continue; if (record.isUnknownBases()) { record.readBases = SAMRecord.NULL_SEQUENCE; } else {
private static byte[] restoreReadBases(final CramCompressionRecord record, final byte[] ref, final int refOffsetZeroBased, final SubstitutionMatrix substitutionMatrix) { if (record.isUnknownBases() || record.readLength == 0) return SAMRecord.NULL_SEQUENCE; final int readLength = record.readLength;
private static byte[] restoreReadBases(final CramCompressionRecord record, final byte[] ref, final int refOffsetZeroBased, final SubstitutionMatrix substitutionMatrix) { if (record.isUnknownBases() || record.readLength == 0) return SAMRecord.NULL_SEQUENCE; final int readLength = record.readLength; final byte[] bases = new byte[readLength];
private static byte[] restoreReadBases(final CramCompressionRecord record, final byte[] ref, final int refOffsetZeroBased, final SubstitutionMatrix substitutionMatrix) { if (record.isUnknownBases() || record.readLength == 0) return SAMRecord.NULL_SEQUENCE; final int readLength = record.readLength; final byte[] bases = new byte[readLength];
if (record.isUnknownBases()) { record.readBases = SAMRecord.NULL_SEQUENCE; } else
if (record.isUnknownBases()) { record.readBases = SAMRecord.NULL_SEQUENCE; } else
if (record.isUnknownBases()) { record.readBases = SAMRecord.NULL_SEQUENCE; } else
if (cramRecord.isUnknownBases()) { cramRecord.readBases = SAMRecord.NULL_SEQUENCE; cramRecord.qualityScores = SAMRecord.NULL_QUALS;
if (cramRecord.isUnknownBases()) { cramRecord.readBases = SAMRecord.NULL_SEQUENCE; cramRecord.qualityScores = SAMRecord.NULL_QUALS;
if (!r.isUnknownBases()) { for (final byte b : r.readBases) { baseCodec.writeData(b);
if (!r.isUnknownBases()) { for (final byte b : r.readBases) { baseCodec.writeData(b);