本文整理了Java中org.broadinstitute.gatk.utils.sam.GATKSAMRecord.setProperPairFlag()
方法的一些代码示例,展示了GATKSAMRecord.setProperPairFlag()
的具体用法。这些代码示例主要来源于Github
/Stackoverflow
/Maven
等平台,是从一些精选项目中提取出来的代码,具有较强的参考意义,能在一定程度帮忙到你。GATKSAMRecord.setProperPairFlag()
方法的具体详情如下:
包路径:org.broadinstitute.gatk.utils.sam.GATKSAMRecord
类名称:GATKSAMRecord
方法名:setProperPairFlag
暂无
代码示例来源:origin: broadgsa/gatk
private GATKSAMRecord makeRead(final int fragmentSize, final int mateStart) {
final byte[] bases = {'A', 'C', 'G', 'T', 'A', 'C', 'G', 'T'};
final byte[] quals = {30, 30, 30, 30, 30, 30, 30, 30};
final String cigar = "8M";
GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(bases, quals, cigar);
read.setProperPairFlag(true);
read.setReadPairedFlag(true);
read.setMateAlignmentStart(mateStart);
read.setInferredInsertSize(fragmentSize);
return read;
}
代码示例来源:origin: broadgsa/gatk
public final static List<GATKSAMRecord> createPair(SAMFileHeader header, String name, int readLen, int leftStart, int rightStart, boolean leftIsFirst, boolean leftIsNegative) {
GATKSAMRecord left = ArtificialSAMUtils.createArtificialRead(header, name, 0, leftStart, readLen);
GATKSAMRecord right = ArtificialSAMUtils.createArtificialRead(header, name, 0, rightStart, readLen);
left.setReadPairedFlag(true);
right.setReadPairedFlag(true);
left.setProperPairFlag(true);
right.setProperPairFlag(true);
left.setFirstOfPairFlag(leftIsFirst);
right.setFirstOfPairFlag(!leftIsFirst);
left.setReadNegativeStrandFlag(leftIsNegative);
left.setMateNegativeStrandFlag(!leftIsNegative);
right.setReadNegativeStrandFlag(!leftIsNegative);
right.setMateNegativeStrandFlag(leftIsNegative);
left.setMateAlignmentStart(right.getAlignmentStart());
right.setMateAlignmentStart(left.getAlignmentStart());
left.setMateReferenceIndex(0);
right.setMateReferenceIndex(0);
int isize = rightStart + readLen - leftStart;
left.setInferredInsertSize(isize);
right.setInferredInsertSize(-isize);
return Arrays.asList(left, right);
}
代码示例来源:origin: broadgsa/gatk
elements.add(new CigarElement(length, CigarOperator.characterToEnum('M')));
record.setCigar(new Cigar(elements));
record.setProperPairFlag(false);
代码示例来源:origin: broadgsa/gatk
@Test(enabled = true)
public void testHardClippingBeforeMergeResultingInCompletelyContainedSecondRead() {
final String adapter = "NNNN";
final int minReadSize = 7;
final GATKSAMRecord readLeftAdapter = makeOverlappingRead(adapter, 30, Utils.dupString("A", 10), Utils.dupBytes((byte)30, 10), "", 30, 10);
final GATKSAMRecord readRightAdapter = makeOverlappingRead("", 30, Utils.dupString("A", minReadSize), Utils.dupBytes((byte)30, minReadSize), adapter, 30, 10);
readLeftAdapter.setCigarString(adapter.length() + "S10M");
readLeftAdapter.setProperPairFlag(true);
readLeftAdapter.setFirstOfPairFlag(true);
readLeftAdapter.setReadNegativeStrandFlag(true);
readLeftAdapter.setMateAlignmentStart(10);
readRightAdapter.setCigarString(minReadSize + "M4S");
readRightAdapter.setProperPairFlag(true);
readRightAdapter.setFirstOfPairFlag(false);
readRightAdapter.setReadNegativeStrandFlag(false);
final int insertSize = minReadSize;
readLeftAdapter.setInferredInsertSize(insertSize);
readRightAdapter.setInferredInsertSize(-insertSize);
final GATKSAMRecord actual = FragmentUtils.mergeOverlappingPairedFragments(readLeftAdapter, readRightAdapter);
Assert.assertNull(actual);
}
代码示例来源:origin: broadgsa/gatk
final int readLength = nClips + goodBases;
GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "read1" , 0, start, readLength);
read.setProperPairFlag(true);
read.setReadPairedFlag(true);
read.setReadUnmappedFlag(false);
代码示例来源:origin: broadgsa/gatk
final GATKSAMRecord expectedMerged = makeOverlappingRead("", 30, common, commonQuals, "", 30, 10);
readLeftAdapter.setCigarString(adapter.length() + "S" + common.length() + "M");
readLeftAdapter.setProperPairFlag(true);
readLeftAdapter.setReadPairedFlag(true);
readLeftAdapter.setFirstOfPairFlag(true);
readLeftAdapter.setMateAlignmentStart(readRightAdapter.getAlignmentStart());
readRightAdapter.setCigarString(common.length() + "M4S");
readRightAdapter.setProperPairFlag(true);
readRightAdapter.setReadPairedFlag(true);
readRightAdapter.setFirstOfPairFlag(false);
代码示例来源:origin: broadgsa/gatk
final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "read1", 0, 10, 10);
read.setReadPairedFlag(true);
read.setProperPairFlag(true);
read.setReadUnmappedFlag(false);
read.setMateUnmappedFlag(false);
bad.setProperPairFlag(false);
代码示例来源:origin: broadgsa/gatk
read.setProperPairFlag(false);
Assert.assertEquals(get.getAdaptor(read), ReadUtils.CANNOT_COMPUTE_ADAPTOR_BOUNDARY);
read.setAlignmentStart(BEFORE);
read.setReadPairedFlag(true);
read.setProperPairFlag(true);
read.setReadNegativeStrandFlag(negFlag);
read.setMateNegativeStrandFlag(!negFlag);
read.setAlignmentStart(BEFORE);
read.setReadPairedFlag(true);
read.setProperPairFlag(true);
read.setReadNegativeStrandFlag(negFlag);
read.setMateNegativeStrandFlag(negFlag);
代码示例来源:origin: broadgsa/gatk
private GATKSAMRecord createReadOffContig(final SAMFileHeader header, final boolean negStrand, final int pre, final int post) {
final int contigLen = header.getSequence(0).getSequenceLength();
final int readLen = pre + contigLen + post;
final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "read1", 0, 1, readLen);
read.setAlignmentStart(1);
read.setCigar(TextCigarCodec.decode(pre + "S" + contigLen + "M" + post + "S"));
read.setBaseQualities(Utils.dupBytes((byte) 30, readLen));
read.setReadBases(Utils.dupBytes((byte)'A', readLen));
read.setMappingQuality(60);
read.setMateAlignmentStart(1);
read.setProperPairFlag(true);
read.setReadPairedFlag(true);
read.setInferredInsertSize(30);
read.setReadNegativeStrandFlag(negStrand);
read.setMateNegativeStrandFlag(! negStrand);
read.setReadGroup(new GATKSAMReadGroupRecord("foo"));
return read;
}
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