Examples with FastqRecord htsjdk.samtools.fastq.FastqRecord used on opensource projects

Example 36 with FastqRecord

use of htsjdk.samtools.fastq.FastqRecord in project jvarkit by lindenb.

the class PadEmptyFastq method copyTo.

private void copyTo(final FastqReader r, final FastqWriter w) {
    int padLength = this.N;
    long nReads = 0L;
    long nFill = 0L;
    String fillN = null;
    String fillQ = null;
    r.setValidationStringency(ValidationStringency.LENIENT);
    while (r.hasNext()) {
        FastqRecord rec = r.next();
        if (++nReads % 1E6 == 0) {
            LOG.info("Read " + nReads + " reads. empty reads=" + nFill);
        }
        if (rec.getReadString().isEmpty()) {
            ++nFill;
            if (padLength < 1) {
                padLength = DEFAULT_LENGTH;
            }
            if (fillN == null) {
                StringBuilder b1 = new StringBuilder();
                while (b1.length() < padLength) b1.append("N");
                fillN = b1.toString();
                fillQ = fillN.replace('N', '#');
            }
            rec = new FastqRecord(rec.getReadName(), fillN, rec.getBaseQualityHeader(), fillQ);
        } else if (padLength < 1) {
            padLength = rec.getReadString().length();
        }
        w.write(rec);
    }
    LOG.info("Done. Read " + nReads + " reads. empty reads=" + nFill);
}

Example 37 with FastqRecord

use of htsjdk.samtools.fastq.FastqRecord in project jvarkit by lindenb.

the class SamRetrieveSeqAndQual method doWork.

@Override
public int doWork(List<String> args) {
    FastqReader[] fastqReaders = null;
    SamReader samReader = null;
    SAMFileWriter samWriter = null;
    SAMRecordIterator iter = null;
    try {
        if (fastqFin == null) {
            LOG.error("undefined fastq file");
            return -1;
        } else {
            LOG.info("opening " + fastqFin);
            FastqReader r1 = new FastqReader(fastqFin);
            if (fastqRin == null) {
                fastqReaders = new FastqReader[] { r1 };
            } else {
                LOG.info("opening " + fastqRin);
                FastqReader r2 = new FastqReader(fastqRin);
                fastqReaders = new FastqReader[] { r1, r2 };
            }
        }
        samReader = super.openSamReader(oneFileOrNull(args));
        final SAMFileHeader.SortOrder sortOrder = samReader.getFileHeader().getSortOrder();
        if (sortOrder == null) {
            LOG.warning("undefined sort order read are in the sam order");
        } else if (!sortOrder.equals(SAMFileHeader.SortOrder.queryname)) {
            LOG.error("Bad Sort Order. Sort this input on read name");
            return -1;
        }
        SAMFileHeader header = samReader.getFileHeader().clone();
        SAMProgramRecord prg = header.createProgramRecord();
        prg.setCommandLine(this.getProgramCommandLine());
        prg.setProgramName(this.getProgramName());
        prg.setProgramVersion(this.getVersion());
        samWriter = writingBamArgs.openSAMFileWriter(bamOut, header, true);
        iter = samReader.iterator();
        SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(header.getSequenceDictionary());
        FastqRecord[] currFastq = new FastqRecord[] { null, null };
        while (iter.hasNext()) {
            SAMRecord rec = progress.watch(iter.next());
            String readName = rec.getReadName();
            int fastq_index = 0;
            if (rec.getReadPairedFlag()) {
                if (fastqReaders.length != 2) {
                    LOG.error("Not paired but number of fastq!=2");
                    return -1;
                }
                fastq_index = (rec.getFirstOfPairFlag() ? 0 : 1);
            } else {
                if (fastqReaders.length != 1) {
                    LOG.error("Not paired but number of fastq!=1");
                    return -1;
                }
                fastq_index = 0;
            }
            if (sortOrder == SAMFileHeader.SortOrder.queryname) {
                while (currFastq[fastq_index] == null || normalizeFastqName(currFastq[fastq_index].getReadName()).compareTo(readName) < 0) {
                    if (!fastqReaders[fastq_index].hasNext()) {
                        LOG.error("Read Missing for " + readName);
                        return -1;
                    }
                    currFastq[fastq_index] = fastqReaders[fastq_index].next();
                    if (normalizeFastqName(currFastq[fastq_index].getReadName()).compareTo(readName) > 0) {
                        LOG.error("Read Missing for " + readName);
                        return -1;
                    }
                }
            } else {
                if (!fastqReaders[fastq_index].hasNext()) {
                    LOG.error("Read Missing for " + readName);
                    return -1;
                }
                currFastq[fastq_index] = fastqReaders[fastq_index].next();
            }
            if (normalizeFastqName(currFastq[fastq_index].getReadName()).compareTo(readName) != 0) {
                LOG.error("Read Missing/Error for " + readName + " current:" + currFastq[fastq_index].getReadName());
                return -1;
            }
            String fastqBases = currFastq[fastq_index].getReadString();
            String fastqQuals = currFastq[fastq_index].getBaseQualityString();
            /* handle orientation */
            if (!rec.getReadUnmappedFlag() && rec.getReadNegativeStrandFlag()) {
                fastqBases = AcidNucleics.reverseComplement(fastqBases);
                StringBuilder sb = new StringBuilder(fastqQuals.length());
                for (int i = fastqQuals.length() - 1; i >= 0; --i) sb.append(fastqQuals.charAt(i));
                fastqQuals = sb.toString();
            }
            /* remove hard clip */
            Cigar cigar = rec.getCigar();
            if (cigar != null) {
                List<CigarElement> ceList = cigar.getCigarElements();
                if (!ceList.isEmpty()) {
                    CigarElement ce = ceList.get(ceList.size() - 1);
                    if (ce.getOperator() == CigarOperator.HARD_CLIP) {
                        fastqBases = fastqBases.substring(0, fastqBases.length() - ce.getLength());
                        fastqQuals = fastqQuals.substring(0, fastqQuals.length() - ce.getLength());
                    }
                    ce = ceList.get(0);
                    if (ce.getOperator() == CigarOperator.HARD_CLIP) {
                        fastqBases = fastqBases.substring(ce.getLength());
                        fastqQuals = fastqQuals.substring(ce.getLength());
                    }
                }
            }
            rec.setBaseQualityString(fastqQuals);
            rec.setReadString(fastqBases);
            samWriter.addAlignment(rec);
        }
        progress.finish();
        return 0;
    } catch (Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        if (fastqReaders != null)
            for (FastqReader r : fastqReaders) CloserUtil.close(r);
        CloserUtil.close(iter);
        CloserUtil.close(samReader);
        CloserUtil.close(samWriter);
    }
}

Example 38 with FastqRecord

use of htsjdk.samtools.fastq.FastqRecord in project jvarkit by lindenb.

the class SamExtractClip method run.

private void run(final SamReader r, final FastqWriter out) {
    int[] startend = new int[2];
    final SAMFileHeader header = r.getFileHeader();
    // w=swf.make(header, System.out);
    SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(header);
    SAMRecordIterator it = r.iterator();
    while (it.hasNext()) {
        final SAMRecord rec = progress.watch(it.next());
        if (rec.getReadUnmappedFlag())
            continue;
        if (rec.isSecondaryOrSupplementary())
            continue;
        if (rec.getDuplicateReadFlag())
            continue;
        final Cigar cigar = rec.getCigar();
        if (cigar == null || cigar.isEmpty())
            continue;
        String suffix = "";
        if (rec.getReadPairedFlag()) {
            suffix = (rec.getFirstOfPairFlag() ? "/1" : "/2");
        }
        startend[0] = 0;
        startend[1] = rec.getReadLength();
        boolean found = false;
        for (int side = 0; side < 2; ++side) {
            final CigarElement ce = cigar.getCigarElement(side == 0 ? 0 : cigar.numCigarElements() - 1);
            if (!ce.getOperator().equals(CigarOperator.S))
                continue;
            if (ce.getLength() < min_clip_length)
                continue;
            found = true;
            final String clippedSeq;
            final String clippedQual;
            if (side == 0) {
                startend[0] = ce.getLength();
                clippedSeq = rec.getReadString().substring(0, startend[0]);
                clippedQual = rec.getBaseQualityString().substring(0, startend[0]);
            } else {
                startend[1] = rec.getReadLength() - ce.getLength();
                clippedSeq = rec.getReadString().substring(startend[1]);
                clippedQual = rec.getBaseQualityString().substring(startend[1]);
            }
            out.write(new FastqRecord(rec.getReadName() + suffix + ";" + side + ";" + rec.getReferenceName() + ";" + rec.getAlignmentStart() + ";" + rec.getFlags() + ";" + rec.getCigarString() + ";" + (side == 0 ? "5'" : "3'"), clippedSeq, "", clippedQual));
        }
        if (!found)
            continue;
        String bases = rec.getReadString();
        String qual = rec.getBaseQualityString();
        if (rec.getReadNegativeStrandFlag()) {
            bases = AcidNucleics.reverseComplement(bases);
            qual = new StringBuilder(qual).reverse().toString();
        }
        if (print_original_read) {
            out.write(new FastqRecord(rec.getReadName() + suffix, bases, "", qual));
        }
        if (print_clipped_read) {
            out.write(new FastqRecord(rec.getReadName() + suffix + ":clipped", bases.substring(startend[0], startend[1]), "", qual.substring(startend[0], startend[1])));
        }
    }
    it.close();
    progress.finish();
}

Example 39 with FastqRecord

use of htsjdk.samtools.fastq.FastqRecord in project jvarkit by lindenb.

the class AbstractFastqReader method next.

public FastqRecord next() {
    if (!hasNext()) {
        throw new NoSuchElementException("next() called when !hasNext()");
    }
    final FastqRecord rec = nextRecord;
    nextRecord = null;
    _has_next_called = false;
    seqHeader = null;
    return rec;
}

Example 40 with FastqRecord

use of htsjdk.samtools.fastq.FastqRecord in project jvarkit by lindenb.

the class FourLinesFastqReaderTest method test2.

public void test2() throws Exception {
    final String fastqs = "@IL31_4368:1:1:996:8507/2\n" + "\n" + "+\n" + "\n" + "@IL31_4368:1:1:996:21421/2\n" + "CAAAAACTTTCACTTTACCTGCCGGGTTTCCCAGTTTACATTCCACTGTTTGAC\n" + "+\n" + ">DBDDB,B9BAA4AAB7BB?7BBB=91;+*@;5<87+*=/*@@?9=73=.7)7*\n";
    FourLinesFastqReader r = new FourLinesFastqReader(new ByteArrayInputStream(fastqs.getBytes()));
    r.setValidationStringency(ValidationStringency.LENIENT);
    Assert.assertTrue(r.hasNext());
    FastqRecord rec = r.next();
    Assert.assertNotNull(rec);
    Assert.assertTrue(rec.getBaseQualityString().isEmpty());
    Assert.assertTrue(rec.getReadString().isEmpty());
    Assert.assertTrue(r.hasNext());
    rec = r.next();
    Assert.assertNotNull(rec);
    Assert.assertFalse(rec.getBaseQualityString().isEmpty());
    Assert.assertFalse(rec.getReadString().isEmpty());
    Assert.assertFalse(r.hasNext());
    r.close();
}