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bbimberbbimber
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Add handler to convert existing BAMs to CRAM
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3 files changed

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‎SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SamtoolsCramConverter.java‎

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package org.labkey.api.sequenceanalysis.pipeline;
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import org.apache.logging.log4j.Logger;
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import org.jetbrains.annotations.Nullable;
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import org.labkey.api.pipeline.PipelineJobException;
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import java.io.File;
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import java.util.ArrayList;
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import java.util.List;
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/**
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* Created by bimber on 11/4/2016.
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*/
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public class SamtoolsCramConverter extends SamtoolsRunner
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{
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public SamtoolsCramConverter(Logger log)
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{
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super(log);
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}
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public File convert(File inputBam, File outputCram, File gzippedFasta, boolean doIndex, @Nullable Integer threads) throws PipelineJobException
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{
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getLogger().info("Converting SAM/BAM to CRAM: " + inputBam.getPath());
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List<String> params = new ArrayList<>();
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params.add(getSamtoolsPath().getPath());
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params.add("view");
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params.add("-C");
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params.add("-o");
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params.add(outputCram.getPath());
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params.add("-T");
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params.add(gzippedFasta.getPath());
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if (threads != null)
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{
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params.add("--threads");
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params.add(String.valueOf(threads));
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}
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params.add(inputBam.getPath());
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execute(params);
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if (doIndex)
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{
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doIndex(outputCram, threads);
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}
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return outputCram;
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}
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private void doIndex(File input, @Nullable Integer threads) throws PipelineJobException
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{
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List<String> params = new ArrayList<>();
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params.add(getSamtoolsPath().getPath());
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params.add("index");
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if (threads != null)
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{
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params.add("--threads");
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params.add(String.valueOf(threads));
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}
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params.add(input.getPath());
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execute(params);
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File idx = new File(input.getPath() + ".crai");
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if (!idx.exists())
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{
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throw new PipelineJobException("Unable to find CRAM index: " + idx.getPath());
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}
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}
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}

‎SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java‎

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import org.labkey.sequenceanalysis.pipeline.AlignmentImportJob;
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import org.labkey.sequenceanalysis.pipeline.CacheGenomePipelineJob;
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import org.labkey.sequenceanalysis.pipeline.CacheGenomeTrigger;
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import org.labkey.sequenceanalysis.pipeline.ConvertToCramHandler;
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import org.labkey.sequenceanalysis.pipeline.IlluminaImportJob;
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import org.labkey.sequenceanalysis.pipeline.ImportFastaSequencesPipelineJob;
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import org.labkey.sequenceanalysis.pipeline.ImportGenomeTrackPipelineJob;
@@ -361,6 +362,7 @@ public static void registerPipelineSteps()
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SequenceAnalysisService.get().registerFileHandler(new MergeLoFreqVcfHandler());
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SequenceAnalysisService.get().registerFileHandler(new PangolinHandler());
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SequenceAnalysisService.get().registerFileHandler(new NextCladeHandler());
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SequenceAnalysisService.get().registerFileHandler(new ConvertToCramHandler());
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SequenceAnalysisService.get().registerReadsetHandler(new MultiQCHandler());
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SequenceAnalysisService.get().registerReadsetHandler(new RestoreSraDataHandler());

‎SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ConvertToCramHandler.java‎

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package org.labkey.sequenceanalysis.pipeline;
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import org.json.JSONObject;
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import org.labkey.api.exp.api.ExpData;
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import org.labkey.api.module.ModuleLoader;
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import org.labkey.api.pipeline.PipelineJob;
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import org.labkey.api.pipeline.PipelineJobException;
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import org.labkey.api.pipeline.RecordedAction;
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import org.labkey.api.sequenceanalysis.SequenceOutputFile;
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import org.labkey.api.sequenceanalysis.pipeline.AbstractParameterizedOutputHandler;
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import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenome;
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import org.labkey.api.sequenceanalysis.pipeline.SamtoolsCramConverter;
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import org.labkey.api.sequenceanalysis.pipeline.SequenceAnalysisJobSupport;
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import org.labkey.api.sequenceanalysis.pipeline.SequenceOutputHandler;
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import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService;
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import org.labkey.api.sequenceanalysis.pipeline.ToolParameterDescriptor;
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import org.labkey.api.util.FileUtil;
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import org.labkey.sequenceanalysis.SequenceAnalysisModule;
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import org.labkey.sequenceanalysis.util.SequenceUtil;
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import java.io.File;
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import java.util.Arrays;
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import java.util.List;
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public class ConvertToCramHandler extends AbstractParameterizedOutputHandler<SequenceOutputHandler.SequenceOutputProcessor>
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{
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public ConvertToCramHandler()
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{
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super(ModuleLoader.getInstance().getModule(SequenceAnalysisModule.class), "Convert To Cram", "This will convert a BAM file to CRAM, replacing the original", null, Arrays.asList(
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ToolParameterDescriptor.create("replaceOriginal", "Replace Original File", "If selected, the input BAM will be deleted and the database record will be switched to use this filepath.", "checkbox", new JSONObject(){{
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put("checked", true);
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}}, true))
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);
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}
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@Override
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public boolean canProcess(SequenceOutputFile o)
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{
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return o.getFile() != null && o.getFile().exists() && SequenceUtil.FILETYPE.bam.getFileType().isType(o.getFile());
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}
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@Override
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public boolean useWorkbooks()
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{
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return true;
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}
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@Override
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public boolean doSplitJobs()
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{
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return true;
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}
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@Override
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public boolean requiresGenome()
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{
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return true;
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}
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@Override
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public boolean doRunRemote()
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{
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return true;
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}
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@Override
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public boolean doRunLocal()
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{
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return false;
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}
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@Override
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public SequenceOutputProcessor getProcessor()
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{
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return new Processor();
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}
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public class Processor implements SequenceOutputProcessor
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{
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@Override
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public void processFilesOnWebserver(PipelineJob job, SequenceAnalysisJobSupport support, List<SequenceOutputFile> inputFiles, JSONObject params, File outputDir, List<RecordedAction> actions, List<SequenceOutputFile> outputsToCreate) throws UnsupportedOperationException, PipelineJobException
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{
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}
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@Override
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public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext ctx) throws UnsupportedOperationException, PipelineJobException
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{
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boolean replaceOriginal = ctx.getParams().optBoolean("replaceOriginal", false);
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ctx.getLogger().info("Replace input BAM: " + replaceOriginal);
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Integer threads = SequencePipelineService.get().getMaxThreads(ctx.getLogger());
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for (SequenceOutputFile so : inputFiles)
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{
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ReferenceGenome genome = ctx.getSequenceSupport().getCachedGenome(so.getLibrary_id());
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File cram = new File(so.getFile().getParentFile(), FileUtil.getBaseName(so.getFile()) + ".cram");
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new SamtoolsCramConverter(ctx.getLogger()).convert(so.getFile(), cram, genome.getWorkingFastaFileGzipped(), true, threads);
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checkCramAndIndex(so);
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if (replaceOriginal)
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{
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ctx.getLogger().info("Deleting original BAM: " + so.getFile().getPath());
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new File(so.getFile().getPath() + ".bai").delete();
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so.getFile().delete();
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}
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}
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}
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private void checkCramAndIndex(SequenceOutputFile so) throws PipelineJobException
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{
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File cram = new File(so.getFile().getParentFile(), FileUtil.getBaseName(so.getFile()) + ".cram");
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if (!cram.exists())
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{
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throw new PipelineJobException("Unable to find file: " + cram.getPath());
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}
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File cramIdx = new File(cram.getPath() + ".crai");
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if (!cramIdx.exists())
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{
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throw new PipelineJobException("Unable to find file: " + cramIdx.getPath());
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}
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}
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@Override
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public void complete(PipelineJob job, List<SequenceOutputFile> inputs, List<SequenceOutputFile> outputsCreated, SequenceAnalysisJobSupport support) throws PipelineJobException
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{
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for (SequenceOutputFile so : inputs)
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{
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File cram = new File(so.getFile().getParentFile(), FileUtil.getBaseName(so.getFile()) + ".cram");
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checkCramAndIndex(so);
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job.getLogger().info("Updating ExpData record with new filepath: " + cram.getPath());
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ExpData d = so.getExpData();
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d.setDataFileURI(cram.toURI());
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d.save(job.getUser());
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}
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}
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}
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}

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