Add reconstruct trios clps

src/main/java/picard/fingerprint/FingerprintChecker.java

@@ -366,10 +366,7 @@ private void getFingerprintFromVc(final Map<String, Fingerprint> fingerprints, f
         for (final String sample : fingerprints.keySet()) {
             final Fingerprint fp = fingerprints.get(sample);
 
-            //PLs are preferred over GTs
-            //TODO: this code is replicated in various places (ReconstructTriosFromVCF for example). Needs refactoring.
-            //TODO: add a way to force using GTs when both are available (why?)
-
+            // PLs are preferred over GTs
             // Get the genotype for the sample and check that it is useful
             final Genotype genotype = usableSnp.getGenotype(sample);
             if (genotype == null) {
@@ -390,7 +387,7 @@ private void getFingerprintFromVc(final Map<String, Fingerprint> fingerprints, f
 
                 if (genotype.isNoCall()) continue;
 
-                // TODO: when multiple genotypes are available for a Haplotype check that they
+                // TODO: when multiple genotypes are available for a Haplotype, check that they
                 // TODO: agree. Not urgent since DownloadGenotypes already does this.
                 // TODO: more urgent now as we convert vcfs to haplotypeProbabilities and
                 // TODO: there could be different VCs with information we'd like to use...
@@ -511,11 +508,8 @@ public Map<FingerprintIdDetails, Fingerprint> fingerprintSamFile(final Path samF
         // Now go through the data at each locus and figure stuff out!
         for (final SamLocusIterator.LocusInfo info : iterator) {
 
-            // if statement to avoid string building.
-            // TODO: replace with lambda version once htsjdk is rev'ed
-            if (Log.isEnabled(Log.LogLevel.DEBUG)) {
-                log.debug("At locus " + info.toString());
-            }
+            log.debug(() -> "At locus " + info.toString());
+
             // TODO: Filter out the locus if the allele balance doesn't make sense for either a
             // TODO: 50/50 het or a hom with some errors; in HS data with deep coverage any base
             // TODO: with major strand bias could cause errors

src/main/java/picard/fingerprint/InferSex.java

@@ -0,0 +1,76 @@
+/*
+ * 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.fingerprint;
+
+import htsjdk.samtools.util.CollectionUtil;
+import htsjdk.samtools.util.IOUtil;
+import htsjdk.samtools.util.Log;
+import org.broadinstitute.barclay.argparser.Argument;
+import picard.cmdline.CommandLineProgram;
+import picard.cmdline.StandardOptionDefinitions;
+import picard.pedigree.PedFile;
+import picard.pedigree.Sex;
+
+import java.io.File;
+import java.util.Map;
+import java.util.Set;
+
+/**
+ * Attempts to use a set of genome data samples to determine sex within the cohort provided.
+ *
+ * @author Tim Fennell
+ * @author Jonathan Barlev
+ * @author Yossi Farjoun
+ */
+
+// Abstract class that provides the outline of a sex inferencing CLP.
+// The implementing class will have to implement getSexInferencer()
+public abstract class InferSex extends CommandLineProgram {
+
+    @Argument(shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME, doc = "Output pedigree file name.")
+    public File OUTPUT;
+
+    @Argument(doc="List of possible names for male sex chromosome(s)")
+    public Set<String> MALE_CHROMS = CollectionUtil.makeSet("Y", "chrY");
+
+    @Argument(doc="List of possible names for female sex chromosome(s)")
+    public Set<String> FEMALE_CHROMS = CollectionUtil.makeSet("X", "chrX");
+
+    final Log log = Log.getInstance(InferSex.class);
+
+    abstract SexInferenceEngine getSexInference();
+
+    @Override
+    protected int doWork() {
+        IOUtil.assertFileIsWritable(OUTPUT);
+
+        // Determine gender for everyone
+        log.info("Determining sample sexes");
+        final Map<String,Sex> sampleSexes =  getSexInference().determineSexes();
+        PedFile.fromSexMap(sampleSexes).write(OUTPUT);
+
+        return 0;
+    }
+}

src/main/java/picard/fingerprint/InferSexFromBAM.java

@@ -0,0 +1,76 @@
+/*
+ * 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.fingerprint;
+
+import htsjdk.samtools.util.IOUtil;
+import org.broadinstitute.barclay.argparser.Argument;
+import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
+import org.broadinstitute.barclay.argparser.ExperimentalFeature;
+import picard.cmdline.StandardOptionDefinitions;
+import picard.cmdline.programgroups.DiagnosticsAndQCProgramGroup;
+
+import java.io.File;
+import java.util.List;
+
+/**
+ * Program to Infer Sex of a cohort of samples from bams. Needs a large cohort with both sexes to
+ * work since it uses a clustering-based algorithm
+ *
+ * See InferSex for more details.
+ *
+ * This class looks at the index information to get average coverage over the sex chromosomes.
+ * it provides that information to the base class.
+ *
+ * Created by jbarlev on 5/30/14.
+ *
+ * @author Jonathan Barlev
+ * @author Yossi Farjoun
+ */
+@CommandLineProgramProperties(
+        summary = "A program that can infer sample sex from a collection of BAM files." +
+                "It compares the coverage over the male and female chromosomes to that over the rest of the" +
+                "genome, and performs clustering to find the answer. It uses the bam index to avoid having to " +
+                "iterate over the whole BAM file.",
+        oneLineSummary = "Infer sample sex from a collection of BAM files",
+        programGroup = DiagnosticsAndQCProgramGroup.class
+)
+@ExperimentalFeature
+public class InferSexFromBAM extends InferSex {
+
+    @Argument(shortName = StandardOptionDefinitions.INPUT_SHORT_NAME, doc = "Input BAM (not SAM) file. Must be indexed.")
+    public List<File> INPUT;
+
+    @Override
+    SexInferenceEngine getSexInference() {
+        return new SexInferenceEngineFromBAM(MALE_CHROMS, FEMALE_CHROMS, INPUT);
+    }
+
+    @Override
+    protected int doWork() {
+        IOUtil.assertFilesAreReadable(INPUT);
+
+        return super.doWork();
+    }
+}

src/main/java/picard/fingerprint/InferSexFromVCF.java

@@ -0,0 +1,87 @@
+/*
+ * 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.fingerprint;
+
+import htsjdk.samtools.util.IOUtil;
+import org.broadinstitute.barclay.argparser.Argument;
+import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
+import org.broadinstitute.barclay.argparser.ExperimentalFeature;
+import picard.cmdline.StandardOptionDefinitions;
+import picard.cmdline.programgroups.DiagnosticsAndQCProgramGroup;
+
+import java.io.File;
+
+/**
+ * Program to Infer Sex of a cohort of samples from a vcf. Needs a large cohort with both sexes to
+ * work since it uses a clustering-based algorithm
+ *
+ * See InferSex for more details.
+ *
+ * This class looks at depth markers on spaced variants in the VCF and provide information from that to the base class.
+ *
+ * Created by jbarlev on 5/30/14.
+ *
+ * @author Jonathan Barlev
+ * @author Yossi Farjoun
+ */
+@CommandLineProgramProperties(
+        summary = "A program that can infer sample sex from a VCF file." +
+                "It compares the coverage over the male and female chromosomes to that over the rest of the" +
+                "genome, and performs clustering to find the answer.",
+        oneLineSummary = "Infer sample sex from a VCF file",
+        programGroup = DiagnosticsAndQCProgramGroup.class
+)
+@ExperimentalFeature
+public class InferSexFromVCF extends InferSex {
+    @Argument(shortName = StandardOptionDefinitions.INPUT_SHORT_NAME, doc = "Input VCF file.")
+    public File INPUT;
+
+    @Argument(shortName = "AUTO_V", doc = "Number determining how many variants are sampled for coverage on each non-sex chromosome. " +
+            "Program will (attempt to) sample coverage at AUTOSOMAL_VARIANTS evenly spaced variants on each non-sex chromosome.")
+    public int AUTOSOMAL_VARIANTS = 10;
+
+    @Argument(shortName = "ALLO_V", doc = "Number determining how many variants are sampled for coverage on each sex chromosome. " +
+            "Program will (attempt to) sample coverage at ALLOSOMAL_VARIANTS evenly spaced variants on each sex chromosome. ")
+    public int ALLOSOMAL_VARIANTS = 100;
+
+    @Argument(shortName = "PAR", doc = "An IntervalList containing the pseudoautosomal region. Used for masking out that region since the regions on one " +
+            "chromosome may get mapped to the other and thus can change the apparent coverage.", optional = true)
+    public File PSEUDOAUTOSOMAL_REGION = null;
+
+    @Argument(doc="Some VCFs do not have variants (called) on Male chromosomes. Consequently, when determining sex, one may wish to give less weight to their Coverage than" +
+            "the memale chromosomes. Do this by dividing the male chromosome coverage values by a factor of Y_COVERAGE_SHRINK_FACTOR.")
+    public double Y_COVERAGE_SHRINK_FACTOR = 2.0;
+
+    @Override
+    SexInferenceEngine getSexInference() {
+        return new SexInferenceEngineFromVCF(MALE_CHROMS, FEMALE_CHROMS, INPUT, AUTOSOMAL_VARIANTS, ALLOSOMAL_VARIANTS, PSEUDOAUTOSOMAL_REGION, Y_COVERAGE_SHRINK_FACTOR);
+    }
+
+    @Override
+    protected int doWork() {
+        IOUtil.assertFileIsReadable(INPUT);
+        return super.doWork();
+    }
+}