From e6b19dc751ec05751bc3e93ce73260ef0742c2a2 Mon Sep 17 00:00:00 2001 From: Adam Rauch Date: Wed, 10 Jan 2024 18:18:23 -0800 Subject: [PATCH] Use the correct @Nullable annotation --- .../sequenceanalysis/run/variant/GenotypeConcordanceStep.java | 2 +- .../sequenceanalysis/run/variant/GenotypeFiltrationStep.java | 2 +- .../labkey/sequenceanalysis/run/variant/KingInferenceStep.java | 3 +-- .../run/variant/MendelianViolationReportStep.java | 2 +- .../run/variant/OutputVariantsStartingInIntervalsStep.java | 3 +-- 5 files changed, 5 insertions(+), 7 deletions(-) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/GenotypeConcordanceStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/GenotypeConcordanceStep.java index d9e2785ea..0ee8d3488 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/GenotypeConcordanceStep.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/GenotypeConcordanceStep.java @@ -7,6 +7,7 @@ import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.vcf.VCFFileReader; import htsjdk.variant.vcf.VCFHeader; +import org.jetbrains.annotations.Nullable; import org.json.JSONObject; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.SequenceAnalysisService; @@ -22,7 +23,6 @@ import org.labkey.sequenceanalysis.pipeline.SequenceTaskHelper; import org.labkey.sequenceanalysis.run.util.VariantAnnotatorWrapper; -import javax.annotation.Nullable; import java.io.File; import java.io.IOException; import java.util.ArrayList; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/GenotypeFiltrationStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/GenotypeFiltrationStep.java index 37c754704..8b63d72eb 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/GenotypeFiltrationStep.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/GenotypeFiltrationStep.java @@ -1,6 +1,7 @@ package org.labkey.sequenceanalysis.run.variant; import htsjdk.samtools.util.Interval; +import org.jetbrains.annotations.Nullable; import org.json.JSONArray; import org.json.JSONObject; import org.labkey.api.pipeline.PipelineJobException; @@ -16,7 +17,6 @@ import org.labkey.api.sequenceanalysis.run.VariantFiltrationWrapper; import org.labkey.sequenceanalysis.pipeline.SequenceTaskHelper; -import javax.annotation.Nullable; import java.io.File; import java.util.ArrayList; import java.util.Arrays; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/KingInferenceStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/KingInferenceStep.java index 831631723..aa7d6da7b 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/KingInferenceStep.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/KingInferenceStep.java @@ -8,6 +8,7 @@ import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.math.NumberUtils; import org.apache.logging.log4j.Logger; +import org.jetbrains.annotations.Nullable; import org.json.JSONObject; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.SequenceAnalysisService; @@ -22,11 +23,9 @@ import org.labkey.api.sequenceanalysis.run.AbstractCommandPipelineStep; import org.labkey.api.sequenceanalysis.run.AbstractCommandWrapper; -import javax.annotation.Nullable; import java.io.File; import java.io.IOException; import java.util.ArrayList; -import java.util.Arrays; import java.util.List; public class KingInferenceStep extends AbstractCommandPipelineStep implements VariantProcessingStep diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/MendelianViolationReportStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/MendelianViolationReportStep.java index 052a1a982..b29befc8a 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/MendelianViolationReportStep.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/MendelianViolationReportStep.java @@ -1,6 +1,7 @@ package org.labkey.sequenceanalysis.run.variant; import htsjdk.samtools.util.Interval; +import org.jetbrains.annotations.Nullable; import org.json.JSONObject; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStep; @@ -14,7 +15,6 @@ import org.labkey.api.sequenceanalysis.pipeline.VariantProcessingStepOutputImpl; import org.labkey.sequenceanalysis.pipeline.ProcessVariantsHandler; -import javax.annotation.Nullable; import java.io.File; import java.util.ArrayList; import java.util.Arrays; diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/OutputVariantsStartingInIntervalsStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/OutputVariantsStartingInIntervalsStep.java index 15174dfcd..2d02bc997 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/OutputVariantsStartingInIntervalsStep.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/OutputVariantsStartingInIntervalsStep.java @@ -2,6 +2,7 @@ import htsjdk.samtools.util.Interval; import org.apache.logging.log4j.Logger; +import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.SequenceAnalysisService; import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStep; @@ -14,12 +15,10 @@ import org.labkey.api.sequenceanalysis.run.AbstractDiscvrSeqWrapper; import org.labkey.api.writer.PrintWriters; -import javax.annotation.Nullable; import java.io.File; import java.io.IOException; import java.io.PrintWriter; import java.util.ArrayList; -import java.util.Arrays; import java.util.List; /**