Java Code Examples for htsjdk.samtools.util.StringUtil#isBlank()

/** Returns read baseName and asserts correct pair read name format:
 * <ul>
 * <li> Paired reads must either have the exact same read names or they must contain at least one "/"
 * <li> and the First pair read name must end with "/1" and second pair read name ends with "/2"
 * <li> The baseName (read name part before the /) must be the same for both read names
 * <li> If the read names are exactly the same but end in "/2" or "/1" then an exception will be thrown
 * </ul>
 */
String getBaseName(final String readName1, final String readName2, final FastqReader freader1, final FastqReader freader2) {
    String [] toks = getReadNameTokens(readName1, 1, freader1);
    final String baseName1 = toks[0] ;
    final String num1 = toks[1] ;

    toks = getReadNameTokens(readName2, 2, freader2);
    final String baseName2 = toks[0] ;
    final String num2 = toks[1];

    if (!baseName1.equals(baseName2)) {
        throw new PicardException(String.format("In paired mode, read name 1 (%s) does not match read name 2 (%s)", baseName1,baseName2));
    }

    final boolean num1Blank = StringUtil.isBlank(num1);
    final boolean num2Blank = StringUtil.isBlank(num2);
    if (num1Blank || num2Blank) {
        if(!num1Blank) throw new PicardException(error(freader1,"Pair 1 number is missing (" +readName1+ "). Both pair numbers must be present or neither."));       //num1 != blank and num2   == blank
        else if(!num2Blank) throw new PicardException(error(freader2, "Pair 2 number is missing (" +readName2+ "). Both pair numbers must be present or neither.")); //num1 == blank and num =2 != blank
    } else {
        if (!num1.equals("1")) throw new PicardException(error(freader1,"Pair 1 number must be 1 ("+readName1+")"));
        if (!num2.equals("2")) throw new PicardException(error(freader2,"Pair 2 number must be 2 ("+readName2+")"));
    }

    return baseName1 ;
}
 

/**
 * Load the file ALT_NAMES containing the alternative contig names
 *
 * @return a <code>Map&lt;src_contig,Set&lt;new_names&gt;&gt;</code>. Never null. May be empty if ALT_NAMES is null.
 * @throws PicardException if there is any error in the file ALT_NAMES
 * @author Pierre Lindenbaum
 */
private Map<String, Set<String>> loadContigAliasesMap() throws PicardException {
    // return an empty map if no mapping file was provided
    if (this.ALT_NAMES == null) {
        return Collections.emptyMap();
    }
    // the map returned by the function
    final Map<String, Set<String>> aliasesByContig = new HashMap<>();
    try {
        for (final String line : IOUtil.slurpLines(this.ALT_NAMES)) {
            if (StringUtil.isBlank(line)) {
                continue;
            }
            final int tab = line.indexOf('\t');
            if (tab == -1) {
                throw new IOException("tabulation missing in " + line);
            }
            final String contigName = line.substring(0, tab);
            final String altName = line.substring(tab + 1);
            // check for empty values
            if (StringUtil.isBlank(contigName)) {
                throw new IOException("empty contig in " + line);
            }
            if (StringUtil.isBlank(altName)) {
                throw new IOException("empty alternative name in " + line);
            }
            if (altName.equals(contigName)) {
                continue;
            }
            try {
                SAMSequenceRecord.validateSequenceName(altName);
            } catch (final SAMException exception) {
                throw new IOException("Illegal alternative reference sequence name in " + line, exception);
            }
            // check alias not previously defined as contig
            if (aliasesByContig.containsKey(altName)) {
                throw new IOException("alternate name " + altName +
                        " previously defined as a contig in " + line);
            }
            // check contig not previously defined as alias
            if (aliasesByContig.keySet().stream()
                    // not an error if defined twice for same contig
                    .filter(K -> !K.equals(contigName))
                    .anyMatch(K -> aliasesByContig.get(K).contains(contigName))) {
                throw new IOException("contig  " + contigName +
                        " previously defined as an alternate name in " + line);
            }
            // add alias
            if (!aliasesByContig.containsKey(contigName)) {
                aliasesByContig.put(contigName, new HashSet<>());
            }
            aliasesByContig.get(contigName).add(altName);
        }
        return aliasesByContig;
    } catch (final IOException e) {
        throw new PicardException("Can't read alias file " + ALT_NAMES, e);
    }
}