This tool uses reduced representation bisulfite sequencing (Rrbs) data to determine cytosine " + "methylation status across all reads of a genomic DNA sequence. For a primer on bisulfite sequencing and cytosine methylation, " + @@ -82,7 +76,18 @@ public class CollectRrbsMetrics extends CommandLineProgram { "The detailed metrics table includes the coordinates of all of the CpG sites for the experiment as well as the conversion rates " + "observed for each site.
" + - "It is possible to launch CollectRrbsMetrics tool by setting all output files or by indicating a base name for metrics files only. See examples:
" + + + "" + + "java -jar picard.jar CollectRrbsMetrics \\" + + "
" + + " R=reference_sequence.fasta \\
" + + " I=input.bam \\
" + + " O=detail_output.txt \\
" + + " CHART=chart_output.pdf \\
" + + " S=summary_output.txt" + + "
" +
"java -jar picard.jar CollectRrbsMetrics \\
" +
" R=reference_sequence.fasta \\
" +
@@ -95,13 +100,11 @@ public class CollectRrbsMetrics extends CommandLineProgram {
" for a complete description of both the detail and summary metrics produced by this tool." +
"
";
-// Path to R file for plotting purposes
+ // Path to R file for plotting purposes
-private static final String R_SCRIPT = "picard/analysis/rrbsQc.R";
+ private static final String R_SCRIPT = "picard/analysis/rrbsQc.R";
- @Argument(doc = "The BAM or SAM file containing aligned reads. Must be coordinate sorted", shortName = StandardOptionDefinitions.INPUT_SHORT_NAME)
- public File INPUT;
- @Argument(doc = "Base name for output files", shortName = StandardOptionDefinitions.METRICS_FILE_SHORT_NAME)
+ @Argument(doc = "Base name for output files", shortName = StandardOptionDefinitions.METRICS_FILE_SHORT_NAME, mutex = {"OUTPUT", "CHART_OUTPUT", "SUMMARY_OUTPUT"})
public String METRICS_FILE_PREFIX;
@Argument(doc = "Minimum read length")
public int MINIMUM_READ_LENGTH = 5;
@@ -112,18 +115,19 @@ public class CollectRrbsMetrics extends CommandLineProgram {
@Argument(doc = "Maximum percentage of mismatches in a read for it to be considered, with a range of 0-1")
public double MAX_MISMATCH_RATE = 0.1;
@Argument(doc = "Set of sequence names to consider, if not specified all sequences will be used", optional = true)
- public Set SEQUENCE_NAMES = new HashSet();
- @Argument(shortName = StandardOptionDefinitions.ASSUME_SORTED_SHORT_NAME,
- doc = "If true, assume that the input file is coordinate sorted even if the header says otherwise.")
- public boolean ASSUME_SORTED = false;
+ public Set SEQUENCE_NAMES = new HashSet<>();
@Argument(shortName = "LEVEL", doc = "The level(s) at which to accumulate metrics. ")
public Set METRIC_ACCUMULATION_LEVEL = CollectionUtil.makeSet(MetricAccumulationLevel.ALL_READS);
+ @Argument(shortName = "CHART", doc = "The PDF file to render the chart to.", mutex = {"METRICS_FILE_PREFIX"})
+ public File CHART_OUTPUT;
+ @Argument(shortName = "S", doc = "The text file to write summary metrics to.", mutex = {"METRICS_FILE_PREFIX"})
+ public File SUMMARY_OUTPUT;
public static final String DETAIL_FILE_EXTENSION = "rrbs_detail_metrics";
public static final String SUMMARY_FILE_EXTENSION = "rrbs_summary_metrics";
public static final String PDF_FILE_EXTENSION = "rrbs_qc.pdf";
- private static final Log log = Log.getInstance(CollectRrbsMetrics.class);
+ private RrbsMetricsCollector metricsCollector;
// return a custom argument collection since this tool uses a (required) argument name
// of "REFERENCE", not "REFERENCE_SEQUENCE"
@@ -147,33 +151,43 @@ public static void main(final String[] args) {
}
@Override
- protected int doWork() {
- if (!METRICS_FILE_PREFIX.endsWith(".")) {
- METRICS_FILE_PREFIX = METRICS_FILE_PREFIX + ".";
- }
- final File SUMMARY_OUT = new File(METRICS_FILE_PREFIX + SUMMARY_FILE_EXTENSION);
- final File DETAILS_OUT = new File(METRICS_FILE_PREFIX + DETAIL_FILE_EXTENSION);
- final File PLOTS_OUT = new File(METRICS_FILE_PREFIX + PDF_FILE_EXTENSION);
- assertIoFiles(SUMMARY_OUT, DETAILS_OUT, PLOTS_OUT);
-
- final SamReader samReader = SamReaderFactory.makeDefault().open(INPUT);
- if (!ASSUME_SORTED && samReader.getFileHeader().getSortOrder() != SAMFileHeader.SortOrder.coordinate) {
- throw new PicardException("The input file " + INPUT.getAbsolutePath() + " does not appear to be coordinate sorted");
+ protected void setup(final SAMFileHeader header, final File samFile) {
+ if (METRICS_FILE_PREFIX != null) {
+ if (!METRICS_FILE_PREFIX.endsWith(".")) {
+ METRICS_FILE_PREFIX = METRICS_FILE_PREFIX + ".";
+ }
+ OUTPUT = new File(METRICS_FILE_PREFIX + DETAIL_FILE_EXTENSION);
+ SUMMARY_OUTPUT = new File(METRICS_FILE_PREFIX + SUMMARY_FILE_EXTENSION);
+ CHART_OUTPUT = new File(METRICS_FILE_PREFIX + PDF_FILE_EXTENSION);
}
+ IOUtil.assertFileIsWritable(OUTPUT);
+ IOUtil.assertFileIsWritable(SUMMARY_OUTPUT);
+ IOUtil.assertFileIsWritable(CHART_OUTPUT);
+ metricsCollector = new RrbsMetricsCollector(
+ METRIC_ACCUMULATION_LEVEL,
+ header.getReadGroups(),
+ C_QUALITY_THRESHOLD,
+ NEXT_BASE_QUALITY_THRESHOLD,
+ MINIMUM_READ_LENGTH,
+ MAX_MISMATCH_RATE
+ );
+ }
- final ReferenceSequenceFileWalker refWalker = new ReferenceSequenceFileWalker(REFERENCE_SEQUENCE);
- final ProgressLogger progressLogger = new ProgressLogger(log);
+ @Override
+ protected void acceptRead(final SAMRecord samRecord, final ReferenceSequence ref) {
+ if (!samRecord.getReadUnmappedFlag() && !isSequenceFiltered(samRecord.getReferenceName())) {
+ metricsCollector.acceptRecord(samRecord, ref);
+ }
+ }
- final RrbsMetricsCollector metricsCollector = new RrbsMetricsCollector(METRIC_ACCUMULATION_LEVEL, samReader.getFileHeader().getReadGroups(),
- C_QUALITY_THRESHOLD, NEXT_BASE_QUALITY_THRESHOLD, MINIMUM_READ_LENGTH, MAX_MISMATCH_RATE);
+ private boolean isSequenceFiltered(final String sequenceName) {
+ return SEQUENCE_NAMES != null
+ && !SEQUENCE_NAMES.isEmpty()
+ && !SEQUENCE_NAMES.contains(sequenceName);
+ }
- for (final SAMRecord samRecord : samReader) {
- progressLogger.record(samRecord);
- if (!samRecord.getReadUnmappedFlag() && !isSequenceFiltered(samRecord.getReferenceName())) {
- final ReferenceSequence referenceSequence = refWalker.get(samRecord.getReferenceIndex());
- metricsCollector.acceptRecord(samRecord, referenceSequence);
- }
- }
+ @Override
+ protected void finish() {
metricsCollector.finish();
final MetricsFile> rrbsMetrics = getMetricsFile();
metricsCollector.addAllLevelsToFile(rrbsMetrics);
@@ -182,34 +196,23 @@ protected int doWork() {
// we get it out split it apart to the two separate MetricsFiles and write them to file
final MetricsFile summaryFile = getMetricsFile();
final MetricsFile detailsFile = getMetricsFile();
- for (final RrbsMetrics rrbsMetric : rrbsMetrics.getMetrics()) {
+ rrbsMetrics.getMetrics().forEach(rrbsMetric -> {
summaryFile.addMetric(rrbsMetric.getSummaryMetrics());
- for (final RrbsCpgDetailMetrics detailMetric : rrbsMetric.getDetailMetrics()) {
- detailsFile.addMetric(detailMetric);
- }
- }
- summaryFile.write(SUMMARY_OUT);
- detailsFile.write(DETAILS_OUT);
- RExecutor.executeFromClasspath(R_SCRIPT, DETAILS_OUT.getAbsolutePath(), SUMMARY_OUT.getAbsolutePath(), PLOTS_OUT.getAbsolutePath());
- CloserUtil.close(samReader);
- return 0;
- }
+ rrbsMetric.getDetailMetrics().forEach(detailsFile::addMetric);
+ });
- private boolean isSequenceFiltered(final String sequenceName) {
- return (SEQUENCE_NAMES != null) && (!SEQUENCE_NAMES.isEmpty()) && (!SEQUENCE_NAMES.contains(sequenceName));
- }
+ summaryFile.write(SUMMARY_OUTPUT);
+ detailsFile.write(OUTPUT);
- private void assertIoFiles(final File summaryFile, final File detailsFile, final File plotsFile) {
- IOUtil.assertFileIsReadable(INPUT);
- IOUtil.assertFileIsReadable(REFERENCE_SEQUENCE);
- IOUtil.assertFileIsWritable(summaryFile);
- IOUtil.assertFileIsWritable(detailsFile);
- IOUtil.assertFileIsWritable(plotsFile);
+ RExecutor.executeFromClasspath(R_SCRIPT,
+ OUTPUT.getAbsolutePath(),
+ SUMMARY_OUTPUT.getAbsolutePath(),
+ CHART_OUTPUT.getAbsolutePath());
}
@Override
protected String[] customCommandLineValidation() {
- final List errorMsgs = new ArrayList();
+ final List errorMsgs = new ArrayList<>();
if (MAX_MISMATCH_RATE < 0 || MAX_MISMATCH_RATE > 1) {
errorMsgs.add("MAX_MISMATCH_RATE must be in the range of 0-1");
}
diff --git a/src/main/java/picard/analysis/SinglePassSamProgram.java b/src/main/java/picard/analysis/SinglePassSamProgram.java
index bb93ed9944..2cda91661a 100644
--- a/src/main/java/picard/analysis/SinglePassSamProgram.java
+++ b/src/main/java/picard/analysis/SinglePassSamProgram.java
@@ -56,7 +56,7 @@ public abstract class SinglePassSamProgram extends CommandLineProgram {
@Argument(shortName = StandardOptionDefinitions.INPUT_SHORT_NAME, doc = "Input SAM or BAM file.")
public File INPUT;
- @Argument(shortName = "O", doc = "File to write the output to.")
+ @Argument(shortName = "O", doc = "File to write the output to.", optional = true)
public File OUTPUT;
@Argument(doc = "If true (default), then the sort order in the header file will be ignored.",
diff --git a/src/test/java/picard/analysis/CollectMultipleMetricsTest.java b/src/test/java/picard/analysis/CollectMultipleMetricsTest.java
index 9406f034a4..7855c02660 100644
--- a/src/test/java/picard/analysis/CollectMultipleMetricsTest.java
+++ b/src/test/java/picard/analysis/CollectMultipleMetricsTest.java
@@ -13,6 +13,7 @@
import org.testng.annotations.BeforeTest;
import org.testng.annotations.Test;
import picard.cmdline.CommandLineProgramTest;
+import picard.metrics.MultilevelMetrics;
import picard.sam.SortSam;
import static picard.analysis.GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector.*;
@@ -33,11 +34,62 @@
public class CollectMultipleMetricsTest extends CommandLineProgramTest {
private static final File TEST_DATA_DIR = new File("testdata/picard/sam");
+ private static final File TEST_DATA_DIR_RRBS = new File("testdata/picard/metrics");
public String getCommandLineProgramName() {
return CollectMultipleMetrics.class.getSimpleName();
}
+ @Test
+ public void testCollectRrbsMetrics() throws IOException {
+ final File input = new File(TEST_DATA_DIR_RRBS, "chrMReads.sam");
+ final File reference = new File(TEST_DATA_DIR_RRBS, "chrM.reference.fasta");
+ final File outfile = File.createTempFile("crmt.", ".rrbs_summary_metrics");
+ outfile.deleteOnExit();
+
+ final File summary = new File(outfile + ".rrbc.summary_metrics");
+ final File detail = new File(outfile + ".rrbc.detail_metrics");
+ final File pdf = new File(outfile + ".rrbc.pdf");
+ summary.deleteOnExit();
+ detail.deleteOnExit();
+ pdf.deleteOnExit();
+
+ final String[] args = new String[] {
+ "INPUT=" + input.getAbsolutePath(),
+ "OUTPUT=" + outfile.getAbsolutePath(),
+ "REFERENCE_SEQUENCE=" + reference.getAbsolutePath(),
+ "PROGRAM=" + null,
+ "PROGRAM=" + CollectMultipleMetrics.Program.CollectRrbsMetrics.name()};
+
+ Assert.assertEquals(runPicardCommandLine(args), 0);
+
+ final RrbsSummaryMetrics metrics = getMultilevelMetrics(summary);
+ Assert.assertEquals(metrics.READS_ALIGNED.intValue(), 5);
+ Assert.assertEquals(metrics.NON_CPG_BASES.intValue(), 15);
+ Assert.assertEquals(metrics.NON_CPG_CONVERTED_BASES.intValue(), 11);
+ Assert.assertEquals(metrics.PCT_NON_CPG_BASES_CONVERTED, 0.733333);
+ Assert.assertEquals(metrics.CPG_BASES_SEEN.intValue(), 5);
+ Assert.assertEquals(metrics.CPG_BASES_CONVERTED.intValue(), 1);
+ Assert.assertEquals(metrics.PCT_CPG_BASES_CONVERTED, 0.2);
+ Assert.assertEquals(metrics.MEAN_CPG_COVERAGE, 1.666667);
+ Assert.assertEquals(metrics.MEDIAN_CPG_COVERAGE.intValue(), 2);
+ Assert.assertEquals(metrics.READS_WITH_NO_CPG.intValue(), 1);
+ Assert.assertEquals(metrics.READS_IGNORED_SHORT.intValue(), 1);
+ Assert.assertEquals(metrics.READS_IGNORED_MISMATCHES.intValue(), 1);
+
+ final RrbsCpgDetailMetrics metricsCpg = getMultilevelMetrics(detail);
+ Assert.assertEquals(metricsCpg.SEQUENCE_NAME, "chrM");
+ Assert.assertEquals(metricsCpg.POSITION.intValue(), 60);
+ Assert.assertEquals(metricsCpg.TOTAL_SITES.intValue(), 1);
+ Assert.assertEquals(metricsCpg.CONVERTED_SITES.intValue(), 1);
+ Assert.assertEquals(metricsCpg.PCT_CONVERTED.intValue(), 1);
+ }
+
+ private T getMultilevelMetrics(final File file) throws FileNotFoundException {
+ final MetricsFile retVal = new MetricsFile();
+ retVal.read(new FileReader(file));
+ return retVal.getMetrics().get(0);
+ }
@Test
public void testAlignmentSummaryViaMultipleMetrics() throws IOException {
diff --git a/src/test/java/picard/analysis/CollectRrbsMetricsTest.java b/src/test/java/picard/analysis/CollectRrbsMetricsTest.java
new file mode 100644
index 0000000000..d932cb8ffa
--- /dev/null
+++ b/src/test/java/picard/analysis/CollectRrbsMetricsTest.java
@@ -0,0 +1,182 @@
+package picard.analysis;
+
+import htsjdk.samtools.metrics.MetricsFile;
+import htsjdk.samtools.util.IOUtil;
+import org.testng.Assert;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+import picard.cmdline.CommandLineProgramTest;
+import picard.metrics.MultilevelMetrics;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.List;
+
+public class CollectRrbsMetricsTest extends CommandLineProgramTest {
+ private static final String CHR_M_SAM = "testdata/picard/metrics/chrMReads.sam";
+ private static final String CHR_M_REFERENCE = "testdata/picard/metrics/chrM.reference.fasta";
+ private static final String CHR_M_SAM_TEST_UNMAPPED = "testdata/picard/sam/collect_rrbs_metrics_test_unmapped.sam";
+ private static final String CHR_M_REFERENCE_TEST_UNMAPPED = "testdata/picard/sam/summary_alignment_stats_test.fasta";
+
+ private File pdf;
+ private File summaryOutput;
+ private File detailOutput;
+ private File tempDir;
+ private String prefix;
+
+ @Override
+ public String getCommandLineProgramName() {
+ return CollectRrbsMetrics.class.getSimpleName();
+ }
+
+ @BeforeClass
+ private void setUp() throws Exception {
+ pdf = File.createTempFile("crmt.", ".pdf");
+ pdf.deleteOnExit();
+ summaryOutput = File.createTempFile("crmt.", ".rrbs_summary_metrics");
+ summaryOutput.deleteOnExit();
+ detailOutput = File.createTempFile("crmt.", "detail.sam");
+ detailOutput.deleteOnExit();
+ tempDir = Files.createTempDirectory("crmt.").toFile();
+ prefix = Paths.get(tempDir.toString(), "crmt.").toString();
+ }
+
+ @AfterClass
+ public void clearTempDir() throws IOException {
+ IOUtil.deleteDirectoryTree(tempDir);
+ }
+
+ @Test
+ public void chrMReads() throws Exception {
+ Assert.assertEquals(
+ runPicardCommandLine(
+ makeArgList(CHR_M_SAM, null, detailOutput.getAbsolutePath(), pdf.getAbsolutePath(), summaryOutput.getAbsolutePath(), CHR_M_REFERENCE)
+ ),
+ 0
+ );
+
+ final RrbsSummaryMetrics metrics = getMultilevelMetrics(summaryOutput);
+ Assert.assertEquals(metrics.READS_ALIGNED.intValue(), 5);
+ Assert.assertEquals(metrics.NON_CPG_BASES.intValue(), 15);
+ Assert.assertEquals(metrics.NON_CPG_CONVERTED_BASES.intValue(), 11);
+ Assert.assertEquals(metrics.PCT_NON_CPG_BASES_CONVERTED, 0.733333);
+ Assert.assertEquals(metrics.CPG_BASES_SEEN.intValue(), 5);
+ Assert.assertEquals(metrics.CPG_BASES_CONVERTED.intValue(), 1);
+ Assert.assertEquals(metrics.PCT_CPG_BASES_CONVERTED, 0.2);
+ Assert.assertEquals(metrics.MEAN_CPG_COVERAGE, 1.666667);
+ Assert.assertEquals(metrics.MEDIAN_CPG_COVERAGE.intValue(), 2);
+ Assert.assertEquals(metrics.READS_WITH_NO_CPG.intValue(), 1);
+ Assert.assertEquals(metrics.READS_IGNORED_SHORT.intValue(), 1);
+ Assert.assertEquals(metrics.READS_IGNORED_MISMATCHES.intValue(), 1);
+ }
+
+ @Test
+ public void testRrbsCpgDetailMetrics() throws Exception {
+ Assert.assertEquals(
+ runPicardCommandLine(
+ makeArgList(CHR_M_SAM, null, detailOutput.getAbsolutePath(), pdf.getAbsolutePath(), summaryOutput.getAbsolutePath(), CHR_M_REFERENCE)
+ ),
+ 0
+ );
+
+ final RrbsCpgDetailMetrics metricsCpg = getMultilevelMetrics(detailOutput);
+ Assert.assertEquals(metricsCpg.SEQUENCE_NAME, "chrM");
+ Assert.assertEquals(metricsCpg.POSITION.intValue(), 60);
+ Assert.assertEquals(metricsCpg.TOTAL_SITES.intValue(), 1);
+ Assert.assertEquals(metricsCpg.CONVERTED_SITES.intValue(), 1);
+ Assert.assertEquals(metricsCpg.PCT_CONVERTED.intValue(), 1);
+ }
+
+ @Test
+ public void testUnmappedReads() throws Exception {
+ Assert.assertEquals(
+ runPicardCommandLine(
+ makeArgList(CHR_M_SAM_TEST_UNMAPPED, null, detailOutput.getAbsolutePath(), pdf.getAbsolutePath(), summaryOutput.getAbsolutePath(), CHR_M_REFERENCE_TEST_UNMAPPED)
+ ),
+ 0
+ );
+
+ final MetricsFile metricsFile = new MetricsFile();
+ metricsFile.read(new FileReader(detailOutput));
+
+ Assert.assertEquals(metricsFile.getMetrics().size(), 2); // this metric skips unmapped reads, so we get 2 reads instead of 3
+ }
+
+ @Test
+ public void testRrbsCpgDetailMetricsByPrefix() throws Exception {
+ Assert.assertEquals(
+ runPicardCommandLine(
+ makeArgList(CHR_M_SAM, prefix, null, null, null, CHR_M_REFERENCE)
+ ),
+ 0
+ );
+
+ final String output = prefix + CollectRrbsMetrics.DETAIL_FILE_EXTENSION;
+ final RrbsCpgDetailMetrics metricsCpg = getMultilevelMetrics(output);
+ Assert.assertEquals(metricsCpg.SEQUENCE_NAME, "chrM");
+ Assert.assertEquals(metricsCpg.POSITION.intValue(), 60);
+ Assert.assertEquals(metricsCpg.TOTAL_SITES.intValue(), 1);
+ Assert.assertEquals(metricsCpg.CONVERTED_SITES.intValue(), 1);
+ Assert.assertEquals(metricsCpg.PCT_CONVERTED.intValue(), 1);
+ }
+
+ private T getMultilevelMetrics(final File file) throws FileNotFoundException {
+ final MetricsFile metricsFile = new MetricsFile();
+ metricsFile.read(new FileReader(file));
+ return metricsFile.getMetrics().get(0);
+ }
+
+ private T getMultilevelMetrics(final String fileName) throws FileNotFoundException {
+ return getMultilevelMetrics(new File(fileName));
+ }
+
+ @Test(dataProvider = "incorrectArguments", expectedExceptions = IllegalArgumentException.class)
+ public void checkingArguments(final String prefix, final String detailOutput, final String chartOutput, final String summaryOutput) {
+ runPicardCommandLine(makeArgList(CHR_M_SAM, prefix, detailOutput, chartOutput, summaryOutput, CHR_M_REFERENCE));
+ }
+
+ @DataProvider(name = "incorrectArguments")
+ public Object[][] makeIncorrectArguments() {
+ return new Object[][]{
+ // METRICS_FILE_PREFIX OUTPUT CHART_OUTPUT SUMMARY_OUTPUT
+ {prefix, detailOutput, null, null},
+ {prefix, null, pdf, null},
+ {prefix, null, null, summaryOutput},
+ {null, detailOutput, pdf, null},
+ {null, detailOutput, null, summaryOutput},
+ {null, null, pdf, summaryOutput},
+ };
+ }
+
+ private List makeArgList(final String input, final String prefix,
+ final String detailOutput, final String chartOutput, final String summaryOutput,
+ final String referenceSequence) {
+ List args = new ArrayList<>();
+ if (input != null) {
+ args.add("INPUT=" + input);
+ }
+ if (prefix != null) {
+ args.add("METRICS_FILE_PREFIX=" + prefix);
+ }
+ if (detailOutput != null) {
+ args.add("OUTPUT=" + detailOutput);
+ }
+ if (chartOutput != null) {
+ args.add("CHART_OUTPUT=" + chartOutput);
+ }
+ if (summaryOutput != null) {
+ args.add("SUMMARY_OUTPUT=" + summaryOutput);
+ }
+ if (referenceSequence != null) {
+ args.add("R=" + referenceSequence);
+ }
+ return args;
+ }
+}
\ No newline at end of file
diff --git a/src/test/java/picard/metrics/CollectRrbsMetricsTest.java b/src/test/java/picard/metrics/CollectRrbsMetricsTest.java
deleted file mode 100644
index 0f254d1b38..0000000000
--- a/src/test/java/picard/metrics/CollectRrbsMetricsTest.java
+++ /dev/null
@@ -1,102 +0,0 @@
-/*
- * The MIT License
- *
- * Copyright (c) 2013 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.metrics;
-
-import htsjdk.samtools.util.IOUtil;
-import htsjdk.samtools.metrics.MetricsFile;
-import org.testng.Assert;
-import org.testng.annotations.AfterTest;
-import org.testng.annotations.BeforeTest;
-import org.testng.annotations.Test;
-import picard.analysis.CollectRrbsMetrics;
-import picard.analysis.RrbsSummaryMetrics;
-
-import java.io.File;
-import java.io.FileReader;
-import java.lang.Exception;import java.lang.Integer;import java.lang.String;import java.util.ArrayList;
-import java.util.List;
-
-/**
- * @author jgentry@broadinstitute.org
- */
-
-public class CollectRrbsMetricsTest {
- public static final String CHR_M_SAM = "testdata/picard/metrics/chrMReads.sam";
- public static final String CHR_M_REFERENCE ="testdata/picard/metrics/chrM.reference.fasta";
-
- private File rootTestDir;
-
- @BeforeTest
- private void setUp() throws Exception {
- rootTestDir = File.createTempFile("crmt.", ".tmp");
- Assert.assertTrue(rootTestDir.delete());
- Assert.assertTrue(rootTestDir.mkdir());
- }
-
- @AfterTest
- private void tearDown() {
- IOUtil.deleteDirectoryTree(rootTestDir);
- }
-
- @Test
- public void chrMReads() throws Exception {
- final MetricsFile metricsFile = getSummaryFile(CHR_M_SAM, CHR_M_REFERENCE, rootTestDir + "/READ_TEST", new ArrayList());
- final RrbsSummaryMetrics metrics = metricsFile.getMetrics().get(0);
- Assert.assertEquals(metrics.READS_ALIGNED.intValue(), 5);
- Assert.assertEquals(metrics.NON_CPG_BASES.intValue(), 15);
- Assert.assertEquals(metrics.NON_CPG_CONVERTED_BASES.intValue(), 11);
- Assert.assertEquals(metrics.PCT_NON_CPG_BASES_CONVERTED, 0.733333);
- Assert.assertEquals(metrics.CPG_BASES_SEEN.intValue(), 5);
- Assert.assertEquals(metrics.CPG_BASES_CONVERTED.intValue(), 1);
- Assert.assertEquals(metrics.PCT_CPG_BASES_CONVERTED, 0.2);
- Assert.assertEquals(metrics.MEAN_CPG_COVERAGE, 1.666667);
- Assert.assertEquals(metrics.MEDIAN_CPG_COVERAGE.intValue(), 2);
- Assert.assertEquals(metrics.READS_WITH_NO_CPG.intValue(), 1);
- Assert.assertEquals(metrics.READS_IGNORED_SHORT.intValue(), 1);
- Assert.assertEquals(metrics.READS_IGNORED_MISMATCHES.intValue(), 1);
- }
-
- private MetricsFile getSummaryFile(final String input, final String reference, final String prefix,
- final List sequences) throws Exception {
- final List argList = new ArrayList();
- argList.add("INPUT=" + input);
- argList.add("METRICS_FILE_PREFIX=" + prefix);
- argList.add("REFERENCE=" + reference);
- for (final String sequence : sequences) {
- argList.add("SEQUENCE_NAMES=" + sequence);
- }
-
- final String[] args = new String[argList.size()];
- argList.toArray(args);
-
- Assert.assertEquals(new CollectRrbsMetrics().instanceMain(args), 0);
-
- final MetricsFile retVal = new MetricsFile();
- retVal.read(new FileReader(prefix + ".rrbs_summary_metrics"));
- return retVal;
- }
-
-
-}
diff --git a/testdata/picard/sam/collect_rrbs_metrics_test_unmapped.sam b/testdata/picard/sam/collect_rrbs_metrics_test_unmapped.sam
new file mode 100644
index 0000000000..990c703cd3
--- /dev/null
+++ b/testdata/picard/sam/collect_rrbs_metrics_test_unmapped.sam
@@ -0,0 +1,10 @@
+@HD VN:1.0 SO:coordinate
+@SQ SN:chr1 LN:101
+@SQ SN:chr2 LN:101
+@SQ SN:chr3 LN:101
+@SQ SN:chr4 LN:101
+@SQ SN:chr5 LN:101
+@RG ID:0 SM:Hi,Daddy! LB:whatever PU:me PL:ILLUMINA
+SL-XAV:1:1:0:1914#0/2 157 * 0 0 * * 0 0 CGTATGCGCTNTTTATGTCGCCCACAGTGCCTAGTATAGCCCCTGCTAATAAAAAGAGATGAATACGTTTACTTAAAAAACTGAAACTAGNAATGTGCAAN (0,7&&*/*0*,)10/).-*&.&*/6669.&-337599;3,&,6/.,5::999987893+387020775777547999::668997448:::9;999::0& RG:Z:0
+SL-XAV:1:1:0:1639#0/2 153 chr4 1 255 101M * 0 0 CGTGATACCANCTCATGTTCACAGCCAAAGCCTGAAGCTGTCTATTATATTTCTCAACCATAAACTTTTGCCTCAGGCATCCGCAGAATGNTTTGCAGCCN '.&.&&'.0+01'2(1'(''-)','+0041/.+032;:867115/5267-.0/)-5.&-26200224,,0+0/0275/5605688::646875568882*& RG:Z:0
+SL-XAV:1:1:0:68#0/2 137 chr5 1 255 101M * 0 0 NTCTCATTTANAAATGGTTATAAAAACATTTATGCTGAAAAGGTGAAGTTCATTAATGAACAGGCTGACTGTCTCACTATCGCGTTCGCANGACGTTATCT &1<<999;;;;<<<87579:556972789977444.'.023.&,7621/54.49.)/53055-22--''+(.'-))6-168/(3&&0(<).))*&&&&&'0 RG:Z:0