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类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;
}
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 }
};
}
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], "*" }
};
}