本文整理汇总了Java中com.google.api.services.genomics.model.Read.setAlignment方法的典型用法代码示例。如果您正苦于以下问题:Java Read.setAlignment方法的具体用法?Java Read.setAlignment怎么用?Java Read.setAlignment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.setAlignment方法的6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: testEquality
import com.google.api.services.genomics.model.Read; //导入方法依赖的package包/类
@Test
public void testEquality() {
Read read1 = new Read();
Read read2 = new Read();
read1.setAlignment(new LinearAlignment());
read1.getAlignment().setPosition(new Position());
read1.getAlignment().getPosition().setReferenceName("FOO");
read2.setAlignment(new LinearAlignment());
read2.getAlignment().setPosition(new Position());
read2.getAlignment().getPosition().setReferenceName("FOO");
Assert.assertEquals(read1, read2, "equal reads not equal");
read2.getAlignment().getPosition().setReferenceName("BAR");
Assert.assertNotEquals(read1, read2, "unequal reads are equal");
}
示例2: 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3: getUnmappedReads
import com.google.api.services.genomics.model.Read; //导入方法依赖的package包/类
private static List<GATKRead> getUnmappedReads() {
List<GATKRead> unmappedReads = new ArrayList<>();
final SAMRecord unmappedFlagSam = basicSAMRecord();
unmappedFlagSam.setReadUnmappedFlag(true);
unmappedReads.add(new SAMRecordToGATKReadAdapter(unmappedFlagSam));
final SAMRecord unmappedContigSam = basicSAMRecord();
unmappedContigSam.setReferenceName(SAMRecord.NO_ALIGNMENT_REFERENCE_NAME);
unmappedReads.add(new SAMRecordToGATKReadAdapter(unmappedContigSam));
final SAMRecord noAlignmentStartSam = basicSAMRecord();
noAlignmentStartSam.setAlignmentStart(SAMRecord.NO_ALIGNMENT_START);
unmappedReads.add(new SAMRecordToGATKReadAdapter(noAlignmentStartSam));
final Read noAlignmentGoogleRead = basicGoogleGenomicsRead();
noAlignmentGoogleRead.setAlignment(null);
unmappedReads.add(new GoogleGenomicsReadToGATKReadAdapter(noAlignmentGoogleRead));
final Read noPositionGoogleRead = basicGoogleGenomicsRead();
noPositionGoogleRead.getAlignment().setPosition(null);
unmappedReads.add(new GoogleGenomicsReadToGATKReadAdapter(noPositionGoogleRead));
final Read noContigGoogleRead = basicGoogleGenomicsRead();
noContigGoogleRead.getAlignment().getPosition().setReferenceName(null);
unmappedReads.add(new GoogleGenomicsReadToGATKReadAdapter(noContigGoogleRead));
final Read starContigGoogleRead = basicGoogleGenomicsRead();
starContigGoogleRead.getAlignment().getPosition().setReferenceName(SAMRecord.NO_ALIGNMENT_REFERENCE_NAME);
unmappedReads.add(new GoogleGenomicsReadToGATKReadAdapter(starContigGoogleRead));
final Read noStartGoogleRead = basicGoogleGenomicsRead();
noStartGoogleRead.getAlignment().getPosition().setPosition(-1l);
unmappedReads.add(new GoogleGenomicsReadToGATKReadAdapter(noStartGoogleRead));
return unmappedReads;
}
示例4: testGetCigarString
import com.google.api.services.genomics.model.Read; //导入方法依赖的package包/类
@Test
public void testGetCigarString() throws Exception {
Read read = new Read();
assertEquals(null, ReadUtils.getCigarString(read));
List<CigarUnit> cigar = Lists.newArrayList(
new CigarUnit().setOperation("ALIGNMENT_MATCH").setOperationLength(100L),
new CigarUnit().setOperation("CLIP_SOFT").setOperationLength(3L));
read.setAlignment(new LinearAlignment().setCigar(cigar));
assertEquals("100M3S", ReadUtils.getCigarString(read));
}
示例5: readHasNoAssignedPositionTestData
import com.google.api.services.genomics.model.Read; //导入方法依赖的package包/类
@DataProvider(name = "ReadHasNoAssignedPositionTestData")
public Object[][] readHasNoAssignedPositionTestData() {
final SAMFileHeader header = ArtificialReadUtils.createArtificialSamHeader();
// To test the "null contig" cases, we need to use a Google Genomics Read, since SAMRecord doesn't allow it
final Read unmappedGoogleReadWithNullContigSetStart = new Read();
unmappedGoogleReadWithNullContigSetStart.setAlignment(new LinearAlignment());
unmappedGoogleReadWithNullContigSetStart.getAlignment().setPosition(new Position());
unmappedGoogleReadWithNullContigSetStart.getAlignment().getPosition().setReferenceName(null);
unmappedGoogleReadWithNullContigSetStart.getAlignment().getPosition().setPosition(10l);
final GATKRead unmappedReadWithNullContigSetStart = new GoogleGenomicsReadToGATKReadAdapter(unmappedGoogleReadWithNullContigSetStart);
final Read unmappedGoogleReadWithNullContigUnsetStart = new Read();
unmappedGoogleReadWithNullContigUnsetStart.setAlignment(new LinearAlignment());
unmappedGoogleReadWithNullContigUnsetStart.getAlignment().setPosition(new Position());
unmappedGoogleReadWithNullContigUnsetStart.getAlignment().getPosition().setReferenceName(null);
unmappedGoogleReadWithNullContigUnsetStart.getAlignment().getPosition().setPosition(Long.valueOf(ReadConstants.UNSET_POSITION));
final GATKRead unmappedReadWithNullContigUnsetStart = new GoogleGenomicsReadToGATKReadAdapter(unmappedGoogleReadWithNullContigUnsetStart);
// We'll also test the improbable case of a SAMRecord marked as mapped, but with an unset contig/start
final SAMRecord mappedSAMWithUnsetContigSetStart = new SAMRecord(header);
mappedSAMWithUnsetContigSetStart.setReferenceName(ReadConstants.UNSET_CONTIG);
mappedSAMWithUnsetContigSetStart.setAlignmentStart(10);
mappedSAMWithUnsetContigSetStart.setReadUnmappedFlag(false);
final GATKRead mappedReadWithUnsetContigSetStart = new SAMRecordToGATKReadAdapter(mappedSAMWithUnsetContigSetStart);
final SAMRecord mappedSAMWithSetContigUnsetStart = new SAMRecord(header);
mappedSAMWithSetContigUnsetStart.setReferenceName("1");
mappedSAMWithSetContigUnsetStart.setAlignmentStart(ReadConstants.UNSET_POSITION);
mappedSAMWithSetContigUnsetStart.setReadUnmappedFlag(false);
final GATKRead mappedReadWithSetContigUnsetStart = new SAMRecordToGATKReadAdapter(mappedSAMWithSetContigUnsetStart);
return new Object[][] {
// Mapped read with position
{ ArtificialReadUtils.createArtificialRead(header, "foo", 0, 5, 10), false },
// Basic unmapped read with no position
{ ArtificialReadUtils.createArtificialUnmappedRead(header, new byte[]{'A'}, new byte[]{30}), true },
// Unmapped read with set position (contig and start)
{ ArtificialReadUtils.createArtificialUnmappedReadWithAssignedPosition(header, "1", 10, new byte[]{'A'}, new byte[]{30}), false },
// Unmapped read with null contig, set start
{ unmappedReadWithNullContigSetStart, true },
// Unmapped read with "*" contig, set start
{ ArtificialReadUtils.createArtificialUnmappedReadWithAssignedPosition(header, ReadConstants.UNSET_CONTIG, 10, new byte[]{'A'}, new byte[]{30}), true },
// Unmapped read with set contig, unset start
{ ArtificialReadUtils.createArtificialUnmappedReadWithAssignedPosition(header, "1", ReadConstants.UNSET_POSITION, new byte[]{'A'}, new byte[]{30}), true },
// Unmapped read with null contig, unset start
{ unmappedReadWithNullContigUnsetStart, true },
// Unmapped read with "*" contig, unset start
{ ArtificialReadUtils.createArtificialUnmappedReadWithAssignedPosition(header, ReadConstants.UNSET_CONTIG, ReadConstants.UNSET_POSITION, new byte[]{'A'}, new byte[]{30}), true },
// "Mapped" read with unset contig, set start
{ mappedReadWithUnsetContigSetStart, true },
// "Mapped" read with set contig, unset start
{ mappedReadWithSetContigUnsetStart, true }
};
}
示例6: getAssignedPositionData
import com.google.api.services.genomics.model.Read; //导入方法依赖的package包/类
@DataProvider(name = "GetAssignedPositionData")
public Object[][] getAssignedPositionData() {
List<Object[]> testCases = new ArrayList<>();
testCases.add(new Object[]{basicReadBackedBySam(), BASIC_READ_CONTIG, BASIC_READ_START});
testCases.add(new Object[]{basicReadBackedByGoogle(), BASIC_READ_CONTIG, BASIC_READ_START});
// SAMRecord, unmapped flag set, but has an assigned position
final SAMRecord unmappedFlagSam = basicSAMRecord();
unmappedFlagSam.setReadUnmappedFlag(true);
testCases.add(new Object[]{new SAMRecordToGATKReadAdapter(unmappedFlagSam), BASIC_READ_CONTIG, BASIC_READ_START});
// SAMRecord, unmapped flag not set, but no contig
final SAMRecord unmappedContigSam = basicSAMRecord();
unmappedContigSam.setReferenceName(SAMRecord.NO_ALIGNMENT_REFERENCE_NAME);
testCases.add(new Object[]{new SAMRecordToGATKReadAdapter(unmappedContigSam), SAMRecord.NO_ALIGNMENT_REFERENCE_NAME, BASIC_READ_START});
// SAMRecord, unmapped flag not set, but no start
final SAMRecord noAlignmentStartSam = basicSAMRecord();
noAlignmentStartSam.setAlignmentStart(SAMRecord.NO_ALIGNMENT_START);
testCases.add(new Object[]{new SAMRecordToGATKReadAdapter(noAlignmentStartSam), BASIC_READ_CONTIG, ReadConstants.UNSET_POSITION});
// Google read, no alignment
final Read noAlignmentGoogleRead = basicGoogleGenomicsRead();
noAlignmentGoogleRead.setAlignment(null);
testCases.add(new Object[]{new GoogleGenomicsReadToGATKReadAdapter(noAlignmentGoogleRead), null, ReadConstants.UNSET_POSITION});
// Google read, no position
final Read noPositionGoogleRead = basicGoogleGenomicsRead();
noPositionGoogleRead.getAlignment().setPosition(null);
testCases.add(new Object[]{new GoogleGenomicsReadToGATKReadAdapter(noPositionGoogleRead), null, ReadConstants.UNSET_POSITION});
// Google read, position with no contig
final Read noContigGoogleRead = basicGoogleGenomicsRead();
noContigGoogleRead.getAlignment().getPosition().setReferenceName(null);
testCases.add(new Object[]{new GoogleGenomicsReadToGATKReadAdapter(noContigGoogleRead), null, BASIC_READ_START});
// Google read, position with * contig
final Read starContigGoogleRead = basicGoogleGenomicsRead();
starContigGoogleRead.getAlignment().getPosition().setReferenceName(SAMRecord.NO_ALIGNMENT_REFERENCE_NAME);
testCases.add(new Object[]{new GoogleGenomicsReadToGATKReadAdapter(starContigGoogleRead), SAMRecord.NO_ALIGNMENT_REFERENCE_NAME, BASIC_READ_START});
// Google read, position with contig but no start
final Read noStartGoogleRead = basicGoogleGenomicsRead();
noStartGoogleRead.getAlignment().getPosition().setPosition(-1l);
testCases.add(new Object[]{new GoogleGenomicsReadToGATKReadAdapter(noStartGoogleRead), BASIC_READ_CONTIG, ReadConstants.UNSET_POSITION});
return testCases.toArray(new Object[][]{});
}