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src/test/java/org/broadinstitute/hellbender/utils/read/FlowBasedReadUtilsUnitTest.java
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package org.broadinstitute.hellbender.utils.read; | ||
import htsjdk.samtools.SAMFileHeader; | ||
import htsjdk.samtools.SAMReadGroupRecord; | ||
import htsjdk.samtools.SamReader; | ||
import htsjdk.samtools.SamReaderFactory; | ||
import org.broadinstitute.hellbender.GATKBaseTest; | ||
import org.testng.annotations.Test; | ||
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import java.io.File; | ||
import java.nio.file.FileSystems; | ||
import java.nio.file.Path; | ||
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public class FlowBasedReadUtilsUnitTest extends GATKBaseTest{ | ||
@Test | ||
void testReadGroupParsing() throws Exception{ | ||
final String testResourceDir = publicTestDir + "org/broadinstitute/hellbender/utils/read/flow/reads/"; | ||
final String inputDir = testResourceDir + "/input/"; | ||
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final Path inputFile = FileSystems.getDefault().getPath(inputDir, "sample_mc.bam"); | ||
final SamReader reader = SamReaderFactory.makeDefault().open(new File(inputFile.toString())); | ||
SAMFileHeader header = reader.getFileHeader(); | ||
SAMReadGroupRecord rg1 = header.getReadGroup("UGAv3-72"); | ||
FlowBasedReadUtils.ReadGroupInfo frg1 = new FlowBasedReadUtils.ReadGroupInfo(rg1); | ||
assert(frg1.maxClass==12); | ||
assert(frg1.flowOrder.startsWith("TGCA")); | ||
SAMReadGroupRecord rg2 = header.getReadGroup("UGAv3-73"); | ||
FlowBasedReadUtils.ReadGroupInfo frg2 = new FlowBasedReadUtils.ReadGroupInfo(rg2); | ||
assert(frg2.maxClass==20); | ||
assert(frg2.flowOrder.startsWith("TGCA")); | ||
} | ||
} |