cramRecord.flags = bitFlagsCodec.readData(); cramRecord.compressionFlags = compressionBitFlagsCodec.readData(); if (refId == Slice.MULTI_REFERENCE) { cramRecord.sequenceId = refIdCodec.readData(); } else { cramRecord.sequenceId = refId; cramRecord.readLength = readLengthCodec.readData(); if (APDelta) { cramRecord.alignmentDelta = alignmentStartCodec.readData(); } else { cramRecord.alignmentStart = alignmentStartCodec.readData(); cramRecord.readGroupID = readGroupCodec.readData(); cramRecord.readName = new String(readNameCodec.readData(), charset); cramRecord.mateFlags = mateBitFlagCodec.readData(); if (!captureReadNames) { cramRecord.readName = new String(readNameCodec.readData(), charset); cramRecord.mateSequenceID = mateReferenceIdCodec.readData(); cramRecord.mateAlignmentStart = mateAlignmentStartCodec.readData(); cramRecord.templateSize = insertSizeCodec.readData(); } else if (cramRecord.isHasMateDownStream()) { cramRecord.recordsToNextFragment = distanceToNextFragmentCodec.readData(); final Integer tagIdList = tagIdListCodec.readData(); final byte[][] ids = tagIdDictionary[tagIdList];
cramRecord.flags = bitFlagsCodec.readData(); cramRecord.compressionFlags = compressionBitFlagsCodec.readData(); if (refId == Slice.MULTI_REFERENCE) { cramRecord.sequenceId = refIdCodec.readData(); } else { cramRecord.sequenceId = refId; cramRecord.readLength = readLengthCodec.readData(); if (APDelta) { cramRecord.alignmentDelta = alignmentStartCodec.readData(); } else { cramRecord.alignmentStart = alignmentStartCodec.readData(); cramRecord.readGroupID = readGroupCodec.readData(); cramRecord.readName = new String(readNameCodec.readData(), charset); cramRecord.mateFlags = mateBitFlagCodec.readData(); if (!captureReadNames) { cramRecord.readName = new String(readNameCodec.readData(), charset); cramRecord.mateSequenceID = mateReferenceIdCodec.readData(); cramRecord.mateAlignmentStart = mateAlignmentStartCodec.readData(); cramRecord.templateSize = insertSizeCodec.readData(); } else if (cramRecord.isHasMateDownStream()) { cramRecord.recordsToNextFragment = distanceToNextFragmentCodec.readData(); final Integer tagIdList = tagIdListCodec.readData(); final byte[][] ids = tagIdDictionary[tagIdList];