Java SAMFileHeader.getSortOrder方法代码示例

import htsjdk.samtools.SAMFileHeader; //导入方法依赖的package包/类
private SAMFileHeader loadHeaders(){
    List<SAMFileHeader> headersList = new ArrayList<SAMFileHeader>();
    SAMFileHeader.SortOrder sortOrder = null;
    for(AlignmentReader reader: readers){
        SAMFileHeader curHeader = reader.getFileHeader();
        if(curHeader != null) {
            headersList.add(curHeader);
            sortOrder = curHeader.getSortOrder();
        }
    }
    if(sortOrder != null){
        SamFileHeaderMerger headerMerger = new SamFileHeaderMerger(sortOrder, headersList, true);
        return headerMerger.getMergedHeader();
    }

    return null;
}
 

import htsjdk.samtools.SAMFileHeader; //导入方法依赖的package包/类
@Override
public void onTraversalStart() {
    final SAMFileHeader headerFromReads = getHeaderForReads();
    // log some information for errors
    final SAMFileHeader.SortOrder order = headerFromReads.getSortOrder();
    if (order.equals(SAMFileHeader.SortOrder.coordinate) || order
            .equals(SAMFileHeader.SortOrder.duplicate)) {
        logger.warn(
                "Input is sorted by {} and ReadTools does not handle FASTQ files in this order.",
                order);
        logger.warn(
                "FASTQ output files are expected to be sorted by queryname, and this could cause downstream problems");
        headerFromReads.setSortOrder(SAMFileHeader.SortOrder.queryname);
    }
    writer = outputBamArgumentCollection.outputWriter(headerFromReads,
            () -> getProgramRecord(headerFromReads), true, getReferenceFile()
    );
}
 

import htsjdk.samtools.SAMFileHeader; //导入方法依赖的package包/类
/**
 * Returns {@code true} if the parameters suggest that the files are pre-sorted; {@code false}
 * otherwise.
 *
 * @param header header for checking the sort order.
 */
private boolean isPresorted(final SAMFileHeader header) {
    // if the requested order is unsorted
    return SAMFileHeader.SortOrder.unsorted == sortOrder
            // if the header is the same sort order than the one requested
            || header.getSortOrder() == sortOrder;
}
 

import htsjdk.samtools.SAMFileHeader; //导入方法依赖的package包/类
private SAMFileHeader getSamFileHeader(final ReadsSourceHandler handler) {
    final SAMFileHeader header = handler.getHeader();
    SAMFileHeader.SortOrder order = header.getSortOrder();
    SAMFileHeader.GroupOrder groupOrder = header.getGroupOrder();
    if (isPaired()) {
        switch (order) {
            // both coordinate/duplicate sorting are not allowed here if it is paired
            case coordinate:
            case duplicate:
                throw new UserException.BadInput(String.format(
                        "Pair-end read source %s sorted by '%s'. ReadTools requires pairs to be together: either sorted or grouped by queryname.",
                        handler.getHandledSource(), order));
            // both unsorted and unknown
            case unsorted:
            case unknown:
                logger.warn(
                        "Pair-end read source {} with '{}' order grouped by '{}': Assuming that reads are grouped by {} (keeping pairs together).",
                        handler.getHandledSource(), order, groupOrder, SAMFileHeader.GroupOrder.query);
                order = SAMFileHeader.SortOrder.unsorted;
                groupOrder = SAMFileHeader.GroupOrder.query;
                break;
            case queryname:
                // TODO - remove this limitation
                logger.warn("Output might reflect '%s' even if '%s' is specified in pair-end source %s. This limitation may be removed in the future.",
                        order, SAMFileHeader.SortOrder.queryname, handler.getHandledSource());
                break;
            default:
                throw new GATKException("Unknown sort order: " + header.getSortOrder());
        }
    }

    // log always a warning for queryname order
    if (SAMFileHeader.SortOrder.queryname.equals(order)) {
        logger.warn(
                "Sort order by '{}' is assumed to follow the Picard specifications. This limitation may be removed in the future.",
                SAMFileHeader.SortOrder.queryname);
    }

    // finally, set the sort order
    header.setSortOrder(order);
    // this should be done like this because of a null pointer exception
    if (! SAMFileHeader.GroupOrder.none.equals(groupOrder)) {
        header.setGroupOrder(groupOrder);
    }

    return header;
}