Optionally extract all fingerprint snps

src/main/java/picard/fingerprint/ExtractFingerprint.java

@@ -82,6 +82,11 @@ public class ExtractFingerprint extends CommandLineProgram {
     @Argument(doc = "When true code will check for readability on input files (this can be slow on cloud access)")
     public boolean TEST_INPUT_READABILITY = true;
 
+
+    @Hidden
+    @Argument(doc = "When false, code will extract variants for every snp in the haplotype database, not only the representative one.")
+    public boolean EXTRACT_REPRESENTATIVES_ONLY = true;
+
     @Override
     protected boolean requiresReference() {
         return true;
@@ -133,7 +138,8 @@ protected int doWork() {
         final String sampleToUse = getSampleToUse(soleEntry.getKey());
 
         try {
-            FingerprintUtils.writeFingerPrint(soleEntry.getValue(), OUTPUT, referenceSequence.getReferenceFile(), sampleToUse, "PLs derived from " + INPUT + " using an assumed contamination of " + this.CONTAMINATION);
+            FingerprintUtils.writeFingerPrint(soleEntry.getValue(), OUTPUT, referenceSequence.getReferenceFile(),
+                    sampleToUse, "PLs derived from " + INPUT + " using an assumed contamination of " + this.CONTAMINATION, EXTRACT_REPRESENTATIVES_ONLY);
         } catch (Exception e) {
             log.error(e);
         }

src/main/java/picard/fingerprint/FingerprintUtils.java

@@ -45,16 +45,10 @@
 
 import java.io.File;
 import java.io.IOException;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Date;
-import java.util.LinkedHashSet;
-import java.util.List;
-import java.util.Objects;
-import java.util.Set;
-import java.util.TreeSet;
+import java.util.*;
 import java.util.function.Function;
 import java.util.stream.Collectors;
+import java.util.stream.Stream;
 
 /**
  * A set of utilities used in the fingerprinting environment
@@ -71,18 +65,20 @@ public class FingerprintUtils {
      * @param referenceSequenceFileName the reference sequence (file)
      * @param sample                    the sample name to use in the vcf
      * @param source                    a "source" comment to use in the VCF
-     * @throws IOException
+     * @param representativeOnly        whether to extract only the representative snps
+     * @throws IOException if two snps in the haplotype map have the same "name"
      */
     public static void writeFingerPrint(final Fingerprint fingerprint,
                                         final File outputFile,
                                         final File referenceSequenceFileName,
                                         final String sample,
-                                        final String source) throws IOException {
+                                        final String source,
+                                        final boolean representativeOnly) throws IOException {
 
         try (final ReferenceSequenceFile ref = ReferenceSequenceFileFactory.getReferenceSequenceFile(referenceSequenceFileName);
              final VariantContextWriter variantContextWriter = getVariantContextWriter(outputFile, referenceSequenceFileName, sample, source, ref)) {
 
-            createVCSetFromFingerprint(fingerprint, ref, sample).forEach(variantContextWriter::add);
+            createVCSetFromFingerprint(fingerprint, ref, sample, representativeOnly).forEach(variantContextWriter::add);
         }
     }
 
@@ -113,18 +109,21 @@ private static VariantContextWriter getVariantContextWriter(final File outputFil
     /**
      * A utility function that takes a fingerprint and returns a VariantContextSet with variants representing the haplotypes in the fingerprint
      *
-     * @param fingerPrint A fingerprint
-     * @param reference   A reference sequence that will be used to create the VariantContexts
-     * @param sample      A sample name that will be used for the genotype field
+     * @param fingerPrint         A fingerprint
+     * @param reference           A reference sequence that will be used to create the VariantContexts
+     * @param sample              A sample name that will be used for the genotype field
+     * @param representativeOnly A boolean specifying whether to create a VC only for the representative Snp (or for all of them if false)
      * @return VariantContextSet with variants representing the haplotypes in the fingerprint
      */
-    public static VariantContextSet createVCSetFromFingerprint(final Fingerprint fingerPrint, final ReferenceSequenceFile reference, final String sample) {
+    public static VariantContextSet createVCSetFromFingerprint(final Fingerprint fingerPrint, final ReferenceSequenceFile reference, final String sample, boolean representativeOnly) {
 
         final VariantContextSet variantContexts = new VariantContextSet(reference.getSequenceDictionary());
 
         // check that the same snp name isn't twice in the fingerprint.
         fingerPrint.values().stream()
-                .map(hp -> hp.getRepresentativeSnp().getName())
+                .flatMap(hp -> representativeOnly ?
+                        Stream.of(hp.getRepresentativeSnp().getName()) :
+                        hp.getHaplotype().getSnps().stream().map(Snp::getName))
                 .filter(Objects::nonNull)
                 .filter(n -> !n.equals(""))
                 .collect(Collectors.groupingBy(Function.identity(), Collectors.counting()))
@@ -138,18 +137,31 @@ public static VariantContextSet createVCSetFromFingerprint(final Fingerprint fin
 
         // convert all the haplotypes to variant contexts and add them to the set.
         fingerPrint.values().stream()
-                .map(hp -> getVariantContext(reference, sample, hp))
+                .flatMap(hp -> getVariantContext(reference, sample, hp, representativeOnly))
                 .forEach(variantContexts::add);
 
         return variantContexts;
     }
 
     @VisibleForTesting
-    static VariantContext getVariantContext(final ReferenceSequenceFile reference,
+    static Stream<VariantContext> getVariantContext(final ReferenceSequenceFile reference,
                                                     final String sample,
-                                                    final HaplotypeProbabilities haplotypeProbabilities) {
-        final Snp snp = haplotypeProbabilities.getRepresentativeSnp();
-        final byte refAllele = StringUtil.toUpperCase(reference.getSubsequenceAt(
+                                                    final HaplotypeProbabilities haplotypeProbabilities,
+                                                    final boolean representative_only) {
+        if (representative_only) {
+            return Stream.of(getVariantContextFromSnp(reference, sample, haplotypeProbabilities, haplotypeProbabilities.getRepresentativeSnp()));
+        } else {
+            return haplotypeProbabilities.getHaplotype().getSnps().stream().map(snp -> getVariantContextFromSnp(reference, sample, haplotypeProbabilities, snp));
+        }
+    }
+
+    @VisibleForTesting
+    static VariantContext getVariantContextFromSnp(final ReferenceSequenceFile reference,
+        final String sample,
+        final HaplotypeProbabilities haplotypeProbabilities,
+        final Snp snp) {
+
+            final byte refAllele = StringUtil.toUpperCase(reference.getSubsequenceAt(
                 snp.getChrom(),
                 snp.getPos(),
                 snp.getPos()).getBases()[0]);

src/main/java/picard/fingerprint/Snp.java

@@ -25,6 +25,7 @@
 package picard.fingerprint;
 
 import htsjdk.samtools.util.CollectionUtil;
+import htsjdk.samtools.util.Locatable;
 import htsjdk.samtools.util.StringUtil;
 import htsjdk.variant.variantcontext.Allele;
 
@@ -36,7 +37,7 @@
  *
  * @author Tim Fennell
  */
-public class Snp implements Comparable<Snp> {
+public class Snp implements Comparable<Snp>, Locatable {
     private final String name;
     private final String chrom;
     private final int pos;
@@ -124,4 +125,19 @@ public int hashCode() {
     public String toString() {
         return this.chrom + ":" + this.pos;
     }
+
+    @Override
+    public String getContig() {
+        return chrom;
+    }
+
+    @Override
+    public int getStart() {
+        return pos;
+    }
+
+    @Override
+    public int getEnd() {
+        return pos;
+    }
 }

src/test/java/picard/fingerprint/CheckFingerprintTest.java

@@ -16,7 +16,6 @@
 import java.io.File;
 import java.io.IOException;
 import java.nio.file.Path;
-import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
@@ -214,7 +213,7 @@ public void testFPToVC() throws IOException {
         tempFile.deleteOnExit();
 
         FingerprintUtils.writeFingerPrint(fingerprint, tempFile, SHIFTED_REFERENCE,
-                "NA12892", null);
+                "NA12892", null, true);
 
         final Fingerprint NA12892FromVCF = checker.fingerprintFiles(Collections.singleton(tempFile.toPath()), 1, 1, TimeUnit.DAYS)
                 .values().stream()

src/test/java/picard/fingerprint/FingerprintCheckerTest.java

@@ -375,7 +375,7 @@ void testCanHandleDeepData(final HaplotypeProbabilitiesFromSequence hp, final in
         final File fasta = new File(TEST_DATA_DIR, "reference.fasta");
 
         try (final ReferenceSequenceFile ref = ReferenceSequenceFileFactory.getReferenceSequenceFile(fasta)) {
-            final VariantContext vc = FingerprintUtils.getVariantContext(ref, "test", hp);
+            final VariantContext vc = FingerprintUtils.getVariantContext(ref, "test", hp, true).iterator().next();
             Assert.assertTrue(MathUtil.max(MathUtil.promote(vc.getGenotype(0).getPL())) > 0);
         }
     }
@@ -551,7 +551,7 @@ public void testWriteFingerprint() throws IOException {
         final Fingerprint fp = fpchecker.fingerprintVcf(vcfInput.toPath()).values().iterator().next();
 
         final File vcfOutput = File.createTempFile("fingerprint", ".vcf");
-        FingerprintUtils.writeFingerPrint(fp, vcfOutput, fasta, "Dummy", "Testing");
+        FingerprintUtils.writeFingerPrint(fp, vcfOutput, fasta, "Dummy", "Testing", true);
 
         VcfTestUtils.assertVcfFilesAreEqual(vcfOutput, vcfExpected);
     }