Examples with TargetTableReader org.broadinstitute.hellbender.tools.exome.TargetTableReader used on opensource projects

Example 1 with TargetTableReader

use of org.broadinstitute.hellbender.tools.exome.TargetTableReader in project gatk by broadinstitute.

the class TargetCodec method canDecode.

@Override
public boolean canDecode(final String path) {
    File file;
    try {
        // Use the URI constructor so that we can handle file:// URIs
        final URI uri = new URI(path);
        file = uri.isAbsolute() ? new File(uri) : new File(path);
    } catch (Exception e) {
        // Contract for canDecode() mandates that all exception be trapped
        return false;
    }
    if (!file.canRead() || !file.isFile()) {
        return false;
    }
    try {
        new TargetTableReader(file).close();
    } catch (final IOException | RuntimeException ex) {
        // whereas RuntimeException would be caused by a formatting error in the file.
        return false;
    }
    //disallow .bed extension
    final String toDecode = AbstractFeatureReader.hasBlockCompressedExtension(path) ? path.substring(0, path.lastIndexOf(".")) : path;
    return !toDecode.toLowerCase().endsWith(BED_EXTENSION);
}

Example 2 with TargetTableReader

use of org.broadinstitute.hellbender.tools.exome.TargetTableReader in project gatk-protected by broadinstitute.

the class TargetCodec method canDecode.

@Override
public boolean canDecode(final String path) {
    File file;
    try {
        // Use the URI constructor so that we can handle file:// URIs
        final URI uri = new URI(path);
        file = uri.isAbsolute() ? new File(uri) : new File(path);
    } catch (Exception e) {
        // Contract for canDecode() mandates that all exception be trapped
        return false;
    }
    if (!file.canRead() || !file.isFile()) {
        return false;
    }
    try {
        new TargetTableReader(file).close();
    } catch (final IOException | RuntimeException ex) {
        // whereas RuntimeException would be caused by a formatting error in the file.
        return false;
    }
    //disallow .bed extension
    final String toDecode = AbstractFeatureReader.hasBlockCompressedExtension(path) ? path.substring(0, path.lastIndexOf(".")) : path;
    return !toDecode.toLowerCase().endsWith(BED_EXTENSION);
}