Examples with TabixFileReader com.github.lindenb.jvarkit.util.tabix.TabixFileReader used on opensource projects

Example 1 with TabixFileReader

use of com.github.lindenb.jvarkit.util.tabix.TabixFileReader in project jvarkit by lindenb.

the class VcfCadd method doWork.

@Override
public int doWork(final List<String> args) {
    try {
        if (this.CADD_FLAG_PHRED.equals(CADD_FLAG_SCORE)) {
            LOG.error("tag phred same as tag score");
            return -1;
        }
        if (this.ccaduri == null || !this.ccaduri.endsWith(".gz")) {
            LOG.error("CCAD uri should end with gz. got " + this.ccaduri);
            return -1;
        }
        LOG.info("Loading index for " + this.ccaduri + ". Please wait...");
        this.tabix = new TabixFileReader(this.ccaduri);
        this.convertToCaddContigs = ContigNameConverter.fromContigSet(this.tabix.getChromosomes());
        LOG.info("End loading index");
        for (; ; ) {
            final String head = this.tabix.readLine();
            if (!head.startsWith("#"))
                break;
            if (head.startsWith("#Chrom\tPos\tRef") || head.startsWith("#Chr\tPos\tRef")) {
                this.headerLabel = Arrays.asList(TAB.split(head));
                break;
            }
        }
        if (this.headerLabel == null || this.headerLabel.isEmpty()) {
            LOG.error("Cannot read tabix file header");
            return -1;
        }
        this.headerLabel2column = new HashMap<>(this.headerLabel.size());
        for (int i = 0; i < this.headerLabel.size(); i++) {
            this.headerLabel2column.put(this.headerLabel.get(i), i);
        }
        Integer col = this.headerLabel2column.get("#Chrom");
        if (col == null)
            col = this.headerLabel2column.get("#Chr");
        if (col == null || col.intValue() != 0) {
            LOG.error("Illegal Header: Cannot get column index of #Chrom at 0");
            return -1;
        }
        col = this.headerLabel2column.get("Pos");
        if (col == null || col.intValue() != 1) {
            LOG.error("Illegal Header: Cannot get column index of 'Pos' at 1");
            return -1;
        }
        col = this.headerLabel2column.get("Ref");
        if (col == null || col.intValue() != 2) {
            LOG.error("Illegal Header: Cannot get column index of 'Ref' at 2");
            return -1;
        }
        col = this.headerLabel2column.get("Alt");
        if (col == null) {
            LOG.error("Illegal Header: Cannot get column index of 'Alt'");
            return -1;
        }
        this.column_index_for_Alt = col.intValue();
        col = this.headerLabel2column.get("RawScore");
        if (col == null) {
            LOG.error("Illegal Header: Cannot get column index of 'RawScore'");
            return -1;
        }
        this.column_index_for_RawScore = col.intValue();
        col = this.headerLabel2column.get("PHRED");
        if (col == null) {
            LOG.error("Illegal Header: Cannot get column index of 'PHRED'");
            return -1;
        }
        this.column_index_for_PHRED = col.intValue();
        for (final String field : this.otherFieldsStr.split("[ \t,;]+")) {
            if (StringUtil.isBlank(field))
                continue;
            col = this.headerLabel2column.get(field);
            if (col == null) {
                LOG.error("Illegal Header: Cannot find user's field " + field + "in " + this.headerLabel);
                return -1;
            }
            this.userFields.add(field);
        }
        return doVcfToVcfPath(args, this.writingVariantsDelegate, this.outputFile);
    } catch (final Throwable err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(tabix);
        tabix = null;
    }
}

Example 2 with TabixFileReader

use of com.github.lindenb.jvarkit.util.tabix.TabixFileReader in project jvarkit by lindenb.

the class SwingIndexCov method buildDefaultDict.

private static SAMSequenceDictionary buildDefaultDict(final Component owner, final String uri) {
    LOG.warn("building default dict for " + uri);
    final Map<String, Integer> contig2len = new LinkedHashMap<>();
    try (TabixFileReader tbr = new TabixFileReader(uri)) {
        for (; ; ) {
            final String line = tbr.readLine();
            if (line == null)
                break;
            if (line.startsWith("#"))
                continue;
            final String[] tokens = CharSplitter.TAB.split(line, 4);
            final String ctg = tokens[0];
            final int len = Math.max(contig2len.getOrDefault(ctg, 0), Integer.parseInt(tokens[2]));
            contig2len.put(ctg, len);
        }
        return new SAMSequenceDictionary(contig2len.entrySet().stream().map(KV -> new SAMSequenceRecord(KV.getKey(), KV.getValue())).collect(Collectors.toList()));
    } catch (final IOException err) {
        throw new RuntimeIOException(err);
    }
}

Example 3 with TabixFileReader

use of com.github.lindenb.jvarkit.util.tabix.TabixFileReader in project jvarkit by lindenb.

the class VcfCadd method beforeVcf.

@Override
protected int beforeVcf() {
    try {
        if (this.CADD_FLAG_PHRED.equals(CADD_FLAG_SCORE)) {
            LOG.error("tag phred same as tag score");
            return -1;
        }
        if (StringUtils.isBlank(this.ccaduri) || !this.ccaduri.endsWith(".gz")) {
            LOG.error("CCAD uri should end with gz. got " + this.ccaduri);
            return -1;
        }
        this.tabix = new TabixFileReader(this.ccaduri);
        this.convertToCaddContigs = ContigNameConverter.fromContigSet(this.tabix.getChromosomes());
        for (; ; ) {
            final String head = this.tabix.readLine();
            if (!head.startsWith("#"))
                break;
            if (head.startsWith("#Chrom\tPos\tRef") || head.startsWith("#Chr\tPos\tRef")) {
                this.headerLabel = Arrays.asList(TAB.split(head));
                break;
            }
        }
        if (this.headerLabel == null || this.headerLabel.isEmpty()) {
            LOG.error("Cannot read tabix file header");
            return -1;
        }
        this.headerLabel2column = new HashMap<>(this.headerLabel.size());
        for (int i = 0; i < this.headerLabel.size(); i++) {
            this.headerLabel2column.put(this.headerLabel.get(i), i);
        }
        Integer col = this.headerLabel2column.get("#Chrom");
        if (col == null)
            col = this.headerLabel2column.get("#Chr");
        if (col == null || col.intValue() != 0) {
            LOG.error("Illegal Header: Cannot get column index of #Chrom at 0");
            return -1;
        }
        col = this.headerLabel2column.get("Pos");
        if (col == null || col.intValue() != 1) {
            LOG.error("Illegal Header: Cannot get column index of 'Pos' at 1");
            return -1;
        }
        col = this.headerLabel2column.get("Ref");
        if (col == null || col.intValue() != 2) {
            LOG.error("Illegal Header: Cannot get column index of 'Ref' at 2");
            return -1;
        }
        col = this.headerLabel2column.get("Alt");
        if (col == null) {
            LOG.error("Illegal Header: Cannot get column index of 'Alt'");
            return -1;
        }
        this.column_index_for_Alt = col.intValue();
        col = this.headerLabel2column.get("RawScore");
        if (col == null) {
            LOG.error("Illegal Header: Cannot get column index of 'RawScore'");
            return -1;
        }
        this.column_index_for_RawScore = col.intValue();
        col = this.headerLabel2column.get("PHRED");
        if (col == null) {
            LOG.error("Illegal Header: Cannot get column index of 'PHRED'");
            return -1;
        }
        this.column_index_for_PHRED = col.intValue();
        for (final String field : this.otherFieldsStr.split("[ \t,;]+")) {
            if (StringUtil.isBlank(field))
                continue;
            col = this.headerLabel2column.get(field);
            if (col == null) {
                LOG.error("Illegal Header: Cannot find user's field " + field + "in " + this.headerLabel);
                return -1;
            }
            this.userFields.add(field);
        }
        return 0;
    } catch (final Throwable err) {
        LOG.error(err);
        return -1;
    }
}