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Java Read.setAlignedSequence方法代码示例

本文整理汇总了Java中com.google.api.services.genomics.model.Read.setAlignedSequence方法的典型用法代码示例。如果您正苦于以下问题:Java Read.setAlignedSequence方法的具体用法?Java Read.setAlignedSequence怎么用?Java Read.setAlignedSequence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.setAlignedSequence方法的3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: createArtificialGoogleGenomicsRead

import com.google.api.services.genomics.model.Read; //导入方法依赖的package包/类
public static Read createArtificialGoogleGenomicsRead( final String name, final String contig, final int start, final byte[] bases, final byte[] quals, final String cigar ) {
    Read googleRead = new Read();

    googleRead.setFragmentName(name);
    googleRead.setAlignment(new LinearAlignment());
    googleRead.getAlignment().setPosition(new Position());
    googleRead.getAlignment().getPosition().setReferenceName(contig);
    googleRead.getAlignment().getPosition().setPosition((long) start - 1);
    googleRead.setAlignedSequence(StringUtil.bytesToString(bases));
    googleRead.getAlignment().setCigar(CigarConversionUtils.convertSAMCigarToCigarUnitList(TextCigarCodec.decode(cigar)));

    List<Integer> convertedQuals = new ArrayList<>();
    for ( byte b : quals ) {
        convertedQuals.add((int)b);
    }
    googleRead.setAlignedQuality(convertedQuals);

    // Create a fully formed read that can be wrapped by a GATKRead and have a valid
    // SAMString without GATKRead throwing missing field exceptions.
    googleRead.setFailedVendorQualityChecks(false);
    googleRead.setSecondaryAlignment(false);
    googleRead.setSupplementaryAlignment(false);
    googleRead.setDuplicateFragment(false);

    Position matePos = new Position();
    matePos.setReverseStrand(false);
    googleRead.setNextMatePosition(matePos);

    return googleRead;
}
 
开发者ID:broadinstitute,项目名称:gatk,代码行数:31,代码来源:ArtificialReadUtils.java

示例2: getLengthData

import com.google.api.services.genomics.model.Read; //导入方法依赖的package包/类
@DataProvider(name = "GetLengthData")
public Object[][] getLengthData() {
    final SAMRecord baselessSam = basicSAMRecord();
    baselessSam.setReadBases(SAMRecord.NULL_SEQUENCE);

    final Read baselessGoogleRead = basicGoogleGenomicsRead();
    baselessGoogleRead.setAlignedSequence(null);

    return new Object[][]{
            { basicReadBackedBySam(), BASIC_READ_BASES.length },
            { basicReadBackedByGoogle(), BASIC_READ_BASES.length },
            { new SAMRecordToGATKReadAdapter(baselessSam), 0 },
            { new GoogleGenomicsReadToGATKReadAdapter(baselessGoogleRead), 0 }
    };
}
 
开发者ID:broadinstitute,项目名称:gatk,代码行数:16,代码来源:GATKReadAdaptersUnitTest.java

示例3: getAndSetBasesData

import com.google.api.services.genomics.model.Read; //导入方法依赖的package包/类
@DataProvider(name = "GetAndSetBasesData")
public Object[][] getAndSetBasesData() {
    final SAMRecord baselessSam = basicSAMRecord();
    baselessSam.setReadBases(null);

    final SAMRecord noAlignedSequenceSam = basicSAMRecord();
    noAlignedSequenceSam.setReadBases(SAMRecord.NULL_SEQUENCE);

    final Read baselessGoogleRead = basicGoogleGenomicsRead();
    baselessGoogleRead.setAlignedSequence(null);

    final Read emptyStringSequenceGoogleRead = basicGoogleGenomicsRead();
    emptyStringSequenceGoogleRead.setAlignedSequence("");

    final Read noAlignedSequenceGoogleRead = basicGoogleGenomicsRead();
    noAlignedSequenceGoogleRead.setAlignedSequence(SAMRecord.NULL_SEQUENCE_STRING);

    return new Object[][]{
            { basicReadBackedBySam(), BASIC_READ_BASES, "ACGT" },
            { basicReadBackedByGoogle(), BASIC_READ_BASES, "ACGT" },
            { new SAMRecordToGATKReadAdapter(baselessSam), new byte[0], "*" },
            { new SAMRecordToGATKReadAdapter(noAlignedSequenceSam), new byte[0], "*" },
            { new GoogleGenomicsReadToGATKReadAdapter(baselessGoogleRead), new byte[0], "*" },
            { new GoogleGenomicsReadToGATKReadAdapter(emptyStringSequenceGoogleRead), new byte[0], "*" },
            { new GoogleGenomicsReadToGATKReadAdapter(noAlignedSequenceGoogleRead), new byte[0], "*" }
    };
}
 
开发者ID:broadinstitute,项目名称:gatk,代码行数:28,代码来源:GATKReadAdaptersUnitTest.java


注:本文中的com.google.api.services.genomics.model.Read.setAlignedSequence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。