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381 changes: 297 additions & 84 deletions
381
adam-apis/src/main/scala/org/bdgenomics/adam/api/java/GenomicDatasetConverters.scala
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adam-apis/src/main/scala/org/bdgenomics/adam/api/java/GenomicRDDConverters.scala
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adam-apis/src/test/java/org/bdgenomics/adam/api/java/JavaADAMSequenceConduit.java
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/** | ||
* Licensed to Big Data Genomics (BDG) under one | ||
* or more contributor license agreements. See the NOTICE file | ||
* distributed with this work for additional information | ||
* regarding copyright ownership. The BDG licenses this file | ||
* to you 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. | ||
*/ | ||
package org.bdgenomics.adam.api.java; | ||
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import java.io.IOException; | ||
import java.nio.file.Files; | ||
import java.nio.file.Path; | ||
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import org.bdgenomics.adam.rdd.ADAMContext; | ||
import org.bdgenomics.adam.rdd.sequence.SequenceDataset; | ||
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/** | ||
* A simple test class for the JavaADAMRDD/Context. Writes an RDD of sequences | ||
* to disk and reads it back. | ||
*/ | ||
final class JavaADAMSequenceConduit { | ||
public static SequenceDataset conduit(final SequenceDataset sequenceDataset, | ||
final ADAMContext ac) throws IOException { | ||
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// make temp directory and save file | ||
Path tempDir = Files.createTempDirectory("javaAC"); | ||
String fileName = tempDir.toString() + "/testRdd.sequences.adam"; | ||
sequenceDataset.save(fileName, true, true); | ||
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// create a new adam context and load the file | ||
JavaADAMContext jac = new JavaADAMContext(ac); | ||
return jac.loadDnaSequences(fileName); | ||
} | ||
} |
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82 changes: 0 additions & 82 deletions
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adam-cli/src/main/scala/org/bdgenomics/adam/cli/ADAM2Fasta.scala
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