Java Code Examples for htsjdk.samtools.SAMReadGroupRecord#getLibrary()

/**
 * Method takes a ReadGroup record and a partition type and returns the appropriate summary string for displaying in output tables.
 * Since each partition type has its own pattern for separating out readgroups this method is intended to handle all of the
 * processing for regroups so that outputs can be properly partitioned in all cases.
 *
 * @param rg readGroupRecord to be processed.
 * @param type partition type to generate read group string for.
 */
public static String getTypeID(final SAMReadGroupRecord rg, final DoCOutputType.Partition type ) {
    switch (type) {
        case sample:
            return rg.getSample();
        case readgroup:
            return rg.getSample()+"_rg_"+rg.getReadGroupId();
        case library:
            return rg.getLibrary();
        case center:
            return rg.getSequencingCenter();
        case platform:
            return rg.getPlatform();
        case sample_by_center:
            return rg.getSample()+"_cn_"+rg.getSequencingCenter();
        case sample_by_platform:
            return rg.getSample()+"_pl_"+rg.getPlatform();
        case sample_by_platform_by_center:
            return rg.getSample()+"_pl_"+rg.getPlatform()+"_cn_"+rg.getSequencingCenter();
        default:
            throw new GATKException(String.format("Invalid aggregation type %s", type));
    }
}
 

/**
 * Gets the library name from the header for the record. If the RG tag is not present on
 * the record, or the library isn't denoted on the read group, a constant string is
 * returned.
 */
public static String getLibraryName(final SAMFileHeader header, final SAMRecord rec) {
    final String readGroupId = (String) rec.getAttribute(ReservedTagConstants.READ_GROUP_ID);

    if (readGroupId != null) {
        final SAMReadGroupRecord rg = header.getReadGroup(readGroupId);
        if (rg != null) {
            final String libraryName = rg.getLibrary();
            if (null != libraryName) return libraryName;
        }
    }

    return UNKNOWN_LIBRARY;
}
 

/**
 * Gets the library name from the header for the read group id. If the read group id is null
 * or the library isn't denoted on the read group, a constant string is
 * returned.
 */
public static String getLibraryName(final SAMFileHeader header, String readGroupId) {
  if (readGroupId != null) {
        final SAMReadGroupRecord rg = header.getReadGroup(readGroupId);
        if (rg != null) {
            final String libraryName = rg.getLibrary();
            if (null != libraryName) return libraryName;
        }
    }

    return UNKNOWN_LIBRARY;
}
 

/**
 * Returns the library associated with the provided read's read group.
 * Or the specified default if no library is found
 *
 * @param read read whose library to retrieve
 * @param header SAM header containing read groups
 * @return the library for the provided read's read group as a String,
 *         or the default value if the read has no read group.
 */
public static String getLibraryForRead(final GATKRead read, final SAMFileHeader header, String defaultLibrary) {
    final SAMReadGroupRecord readGroup = ReadUtils.getSAMReadGroupRecord(read, header);
    if (readGroup != null) {
        String library = readGroup.getLibrary();
        return library==null? defaultLibrary : library;
    } else {
        if (read.getReadGroup() == null) {
            throw new UserException.ReadMissingReadGroup(read);
        } else {
            throw new UserException.HeaderMissingReadGroup(read);
        }
    }
}
 

public FingerprintIdDetails(final SAMReadGroupRecord rg, final String file) {
    this(rg.getPlatformUnit(), file);
    this.sample = rg.getSample();
    this.library = rg.getLibrary();
}
 

@Override
protected String getKey(SAMReadGroupRecord rg) {
    return rg.getLibrary();
}
 

@Override
protected String getKey(SAMReadGroupRecord rg) {
    return rg.getLibrary();
}
 

@Override
protected String getKey(SAMReadGroupRecord rg) {
    return rg.getLibrary();
}
 

/**
 * Takes an AlignmentContext object and extracts all the reads that pass the provided filters, and then returns a
 * count breakdown for each base (plus D and N bases) present at the site.
 *
 * NOTE: this currently doesn't support counts by fragments as was the case in gatk3
 */
private static Map<SAMReadGroupRecord,int[]> getBaseCountsByReadGroup(final AlignmentContext context, final byte minBaseQ, final byte maxBaseQ, final CountPileupType countType, final SAMFileHeader header) {
    Map<SAMReadGroupRecord, int[]> countsByRG = new HashMap<>();

    Map<String, int[]> countsByRGName = new HashMap<>();
    Map<String, SAMReadGroupRecord> RGByName = new HashMap<>();

    List<PileupElement> countPileup = new ArrayList<>(context.getBasePileup().size());

    switch (countType) {

        case COUNT_READS:
            for (PileupElement read : context.getBasePileup()) {
                if (elementWithinQualRange(read, minBaseQ, maxBaseQ)) {
                    countPileup.add(read);
                }
            }
            break;

        // TODO see reconcile FragmentUtils.create() and its various idiosyncrasies to re-enable this feature see https://github.com/broadinstitute/gatk/issues/6491
        case COUNT_FRAGMENTS: // ignore base identities and put in FIRST base that passes filters:
            throw new UnsupportedOperationException("Fragment based counting is currently unsupported");

        case COUNT_FRAGMENTS_REQUIRE_SAME_BASE:
            throw new UnsupportedOperationException("Fragment based counting is currently unsupported");

        default:
            throw new UserException("Must use valid CountPileupType");
    }

    for (PileupElement e : countPileup) {
        SAMReadGroupRecord readGroup = ReadUtils.getSAMReadGroupRecord(e.getRead(), header);
        Utils.nonNull(readGroup, String.format("Read %s was missing read group information", e.getRead()));

        // uniqueReadGroupID is unique across the library, read group ID, and the sample
        String uniqueReadGroupId = readGroup.getSample() + "_" + readGroup.getReadGroupId() + "_" + readGroup.getLibrary() + "_" + readGroup.getPlatformUnit();
        int[] counts = countsByRGName.get(uniqueReadGroupId);
        if (counts == null) {
            counts = new int[6];
            countsByRGName.put(uniqueReadGroupId, counts);
            RGByName.put(uniqueReadGroupId, readGroup);
        }

        updateCounts(counts, e);
    }

    for (String readGroupId : RGByName.keySet()) {
        countsByRG.put(RGByName.get(readGroupId), countsByRGName.get(readGroupId));
    }

    return countsByRG;
}