Java FastqRecord.getBaseQualityHeader方法代码示例

import htsjdk.samtools.fastq.FastqRecord; //导入方法依赖的package包/类
/**
 * Creates a GATKRead from a FastqRecord and a header.
 *
 * @param header the header for the record.
 * @param record the record to use as GATKRead.
 */
public FastqGATKRead(final SAMFileHeader header, final FastqRecord record) {
    super(new SAMRecord(header));
    Utils.nonNull(record, "null record");
    // update the record with the read name information
    FastqReadNameEncoding.updateReadFromReadName(this, record.getReadName());
    // set the bases and the qualities
    this.setBases(record.getReadBases());
    this.setBaseQualities(record.getBaseQualities());
    // add the comments in the quality header to the comment if present
    final String baseQualHeader = record.getBaseQualityHeader();
    if (baseQualHeader != null) {
        // the default tag in the specs is CO
        this.setAttribute(SAMTag.CO.toString(), baseQualHeader);
    }
    this.setIsUnmapped();
    if (this.isPaired()) {
        this.setMateIsUnmapped();
    }
}
 

import htsjdk.samtools.fastq.FastqRecord; //导入方法依赖的package包/类
private static FastqRecord createNewFastqRecordWithAdditionalAnnotation(FastqRecord record, String additionalAnnotation, String sequence, String quality) {
	String seqHeaderPrefix = record.getReadHeader();
	String seqLine = record.getReadString();
	if (sequence != null) {
		seqLine = sequence;
	}
	String qualHeaderPrefix = record.getBaseQualityHeader();
	if (qualHeaderPrefix != null) {
		qualHeaderPrefix += additionalAnnotation;
	} else {
		qualHeaderPrefix = additionalAnnotation;
	}
	String qualLine = record.getBaseQualityString();
	if (quality != null) {
		qualLine = quality;
	}
	FastqRecord newRecord = new FastqRecord(seqHeaderPrefix, seqLine, qualHeaderPrefix, qualLine);
	return newRecord;
}
 

import htsjdk.samtools.fastq.FastqRecord; //导入方法依赖的package包/类
public static void reverseCompliment(File inputFastqFile, File outputFastqFile) {

		try (FastqWriter writer = new FastqWriter(outputFastqFile)) {
			try (FastqReader reader = new FastqReader(inputFastqFile)) {
				while (reader.hasNext()) {
					FastqRecord record = reader.next();

					ISequence sequence = new NucleotideCodeSequence(record.getReadString());
					ISequence newSequence = sequence.getCompliment();

					String qualityString = record.getBaseQualityString();
					String newQualityString = qualityString;// StringUtil.reverse(qualityString);

					FastqRecord newRecord = new FastqRecord(record.getReadHeader(), newSequence.toString(), record.getBaseQualityHeader(), newQualityString);
					writer.write(newRecord);

				}
			}
		}
	}
 

import htsjdk.samtools.fastq.FastqRecord; //导入方法依赖的package包/类
public void write(FastqRecord record) {
	try {
		String recordAsString = FastqConstants.SEQUENCE_HEADER + record.getReadHeader() + StringUtil.NEWLINE + record.getReadString() + StringUtil.NEWLINE + FastqConstants.QUALITY_HEADER
				+ (record.getBaseQualityHeader() == null ? "" : record.getBaseQualityHeader()) + StringUtil.NEWLINE + record.getBaseQualityString() + StringUtil.NEWLINE;
		writer.write(recordAsString.getBytes());
	} catch (IOException e) {
		throw new IllegalStateException(e.getMessage(), e);
	}
}
 

import htsjdk.samtools.fastq.FastqRecord; //导入方法依赖的package包/类
static FastqRecord trim(FastqRecord record, int firstBaseToKeep, int lastBaseToKeep, boolean performThreePrimeTrimming, int recordIndex) {
	String readName = record.getReadHeader();
	String readString = record.getReadString();
	String readQuality = record.getBaseQualityString();

	TrimmedRead trimmedRead = trim(readString, readQuality, firstBaseToKeep, lastBaseToKeep, performThreePrimeTrimming);

	FastqRecord newRecord = new FastqRecord(readName, trimmedRead.getTrimmedReadString(), record.getBaseQualityHeader(), trimmedRead.getTrimmedReadQuality());
	return newRecord;

}
 

import htsjdk.samtools.fastq.FastqRecord; //导入方法依赖的package包/类
Record(final FastqRecord rec)
{
name=rec.getReadName();
sequence=rec.getReadString();
name2=rec.getBaseQualityHeader();
qualities=rec.getBaseQualityString();
}
 

import htsjdk.samtools.fastq.FastqRecord; //导入方法依赖的package包/类
private void run(FastqReader r,PrintStream out)
{
String s;
long nRec=0L;
r.setValidationStringency(ValidationStringency.LENIENT);
while(r.hasNext())
	{
	if(++nRec%1E6==0)
		{
		LOG.info("N-Reads:"+nRec);
		}
	FastqRecord fastq=r.next();
	
	
	out.print(FastqConstants.SEQUENCE_HEADER);
	out.println(fastq.getReadName());
	s=fastq.getReadString();

	if((this.only_R2 && nRec%2==1) || (this.only_R1 && nRec%2==0) ) //interleaced
		{
		out.print(s);
		}
	else
		{
		for(int i=s.length()-1;i>=0;i--)
			{
			out.print(AcidNucleics.complement(s.charAt(i)));
			}
		}
	out.println();
	
	out.print(FastqConstants.QUALITY_HEADER);
	s=fastq.getBaseQualityHeader();
	if(s!=null) out.print(s);
	out.println();
	
	s=fastq.getBaseQualityString();
	if((this.only_R2 && nRec%2==1) || (this.only_R1 && nRec%2==0) ) //interleaced
		{
		out.print(s);
		}
	else
		{
		for(int i=s.length()-1;i>=0;i--)
			{
			out.print(s.charAt(i));
			}
		}
	out.println();
	if(out.checkError()) break;
	}
out.flush();
LOG.info("Done. N-Reads:"+nRec);
}