Java Code Examples for htsjdk.samtools.SAMUtils#fastqToPhred()

The following examples show how to use htsjdk.samtools.SAMUtils#fastqToPhred() . You can vote up the ones you like or vote down the ones you don't like, and go to the original project or source file by following the links above each example. You may check out the related API usage on the sidebar.
Example 1
Source File: Read.java    From cramtools with Apache License 2.0 6 votes vote down vote up 
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();
}
Example 2
Source File: FastqToSam.java    From picard with MIT License 5 votes vote down vote up 
/** 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 ;
        }
}
Example 3
Source File: SamToFastq.java    From picard with MIT License 4 votes vote down vote up 
private 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(CLIP_TRIM)) {
                readString = clip(readString, clipPoint, null, !read.getReadNegativeStrandFlag());
                baseQualities = clip(baseQualities, clipPoint, null, !read.getReadNegativeStrandFlag());
            } else if (CLIPPING_ACTION.equalsIgnoreCase(CLIP_TO_N)) {
                readString = clip(readString, clipPoint, CLIP_TO_N.charAt(0), !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));
}