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Re-added --only-output-calls-starting-in-intervals as a deprecated argument with warning. #9000

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merged 3 commits into from
Oct 17, 2024
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Re-added --only-output-calls-starting-in-intervals as a deprecated argument with warning. #9000

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89644a7
added the old arguments as depricated decorators to the new filtering…
jamesemery Oct 15, 2024
958c9a2
never submit a short PR
jamesemery Oct 16, 2024
6f7ab10
one more comment
jamesemery Oct 16, 2024
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25 changes: 20 additions & 5 deletions src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand Down Expand Up @@ -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;
Expand All @@ -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
*
Expand Down Expand Up @@ -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,
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I think this was previously advanced as well, I'd tag it again.

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Also, I believe we should be using barclay's @DeprecatedFeature instead of java deprecated. You can include a "detail" message in it that explains what to use instead.

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<>();
Expand Down Expand Up @@ -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 ) {
Expand Down
18 changes: 18 additions & 0 deletions ...ain/java/org/broadinstitute/hellbender/tools/walkers/gnarlyGenotyper/GnarlyGenotyper.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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.*;
Expand Down Expand Up @@ -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,
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Same comments as above.

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 " +
Expand Down Expand Up @@ -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());
Expand Down
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