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Merge pull request #256 from LabKey/fb_merge_23.11_to_develop
Merge discvr-23.11 to develop
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134 changes: 134 additions & 0 deletions
134
SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/BcftoolsFillTagsStep.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,134 @@ | ||
| package org.labkey.sequenceanalysis.run.analysis; | ||
|
|
||
| import htsjdk.samtools.util.Interval; | ||
| import org.apache.commons.lang3.StringUtils; | ||
| import org.json.JSONObject; | ||
| import org.labkey.api.pipeline.PipelineJobException; | ||
| import org.labkey.api.sequenceanalysis.SequenceAnalysisService; | ||
| import org.labkey.api.sequenceanalysis.pipeline.AbstractVariantProcessingStepProvider; | ||
| import org.labkey.api.sequenceanalysis.pipeline.BcftoolsRunner; | ||
| import org.labkey.api.sequenceanalysis.pipeline.PipelineContext; | ||
| import org.labkey.api.sequenceanalysis.pipeline.PipelineStepProvider; | ||
| import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenome; | ||
| import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService; | ||
| import org.labkey.api.sequenceanalysis.pipeline.ToolParameterDescriptor; | ||
| import org.labkey.api.sequenceanalysis.pipeline.VariantProcessingStep; | ||
| import org.labkey.api.sequenceanalysis.pipeline.VariantProcessingStepOutputImpl; | ||
| import org.labkey.api.sequenceanalysis.run.AbstractCommandPipelineStep; | ||
| import org.labkey.sequenceanalysis.pipeline.SequenceTaskHelper; | ||
|
|
||
| import javax.annotation.Nullable; | ||
| import java.io.File; | ||
| import java.io.IOException; | ||
| import java.util.ArrayList; | ||
| import java.util.Arrays; | ||
| import java.util.List; | ||
| import java.util.stream.Collectors; | ||
|
|
||
| public class BcftoolsFillTagsStep extends AbstractCommandPipelineStep<BcftoolsRunner> implements VariantProcessingStep | ||
| { | ||
| public BcftoolsFillTagsStep(PipelineStepProvider<?> provider, PipelineContext ctx) | ||
| { | ||
| super(provider, ctx, new BcftoolsRunner(ctx.getLogger())); | ||
| } | ||
|
|
||
| public static class Provider extends AbstractVariantProcessingStepProvider<BcftoolsFillTagsStep> implements VariantProcessingStep.RequiresPedigree, VariantProcessingStep.SupportsScatterGather | ||
| { | ||
| public Provider() | ||
| { | ||
| super("BcftoolsFillTagsStep", "Bcftools Fill-tags", "bcftools", "Annotate variants using bcftools fill-tags", Arrays.asList( | ||
| ToolParameterDescriptor.create("hwe", "HWE", "If selected, HWE will be annotated", "checkbox", new JSONObject(){{ | ||
| put("checked", true); | ||
| }}, true), | ||
| ToolParameterDescriptor.create("exchet", "Excess Het", "If selected, ExcHet will be annotated.", "checkbox", new JSONObject(){{ | ||
| put("checked", true); | ||
| }}, true) | ||
| ), null, ""); | ||
| } | ||
|
|
||
| @Override | ||
| public BcftoolsFillTagsStep create(PipelineContext ctx) | ||
| { | ||
| return new BcftoolsFillTagsStep(this, ctx); | ||
| } | ||
| } | ||
|
|
||
| @Override | ||
| public VariantProcessingStep.Output processVariants(File inputVCF, File outputDirectory, ReferenceGenome genome, @Nullable List<Interval> intervals) throws PipelineJobException | ||
| { | ||
| VariantProcessingStepOutputImpl output = new VariantProcessingStepOutputImpl(); | ||
|
|
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| List<String> options = new ArrayList<>(); | ||
| options.add(getWrapper().getBcfToolsPath().getPath()); | ||
| options.add("+fill-tags"); | ||
|
|
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| options.add(inputVCF.getPath()); | ||
|
|
||
| if (intervals != null) | ||
| { | ||
| options.add("--regions"); | ||
| options.add(intervals.stream().map(interval -> interval.getContig() + ":" + interval.getStart() + "-" + interval.getEnd()).collect(Collectors.joining(","))); | ||
| } | ||
|
|
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| options.add("-O"); | ||
| options.add("z9"); | ||
|
|
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| Integer threads = SequencePipelineService.get().getMaxThreads(getPipelineCtx().getLogger()); | ||
| if (threads != null) | ||
| { | ||
| options.add("--threads"); | ||
| options.add(threads.toString()); | ||
| } | ||
|
|
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| File outputVcf = new File(outputDirectory, SequenceTaskHelper.getUnzippedBaseName(inputVCF) + ".ft.vcf.gz"); | ||
| options.add("-o"); | ||
| options.add(outputVcf.getPath()); | ||
|
|
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| List<String> annotations = new ArrayList<>(); | ||
| if (getProvider().getParameterByName("hwe").extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), Boolean.class, false)) | ||
| { | ||
| annotations.add("hwe"); | ||
| } | ||
|
|
||
| if (getProvider().getParameterByName("exchet").extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), Boolean.class, false)) | ||
| { | ||
| annotations.add("exchet"); | ||
| } | ||
|
|
||
| if (annotations.isEmpty()) | ||
| { | ||
| throw new PipelineJobException("No annotations were selected"); | ||
| } | ||
|
|
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| options.add("-t"); | ||
| options.add(StringUtils.join(annotations, ",")); | ||
|
|
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| BcftoolsRunner wrapper = getWrapper(); | ||
|
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| String bcfPluginDir = StringUtils.trimToNull(System.getenv("BCFTOOLS_PLUGINS")); | ||
| if (bcfPluginDir != null) | ||
| { | ||
| getPipelineCtx().getLogger().debug("Setting BCFTOOLS_PLUGINS environment variable: " + bcfPluginDir); | ||
| wrapper.addToEnvironment("BCFTOOLS_PLUGINS", bcfPluginDir); | ||
| } | ||
|
|
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| wrapper.execute(options); | ||
| if (!outputVcf.exists()) | ||
| { | ||
| throw new PipelineJobException("output not found: " + outputVcf); | ||
| } | ||
|
|
||
| try | ||
| { | ||
| SequenceAnalysisService.get().ensureVcfIndex(outputVcf, getWrapper().getLogger()); | ||
| } | ||
| catch (IOException e) | ||
| { | ||
| throw new PipelineJobException(e); | ||
| } | ||
|
|
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| output.setVcf(outputVcf); | ||
|
|
||
| return output; | ||
| } | ||
| } |
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