PF_HQ_ALIGNED_READS, 0);
Assert.assertEquals(metrics.PF_HQ_ALIGNED_Q20_BASES, 0);
Assert.assertEquals(metrics.PF_HQ_MEDIAN_MISMATCHES, 0.0);
Assert.assertEquals(metrics.PF_ALIGNED_BASES, 0);
Assert.assertEquals(metrics.PF_MISMATCH_RATE, 0.0);
Assert.assertEquals(metrics.BAD_CYCLES, 3);
break;
case PAIR:
Assert.assertEquals(metrics.TOTAL_READS, 8);
Assert.assertEquals(metrics.PF_READS, 8);
Assert.assertEquals(metrics.PF_NOISE_READS, 1);
Assert.assertEquals(metrics.PF_HQ_ALIGNED_READS, 0);
Assert.assertEquals(metrics.PF_HQ_ALIGNED_Q20_BASES, 0);
Assert.assertEquals(metrics.PF_HQ_MEDIAN_MISMATCHES, 0.0);
Assert.assertEquals(metrics.PF_ALIGNED_BASES, 0);
Assert.assertEquals(metrics.PF_MISMATCH_RATE, 0.0);
Assert.assertEquals(metrics.BAD_CYCLES, 22);
break;
case UNPAIRED:
default:
Assert.fail("Data does not contain this category: " + metrics.CATEGORY);
}
}
else if (metrics.LIBRARY.equals("lib1")) {
// Only one read group in this library so library and RG metrics should be identical
switch (metrics.CATEGORY) {
case FIRST_OF_PAIR:
Assert.assertEquals(metrics.TOTAL_READS, 2);
Assert.assertEquals(metrics.PF_READS, 2);
Assert.assertEquals(metrics.PF_NOISE_READS, 0);
Assert.assertEquals(metrics.BAD_CYCLES, 19);
break;
case SECOND_OF_PAIR:
Assert.assertEquals(metrics.TOTAL_READS, 2);
Assert.assertEquals(metrics.PF_READS, 2);
Assert.assertEquals(metrics.PF_NOISE_READS, 1);
Assert.assertEquals(metrics.BAD_CYCLES, 3);
break;
case PAIR:
Assert.assertEquals(metrics.TOTAL_READS, 4);
Assert.assertEquals(metrics.PF_READS, 4);
Assert.assertEquals(metrics.PF_NOISE_READS, 1);
Assert.assertEquals(metrics.BAD_CYCLES, 22);
break;
case UNPAIRED:
default:
Assert.fail("Data does not contain this category: " + metrics.CATEGORY);
}
}
else if (metrics.LIBRARY.equals("lib2")) {
if (metrics.READ_GROUP == null) {
switch (metrics.CATEGORY) {
case FIRST_OF_PAIR:
Assert.assertEquals(metrics.TOTAL_READS, 2);
Assert.assertEquals(metrics.PF_READS, 2);
Assert.assertEquals(metrics.PF_NOISE_READS, 0);
Assert.assertEquals(metrics.BAD_CYCLES, 19);
break;
case SECOND_OF_PAIR:
Assert.assertEquals(metrics.TOTAL_READS, 2);
Assert.assertEquals(metrics.PF_READS, 2);
Assert.assertEquals(metrics.PF_NOISE_READS, 0);
Assert.assertEquals(metrics.BAD_CYCLES, 3);
break;
case PAIR:
Assert.assertEquals(metrics.TOTAL_READS, 4);
Assert.assertEquals(metrics.PF_READS, 4);
Assert.assertEquals(metrics.PF_NOISE_READS, 0);
Assert.assertEquals(metrics.BAD_CYCLES, 22);
break;
case UNPAIRED:
default:
Assert.fail("Data does not contain this category: " + metrics.CATEGORY);
}
}
else if (metrics.READ_GROUP.equals("i")) {
switch (metrics.CATEGORY) {
case FIRST_OF_PAIR:
Assert.assertEquals(metrics.TOTAL_READS, 1);
Assert.assertEquals(metrics.PF_READS, 1);
Assert.assertEquals(metrics.PF_NOISE_READS, 0);
Assert.assertEquals(metrics.BAD_CYCLES, 19);
break;
case SECOND_OF_PAIR:
Assert.assertEquals(metrics.TOTAL_READS, 1);
Assert.assertEquals(metrics.PF_READS, 1);
Assert.assertEquals(metrics.PF_NOISE_READS, 0);
Assert.assertEquals(metrics.BAD_CYCLES, 3);
break;
case PAIR:
Assert.assertEquals(metrics.TOTAL_READS, 2);
Assert.assertEquals(metrics.PF_READS, 2);
Assert.assertEquals(metrics.PF_NOISE_READS, 0);
Assert.assertEquals(metrics.BAD_CYCLES, 22);
break;
case UNPAIRED:
default:
Assert.fail("Data does not contain this category: " + metrics.CATEGORY);
}
}
else if (metrics.READ_GROUP.equals("i2")) {
switch (metrics.CATEGORY) {
case FIRST_OF_PAIR:
Assert.assertEquals(metrics.TOTAL_READS, 1);
Assert.assertEquals(metrics.PF_READS, 1);
Assert.assertEquals(metrics.PF_NOISE_READS, 0);
Assert.assertEquals(metrics.BAD_CYCLES, 27);
break;
case SECOND_OF_PAIR:
Assert.assertEquals(metrics.TOTAL_READS, 1);
Assert.assertEquals(metrics.PF_READS, 1);
Assert.assertEquals(metrics.PF_NOISE_READS, 0);
Assert.assertEquals(metrics.BAD_CYCLES, 3);
break;
case PAIR:
Assert.assertEquals(metrics.TOTAL_READS, 2);
Assert.assertEquals(metrics.PF_READS, 2);
Assert.assertEquals(metrics.PF_NOISE_READS, 0);
Assert.assertEquals(metrics.BAD_CYCLES, 30);
break;
case UNPAIRED:
default:
Assert.fail("Data does not contain this category: " + metrics.CATEGORY);
}
}
else {
Assert.fail("Data does not contain this read group: " + metrics.READ_GROUP);
}
}
else {
Assert.fail("Data does not contain this library: " + metrics.LIBRARY);
}
}
else {
Assert.fail("Data does not contain this sample: " + metrics.SAMPLE);
}
}
}
}