{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments/48321851","id":48321851,"diff_hunk":"@@ -0,0 +1,430 @@\n+package org.broadinstitute.hellbender.tools.walkers.variantutils;\n+\n+import htsjdk.variant.variantcontext.Allele;\n+import htsjdk.variant.variantcontext.VariantContext;\n+import htsjdk.variant.vcf.VCFConstants;\n+import htsjdk.variant.vcf.VCFHeader;\n+import org.broadinstitute.hellbender.cmdline.Advanced;\n+import org.broadinstitute.hellbender.cmdline.Argument;\n+import org.broadinstitute.hellbender.cmdline.CommandLineProgramProperties;\n+import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;\n+import org.broadinstitute.hellbender.cmdline.programgroups.VariantProgramGroup;\n+import org.broadinstitute.hellbender.engine.FeatureContext;\n+import org.broadinstitute.hellbender.engine.ReadsContext;\n+import org.broadinstitute.hellbender.engine.ReferenceContext;\n+import org.broadinstitute.hellbender.engine.VariantWalker;\n+import org.broadinstitute.hellbender.exceptions.UserException;\n+import org.broadinstitute.hellbender.utils.Utils;\n+import org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils;\n+import org.broadinstitute.hellbender.utils.variant.VcfUtils;\n+\n+import java.io.FileNotFoundException;\n+import java.io.PrintStream;\n+import java.lang.reflect.Array;\n+import java.util.*;\n+import java.util.function.Function;\n+\n+/**\n+ * Extract specific fields from a VCF file to a tab-delimited table\n+ *\n+ * <p>\n+ * This tool is designed to extract fields from the VCF to a table format that is more convenient to work with in\n+ * downstream analyses.</p>\n+ *\n+ * <p>The user specifies one or more\n+ * fields to print with the -F NAME, each of which appears as a single column in\n+ * the output file, with a header named NAME, and the value of this field in the VCF\n+ * one per line.  NAME can be any standard VCF column (CHROM, ID, QUAL) or any binding\n+ * in the INFO field (AC=10).  In addition, there are specially supported values like\n+ * EVENTLENGTH (length of the event), TRANSITION (for SNPs), HET (count of het genotypes),\n+ * HOM-REF (count of homozygous reference genotypes), HOM-VAR (count of homozygous variant\n+ * genotypes), NO-CALL (count of no-call genotypes), TYPE (the type of event), VAR (count of\n+ * non-reference genotypes), NSAMPLES (number of samples), NCALLED (number of called samples),\n+ * GQ (from the genotype field; works only for a file with a single sample), and MULTI-ALLELIC\n+ * (is the record from a multi-allelic site).  </p>\n+ *\n+ * </p>\n+ *\n+ * <h3>Input</h3>\n+ * <p>\n+ * <ul>\n+ *     <li>A VCF file</li>\n+ *     <li>A list of -F fields to write</li>\n+ * </ul>\n+ * </p>\n+ *\n+ * <h3>Output</h3>\n+ * <p>\n+ * A tab-delimited file containing the values of the requested fields in the VCF file\n+ * </p>\n+ *\n+ * <h3>Usage example</h3>\n+ * <pre>\n+ *     ./gatk-launch \\\n+ *     -R reference.fasta\n+ *     -T VariantsToTable \\\n+ *     -V file.vcf \\\n+ *     -F CHROM -F POS -F ID -F QUAL -F AC \\\n+ *     -o results.table\n+ * </pre>\n+ * <p>would produce a file that looks like:</p>\n+ * <pre>\n+ *     CHROM    POS ID      QUAL    AC\n+ *     1        10  .       50      1\n+ *     1        20  rs10    99      10\n+ *     et cetera...\n+ * </pre>\n+ *\n+ * <h3>Caveat</h3>\n+ * <p>If a VCF record is missing a value, then the tool by default throws an error, but the special value NA can\n+ * be emitted instead if requested at the command line using --allowMissingData.</p>\n+ *\n+ * @author Mark DePristo\n+ * @since 2010\n+ */\n+@CommandLineProgramProperties(\n+        summary = \"This tool is designed to extract fields from the VCF to a table format \" +\n+                \"that is more convenient to work with in \" +\n+                \"downstream analyses\",\n+        oneLineSummary = \"Extract specific fields from a VCF file to a tab-delimited table\",\n+        programGroup = VariantProgramGroup.class\n+)\n+public final class VariantsToTable extends VariantWalker {\n+\n+    @Argument(fullName = StandardArgumentDefinitions.OUTPUT_LONG_NAME,\n+            shortName = StandardArgumentDefinitions.OUTPUT_SHORT_NAME,\n+            doc=\"File to which results should be written\")\n+    private String out = null;\n+\n+    /**\n+     * -F NAME can be any standard VCF column (CHROM, ID, QUAL) or any binding in the INFO field (e.g., AC=10).\n+     * Note that to capture GENOTYPE (FORMAT) field values, see the GF argument.  This argument accepts any number\n+     * of inputs.  So -F CHROM -F POS is allowed.\n+     */\n+    @Argument(fullName=\"fields\", shortName=\"F\", doc=\"The name of each field to capture for output in the table\", optional=true)\n+    private List<String> fieldsToTake = new ArrayList<>();\n+\n+    /**\n+     * -GF NAME can be any binding in the FORMAT field (e.g., GQ, PL).\n+     * Note this argument accepts any number of inputs.  So -GF GQ -GF PL is allowed.\n+     */\n+    @Argument(fullName=\"genotypeFields\", shortName=\"GF\", doc=\"The name of each genotype field to capture for output in the table\", optional=true)\n+    private List<String> genotypeFieldsToTake = new ArrayList<>();\n+\n+    /**\n+     * By default this tool only emits values for fields where the FILTER field is either PASS or . (unfiltered).\n+     * Throwing this flag will cause VariantsToTable to emit values regardless of the FILTER field value.\n+     */\n+    @Advanced\n+    @Argument(fullName=\"showFiltered\", shortName=\"raw\", doc=\"If provided, field values from filtered records will be included in the output\", optional=true)\n+    private boolean showFiltered = false;\n+\n+    /**\n+     * By default, records with multiple ALT alleles will comprise just one line of output; note that in general this can make your resulting file\n+     * unreadable/malformed for certain tools like R, as the representation of multi-allelic INFO field values are often comma-separated lists\n+     * of values.  Using the flag will cause multi-allelic records to be split into multiple lines of output (one for each allele in the ALT field);\n+     * INFO field values that are not lists are copied for each of the output records while only the appropriate entry is used for lists.\n+     */\n+    @Argument(fullName=\"splitMultiAllelic\", shortName=\"SMA\", doc=\"If provided, we will split multi-allelic records into multiple lines of output\", optional=true)\n+    private boolean splitMultiAllelic = false;\n+\n+    /**\n+     * By default, this tool emits one line per usable VCF record (or per allele if the -SMA flag is provided).  Using the -moltenize flag\n+     * will cause records to be split into multiple lines of output: one for each field provided with -F or one for each combination of sample\n+     * and field provided with -GF.  Note that the \"Sample\" column for -F fields will always be \"site\".\n+     */\n+    @Advanced\n+    @Argument(fullName=\"moltenize\", shortName=\"moltenize\", doc=\"If provided, we will produce molten output\", optional=true)\n+    private boolean moltenizeOutput = false;\n+\n+    /**\n+     * By default, this tool throws a UserException when it encounters a field without a value in some record.  This\n+     * is generally useful when you mistype -F CHROM, so that you get a friendly warning about CHROM not being\n+     * found before the tool runs through 40M 1000G records.  However, in some cases you genuinely want to allow such\n+     * fields (e.g., AC not being calculated for filtered records, if included).  When provided, this 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#21 \r\n@cmnbroad please review\r\n\r\n@vdauwera FYI - new tool 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