Examples with IndexedFastaSequenceFile htsjdk.samtools.reference.IndexedFastaSequenceFile used on opensource projects

Example 56 with IndexedFastaSequenceFile

use of htsjdk.samtools.reference.IndexedFastaSequenceFile in project jvarkit by lindenb.

the class Bam2Raster method doWork.

@Override
public int doWork(final List<String> args) {
    if (this.regionStr == null) {
        LOG.error("Region was not defined.");
        return -1;
    }
    if (this.WIDTH < 100) {
        LOG.info("adjusting WIDTH to 100");
        this.WIDTH = 100;
    }
    SamReader samFileReader = null;
    try {
        final SamReaderFactory srf = super.createSamReaderFactory();
        if (this.referenceFile != null) {
            LOG.info("loading reference");
            this.indexedFastaSequenceFile = new IndexedFastaSequenceFile(this.referenceFile);
            srf.referenceSequence(this.referenceFile);
        }
        final IntervalParser intervalParser = new IntervalParser(this.indexedFastaSequenceFile == null ? null : this.indexedFastaSequenceFile.getSequenceDictionary()).setFixContigName(true);
        this.interval = intervalParser.parse(this.regionStr);
        if (this.interval == null) {
            LOG.error("Cannot parse interval " + regionStr + " or chrom doesn't exists in sam dictionary.");
            return -1;
        }
        LOG.info("Interval is " + this.interval);
        loadVCFs();
        for (final String bamFile : IOUtils.unrollFiles(args)) {
            samFileReader = srf.open(SamInputResource.of(bamFile));
            final SAMFileHeader header = samFileReader.getFileHeader();
            final SAMSequenceDictionary dict = header.getSequenceDictionary();
            if (dict == null) {
                LOG.error("no dict in " + bamFile);
                return -1;
            }
            if (dict.getSequence(this.interval.getContig()) == null) {
                LOG.error("no such chromosome in " + bamFile + " " + this.interval);
                return -1;
            }
            scan(samFileReader);
            samFileReader.close();
            samFileReader = null;
        }
        if (this.key2partition.isEmpty()) {
            LOG.error("No data was found.(not Read-Group specified ?");
            return -1;
        }
        this.key2partition.values().stream().forEach(P -> P.build());
        saveImages(this.key2partition.values().stream().map(P -> P.image).collect(Collectors.toList()));
        return RETURN_OK;
    } catch (Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(indexedFastaSequenceFile);
        CloserUtil.close(samFileReader);
        indexedFastaSequenceFile = null;
    }
}

Example 57 with IndexedFastaSequenceFile

use of htsjdk.samtools.reference.IndexedFastaSequenceFile in project jvarkit by lindenb.

the class LowResBam2Raster method doWork.

@Override
public int doWork(final List<String> args) {
    if (this.regionStr == null) {
        LOG.error("Region was not defined.");
        return -1;
    }
    if (this.WIDTH < 100) {
        LOG.info("adjusting WIDTH to 100");
        this.WIDTH = 100;
    }
    if (this.gcWinSize <= 0) {
        LOG.info("adjusting GC win size to 5");
        this.gcWinSize = 5;
    }
    SamReader samFileReader = null;
    try {
        if (this.referenceFile != null) {
            LOG.info("loading reference");
            this.indexedFastaSequenceFile = new IndexedFastaSequenceFile(this.referenceFile);
        }
        final SamReaderFactory srf = super.createSamReaderFactory();
        this.interval = new IntervalParser(this.indexedFastaSequenceFile == null ? null : this.indexedFastaSequenceFile.getSequenceDictionary()).parse(this.regionStr);
        if (this.interval == null) {
            LOG.error("Cannot parse interval " + regionStr + " or chrom doesn't exists in sam dictionary.");
            return -1;
        }
        LOG.info("Interval is " + this.interval);
        loadVCFs();
        if (this.knownGeneUrl != null) {
            IntervalTreeMap<List<KnownGene>> map = KnownGene.loadUriAsIntervalTreeMap(this.knownGeneUrl, (KG) -> (KG.getContig().equals(this.interval.getContig()) && !(KG.getEnd() < this.interval.getStart() || KG.getStart() + 1 > this.interval.getEnd())));
            this.knownGenes.addAll(map.values().stream().flatMap(L -> L.stream()).collect(Collectors.toList()));
        }
        for (final String bamFile : IOUtils.unrollFiles(args)) {
            samFileReader = srf.open(SamInputResource.of(bamFile));
            final SAMFileHeader header = samFileReader.getFileHeader();
            final SAMSequenceDictionary dict = header.getSequenceDictionary();
            if (dict == null) {
                LOG.error("no dict in " + bamFile);
                return -1;
            }
            if (dict.getSequence(this.interval.getContig()) == null) {
                LOG.error("no such chromosome in " + bamFile + " " + this.interval);
                return -1;
            }
            scan(samFileReader);
            samFileReader.close();
            samFileReader = null;
        }
        if (this.key2partition.isEmpty()) {
            LOG.error("No data was found. no Read-Group specified ? no data in that region ?");
            return -1;
        }
        this.key2partition.values().stream().forEach(P -> P.make());
        saveImages(this.key2partition.values().stream().map(P -> P.image).collect(Collectors.toList()));
        return RETURN_OK;
    } catch (final Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(samFileReader);
    }
}