Java SAMUtils.fastqToPhred方法代码示例

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();
}
 

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 ;
        }
}
 

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);	
    }
 

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);	
    }
 

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));
}
 

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));
}
 

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));
}
 

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));
}
 

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));

}
 

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));
}
 

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));
}
 

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;
}