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Java Read.setReadGroupId方法代码示例

本文整理汇总了Java中com.google.api.services.genomics.model.Read.setReadGroupId方法的典型用法代码示例。如果您正苦于以下问题:Java Read.setReadGroupId方法的具体用法?Java Read.setReadGroupId怎么用?Java Read.setReadGroupId使用的例子?那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在com.google.api.services.genomics.model.Read的用法示例。


在下文中一共展示了Read.setReadGroupId方法的2个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于系统推荐出更棒的Java代码示例。

示例1: basicGoogleGenomicsRead

import com.google.api.services.genomics.model.Read; //导入方法依赖的package包/类
/**
 * Creates a basic mapped Google read with a mapped mate.
 * @return GoogleGenomicsRead
 */
private static Read basicGoogleGenomicsRead() {
    final Read read = ArtificialReadUtils.createArtificialGoogleGenomicsRead(
            BASIC_READ_NAME,
            BASIC_READ_CONTIG,
            BASIC_READ_START,
            BASIC_READ_BASES,
            BASIC_READ_BASE_QUALITIES,
            BASIC_READ_CIGAR
    );
    read.setReadGroupId(BASIC_READ_GROUP);
    read.getAlignment().getPosition().setReverseStrand(false);
    read.getAlignment().setMappingQuality(BASIC_READ_MAPPING_QUALITY);
    read.setNextMatePosition(new Position());
    read.getNextMatePosition().setReferenceName(BASIC_READ_MATE_CONTIG);
    read.getNextMatePosition().setPosition((long) BASIC_READ_MATE_START - 1);
    read.getNextMatePosition().setReverseStrand(false);
    read.setNumberReads(2);
    read.setReadNumber(0);
    read.setProperPlacement(false);
    Map<String, List<Object>> infoMap = new LinkedHashMap<>();
    infoMap.put(SAMTag.PG.name(), Collections.singletonList(BASIC_PROGRAM));
    read.setInfo(infoMap);

    return read;
}
 
开发者ID:broadinstitute,项目名称:gatk,代码行数:30,代码来源:GATKReadAdaptersUnitTest.java

示例2: getAndSetReadGroupData

import com.google.api.services.genomics.model.Read; //导入方法依赖的package包/类
@DataProvider(name = "GetAndSetReadGroupData")
public Object[][] getAndSetReadGroupData() {
    SAMRecord noRGSam = basicSAMRecord();
    noRGSam.clearAttributes();

    Read noRGGoogleRead = basicGoogleGenomicsRead();
    noRGGoogleRead.setReadGroupId(null);

    return new Object[][] {
            { basicReadBackedBySam(), BASIC_READ_GROUP },
            { basicReadBackedByGoogle(), BASIC_READ_GROUP },
            { new SAMRecordToGATKReadAdapter(noRGSam), null },
            { new GoogleGenomicsReadToGATKReadAdapter(noRGGoogleRead), null }
    };
}
 
开发者ID:broadinstitute,项目名称:gatk,代码行数:16,代码来源:GATKReadAdaptersUnitTest.java


注:本文中的com.google.api.services.genomics.model.Read.setReadGroupId方法示例由纯净天空整理自Github/MSDocs等开源代码及文档管理平台,相关代码片段筛选自各路编程大神贡献的开源项目,源码版权归原作者所有,传播和使用请参考对应项目的License;未经允许,请勿转载。