Merge pull request #1369 from broadinstitute/gg_GL-53_ContaminationQc…

…Metric

CreateVerifyIDIntensityContaminationMetricsFile

src/main/java/picard/arrays/CreateVerifyIDIntensityContaminationMetricsFile.java

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+/*
+ * The MIT License
+ *
+ * Copyright (c) 2019 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.arrays;
+
+import htsjdk.samtools.metrics.MetricsFile;
+import htsjdk.samtools.util.IOUtil;
+import org.broadinstitute.barclay.argparser.Argument;
+import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
+import org.broadinstitute.barclay.help.DocumentedFeature;
+import picard.PicardException;
+import picard.cmdline.CommandLineProgram;
+import picard.cmdline.StandardOptionDefinitions;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+/**
+ * A simple program to create a standard picard metrics file
+ * from the output of VerifyIDIntensity
+ */
+@CommandLineProgramProperties(
+        summary = CreateVerifyIDIntensityContaminationMetricsFile.USAGE_DETAILS,
+        oneLineSummary = "Program to generate a picard metrics file from the output of the VerifyIDIntensity tool.",
+        programGroup = picard.cmdline.programgroups.GenotypingArraysProgramGroup.class
+)
+
+@DocumentedFeature
+public class CreateVerifyIDIntensityContaminationMetricsFile extends CommandLineProgram {
+    static final String USAGE_DETAILS =
+            "CreateVerifyIDIntensityContaminationMetricsFile takes an output file as generated by the VerifyIDIntensity tool and creates a picard metrics file. " +
+                    "VerifyIDIntensity <a href='https://genome.sph.umich.edu/wiki/VerifyIDintensity'>VerifyIDintensity</a> is a tool for " +
+                    "detecting and estimating sample contamination of Illumina genotyping array data." +
+                    "<h4>Usage example:</h4>" +
+                    "<pre>" +
+                    "java -jar picard.jar CreateVerifyIDIntensityContaminationMetricsFile \\<br />" +
+                    "      INPUT=VerifyIDIntensityOutput.txt \\<br />" +
+                    "      OUTPUT=outputBaseName" +
+                    "</pre>";
+
+    @Argument(shortName = StandardOptionDefinitions.INPUT_SHORT_NAME, doc = "The output of VerifyIDIntensity(typically captured stdout).")
+    public File INPUT;
+
+    @Argument(shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME, doc = "Basename for the metrics file that will be written." +
+            " Resulting file will be <OUTPUT>." + FILE_EXTENSION)
+    public File OUTPUT;
+
+    public static final String FILE_EXTENSION = "verifyidintensity_metrics";
+
+    @Override
+    protected int doWork() {
+        IOUtil.assertFileIsReadable(INPUT);
+        final File metricsFile = new File(OUTPUT + "." + FILE_EXTENSION);
+        IOUtil.assertFileIsWritable(metricsFile);
+
+        final MetricsFile<VerifyIDIntensityContaminationMetrics, ?> verifyIDIntensityContaminationMetricsFile = getMetricsFile();
+
+        final Pattern HEADER_PATTERN = Pattern.compile("^ID\\s+%Mix\\s+LLK\\s+LLK0\\s*$");
+        final Pattern DASHES_PATTERN = Pattern.compile("^[-]+$");
+        final Pattern DATA_PATTERN = Pattern.compile("^(\\d+)\\s+(\\d*\\.\\d+)\\s+(\\d+)\\s+(\\d+)\\s*$");
+        try (BufferedReader br = new BufferedReader(new FileReader(INPUT))) {
+            String line;
+            line = br.readLine();
+            lineMatch(line, HEADER_PATTERN);
+            line = br.readLine();
+            lineMatch(line, DASHES_PATTERN);
+            while ((line = br.readLine()) != null) {
+                final Matcher m = lineMatch(line, DATA_PATTERN);
+                // Load up and store the metrics
+                final VerifyIDIntensityContaminationMetrics metrics = new VerifyIDIntensityContaminationMetrics();
+                metrics.ID = Integer.parseInt(m.group(1));
+                metrics.PCT_MIX = Double.parseDouble(m.group(2));
+                metrics.LLK = Long.parseLong(m.group(3));
+                metrics.LLK0 = Long.parseLong(m.group(4));
+
+                verifyIDIntensityContaminationMetricsFile.addMetric(metrics);
+            }
+            verifyIDIntensityContaminationMetricsFile.write(metricsFile);
+        } catch (IOException e) {
+            throw new PicardException("Error parsing VerifyIDIntensity Output", e);
+        }
+        return 0;
+    }
+
+    private Matcher lineMatch(final String line, final Pattern patternToMatch) {
+        Matcher m = patternToMatch.matcher(line);
+        if (!m.matches()) {
+            throw new PicardException("Unrecognized line: " + line + " in " + INPUT.getAbsolutePath());
+        }
+        return m;
+    }
+}

src/main/java/picard/arrays/VerifyIDIntensityContaminationMetrics.java

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+package picard.arrays;
+
+import htsjdk.samtools.metrics.MetricBase;
+
+public class VerifyIDIntensityContaminationMetrics extends MetricBase {
+    /** The ID of this entry */
+    public int ID;
+
+    /** The percent mixture (contamination) of the sample for ID */
+    public double PCT_MIX;
+
+    /** The log likelihood */
+    public long LLK;
+
+    /** The log likelihood 0 */
+    public long LLK0;
+}

src/test/java/picard/arrays/CreateVerifyIDIntensityContaminationMetricsFileTest.java

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+package picard.arrays;
+
+import htsjdk.samtools.metrics.MetricsFile;
+import org.testng.Assert;
+import org.testng.annotations.Test;
+import picard.PicardException;
+
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+
+public class CreateVerifyIDIntensityContaminationMetricsFileTest {
+
+    private static final File TEST_DATA_DIR = new File("testdata/picard/arrays");
+    private static final File TEST_INPUT_FILE = new File(TEST_DATA_DIR, "VerifyIDIntensity.txt");
+    private static final File TEST_BAD_INPUT_FILE = new File(TEST_DATA_DIR, "input.vcf");
+
+    @Test
+    public void testCreateVerifyIDIntensityContaminationMetricsFile() throws IOException {
+        final File outputBase = File.createTempFile("testCreateVerifyIDIntensityContaminationMetricsFile", "");
+        final File output = new File(outputBase.getAbsolutePath() + "." + CreateVerifyIDIntensityContaminationMetricsFile.FILE_EXTENSION);
+        output.deleteOnExit();
+        System.out.println(outputBase.getAbsolutePath());
+        System.out.println(output.getAbsolutePath());
+
+        final CreateVerifyIDIntensityContaminationMetricsFile createVerifyIDIntensityContaminationMetricsFile = new CreateVerifyIDIntensityContaminationMetricsFile();
+        createVerifyIDIntensityContaminationMetricsFile.INPUT = TEST_INPUT_FILE;
+        createVerifyIDIntensityContaminationMetricsFile.OUTPUT = outputBase;
+
+        Assert.assertEquals(createVerifyIDIntensityContaminationMetricsFile.instanceMain(new String[0]), 0);
+
+        final MetricsFile<VerifyIDIntensityContaminationMetrics, Comparable<?>> metrics = new MetricsFile<>();
+        metrics.read(new FileReader(output));
+
+        Assert.assertEquals(metrics.getMetrics().size(), 2);
+        Assert.assertEquals(metrics.getMetrics().get(0).ID, 0);
+        Assert.assertEquals(metrics.getMetrics().get(0).PCT_MIX, 0.214766);
+        Assert.assertEquals(metrics.getMetrics().get(0).LLK, 157575);
+        Assert.assertEquals(metrics.getMetrics().get(0).LLK0, 177169);
+
+        Assert.assertEquals(metrics.getMetrics().get(1).ID, 1);
+        Assert.assertEquals(metrics.getMetrics().get(1).PCT_MIX, 0.214767);
+        Assert.assertEquals(metrics.getMetrics().get(1).LLK, 157576);
+        Assert.assertEquals(metrics.getMetrics().get(1).LLK0, 177170);
+    }
+
+    @Test(expectedExceptions = PicardException.class)
+    public void testFailCreateVerifyIDIntensityContaminationMetricsFile() throws IOException {
+        final File outputBase = File.createTempFile("testFailCreateVerifyIDIntensityContaminationMetricsFile", "");
+        final File output = new File(outputBase.getAbsolutePath() + "." + CreateVerifyIDIntensityContaminationMetricsFile.FILE_EXTENSION);
+        output.deleteOnExit();
+        System.out.println(outputBase.getAbsolutePath());
+        System.out.println(output.getAbsolutePath());
+
+        final CreateVerifyIDIntensityContaminationMetricsFile createVerifyIDIntensityContaminationMetricsFile = new CreateVerifyIDIntensityContaminationMetricsFile();
+        createVerifyIDIntensityContaminationMetricsFile.INPUT = TEST_BAD_INPUT_FILE;
+        createVerifyIDIntensityContaminationMetricsFile.OUTPUT = outputBase;
+
+        Assert.assertEquals(createVerifyIDIntensityContaminationMetricsFile.instanceMain(new String[0]), 1);
+    }
+}

testdata/picard/arrays/VerifyIDIntensity.txt

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+ID	%Mix		LLK		LLK0	
+-----------------------------------------------------------------
+0	0.214766	157575	177169
+1	0.214767	157576	177170