Examples with RuntimeIOException htsjdk.samtools.util.RuntimeIOException used on opensource projects

Example 11 with RuntimeIOException

use of htsjdk.samtools.util.RuntimeIOException in project jvarkit by lindenb.

the class VcfCalledWithAnotherMethod method doVcfToVcf.

protected int doVcfToVcf(final String inputName, final VcfIterator in, final VariantContextWriter out) {
    final List<ExternalVcf> externalVcfs = new ArrayList<>();
    try {
        final VCFHeader header = in.getHeader();
        this.dictionary = header.getSequenceDictionary();
        /**
         * open primitive input
         */
        if (this.dictionary == null) {
            LOG.error("no dictionary in input");
            return -1;
        }
        final Set<File> samtoolsFiles = new HashSet<>();
        this.externalVcfStrs.stream().filter(S -> S.endsWith(".list")).map(S -> Paths.get(S)).forEach(P -> {
            try {
                samtoolsFiles.addAll(Files.readAllLines(P).stream().filter(L -> !(L.startsWith("#") || L.trim().isEmpty())).map(S -> new File(S)).collect(Collectors.toSet()));
            } catch (final Exception err) {
                throw new RuntimeIOException(err);
            }
        });
        samtoolsFiles.addAll(this.externalVcfStrs.stream().filter(S -> !S.endsWith(".list")).map(S -> new File(S)).collect(Collectors.toSet()));
        externalVcfs.addAll(samtoolsFiles.stream().map(F -> new ExternalVcf(F)).collect(Collectors.toList()));
        /**
         * check for uniq keys
         */
        final Set<String> uniqKeys = new HashSet<>();
        for (final ExternalVcf extvcf : externalVcfs) {
            int n = 0;
            for (; ; ) {
                final String newkey = extvcf.key + (n == 0 ? "" : "_" + n);
                if (!uniqKeys.contains(newkey)) {
                    extvcf.key = newkey;
                    uniqKeys.add(newkey);
                    break;
                }
                ++n;
            }
        }
        final VCFHeader h2 = new VCFHeader(header);
        for (final ExternalVcf extvcf : externalVcfs) {
            h2.addMetaDataLine(new VCFHeaderLine("otherVcf:" + extvcf.key, extvcf.vcfFile.getPath()));
        }
        final VCFFilterHeaderLine variantNotFoundElsewhereFILTER = (filterNameVariantNotFoundElseWhere.isEmpty() ? null : new VCFFilterHeaderLine(filterNameVariantNotFoundElseWhere, "Variant Was not found in other VCFs: " + externalVcfs.stream().map(S -> S.vcfFile.getPath()).collect(Collectors.joining(", "))));
        if (variantNotFoundElsewhereFILTER != null) {
            h2.addMetaDataLine(variantNotFoundElsewhereFILTER);
        }
        final VCFInfoHeaderLine variantFoundElseWhereKeys = new VCFInfoHeaderLine(this.infoFoundKey, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "Variant was found in the VCFs designed by those keys");
        h2.addMetaDataLine(variantFoundElseWhereKeys);
        final VCFInfoHeaderLine variantFoundElseWhereCount = new VCFInfoHeaderLine(this.infoFoundKey, 1, VCFHeaderLineType.Integer, "Number of times the Variant was found  in the VCFs");
        h2.addMetaDataLine(variantFoundElseWhereCount);
        final VCFFormatHeaderLine genotypeCountSame = new VCFFormatHeaderLine(this.formatCountSame, 1, VCFHeaderLineType.Integer, "Number of times the Genotype was found the same in other VCFs");
        h2.addMetaDataLine(genotypeCountSame);
        final VCFFormatHeaderLine genotypeCountDiscordant = new VCFFormatHeaderLine(this.formatCountDiscordant, 1, VCFHeaderLineType.Integer, "Number of times the Genotype was found dicordant in other VCFs");
        h2.addMetaDataLine(genotypeCountDiscordant);
        super.addMetaData(h2);
        final VariantContextWriter w = super.openVariantContextWriter(outputFile);
        w.writeHeader(h2);
        final SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(this.dictionary);
        while (in.hasNext()) {
            final VariantContext ctx = progress.watch(in.next());
            final List<GenotypeCount> genotypeCounts = ctx.getGenotypes().stream().map(G -> new GenotypeCount(G)).collect(Collectors.toList());
            final VariantContextBuilder vcb = new VariantContextBuilder(ctx);
            final Set<String> variantFoundInOtherVcfs = new HashSet<>();
            for (final ExternalVcf extvcf : externalVcfs) {
                final List<VariantContext> otherVariants = extvcf.get(ctx);
                if (otherVariants.stream().filter(CTX2 -> {
                    if (ctx.getAlternateAlleles().isEmpty())
                        return true;
                    for (final Allele a : ctx.getAlternateAlleles()) {
                        if (CTX2.hasAllele(a))
                            return true;
                    }
                    return false;
                }).findAny().isPresent()) {
                    variantFoundInOtherVcfs.add(extvcf.key);
                }
                for (final GenotypeCount gt : genotypeCounts) {
                    for (final VariantContext otherVariant : otherVariants) {
                        final Genotype otherGt = otherVariant.getGenotype(gt.gt.getSampleName());
                        if (otherGt == null)
                            continue;
                        if (gt.gt.sameGenotype(otherGt) || (this.noCallSameAsHomRef && ((gt.gt.isNoCall() && otherGt.isHomRef()) || (gt.gt.isHomRef() && otherGt.isNoCall())))) {
                            gt.countSame++;
                        } else {
                            gt.countDiscordant++;
                        }
                    }
                }
            }
            vcb.genotypes(genotypeCounts.stream().map(G -> {
                final GenotypeBuilder gb = new GenotypeBuilder(G.gt);
                gb.attribute(genotypeCountSame.getID(), G.countSame);
                gb.attribute(genotypeCountDiscordant.getID(), G.countDiscordant);
                return gb.make();
            }).collect(Collectors.toList()));
            vcb.attribute(variantFoundElseWhereCount.getID(), variantFoundInOtherVcfs.size());
            if (variantFoundInOtherVcfs.isEmpty()) {
                if (variantNotFoundElsewhereFILTER != null) {
                    vcb.filter(variantNotFoundElsewhereFILTER.getID());
                }
            } else {
                if (variantNotFoundElsewhereFILTER != null && !ctx.isFiltered()) {
                    vcb.passFilters();
                }
                vcb.attribute(variantFoundElseWhereKeys.getID(), new ArrayList<>(variantFoundInOtherVcfs));
            }
            w.add(vcb.make());
        }
        progress.finish();
        while (!externalVcfs.isEmpty()) externalVcfs.remove(0).close();
        return RETURN_OK;
    } catch (Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        while (!externalVcfs.isEmpty()) externalVcfs.remove(0).close();
    }
}

Example 12 with RuntimeIOException

use of htsjdk.samtools.util.RuntimeIOException in project jvarkit by lindenb.

the class PubmedOrcidGraph method dumpGexf.

private void dumpGexf() {
    final XMLOutputFactory xof = XMLOutputFactory.newFactory();
    PrintWriter pw = null;
    XMLStreamWriter w = null;
    DatabaseEntry key = new DatabaseEntry();
    DatabaseEntry data = new DatabaseEntry();
    Cursor c = null;
    try {
        pw = openFileOrStdoutAsPrintWriter(this.outputFile);
        w = xof.createXMLStreamWriter(pw);
        w.writeStartDocument("UTF-8", "1.0");
        w.writeStartElement("gexf");
        w.writeAttribute("xmlns", GexfConstants.XMLNS);
        w.writeAttribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance");
        w.writeAttribute("xsi:schemaLocation", GexfConstants.XSI_SCHEMA_LOCATION);
        w.writeAttribute("version", GexfConstants.VERSION);
        /* meta */
        w.writeStartElement("meta");
        w.writeAttribute("lastmodifieddate", "2017-04-03");
        w.writeStartElement("creator");
        w.writeCharacters("PumedOrcidGraph");
        w.writeEndElement();
        w.writeStartElement("description");
        w.writeCharacters("PumedOrcidGraph");
        w.writeEndElement();
        w.writeEndElement();
        /* graph */
        w.writeStartElement("graph");
        w.writeAttribute("mode", "static");
        w.writeAttribute("defaultedgetype", "undirected");
        /* attributes */
        w.writeStartElement("attributes");
        w.writeAttribute("class", "node");
        w.writeAttribute("mode", "static");
        gexfAttDecl(w, "orcid", "string");
        gexfAttDecl(w, "foreName", "string");
        gexfAttDecl(w, "lastName", "string");
        gexfAttDecl(w, "initials", "string");
        gexfAttDecl(w, "affiliation", "string");
        // attributes
        w.writeEndElement();
        if (!this.hide_edge_attributes) {
            w.writeStartElement("attributes");
            w.writeAttribute("class", "edge");
            w.writeAttribute("mode", "static");
            gexfAttDecl(w, "pmid", "string");
            gexfAttDecl(w, "title", "string");
            gexfAttDecl(w, "doi", "string");
            gexfAttDecl(w, "year", "string");
            gexfAttDecl(w, "journal", "string");
            // attributes
            w.writeEndElement();
        }
        /* nodes */
        w.writeStartElement("nodes");
        c = this.authorDatabase.openCursor(txn, null);
        while (c.getNext(key, data, LockMode.DEFAULT) == OperationStatus.SUCCESS) {
            final Author au = this.authorBinding.entryToObject(data);
            if (NAME_NOT_FOUND.equals(au.foreName)) {
                w.writeComment("Orcid " + au.orcid + " not found in pubmed");
                continue;
            }
            au.gexf(w);
        }
        c.close();
        // nodes
        w.writeEndElement();
        w.writeStartElement("edges");
        key = new DatabaseEntry();
        c = this.linkDatabase.openCursor(txn, null);
        while (c.getNext(key, data, LockMode.DEFAULT) == OperationStatus.SUCCESS) {
            final Link L = this.linkBinding.entryToObject(data);
            w.writeStartElement("edge");
            w.writeAttribute("id", "E" + (++ID_GENERATOR));
            w.writeAttribute("type", "undirected");
            w.writeAttribute("weight", String.valueOf(L.pmids.size()));
            w.writeAttribute("source", L.orcid1);
            w.writeAttribute("target", L.orcid2);
            for (String pmid : L.pmids) {
                DatabaseEntry key2 = new DatabaseEntry();
                DatabaseEntry data2 = new DatabaseEntry();
                StringBinding.stringToEntry(pmid, key2);
                if (this.articleDatabase.get(txn, key2, data2, LockMode.DEFAULT) != OperationStatus.SUCCESS) {
                    throw new JvarkitException.BerkeleyDbError("cannot get article");
                }
                final Article article = this.articleBinding.entryToObject(data2);
                if (this.all_links_between_authors) {
                    w.writeAttribute("label", String.valueOf(L.pmids.size()));
                } else {
                    w.writeAttribute("label", "" + article.ArticleTitle + ". " + article.ISOAbbreviation + ". (" + article.Year + ")");
                }
                if (!this.hide_edge_attributes) {
                    w.writeStartElement("attributes");
                    w.writeEmptyElement("attribute");
                    w.writeAttribute("for", "pmid");
                    w.writeAttribute("value", article.pmid);
                    w.writeEmptyElement("attribute");
                    w.writeAttribute("for", "title");
                    w.writeAttribute("value", article.ArticleTitle);
                    w.writeEmptyElement("attribute");
                    w.writeAttribute("for", "doi");
                    w.writeAttribute("value", article.doi);
                    w.writeEmptyElement("attribute");
                    w.writeAttribute("for", "year");
                    w.writeAttribute("value", article.Year);
                    w.writeEmptyElement("attribute");
                    w.writeAttribute("for", "journal");
                    w.writeAttribute("value", article.ISOAbbreviation);
                    // attributes
                    w.writeEndElement();
                }
                break;
            }
            // 
            // edge
            w.writeEndElement();
        }
        c.close();
        // edges
        w.writeEndElement();
        w.writeEndElement();
        w.writeEndDocument();
        w.flush();
        pw.flush();
        pw.close();
        pw = null;
    } catch (Exception err) {
        throw new RuntimeIOException(err);
    } finally {
        CloserUtil.close(w);
        CloserUtil.close(pw);
    }
}

Example 13 with RuntimeIOException

use of htsjdk.samtools.util.RuntimeIOException in project gatk by broadinstitute.

the class NormalizeFasta method doWork.

@Override
protected Object doWork() {
    IOUtil.assertFileIsReadable(INPUT);
    IOUtil.assertFileIsWritable(OUTPUT);
    Utils.validateArg(!INPUT.getAbsoluteFile().equals(OUTPUT.getAbsoluteFile()), "Input and output cannot be the same file.");
    try (final ReferenceSequenceFile ref = ReferenceSequenceFileFactory.getReferenceSequenceFile(INPUT, TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE);
        final BufferedWriter out = IOUtil.openFileForBufferedWriting(OUTPUT)) {
        ReferenceSequence seq = null;
        while ((seq = ref.nextSequence()) != null) {
            final String name = seq.getName();
            final byte[] bases = seq.getBases();
            try {
                out.write(">");
                out.write(name);
                out.newLine();
                if (bases.length == 0) {
                    logger.warn("Sequence " + name + " contains 0 bases.");
                } else {
                    for (int i = 0; i < bases.length; ++i) {
                        if (i > 0 && i % LINE_LENGTH == 0)
                            out.write("\n");
                        out.write(bases[i]);
                    }
                    out.write("\n");
                }
            } catch (IOException ioe) {
                throw new RuntimeIOException("Error writing to file " + OUTPUT.getAbsolutePath(), ioe);
            }
        }
    } catch (IOException e) {
        throw new RuntimeIOException(e);
    }
    return null;
}

Example 14 with RuntimeIOException

use of htsjdk.samtools.util.RuntimeIOException in project gatk by broadinstitute.

the class BucketUtils method dirSize.

/**
     * Returns the total file size of all files in a directory, or the file size if the path specifies a file.
     * Note that sub-directories are ignored - they are not recursed into.
     * Only supports HDFS and local paths.
     *
     * @param path The URL to the file or directory whose size to return
     * @return the total size of all files in bytes
     */
public static long dirSize(String path) {
    try {
        // GCS case (would work with local too)
        if (isCloudStorageUrl(path)) {
            java.nio.file.Path p = getPathOnGcs(path);
            return Files.list(p).mapToLong(q -> {
                try {
                    return (Files.isRegularFile(q) ? Files.size(q) : 0);
                } catch (IOException e) {
                    throw new RuntimeIOException(e);
                }
            }).sum();
        }
        // local file or HDFS case
        Path hadoopPath = new Path(path);
        FileSystem fs = new Path(path).getFileSystem(new Configuration());
        FileStatus status = fs.getFileStatus(hadoopPath);
        if (status == null) {
            throw new UserException.CouldNotReadInputFile(path, "File not found.");
        }
        long size = 0;
        if (status.isDirectory()) {
            for (FileStatus st : fs.listStatus(status.getPath())) {
                if (st.isFile()) {
                    size += st.getLen();
                }
            }
        } else {
            size += status.getLen();
        }
        return size;
    } catch (RuntimeIOException | IOException e) {
        throw new UserException("Failed to determine total input size of " + path + "\n Caused by:" + e.getMessage(), e);
    }
}

Example 15 with RuntimeIOException

use of htsjdk.samtools.util.RuntimeIOException in project gatk by broadinstitute.

the class AbstractInputParser method parseLine.

/**
     * This method represents the most efficient way (so far) to parse a line of whitespace-delimited text
     *
     * @param line the line to parse
     * @return  an array of all the "words"
     */
private String[] parseLine(final byte[] line) {
    if (getWordCount() == 0) {
        calculateWordCount(line);
    }
    final String[] parts = new String[getWordCount()];
    boolean delimiter = true;
    int index = 0;
    int start = 0;
    try {
        for (int i = 0; i < line.length; i++) {
            if (isDelimiter(line[i])) {
                if (!delimiter) {
                    parts[index++] = new String(line, start, i - start);
                } else if (!isTreatGroupedDelimitersAsOne()) {
                    parts[index++] = null;
                }
                delimiter = true;
            } else {
                if (delimiter)
                    start = i;
                delimiter = false;
            }
        }
        if (!delimiter) {
            parts[index] = new String(line, start, line.length - start);
        }
    } catch (ArrayIndexOutOfBoundsException e) {
        throw new RuntimeIOException("Unexpected number of elements found when parsing file " + this.getFileName() + ": " + index + ".  Expected a maximum of " + this.getWordCount() + " elements per line:" + new String(line, 0, line.length), e);
    }
    return parts;
}