Examples with SAMRecordIterator htsjdk.samtools.SAMRecordIterator used on opensource projects

Example 41 with SAMRecordIterator

use of htsjdk.samtools.SAMRecordIterator in project jvarkit by lindenb.

the class BamClipToInsertion method doWork.

@Override
public int doWork(final List<String> args) {
    SAMRecordIterator iter = null;
    SamReader sfr = null;
    SAMFileWriter sfw = null;
    try {
        sfr = super.openSamReader(oneFileOrNull(args));
        final SAMFileHeader header1 = sfr.getFileHeader();
        if (header1 == null) {
            LOG.error("File header missing");
            return -1;
        }
        if (header1.getSortOrder() != SortOrder.coordinate) {
            LOG.error("Input is not sorted on coordinate.");
            return -1;
        }
        final SAMFileHeader header2 = header1.clone();
        header2.addComment(getProgramName() + ":" + getVersion() + ":" + getProgramCommandLine());
        header2.setSortOrder(SortOrder.unsorted);
        sfw = this.writingBamArgs.openSAMFileWriter(output, header2, true);
        final SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(header1);
        iter = sfr.iterator();
        String curContig = null;
        LinkedList<SamAndCigar> buffer = new LinkedList<>();
        for (; ; ) {
            SAMRecord rec = null;
            if (iter.hasNext()) {
                rec = progress.watch(iter.next());
                // ignore unmapped reads
                if (rec.getReadUnmappedFlag()) {
                    sfw.addAlignment(rec);
                    continue;
                }
            }
            if (rec == null || (curContig != null && !curContig.equals(rec.getReferenceName()))) {
                for (final SamAndCigar r : buffer) sfw.addAlignment(r.getSAMRecord());
                buffer.clear();
                // we're done
                if (rec == null)
                    break;
                curContig = rec.getReferenceName();
            }
            final SamAndCigar sac = new SamAndCigar(rec);
            if (!sac.containsIorS) {
                sfw.addAlignment(rec);
                continue;
            }
            buffer.add(sac);
            int i = 0;
            while (i < buffer.size()) {
                final SamAndCigar ri = buffer.get(i);
                if (ri.getSAMRecord().getUnclippedEnd() < rec.getUnclippedStart()) {
                    for (int j = 0; j < buffer.size(); ++j) {
                        if (i == j)
                            continue;
                        ri.merge(buffer.get(j));
                    }
                    sfw.addAlignment(ri.build());
                    buffer.remove(i);
                } else {
                    ++i;
                }
            }
        }
        progress.finish();
        LOG.info("done");
        return RETURN_OK;
    } catch (Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(iter);
        CloserUtil.close(sfr);
        CloserUtil.close(sfw);
    }
}

Example 42 with SAMRecordIterator

use of htsjdk.samtools.SAMRecordIterator in project jvarkit by lindenb.

the class BamTile method doWork.

@Override
public int doWork(final List<String> args) {
    SAMRecordIterator iter = null;
    SamReader sfr = null;
    SAMFileWriter sfw = null;
    try {
        sfr = openSamReader(oneFileOrNull(args));
        final SAMFileHeader header1 = sfr.getFileHeader();
        if (header1 == null) {
            LOG.error("File header missing");
            return -1;
        }
        if (header1.getSortOrder() != SAMFileHeader.SortOrder.coordinate) {
            LOG.error("File header not sorted on coordinate");
            return -1;
        }
        final SAMFileHeader header2 = header1.clone();
        header2.addComment("BamTile:" + getVersion() + ":" + getProgramCommandLine());
        sfw = this.writingBamArgs.openSAMFileWriter(this.outputFile, header2, true);
        final SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(header1);
        iter = sfr.iterator();
        final LinkedList<SAMRecord> buffer = new LinkedList<>();
        for (; ; ) {
            SAMRecord rec = null;
            if (iter.hasNext()) {
                rec = progress.watch(iter.next());
                if (rec.getReadUnmappedFlag())
                    continue;
                if (this.filterOut.filterOut(rec))
                    continue;
                if (!buffer.isEmpty()) {
                    final SAMRecord last = buffer.getLast();
                    if (this.no_overlap) {
                        if (last.getReferenceIndex() == rec.getReferenceIndex() && last.getEnd() >= rec.getStart()) {
                            continue;
                        }
                    } else {
                        if (last.getReferenceIndex() == rec.getReferenceIndex() && last.getAlignmentStart() <= rec.getAlignmentStart() && last.getAlignmentEnd() >= rec.getAlignmentEnd()) {
                            continue;
                        }
                    }
                }
            }
            if (rec == null || (!buffer.isEmpty() && buffer.getLast().getReferenceIndex() != rec.getReferenceIndex())) {
                while (!buffer.isEmpty()) {
                    sfw.addAlignment(buffer.removeFirst());
                }
                if (rec == null)
                    break;
            }
            buffer.add(rec);
            if (!this.no_overlap && buffer.size() > 2) {
                final int index = buffer.size();
                final SAMRecord prev = buffer.get(index - 3);
                final SAMRecord curr = buffer.get(index - 2);
                final SAMRecord next = buffer.get(index - 1);
                if (prev.getAlignmentEnd() >= next.getAlignmentStart() || curr.getAlignmentEnd() <= prev.getAlignmentEnd()) {
                    buffer.remove(index - 2);
                } else if (curr.getAlignmentStart() == prev.getAlignmentStart() && curr.getAlignmentEnd() > prev.getAlignmentEnd()) {
                    buffer.remove(index - 3);
                }
            }
            while (buffer.size() > 3) {
                sfw.addAlignment(buffer.removeFirst());
            }
        }
        progress.finish();
        sfw.close();
        sfw = null;
        iter.close();
        iter = null;
        sfr.close();
        sfr = null;
        LOG.info("done");
        return RETURN_OK;
    } catch (final Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(iter);
        CloserUtil.close(sfr);
        CloserUtil.close(sfw);
    }
}

Example 43 with SAMRecordIterator

use of htsjdk.samtools.SAMRecordIterator in project jvarkit by lindenb.

the class BamToSql method doWork.

@Override
public int doWork(List<String> args) {
    if (this.faidxFile == null) {
        LOG.error("ref sequence faidx not defined");
        return -1;
    }
    SAMRecordIterator iter = null;
    SamReader sfr = null;
    PrintWriter out = null;
    GenomicSequence genomicSequence = null;
    IndexedFastaSequenceFile indexedFastaSequenceFile = null;
    args = new ArrayList<String>(IOUtils.unrollFiles(args));
    try {
        out = super.openFileOrStdoutAsPrintWriter(this.outputFile);
        indexedFastaSequenceFile = new IndexedFastaSequenceFile(this.faidxFile);
        out.println("CREATE TABLE IF NOT EXISTS SamFile");
        out.println("(");
        out.println("id INTEGER PRIMARY KEY,");
        out.println("filename TEXT");
        out.println(");");
        out.println("CREATE TABLE IF NOT EXISTS Dictionary");
        out.println("(");
        out.println("id INTEGER PRIMARY KEY,");
        out.println("name TEXT NOT NULL,");
        out.println("length INT NOT NULL,");
        out.println("tid INT NOT NULL,");
        out.println("samfile_id INT NOT NULL,");
        out.println("FOREIGN KEY(samfile_id) REFERENCES SamFile(id)");
        out.println(");");
        out.println("CREATE TABLE IF NOT EXISTS ReadGroup");
        out.println("(");
        out.println("id INTEGER PRIMARY KEY,");
        out.println("groupId TEXT NOT NULL,");
        out.println("sample TEXT NOT NULL,");
        out.println("samfile_id INT NOT NULL,");
        out.println("FOREIGN KEY(samfile_id) REFERENCES SamFile(id)");
        out.println(");");
        out.println("CREATE TABLE IF NOT EXISTS Read");
        out.println("(");
        out.println("id INTEGER PRIMARY KEY,");
        out.println("name TEXT NOT NULL,");
        out.println("flag INTEGER NOT NULL,");
        if (this.printflag) {
            for (final SAMFlag flg : SAMFlag.values()) {
                out.println(flg.name() + " INTEGER NOT NULL,");
            }
        }
        out.println("rname TEXT,");
        out.println("pos INTEGER,");
        out.println("mapq INTEGER NOT NULL,");
        out.println("cigar TEXT,");
        out.println("rnext TEXT,");
        out.println("pnext INTEGER,");
        out.println("tlen INTEGER,");
        out.println("sequence TEXT NOT NULL,");
        out.println("qualities TEXT NOT NULL,");
        out.println("samfile_id INT NOT NULL,");
        out.println("group_id INT,");
        out.println("FOREIGN KEY(samfile_id) REFERENCES SamFile(id),");
        out.println("FOREIGN KEY(group_id) REFERENCES ReadGroup(id)");
        out.println(");");
        out.println("CREATE TABLE IF NOT EXISTS Cigar");
        out.println("(");
        out.println("id INTEGER PRIMARY KEY,");
        out.println("read_pos INT ,");
        out.println("read_base TEXT,");
        out.println("read_qual INT ,");
        out.println("ref_pos INT ,");
        out.println("ref_base TEXT,");
        out.println("operator TEXT NOT NULL,");
        out.println("read_id INT NOT NULL,");
        out.println("FOREIGN KEY(read_id) REFERENCES Read(id)");
        out.println(");");
        out.println("begin transaction;");
        int samIndex = 0;
        do {
            final String inputName;
            if (samIndex == 0 && args.isEmpty()) {
                sfr = openSamReader(null);
                inputName = "<stdin>";
            } else {
                inputName = args.get(samIndex);
                sfr = openSamReader(inputName);
            }
            final SAMFileHeader header1 = sfr.getFileHeader();
            if (header1 == null) {
                throw new JvarkitException.FileFormatError("File header missing");
            }
            final SAMSequenceDictionary dict = header1.getSequenceDictionary();
            if (dict == null) {
                throw new JvarkitException.DictionaryMissing("No Dictionary in input");
            }
            final IntervalParser intervalParser = new IntervalParser(dict);
            final Interval userInterval;
            iter = null;
            if (this.regionStr == null || this.regionStr.isEmpty()) {
                LOG.warn("You're currently scanning the whole BAM ???!!!");
                iter = sfr.iterator();
                userInterval = null;
            } else {
                userInterval = intervalParser.parse(this.regionStr);
                if (userInterval == null) {
                    throw new JvarkitException.UserError("cannot parse interval " + this.regionStr);
                }
                iter = sfr.query(userInterval.getContig(), userInterval.getStart(), userInterval.getEnd(), false);
            }
            out.println(String.join(" ", "insert into SamFile(filename) values(", quote(inputName), ");"));
            for (int i = 0; i < dict.size(); ++i) {
                final SAMSequenceRecord ssr = dict.getSequence(i);
                out.println("insert into Dictionary(name,length,tid,samfile_id) select " + quote(inputName) + "," + ssr.getSequenceLength() + "," + i + ",max(id) from SamFile;");
            }
            for (final SAMReadGroupRecord g : header1.getReadGroups()) {
                out.println("insert into ReadGroup(groupId,sample,samfile_id) select " + quote(g.getId()) + "," + quote(g.getSample()) + "," + "max(id) from SamFile;");
            }
            final SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(header1);
            while (iter.hasNext()) {
                final SAMRecord rec = progress.watch(iter.next());
                final StringBuilder sql = new StringBuilder();
                sql.append("insert into Read(" + "name,flag,");
                if (this.printflag) {
                    for (final SAMFlag flg : SAMFlag.values()) {
                        sql.append(flg.name()).append(",");
                    }
                }
                sql.append("rname,pos,mapq,cigar,rnext,pnext,tlen,sequence,qualities,group_id,samfile_id) select ");
                sql.append(quote(rec.getReadName())).append(",");
                sql.append(rec.getFlags()).append(",");
                if (this.printflag) {
                    for (final SAMFlag flg : SAMFlag.values()) {
                        sql.append(flg.isSet(rec.getFlags()) ? 1 : 0);
                        sql.append(",");
                    }
                }
                if (rec.getReferenceName() == null || rec.getReferenceName().equals(SAMRecord.NO_ALIGNMENT_REFERENCE_NAME)) {
                    sql.append("NULL,NULL");
                } else {
                    sql.append(quote(rec.getReferenceName()));
                    sql.append(",");
                    sql.append(rec.getAlignmentStart());
                }
                sql.append(",");
                sql.append(rec.getMappingQuality());
                sql.append(",");
                // cigar
                if (rec.getCigarString() == null || rec.getCigarString().equals(SAMRecord.NO_ALIGNMENT_CIGAR)) {
                    sql.append("NULL");
                } else {
                    sql.append(quote(rec.getCigarString()));
                }
                sql.append(",");
                // rnext
                if (rec.getMateReferenceName() == null || rec.getMateReferenceName().equals(SAMRecord.NO_ALIGNMENT_REFERENCE_NAME)) {
                    sql.append("NULL,NULL");
                } else {
                    sql.append(quote(rec.getMateReferenceName()));
                    sql.append(",");
                    sql.append(rec.getMateAlignmentStart());
                }
                sql.append(",");
                // tlen
                sql.append(rec.getInferredInsertSize());
                sql.append(",");
                // sequence
                sql.append(quote(rec.getReadString()));
                sql.append(",");
                // qualities
                sql.append(quote(rec.getBaseQualityString()));
                sql.append(",");
                if (rec.getReadGroup() == null) {
                    sql.append("NULL");
                } else {
                    sql.append("G.id");
                }
                sql.append(",F.id FROM SamFile as F");
                if (rec.getReadGroup() != null) {
                    sql.append(" , ReadGroup as G where G.groupId=").append(quote(rec.getReadGroup().getId())).append(" and F.id = G.samfile_id ");
                }
                sql.append("  ORDER BY F.id DESC LIMIT 1;");
                out.println(sql.toString());
                if (this.printcigar && !rec.getReadUnmappedFlag() && rec.getCigar() != null) {
                    if (genomicSequence == null || !genomicSequence.getChrom().equals(rec.getReferenceName())) {
                        genomicSequence = new GenomicSequence(indexedFastaSequenceFile, rec.getReferenceName());
                    }
                    int ref = rec.getUnclippedStart();
                    final byte[] bases = rec.getReadBases();
                    final byte[] quals = rec.getBaseQualities();
                    int read = 0;
                    for (final CigarElement ce : rec.getCigar()) {
                        final CigarOperator op = ce.getOperator();
                        if (op.equals(CigarOperator.P))
                            continue;
                        for (int i = 0; i < ce.getLength(); ++i) {
                            sql.setLength(0);
                            boolean in_user_interval = true;
                            sql.append("insert into Cigar(operator,read_pos,read_base,read_qual,ref_pos,ref_base,read_id) ");
                            sql.append("select '");
                            sql.append(op.name());
                            sql.append("',");
                            if (userInterval != null && !(rec.getReferenceName().equals(userInterval.getContig()) && ref >= userInterval.getStart() && ref <= userInterval.getEnd())) {
                                in_user_interval = false;
                            }
                            switch(op) {
                                case I:
                                    {
                                        sql.append(read);
                                        sql.append(",");
                                        sql.append("'" + (char) bases[read] + "',");
                                        sql.append("" + quals[read] + "");
                                        sql.append(",");
                                        sql.append("NULL,NULL");
                                        read++;
                                        break;
                                    }
                                case D:
                                case N:
                                case // yes H (hard clip)
                                H:
                                    {
                                        sql.append("NULL,NULL,NULL,");
                                        sql.append(ref);
                                        sql.append(",'");
                                        sql.append((ref < 1 || ref - 1 >= genomicSequence.length()) ? '*' : genomicSequence.charAt(ref - 1));
                                        sql.append("'");
                                        ref++;
                                        break;
                                    }
                                case M:
                                case X:
                                case EQ:
                                case // yes S, soft clip
                                S:
                                    {
                                        sql.append(read);
                                        sql.append(",");
                                        sql.append("'" + (char) bases[read] + "',");
                                        sql.append("" + quals[read] + "");
                                        sql.append(",");
                                        sql.append(ref);
                                        sql.append(",'");
                                        sql.append((ref < 1 || ref - 1 >= genomicSequence.length()) ? '*' : genomicSequence.charAt(ref - 1));
                                        sql.append("'");
                                        ref++;
                                        read++;
                                        break;
                                    }
                                default:
                                    throw new IllegalStateException();
                            }
                            sql.append(", id from Read ORDER BY id DESC LIMIT 1;");
                            if (in_user_interval)
                                out.println(sql.toString());
                        }
                    }
                }
            }
            iter.close();
            iter = null;
            sfr.close();
            sfr = null;
            progress.finish();
            samIndex++;
        } while (samIndex < args.size());
        out.println("COMMIT;");
        out.flush();
        out.close();
        LOG.info("done");
        return 0;
    } catch (Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(iter);
        CloserUtil.close(sfr);
        CloserUtil.close(out);
        CloserUtil.close(indexedFastaSequenceFile);
    }
}

Example 44 with SAMRecordIterator

use of htsjdk.samtools.SAMRecordIterator in project jvarkit by lindenb.

the class SamClipIndelFraction method doWork.

@Override
public int doWork(final List<String> args) {
    SamReader sfr = null;
    SAMRecordIterator iter = null;
    PrintWriter pw = null;
    try {
        sfr = openSamReader(oneFileOrNull(args));
        pw = super.openFileOrStdoutAsPrintWriter(outputFile);
        long total_bases_count = 0L;
        long count_clipped_reads = 0L;
        long count_clipped_left_reads = 0L;
        long count_clipped_right_reads = 0L;
        long count_unclipped_reads = 0L;
        long count_unmapped_reads = 0L;
        SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(sfr.getFileHeader()).logger(LOG);
        Counter<Integer> counter = new Counter<>();
        iter = sfr.iterator();
        while (iter.hasNext()) {
            final SAMRecord record = progress.watch(iter.next());
            if (record.getReadUnmappedFlag()) {
                ++count_unmapped_reads;
                continue;
            }
            final Cigar cigar = record.getCigar();
            int left_clip_length = 0;
            int right_clip_length = 0;
            int deletion_N_length = 0;
            int deletion_D_length = 0;
            int insertion_length = 0;
            boolean onLeft = true;
            for (int i = 0; i < cigar.numCigarElements(); ++i) {
                final CigarElement ce = cigar.getCigarElement(i);
                final CigarOperator op = ce.getOperator();
                switch(op) {
                    case N:
                        {
                            onLeft = false;
                            deletion_D_length += ce.getLength();
                            total_bases_count += ce.getLength();
                            break;
                        }
                    case D:
                        {
                            onLeft = false;
                            deletion_N_length += ce.getLength();
                            total_bases_count += ce.getLength();
                            break;
                        }
                    case I:
                        {
                            onLeft = false;
                            insertion_length += ce.getLength();
                            total_bases_count += ce.getLength();
                            break;
                        }
                    case S:
                    case H:
                        {
                            if (onLeft) {
                                if (record.getReadNegativeStrandFlag()) {
                                    right_clip_length += ce.getLength();
                                } else {
                                    left_clip_length += ce.getLength();
                                }
                            } else {
                                if (record.getReadNegativeStrandFlag()) {
                                    left_clip_length += ce.getLength();
                                } else {
                                    right_clip_length += ce.getLength();
                                }
                            }
                            total_bases_count += ce.getLength();
                            break;
                        }
                    default:
                        {
                            onLeft = false;
                            if (op.consumesReadBases()) {
                                total_bases_count += ce.getLength();
                            }
                            break;
                        }
                }
            }
            if (left_clip_length + right_clip_length == 0) {
                count_unclipped_reads++;
            } else {
                if (left_clip_length > 0)
                    count_clipped_left_reads++;
                if (right_clip_length > 0)
                    count_clipped_right_reads++;
                count_clipped_reads++;
            }
            switch(type) {
                case leftclip:
                    counter.incr(left_clip_length);
                    break;
                case rightclip:
                    counter.incr(right_clip_length);
                    break;
                case allclip:
                    counter.incr(left_clip_length + right_clip_length);
                    break;
                case deletion:
                    counter.incr(deletion_D_length + deletion_N_length);
                    break;
                case insert:
                    counter.incr(insertion_length);
                    break;
                default:
                    LOG.error("Bad type: " + type);
                    return -1;
            }
        }
        progress.finish();
        pw.println("##UNMAPPED_READS=" + count_unmapped_reads);
        pw.println("##MAPPED_READS=" + (count_clipped_reads + count_unclipped_reads));
        pw.println("##CLIPPED_READS=" + count_clipped_reads);
        pw.println("##CLIPPED_READS_5_PRIME=" + count_clipped_left_reads);
        pw.println("##CLIPPED_READS_3_PRIME=" + count_clipped_right_reads);
        pw.println("##UNCLIPPED_READS=" + count_unclipped_reads);
        pw.println("##COUNT_BASES=" + total_bases_count);
        pw.print("#");
        switch(type) {
            case leftclip:
                pw.print("CLIP_5_PRIME");
                break;
            case rightclip:
                pw.print("CLIP_3_PRIME");
                break;
            case allclip:
                pw.print("CLIP");
                break;
            case deletion:
                pw.print("DELETION");
                break;
            case insert:
                pw.print("INSERTION");
                break;
            default:
                LOG.error("Bad type: " + type);
                return -1;
        }
        pw.println("\tCOUNT\tFRACTION_OF_MAPPED_READS");
        for (final Integer size : new TreeSet<Integer>(counter.keySet())) {
            pw.print(size);
            pw.print('\t');
            pw.print(counter.count(size));
            pw.print('\t');
            pw.println(counter.count(size) / (double) (count_unclipped_reads + count_unclipped_reads));
        }
        pw.flush();
        pw.close();
        pw = null;
        return 0;
    } catch (final Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(iter);
        CloserUtil.close(sfr);
        CloserUtil.close(pw);
    }
}

Example 45 with SAMRecordIterator

use of htsjdk.samtools.SAMRecordIterator in project jvarkit by lindenb.

the class SamReadLengthDistribution method scan.

private void scan(final SamReader in) throws IOException {
    final SAMRecordIterator iter = in.iterator();
    while (iter.hasNext()) {
        final SAMRecord rec = iter.next();
        String sampleName = this.partition.getPartion(rec);
        if (sampleName == null || sampleName.isEmpty())
            sampleName = "__UNDEFINED_" + this.partition.name().toUpperCase() + "_";
        Counter<Integer> counter = this.lengths.get(sampleName);
        if (counter == null) {
            counter = new Counter<>();
            this.lengths.put(sampleName, counter);
        }
        final int len = rec.getReadLength();
        counter.incr(len);
        this.max_length = Math.max(max_length, len);
    }
    iter.close();
}