本文整理汇总了Java中htsjdk.samtools.SAMUtils类的典型用法代码示例。如果您正苦于以下问题：Java SAMUtils类的具体用法？Java SAMUtils怎么用？Java SAMUtils使用的例子？那么恭喜您, 这里精选的类代码示例或许可以为您提供帮助。
SAMUtils类属于htsjdk.samtools包，在下文中一共展示了SAMUtils类的20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，您的评价将有助于我们的系统推荐出更棒的Java代码示例。
示例1: setBaseQualities
import htsjdk.samtools.SAMUtils; //导入依赖的package包/类
/**
* Setters and Accessors for base insertion and base deletion quality scores
*/
public void setBaseQualities( final byte[] quals, final EventType errorModel ) {
switch( errorModel ) {
case BASE_SUBSTITUTION:
setBaseQualities(quals);
break;
case BASE_INSERTION:
setAttribute( GATKSAMRecord.BQSR_BASE_INSERTION_QUALITIES, quals == null ? null : SAMUtils.phredToFastq(quals) );
break;
case BASE_DELETION:
setAttribute( GATKSAMRecord.BQSR_BASE_DELETION_QUALITIES, quals == null ? null : SAMUtils.phredToFastq(quals) );
break;
default:
throw new ReviewedGATKException("Unrecognized Base Recalibration type: " + errorModel );
}
}
开发者ID:PAA-NCIC，项目名称:SparkSeq，代码行数:19，代码来源:GATKSAMRecord.java
示例2: initializeCachedData
import htsjdk.samtools.SAMUtils; //导入依赖的package包/类
private void initializeCachedData() {
for ( int i = 0; i < 256; i++ )
for ( int j = 0; j < 256; j++ )
for ( int q = 0; q <= SAMUtils.MAX_PHRED_SCORE; q++ ) {
EPSILONS[i][j][q] = 1.0;
}
for ( char b1 : "ACGTacgt".toCharArray() ) {
for ( char b2 : "ACGTacgt".toCharArray() ) {
for ( int q = 0; q <= SAMUtils.MAX_PHRED_SCORE; q++ ) {
double qual = qual2prob[q < minBaseQual ? minBaseQual : q];
double e = Character.toLowerCase(b1) == Character.toLowerCase(b2) ? 1 - qual : qual * EM;
EPSILONS[(byte)b1][(byte)b2][q] = e;
}
}
}
}
开发者ID:PAA-NCIC，项目名称:SparkSeq，代码行数:18，代码来源:BAQ.java
示例3: qualToUse
import htsjdk.samtools.SAMUtils; //导入依赖的package包/类
/**
* Helper function that returns the phred-scaled base quality score we should use for calculating
* likelihoods for a pileup element. May return 0 to indicate that the observation is bad, and may
* cap the quality score by the mapping quality of the read itself.
*
* @param p Pileup element
* @param ignoreBadBases Should we ignore bad bases?
* @param capBaseQualsAtMappingQual Should we cap the base qualities at the mapping quality of the read?
* @param minBaseQual Minimum allowed base quality
* @return the actual base quality to use
*/
private static byte qualToUse(PileupElement p, boolean ignoreBadBases, boolean capBaseQualsAtMappingQual, int minBaseQual) {
if ( ignoreBadBases && !BaseUtils.isRegularBase( p.getBase() ) )
return 0;
byte qual = p.getQual();
if ( qual > SAMUtils.MAX_PHRED_SCORE )
throw new UserException.MisencodedBAM(p.getRead(), "we encountered an extremely high quality score (" + (int)qual + ")");
if ( capBaseQualsAtMappingQual )
qual = (byte) Math.min( 0xff & qual, p.getMappingQual());
if ( (int)qual < minBaseQual )
qual = (byte)0;
return qual;
}
开发者ID:PAA-NCIC，项目名称:SparkSeq，代码行数:27，代码来源:DiploidSNPGenotypeLikelihoods.java
示例4: initializeCachedData
import htsjdk.samtools.SAMUtils; //导入依赖的package包/类
private void initializeCachedData() {
for (int i = 0; i < 256; i++)
for (int j = 0; j < 256; j++)
for (int q = 0; q <= SAMUtils.MAX_PHRED_SCORE; q++) {
EPSILONS[i][j][q] = 1.0;
}
for (char b1 : "ACGTacgt".toCharArray()) {
for (char b2 : "ACGTacgt".toCharArray()) {
for (int q = 0; q <= SAMUtils.MAX_PHRED_SCORE; q++) {
double qual = qual2prob[q < minBaseQual ? minBaseQual : q];
double e = Character.toLowerCase(b1) == Character
.toLowerCase(b2) ? 1 - qual : qual * EM;
EPSILONS[(byte) b1][(byte) b2][q] = e;
}
}
}
}
开发者ID:seppinho，项目名称:mutation-server，代码行数:19，代码来源:BaqAlt.java
示例5: apply
import htsjdk.samtools.SAMUtils; //导入依赖的package包/类
@Override
public GATKRead apply(final GATKRead read) {
// get the qualities
final byte[] quals = read.getBaseQualities();
try {
// transform them in place
for (int i = 0; i < quals.length; ++i) {
if (quals[i] < MIN_SOLEXA_BEFORE_CONVERSION) {
// throw an exception if they are missencoded
throwException();
}
// convert to Solexa
quals[i] = SOLEXA_QUALITY_CONVERTER
.solexaCharToPhredBinary((byte) SAMUtils.phredToFastq(quals[i]));
}
} catch (IndexOutOfBoundsException e) {
// if there is an index exception, that means that the qualities are not correctly encoded
throwException();
}
// set the base qualities
read.setBaseQualities(quals);
return read;
}
开发者ID:magicDGS，项目名称:ReadTools，代码行数:24，代码来源:SolexaToSangerReadTransformer.java
示例6: doWork
import htsjdk.samtools.SAMUtils; //导入依赖的package包/类
@Override
protected int doWork() {
final File output =
OUTPUT == null
? new File(INPUT.getParentFile(), getOutputFileName(INPUT))
: OUTPUT;
IOUtil.assertFileIsWritable(output);
final String hashText = SAMUtils.calculateReadGroupRecordChecksum(INPUT, REFERENCE_SEQUENCE);
try {
final FileWriter outputWriter = new FileWriter(output);
outputWriter.write(hashText);
outputWriter.close();
} catch (final IOException ioe) {
throw new PicardException(
"Could not write the computed hash (" + hashText + ") to the output file: " + ioe.getMessage(), ioe);
}
return 0;
}
开发者ID:broadinstitute，项目名称:picard，代码行数:21，代码来源:CalculateReadGroupChecksum.java
示例7: MultiHitAlignedReadIterator
import htsjdk.samtools.SAMUtils; //导入依赖的package包/类
/**
*
* @param querynameOrderIterator
* @param primaryAlignmentSelectionStrategy Algorithm for selecting primary alignment when it is not clear from
* the input what should be primary.
*/
MultiHitAlignedReadIterator(final CloseableIterator<SAMRecord> querynameOrderIterator,
final PrimaryAlignmentSelectionStrategy primaryAlignmentSelectionStrategy) {
this.primaryAlignmentSelectionStrategy = primaryAlignmentSelectionStrategy;
peekIterator = new PeekableIterator<SAMRecord>(new FilteringSamIterator(querynameOrderIterator,
new SamRecordFilter() {
// Filter unmapped reads.
public boolean filterOut(final SAMRecord record) {
return record.getReadUnmappedFlag() || SAMUtils.cigarMapsNoBasesToRef(record.getCigar());
}
public boolean filterOut(final SAMRecord first, final SAMRecord second) {
return ((first.getReadUnmappedFlag() || SAMUtils.cigarMapsNoBasesToRef(first.getCigar()))
&& (second.getReadUnmappedFlag() || SAMUtils.cigarMapsNoBasesToRef(second.getCigar())));
}
}));
advance();
}
开发者ID:broadinstitute，项目名称:picard，代码行数:25，代码来源:MultiHitAlignedReadIterator.java
示例8: testUsingOriginalQualities
import htsjdk.samtools.SAMUtils; //导入依赖的package包/类
@Test
public void testUsingOriginalQualities() throws Exception {
final MeanQualityByCycleSpark.HistogramGenerator hg = new MeanQualityByCycleSpark.HistogramGenerator(true);
Assert.assertEquals(hg.useOriginalQualities, true);
GATKRead read1 = ArtificialReadUtils.createArtificialRead("aa".getBytes(), new byte[]{50, 50}, "2M");
hg.addRead(read1);
assertEqualsLongArray(hg.firstReadCountsByCycle, new long[0]);
assertEqualsDoubleArray(hg.firstReadTotalsByCycle, new double[0], 1e-05);
assertEqualsLongArray(hg.secondReadCountsByCycle, new long[0]);
assertEqualsDoubleArray(hg.secondReadTotalsByCycle, new double[0], 1e-05);
GATKRead read2 = ArtificialReadUtils.createArtificialRead("aa".getBytes(), new byte[]{50, 50}, "2M");
read2.setAttribute(SAMTag.OQ.name(), SAMUtils.phredToFastq(new byte[]{30, 40}));
hg.addRead(read2);
assertEqualsLongArray(hg.firstReadCountsByCycle, new long[]{0, 1, 1});
assertEqualsDoubleArray(hg.firstReadTotalsByCycle, new double[]{0, 30, 40}, 1e-05);
assertEqualsLongArray(hg.secondReadCountsByCycle, new long[]{0, 0, 0});
assertEqualsDoubleArray(hg.secondReadTotalsByCycle, new double[]{0, 0, 0}, 1e-05);
}
开发者ID:broadinstitute，项目名称:gatk，代码行数:22，代码来源:MeanQualityHistogramGeneratorUnitTest.java
示例9: reset
import htsjdk.samtools.SAMUtils; //导入依赖的package包/类
void reset(EvidenceRecord evidenceRecord) {
this.evidenceRecord = evidenceRecord;
negative = "-".equals(evidenceRecord.Strand);
baseBuf.clear();
scoreBuf.clear();
if (evidenceRecord.Strand.equals("+")) {
baseBuf.put(evidenceRecord.Sequence.getBytes());
scoreBuf.put(SAMUtils.fastqToPhred(evidenceRecord.Scores));
} else {
byte[] bytes = evidenceRecord.Sequence.getBytes();
SequenceUtil.reverseComplement(bytes);
baseBuf.put(bytes);
bytes = SAMUtils.fastqToPhred(evidenceRecord.Scores);
SequenceUtil.reverseQualities(bytes);
scoreBuf.put(bytes);
}
baseBuf.flip();
scoreBuf.flip();
firstHalf.clear();
secondHalf.clear();
}
开发者ID:enasequence，项目名称:cramtools，代码行数:25，代码来源:Read.java
示例10: firstSAMRecord
import htsjdk.samtools.SAMUtils; //导入依赖的package包/类
SAMRecord firstSAMRecord(SAMFileHeader header) {
SAMRecord r = new SAMRecord(header);
r.setReadName(evidenceRecord.getReadName());
r.setReferenceName(evidenceRecord.Chromosome);
r.setAlignmentStart(Integer.valueOf(evidenceRecord.OffsetInReference) + 1);
r.setMappingQuality(Integer.valueOf(evidenceRecord.ScoreAllele0));
r.setReadPairedFlag(true);
r.setReadUnmappedFlag(false);
r.setReadNegativeStrandFlag(negative);
r.setFirstOfPairFlag(evidenceRecord.side == 0);
r.setSecondOfPairFlag(!r.getFirstOfPairFlag());
r.setCigar(new Cigar(Utils.toCigarOperatorList(firstHalf.samCigarElements)));
r.setReadBases(Utils.toByteArray(firstHalf.readBasesBuf));
r.setBaseQualities(Utils.toByteArray(firstHalf.readScoresBuf));
r.setAttribute("GC", Utils.toString(firstHalf.gcList));
r.setAttribute("GS", Utils.toString(firstHalf.gsBuf));
r.setAttribute("GQ", SAMUtils.phredToFastq(Utils.toByteArray(firstHalf.gqBuf)));
return r;
}
开发者ID:enasequence，项目名称:cramtools，代码行数:24，代码来源:Read.java
示例11: secondSAMRecord
import htsjdk.samtools.SAMUtils; //导入依赖的package包/类
SAMRecord secondSAMRecord(SAMFileHeader header) {
SAMRecord r = new SAMRecord(header);
r.setReadName(evidenceRecord.getReadName());
r.setReferenceName(evidenceRecord.Chromosome);
r.setAlignmentStart(Integer.valueOf(evidenceRecord.MateOffsetInReference) + 1);
r.setMappingQuality(Integer.valueOf(evidenceRecord.ScoreAllele0));
r.setReadPairedFlag(true);
r.setReadUnmappedFlag(false);
r.setReadNegativeStrandFlag(negative);
r.setFirstOfPairFlag(evidenceRecord.side == 1);
r.setSecondOfPairFlag(!r.getFirstOfPairFlag());
r.setCigar(new Cigar(Utils.toCigarOperatorList(secondHalf.samCigarElements)));
r.setReadBases(Utils.toByteArray(secondHalf.readBasesBuf));
r.setBaseQualities(Utils.toByteArray(secondHalf.readScoresBuf));
r.setAttribute("GC", Utils.toString(secondHalf.gcList));
r.setAttribute("GS", Utils.toString(secondHalf.gsBuf));
r.setAttribute("GQ", SAMUtils.phredToFastq(Utils.toByteArray(secondHalf.gqBuf)));
return r;
}
开发者ID:enasequence，项目名称:cramtools，代码行数:24，代码来源:Read.java
示例12: analyseSamRecord
import htsjdk.samtools.SAMUtils; //导入依赖的package包/类
private void analyseSamRecord(final SAMRecord rec) {
if(rec.getReadUnmappedFlag()) return;
if(rec.getReadFailsVendorQualityCheckFlag()) return;
if(rec.isSecondaryOrSupplementary()) return;
if(rec.getDuplicateReadFlag()) return;
final List<SAMRecord> others= SAMUtils.getOtherCanonicalAlignments(rec);
if(others.isEmpty()) return;
String sample=this.defaultSampleName;
final SAMReadGroupRecord g=rec.getReadGroup();
if(g!=null) {
final String sa = g.getSample();
if(sa!=null) sample=sa;
}
IntervalTreeMap<Set<Arc>> database = this.sample2database.get(sample);
if(database==null) {
database=new IntervalTreeMap<Set<Arc>>();
this.sample2database.put(sample, database);
}
for(final SAMRecord other:others)
{
analyseSamPair(database,rec,other);
}
}
开发者ID:lindenb，项目名称:jvarkit，代码行数:27，代码来源:SamScanSplitReads.java
示例13: fillCache
import htsjdk.samtools.SAMUtils; //导入依赖的package包/类
private void fillCache() {
// cache Q(j,k) = log10(j/2N*(1-ek) + (2N-j)/2N*ek) for j = 0:2N
logMismatchProbabilityArray = new double[1+numChromosomes][1+SAMUtils.MAX_PHRED_SCORE];
for (int i=0; i <= numChromosomes; i++) {
for (int j=0; j <= SAMUtils.MAX_PHRED_SCORE; j++) {
double phi = (double)i/numChromosomes;
logMismatchProbabilityArray[i][j] = Math.log10(phi * (1.0-qualVec[j]) + qualVec[j]/3.0 * (1.0-phi));
}
}
}
开发者ID:PAA-NCIC，项目名称:SparkSeq，代码行数:12，代码来源:GeneralPloidyGenotypeLikelihoods.java
示例14: writeDebugLikelihoods
import htsjdk.samtools.SAMUtils; //导入依赖的package包/类
private void writeDebugLikelihoods(final GATKSAMRecord processedRead, final Haplotype haplotype, final double log10l) {
likelihoodsStream.printf("%s %s %s %s %s %s %f%n",
haplotype.getBaseString(),
new String(processedRead.getReadBases()),
SAMUtils.phredToFastq(processedRead.getBaseQualities()),
SAMUtils.phredToFastq(processedRead.getBaseInsertionQualities()),
SAMUtils.phredToFastq(processedRead.getBaseDeletionQualities()),
SAMUtils.phredToFastq(constantGCP),
log10l);
}
开发者ID:PAA-NCIC，项目名称:SparkSeq，代码行数:11，代码来源:PairHMMLikelihoodCalculationEngine.java
示例15: writeDebugLikelihoods
import htsjdk.samtools.SAMUtils; //导入依赖的package包/类
private void writeDebugLikelihoods(final GATKRead processedRead, final Haplotype haplotype, final double log10l){
// Note: the precision of log10l in the debug output is only ~6 digits (ie., not all digits are necessarily printed)
likelihoodsStream.printf("%s %s %s %s %s %s %f%n",
haplotype.getBaseString(),
new String(processedRead.getBases()),
SAMUtils.phredToFastq(processedRead.getBaseQualities()),
SAMUtils.phredToFastq(ReadUtils.getBaseInsertionQualities(processedRead)),
SAMUtils.phredToFastq(ReadUtils.getBaseDeletionQualities(processedRead)),
SAMUtils.phredToFastq(constantGCP),
log10l);
}
开发者ID:broadinstitute，项目名称:gatk-protected，代码行数:12，代码来源:PairHMMLikelihoodCalculationEngine.java
示例16: testConvertQualities
import htsjdk.samtools.SAMUtils; //导入依赖的package包/类
@Test(dataProvider = "solexaQuals")
public void testConvertQualities(final String solexaQualityString,
final String expectedSolexaQuals) throws Exception {
final GATKRead read = ArtificialReadUtils.createArtificialUnmappedRead(header,
Utils.dupBytes((byte) 'A', solexaQualityString.length()),
SAMUtils.fastqToPhred(solexaQualityString)
);
Assert.assertEquals(ReadUtils.getBaseQualityString(transformer.apply(read)),
expectedSolexaQuals);
}
开发者ID:magicDGS，项目名称:ReadTools，代码行数:11，代码来源:SolexaToSangerReadTransformerUnitTest.java
示例17: testBadQualities
import htsjdk.samtools.SAMUtils; //导入依赖的package包/类
@Test(dataProvider = "badQuals", expectedExceptions = UserException.BadInput.class)
public void testBadQualities(final String badQual) {
final GATKRead read = ArtificialReadUtils.createArtificialUnmappedRead(
header, new byte[] {'A'}, SAMUtils.fastqToPhred(badQual));
transformer.apply(read);
log(ReadUtils.getBaseQualityString(read));
}
开发者ID:magicDGS，项目名称:ReadTools，代码行数:8，代码来源:SolexaToSangerReadTransformerUnitTest.java
示例18: testCorrectQuals
import htsjdk.samtools.SAMUtils; //导入依赖的package包/类
@Test(dataProvider = "standardQuals")
public void testCorrectQuals(final String qualities) throws Exception {
final GATKRead read = ArtificialReadUtils.createArtificialUnmappedRead(header,
Utils.dupBytes((byte) 'A', qualities.length()),
SAMUtils.fastqToPhred(qualities)
);
final CheckQualityReadTransformer transformer =
new CheckQualityReadTransformer();
final GATKRead copy = read.deepCopy();
Assert.assertEquals(transformer.apply(read), copy);
transformer.currentReadCounter.set(1001);
Assert.assertEquals(transformer.apply(read), copy);
}
开发者ID:magicDGS，项目名称:ReadTools，代码行数:14，代码来源:CheckQualityReadTransformerUnitTest.java
示例19: testBadQualitiesNoThrown
import htsjdk.samtools.SAMUtils; //导入依赖的package包/类
@Test(dataProvider = "badQuals")
public void testBadQualitiesNoThrown(final String badQual) throws Exception {
final GATKRead read = ArtificialReadUtils.createArtificialUnmappedRead(
header, new byte[] {'A'}, SAMUtils.fastqToPhred(badQual));
final CheckQualityReadTransformer transformer =
new CheckQualityReadTransformer();
transformer.apply(read);
}
开发者ID:magicDGS，项目名称:ReadTools，代码行数:9，代码来源:CheckQualityReadTransformerUnitTest.java
示例20: testBadQualitiesCheck
import htsjdk.samtools.SAMUtils; //导入依赖的package包/类
@Test(dataProvider = "badQuals", expectedExceptions = UserException.MisencodedQualityScoresRead.class)
public void testBadQualitiesCheck(final String badQual) throws Exception {
final GATKRead read = ArtificialReadUtils.createArtificialUnmappedRead(
header, new byte[] {'A'}, SAMUtils.fastqToPhred(badQual));
final CheckQualityReadTransformer transformer =
new CheckQualityReadTransformer();
transformer.currentReadCounter.set(1001);
transformer.apply(read);
log(String.valueOf(read.getBaseQuality(0)));
}
开发者ID:magicDGS，项目名称:ReadTools，代码行数:11，代码来源:CheckQualityReadTransformerUnitTest.java
注：本文中的htsjdk.samtools.SAMUtils类示例整理自Github/MSDocs等源码及文档管理平台，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。 |
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