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Merge pull request #2522 from opencb/TASK-6722
TASK-6722 - Variant Walker to enable user defined variant analysis
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84 changes: 84 additions & 0 deletions
84
opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/VariantWalkerTool.java
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| Original file line number | Diff line number | Diff line change |
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| /* | ||
| * Copyright 2015-2020 OpenCB | ||
| * | ||
| * Licensed under the Apache License, Version 2.0 (the "License"); | ||
| * you may not use this file except in compliance with the License. | ||
| * You may obtain a copy of the License at | ||
| * | ||
| * http://www.apache.org/licenses/LICENSE-2.0 | ||
| * | ||
| * Unless required by applicable law or agreed to in writing, software | ||
| * distributed under the License is distributed on an "AS IS" BASIS, | ||
| * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| * See the License for the specific language governing permissions and | ||
| * limitations under the License. | ||
| */ | ||
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| package org.opencb.opencga.analysis.variant; | ||
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| import org.apache.solr.common.StringUtils; | ||
| import org.opencb.commons.datastore.core.Query; | ||
| import org.opencb.commons.datastore.core.QueryOptions; | ||
| import org.opencb.opencga.analysis.tools.OpenCgaTool; | ||
| import org.opencb.opencga.core.models.common.Enums; | ||
| import org.opencb.opencga.core.models.variant.VariantWalkerParams; | ||
| import org.opencb.opencga.core.tools.annotations.Tool; | ||
| import org.opencb.opencga.core.tools.annotations.ToolParams; | ||
| import org.opencb.opencga.storage.core.variant.io.VariantWriterFactory; | ||
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| import java.nio.file.Path; | ||
| import java.util.Arrays; | ||
| import java.util.List; | ||
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| @Tool(id = VariantWalkerTool.ID, description = VariantWalkerTool.DESCRIPTION, | ||
| scope = Tool.Scope.PROJECT, resource = Enums.Resource.VARIANT) | ||
| public class VariantWalkerTool extends OpenCgaTool { | ||
| public static final String ID = "variant-walk"; | ||
| public static final String DESCRIPTION = "Filter and walk variants from the variant storage to produce a file"; | ||
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| @ToolParams | ||
| protected VariantWalkerParams toolParams = new VariantWalkerParams(); | ||
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| private VariantWriterFactory.VariantOutputFormat format; | ||
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| @Override | ||
| protected void check() throws Exception { | ||
| super.check(); | ||
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| if (StringUtils.isEmpty(toolParams.getInputFormat())) { | ||
| toolParams.setInputFormat(VariantWriterFactory.VariantOutputFormat.VCF.toString()); | ||
| } | ||
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| format = VariantWriterFactory.toOutputFormat(toolParams.getInputFormat(), toolParams.getOutputFileName()); | ||
| if (format.isBinary()) { | ||
| throw new IllegalArgumentException("Binary format not supported for VariantWalkerTool"); | ||
| } | ||
| if (!format.isPlain()) { | ||
| format = format.inPlain(); | ||
| } | ||
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| if (StringUtils.isEmpty(toolParams.getOutputFileName())) { | ||
| toolParams.setOutputFileName("output.txt.gz"); | ||
| } else if (!toolParams.getOutputFileName().endsWith(".gz")) { | ||
| toolParams.setOutputFileName(toolParams.getOutputFileName() + ".gz"); | ||
| } | ||
| } | ||
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| @Override | ||
| protected List<String> getSteps() { | ||
| return Arrays.asList(ID, "move-files"); | ||
| } | ||
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| @Override | ||
| protected void run() throws Exception { | ||
| step(ID, () -> { | ||
| Path outDir = getOutDir(); | ||
| String outputFile = outDir.resolve(toolParams.getOutputFileName()).toString(); | ||
| Query query = toolParams.toQuery(); | ||
| QueryOptions queryOptions = new QueryOptions().append(QueryOptions.INCLUDE, toolParams.getInclude()) | ||
| .append(QueryOptions.EXCLUDE, toolParams.getExclude()); | ||
| variantStorageManager.walkData(outputFile, | ||
| format, query, queryOptions, toolParams.getDockerImage(), toolParams.getCommandLine(), token); | ||
| }); | ||
| } | ||
| } |
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