本文整理汇总了Java中htsjdk.samtools.SAMUtils.fastqToPhred方法的典型用法代码示例。如果您正苦于以下问题:Java SAMUtils.fastqToPhred方法的具体用法?Java SAMUtils.fastqToPhred怎么用?Java SAMUtils.fastqToPhred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htsjdk.samtools.SAMUtils
的用法示例。
在下文中一共展示了SAMUtils.fastqToPhred方法的12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: reset
import htsjdk.samtools.SAMUtils; //导入方法依赖的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();
}
示例2: convertQuality
import htsjdk.samtools.SAMUtils; //导入方法依赖的package包/类
/** Based on the type of quality scores coming in, converts them to a numeric byte[] in phred scale. */
void convertQuality(final byte[] quals, final FastqQualityFormat version) {
switch (version) {
case Standard:
SAMUtils.fastqToPhred(quals);
break ;
case Solexa:
solexaQualityConverter.convertSolexaQualityCharsToPhredBinary(quals);
break ;
case Illumina:
solexaQualityConverter.convertSolexa_1_3_QualityCharsToPhredBinary(quals);
break ;
}
}
示例3: visit
import htsjdk.samtools.SAMUtils; //导入方法依赖的package包/类
@Override
public void visit(final FastqRecord rec) {
final byte quals[]= rec.getBaseQualityString().getBytes();
if(quals==null || quals.length==0) return;
SAMUtils.fastqToPhred(quals);
_visit(quals);
}
示例4: visit
import htsjdk.samtools.SAMUtils; //导入方法依赖的package包/类
@Override
public void visit(final FastqRecord rec) {
byte quals[]= rec.getBaseQualityString().getBytes();
if(quals==null || quals.length==0) return;
SAMUtils.fastqToPhred(quals);
_visit(quals);
}
示例5: getExistingBaseInsertionQualities
import htsjdk.samtools.SAMUtils; //导入方法依赖的package包/类
/**
* @return the base deletion quality or null if read doesn't have one
*/
public byte[] getExistingBaseInsertionQualities() {
return SAMUtils.fastqToPhred( getStringAttribute(BQSR_BASE_INSERTION_QUALITIES));
}
示例6: getExistingBaseDeletionQualities
import htsjdk.samtools.SAMUtils; //导入方法依赖的package包/类
/**
* @return the base deletion quality or null if read doesn't have one
*/
public byte[] getExistingBaseDeletionQualities() {
return SAMUtils.fastqToPhred( getStringAttribute(BQSR_BASE_DELETION_QUALITIES));
}
示例7: getExistingBaseDeletionQualities
import htsjdk.samtools.SAMUtils; //导入方法依赖的package包/类
public static byte[] getExistingBaseDeletionQualities(SAMRecord sam) {
return SAMUtils.fastqToPhred(sam
.getStringAttribute(BQSR_BASE_DELETION_QUALITIES));
}
示例8: getExistingBaseInsertionQualities
import htsjdk.samtools.SAMUtils; //导入方法依赖的package包/类
public static byte[] getExistingBaseInsertionQualities(SAMRecord sam) {
return SAMUtils.fastqToPhred(sam
.getStringAttribute(BQSR_BASE_INSERTION_QUALITIES));
}
示例9: writeRecord
import htsjdk.samtools.SAMUtils; //导入方法依赖的package包/类
void writeRecord(final SAMRecord read, final Integer mateNumber, final FastqWriter writer,
final int basesToTrim, final Integer maxBasesToWrite) {
final String seqHeader = mateNumber == null ? read.getReadName() : read.getReadName() + "/" + mateNumber;
String readString = read.getReadString();
String baseQualities = read.getBaseQualityString();
// If we're clipping, do the right thing to the bases or qualities
if (CLIPPING_ATTRIBUTE != null) {
Integer clipPoint = (Integer) read.getAttribute(CLIPPING_ATTRIBUTE);
if (clipPoint != null && clipPoint < CLIPPING_MIN_LENGTH) {
clipPoint = Math.min(readString.length(), CLIPPING_MIN_LENGTH);
}
if (clipPoint != null) {
if (CLIPPING_ACTION.equalsIgnoreCase("X")) {
readString = clip(readString, clipPoint, null, !read.getReadNegativeStrandFlag());
baseQualities = clip(baseQualities, clipPoint, null, !read.getReadNegativeStrandFlag());
}
else if (CLIPPING_ACTION.equalsIgnoreCase("N")) {
readString = clip(readString, clipPoint, 'N', !read.getReadNegativeStrandFlag());
}
else {
final char newQual = SAMUtils.phredToFastq(new byte[]{(byte) Integer.parseInt(CLIPPING_ACTION)}).charAt(0);
baseQualities = clip(baseQualities, clipPoint, newQual, !read.getReadNegativeStrandFlag());
}
}
}
if (RE_REVERSE && read.getReadNegativeStrandFlag()) {
readString = SequenceUtil.reverseComplement(readString);
baseQualities = StringUtil.reverseString(baseQualities);
}
if (basesToTrim > 0) {
readString = readString.substring(basesToTrim);
baseQualities = baseQualities.substring(basesToTrim);
}
// Perform quality trimming if desired, making sure to leave at least one base!
if (QUALITY != null) {
final byte[] quals = SAMUtils.fastqToPhred(baseQualities);
final int qualityTrimIndex = Math.max(1, TrimmingUtil.findQualityTrimPoint(quals, QUALITY));
if (qualityTrimIndex < quals.length) {
readString = readString.substring(0, qualityTrimIndex);
baseQualities = baseQualities.substring(0, qualityTrimIndex);
}
}
if (maxBasesToWrite != null && maxBasesToWrite < readString.length()) {
readString = readString.substring(0, maxBasesToWrite);
baseQualities = baseQualities.substring(0, maxBasesToWrite);
}
writer.write(new FastqRecord(seqHeader, readString, "", baseQualities));
}
示例10: getExistingBaseInsertionQualities
import htsjdk.samtools.SAMUtils; //导入方法依赖的package包/类
/**
* @return the base deletion quality or null if read doesn't have one
*/
public static byte[] getExistingBaseInsertionQualities(final GATKRead read) {
return SAMUtils.fastqToPhred(read.getAttributeAsString(BQSR_BASE_INSERTION_QUALITIES));
}
示例11: getExistingBaseDeletionQualities
import htsjdk.samtools.SAMUtils; //导入方法依赖的package包/类
/**
* @return the base deletion quality or null if read doesn't have one
*/
public static byte[] getExistingBaseDeletionQualities(final GATKRead read) {
return SAMUtils.fastqToPhred( read.getAttributeAsString(BQSR_BASE_DELETION_QUALITIES));
}
示例12: getOriginalBaseQualities
import htsjdk.samtools.SAMUtils; //导入方法依赖的package包/类
/**
* Retrieve the original base qualities of the given read, if present,
* as stored in the OQ attribute.
*
* @param read read to check
* @return original base qualities as stored in the OQ attribute, or null
* if the OQ attribute is not present
*/
public static byte[] getOriginalBaseQualities( final GATKRead read ) {
if ( ! read.hasAttribute(ORIGINAL_BASE_QUALITIES_TAG) ) {
return null;
}
final String oqString = read.getAttributeAsString(ORIGINAL_BASE_QUALITIES_TAG);
return !oqString.isEmpty() ? SAMUtils.fastqToPhred(oqString) : null;
}