Re-added --only-output-calls-starting-in-intervals as a deprecated …

…argument. (#9000)
broadinstitute · Oct 17, 2024 · 87e9f1f · 87e9f1f
1 parent a377b07
commit 87e9f1f
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Showing 2 changed files with 38 additions and 5 deletions.
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs.java
@@ -7,11 +7,7 @@
 import htsjdk.variant.variantcontext.writer.VariantContextWriter;
 import htsjdk.variant.vcf.VCFHeader;
 import htsjdk.variant.vcf.VCFHeaderLine;
-import org.broadinstitute.barclay.argparser.Argument;
-import org.broadinstitute.barclay.argparser.ArgumentCollection;
-import org.broadinstitute.barclay.argparser.CommandLineException;
-import org.broadinstitute.barclay.argparser.CommandLinePluginDescriptor;
-import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
+import org.broadinstitute.barclay.argparser.*;
 import org.broadinstitute.barclay.help.DocumentedFeature;
 import org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptor;
 import org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKReadFilterPluginDescriptor;
@@ -42,6 +38,7 @@
 import org.broadinstitute.hellbender.utils.SimpleInterval;
 import org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils;
 import org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotation;
+import org.broadinstitute.hellbender.utils.variant.writers.IntervalFilteringVcfWriter;
 
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -52,6 +49,8 @@
 import java.util.Set;
 import java.util.stream.Collectors;
 
+import static org.broadinstitute.hellbender.utils.variant.writers.IntervalFilteringVcfWriter.Mode.STARTS_IN;
+
 /**
  * Perform joint genotyping on one or more samples pre-called with HaplotypeCaller
  *
@@ -171,6 +170,17 @@ public final class GenotypeGVCFs extends VariantLocusWalker {
     @ArgumentCollection
     private GenomicsDBArgumentCollection genomicsdbArgs = new GenomicsDBArgumentCollection();
 
+    /**
+     * This option can only be activated if intervals are specified.
+     */
+    @DeprecatedFeature
+    @Advanced
+    @Argument(fullName= ONLY_OUTPUT_CALLS_STARTING_IN_INTERVALS_FULL_NAME,
+            doc="Restrict variant output to sites that start within provided intervals, equivalent to '--"+StandardArgumentDefinitions.VARIANT_OUTPUT_INTERVAL_FILTERING_MODE_LONG_NAME+" STARTS_IN'",
+            optional=true,
+            mutex = {StandardArgumentDefinitions.VARIANT_OUTPUT_INTERVAL_FILTERING_MODE_LONG_NAME})
+    private boolean onlyOutputCallsStartingInIntervals = false;
+
     @Argument(fullName = FORCE_OUTPUT_INTERVALS_NAME,
             suppressFileExpansion = true, doc = "sites at which to output genotypes even if non-variant in samples", optional = true)
     protected final List<String> forceOutputIntervalStrings = new ArrayList<>();
@@ -253,6 +263,11 @@ public void onTraversalStart() {
             logger.warn("Note that the Mutect2 reference confidence mode is in BETA -- the likelihoods model and output format are subject to change in subsequent versions.");
         }
 
+        if (onlyOutputCallsStartingInIntervals) {
+            logger.warn("The --" + ONLY_OUTPUT_CALLS_STARTING_IN_INTERVALS_FULL_NAME + " option is deprecated. Please use '--" + StandardArgumentDefinitions.VARIANT_OUTPUT_INTERVAL_FILTERING_MODE_LONG_NAME + " STARTS_IN' for an equivalent filtering.");
+            this.userOutputVariantIntervalFilteringMode = STARTS_IN;
+        }
+
         forceOutputIntervalsPresent = !forceOutputIntervalStrings.isEmpty();
 
         if (includeNonVariants && forceOutputIntervalsPresent ) {

diff --git a/...ain/java/org/broadinstitute/hellbender/tools/walkers/gnarlyGenotyper/GnarlyGenotyper.java b/...ain/java/org/broadinstitute/hellbender/tools/walkers/gnarlyGenotyper/GnarlyGenotyper.java
@@ -38,6 +38,7 @@
 import org.broadinstitute.hellbender.utils.variant.GATKVCFHeaderLines;
 import org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils;
 import org.broadinstitute.hellbender.utils.variant.writers.GVCFWriter;
+import org.broadinstitute.hellbender.utils.variant.writers.IntervalFilteringVcfWriter;
 import org.reflections.Reflections;
 
 import java.util.*;
@@ -108,6 +109,17 @@ public final class GnarlyGenotyper extends VariantWalker {
     @Argument(fullName = "keep-all-sites", doc="Retain low quality and non-variant sites, applying appropriate filters", optional=true)
     private boolean keepAllSites = false;
 
+    /**
+     * This option can only be activated if intervals are specified.
+     */
+    @DeprecatedFeature
+    @Advanced
+    @Argument(fullName= GenotypeGVCFs.ONLY_OUTPUT_CALLS_STARTING_IN_INTERVALS_FULL_NAME,
+            doc="Restrict variant output to sites that start within provided intervals, equivalent to '--"+StandardArgumentDefinitions.VARIANT_OUTPUT_INTERVAL_FILTERING_MODE_LONG_NAME+" STARTS_IN'",
+            optional=true,
+            mutex = {StandardArgumentDefinitions.VARIANT_OUTPUT_INTERVAL_FILTERING_MODE_LONG_NAME})
+    private boolean onlyOutputCallsStartingInIntervals = false;
+
     @Argument(fullName = GenomicsDBImport.MERGE_INPUT_INTERVALS_LONG_NAME,
             shortName = GenomicsDBImport.MERGE_INPUT_INTERVALS_LONG_NAME,
             doc = "Boolean flag to read in all data in between intervals.  Improves performance reading from GenomicsDB " +
@@ -168,6 +180,12 @@ protected GenomicsDBOptions getGenomicsDBOptions() {
 
     @Override
     public void onTraversalStart() {
+
+        if (onlyOutputCallsStartingInIntervals) {
+            logger.warn("The --" + GenotypeGVCFs.ONLY_OUTPUT_CALLS_STARTING_IN_INTERVALS_FULL_NAME + " option is deprecated. Please use '--" + StandardArgumentDefinitions.VARIANT_OUTPUT_INTERVAL_FILTERING_MODE_LONG_NAME + " STARTS_IN' for an equivalent filtering.");
+            this.userOutputVariantIntervalFilteringMode = IntervalFilteringVcfWriter.Mode.STARTS_IN;
+        }
+
         final VCFHeader inputVCFHeader = getHeaderForVariants();
 
         final SampleList samples = new IndexedSampleList(inputVCFHeader.getGenotypeSamples());