Java SAMSequenceDictionary.getSequenceIndex方法代码示例

import htsjdk.samtools.SAMSequenceDictionary; //导入方法依赖的package包/类
/**
 * Converts an interval in SimpleInterval format into an htsjdk QueryInterval.
 *
 * In doing so, a header lookup is performed to convert from contig name to index
 *
 * @param interval interval to convert
 * @param sequenceDictionary sequence dictionary used to perform the conversion
 * @return an equivalent interval in QueryInterval format
 */
private static QueryInterval convertSimpleIntervalToQueryInterval( final Interval interval,	final SAMSequenceDictionary sequenceDictionary ) {
	if (interval == null) {
		throw new IllegalArgumentException("interval may not be null");
	}
	if (sequenceDictionary == null) {
		throw new IllegalArgumentException("sequence dictionary may not be null");
	}

	final int contigIndex = sequenceDictionary.getSequenceIndex(interval.getContig());
	if ( contigIndex == -1 ) {
		throw new IllegalArgumentException("Contig " + interval.getContig() + " not present in reads sequence " +
				"dictionary");
	}

	return new QueryInterval(contigIndex, interval.getStart(), interval.getEnd());
}
 

import htsjdk.samtools.SAMSequenceDictionary; //导入方法依赖的package包/类
/** Read a file of contig names that will be ignored when checking for inter-contig pairs. */
private static Set<Integer> readCrossContigsToIgnoreFile( final String crossContigsToIgnoreFile,
                                                          final SAMSequenceDictionary dictionary ) {
    final Set<Integer> ignoreSet = new HashSet<>();
    try ( final BufferedReader rdr =
                  new BufferedReader(
                          new InputStreamReader(BucketUtils.openFile(crossContigsToIgnoreFile))) ) {
        String line;
        while ( (line = rdr.readLine()) != null ) {
            final int tigId = dictionary.getSequenceIndex(line);
            if ( tigId == -1 ) {
                throw new UserException("crossContigToIgnoreFile contains an unrecognized contig name: "+line);
            }
            ignoreSet.add(tigId);
        }
    }
    catch ( final IOException ioe ) {
        throw new UserException("Can't read crossContigToIgnore file "+crossContigsToIgnoreFile, ioe);
    }
    return ignoreSet;
}
 

import htsjdk.samtools.SAMSequenceDictionary; //导入方法依赖的package包/类
public static int compareContigs(final GenomeLocation first, final GenomeLocation second, final SAMSequenceDictionary dictionary) {
    Utils.nonNull(first);
    Utils.nonNull(second);
    Utils.nonNull(dictionary);

    final int firstRefIndex = dictionary.getSequenceIndex(first.getContig());
    final int secondRefIndex = dictionary.getSequenceIndex(second.getContig());
    if (firstRefIndex == -1 || secondRefIndex == -1) {
        throw new IllegalArgumentException("Can't do comparison because Locatables' contigs not found in sequence dictionary");
    }
    // compare the contigs
    return Integer.compare(firstRefIndex, secondRefIndex);
}
 

import htsjdk.samtools.SAMSequenceDictionary; //导入方法依赖的package包/类
static Location parseLocationString(final String location, final SAMSequenceDictionary dictionary) throws RuntimeException {
    final Location result = new Location();

    final String[] split = location.split(":");
    if (split.length != 2) {
        throw new RuntimeException(location + " is not a valid location string");
    }

    final String chromosome = split[0];
    result.ReferenceName = chromosome;
    try {
        result.Position = Integer.parseInt(split[1]);
    } catch (NumberFormatException e) {
        throw new RuntimeException(location + " is not a valid location string");
    }

    // query the position
    result.ReferenceIndex = dictionary.getSequenceIndex(chromosome);
    if (result.ReferenceIndex < 0) {
        if (!chromosome.startsWith("chr")) {
            result.ReferenceIndex = dictionary.getSequenceIndex("chr" + chromosome);
        } else {
            result.ReferenceIndex = dictionary.getSequenceIndex(chromosome.substring(3));
        }
    }
    if (result.ReferenceIndex < 0) {
        throw new RuntimeException(chromosome + " is not in the BAM");
    }

    return result;
}
 

import htsjdk.samtools.SAMSequenceDictionary; //导入方法依赖的package包/类
public int compareLoci(ReadsAtLocus that, SAMSequenceDictionary dict) {
	int compare = dict.getSequenceIndex(this.getChromosome()) - dict.getSequenceIndex(that.getChromosome());
	if (compare == 0) {
		compare = this.getPosition() - that.getPosition();
	}
	
	return compare;
}
 

import htsjdk.samtools.SAMSequenceDictionary; //导入方法依赖的package包/类
/**
 * @return <code>true</code> if the locatable is to the right of the given interval
 */
private static <I extends Locatable, L extends Locatable> boolean toRightOf(I interval, L locatable, SAMSequenceDictionary sequenceDictionary) {
    int intervalContigIndex = sequenceDictionary.getSequenceIndex(interval.getContig());
    int locatableContigIndex = sequenceDictionary.getSequenceIndex(locatable.getContig());
    return (intervalContigIndex == locatableContigIndex && interval.getEnd() < locatable.getStart()) // locatable on same contig, to the right
            || intervalContigIndex < locatableContigIndex; // locatable on subsequent contig
}
 

import htsjdk.samtools.SAMSequenceDictionary; //导入方法依赖的package包/类
/**
 * Determines the relative contig ordering of first and second using the provided sequence dictionary
 *
 * @param first first Locatable
 * @param second second Locatable
 * @param dictionary sequence dictionary used to determine contig ordering
 * @return 0 if the two contigs are the same, a negative value if first's contig comes before second's contig,
 *         or a positive value if first's contig comes after second's contig
 */
public static int compareContigs(final Locatable first, final Locatable second, final SAMSequenceDictionary dictionary) {
    Utils.nonNull(first);
    Utils.nonNull(second);
    Utils.nonNull(dictionary);

    final int firstRefIndex = dictionary.getSequenceIndex(first.getContig());
    final int secondRefIndex = dictionary.getSequenceIndex(second.getContig());
    if (firstRefIndex == -1 || secondRefIndex == -1) {
        throw new IllegalArgumentException("Can't do comparison because Locatables' contigs not found in sequence dictionary");
    }
    // compare the contigs
    return Integer.compare(firstRefIndex, secondRefIndex);
}
 

import htsjdk.samtools.SAMSequenceDictionary; //导入方法依赖的package包/类
/**
 * Converts an interval in SimpleInterval format into an htsjdk QueryInterval.
 *
 * In doing so, a header lookup is performed to convert from contig name to index
 *
 * @param interval interval to convert
 * @param sequenceDictionary sequence dictionary used to perform the conversion
 * @return an equivalent interval in QueryInterval format
 */
public static QueryInterval convertSimpleIntervalToQueryInterval( final SimpleInterval interval, final SAMSequenceDictionary sequenceDictionary ) {
    Utils.nonNull(interval);
    Utils.nonNull(sequenceDictionary);

    final int contigIndex = sequenceDictionary.getSequenceIndex(interval.getContig());
    if ( contigIndex == -1 ) {
        throw new UserException("Contig " + interval.getContig() + " not present in reads sequence dictionary");
    }

    return new QueryInterval(contigIndex, interval.getStart(), interval.getEnd());
}
 

import htsjdk.samtools.SAMSequenceDictionary; //导入方法依赖的package包/类
public static SVIntervalTree<String> readBreakpointsFromTruthVCF(final String truthVCF,
                                                                 final SAMSequenceDictionary dictionary,
                                                                 final int padding ) {
    SVIntervalTree<String> breakpoints = new SVIntervalTree<>();
    try ( final FeatureDataSource<VariantContext> dataSource =
                  new FeatureDataSource<>(truthVCF, null, 0, VariantContext.class) ) {
        for ( final VariantContext vc : dataSource ) {
            final StructuralVariantType svType = vc.getStructuralVariantType();
            if ( svType == null ) continue;
            final String eventName = vc.getID();
            final int contigID = dictionary.getSequenceIndex(vc.getContig());
            if ( contigID < 0 ) {
                throw new UserException("VCF contig " + vc.getContig() + " does not appear in dictionary.");
            }
            final int start = vc.getStart();
            switch ( svType ) {
                case DEL:
                case INV:
                case CNV:
                    final int end = vc.getEnd();
                    breakpoints.put(new SVInterval(contigID,start-padding, end+padding), eventName);
                    break;
                case INS:
                case DUP:
                case BND:
                    breakpoints.put(new SVInterval(contigID,start-padding, start+padding), eventName);
                    break;
            }
        }
    }
    return breakpoints;
}
 

import htsjdk.samtools.SAMSequenceDictionary; //导入方法依赖的package包/类
public void parseSJString(String sjString, SAMSequenceDictionary dict) {
    String columns[] = sjString.split("\t");
    this.type = -1;
    this.secondary_key = dict.getSequenceIndex(columns[0]);
}