// ********************************************************************************************
void HuffmanEncoder::StoreTree(BitStream& bit_stream, HuffmanEncoder& tree)
{
static uchar* mem_buf = NULL;
static uint32 mem_size;
tree.StoreTree(mem_buf, mem_size);
my_assert(mem_size > 0);
my_assert(mem_buf);
bit_stream.FlushPartialWordBuffer();
bit_stream.PutWord(mem_size);
bit_stream.PutBytes(mem_buf, mem_size);
delete [] mem_buf;
}
// ********************************************************************************************
void Block::Process(BitStream &bit_stream, LzMatcher &lz_matcher, std::vector<Field> &fields, uint32 /*n_fields*/,
uint32 fastq_flags, uchar *sym_code, HuffmanEncoder::Code *sym_huf_codes,
uchar *qua_code, HuffmanEncoder::Code **qua_huf_codes, uint32 /*max_run_len*/,
HuffmanEncoder::Code **run_huf_codes, uint32 n_qualities, uint32 _global_max_sequence_length,
uint32 max_quality_length, uint32 block_no, uint32 _quality_stats_mode)
{
global_max_sequence_length = _global_max_sequence_length;
#if (D_RESERVE_BYTES_PER_BLOCK)
{
uchar bytes[Block::RESERVED_BYTES];
std::fill(bytes, bytes+Block::RESERVED_BYTES, INVALID_BYTE);
bit_stream.PutBytes(bytes, Block::RESERVED_BYTES);
}
#endif
if ((fastq_flags & FLAG_PLUS_ONLY) == 0)
{
for (uint32 i = 0; i < rec_count; ++i)
{
bit_stream.PutBit(records[i].plus_len == 1);
}
}
uint32 quality_len_bits = BitStream::BitLength(max_quality_length);
if ((fastq_flags & FLAG_VARIABLE_LENGTH) != 0)
{
for (uint32 i = 0; i < rec_count; ++i)
{
bit_stream.PutBits(records[i].quality_len, quality_len_bits);
}
}
if ((fastq_flags & FLAG_LINE_BREAKS) != 0)
{
uint32 max_line_break_len = 0;
for (uint32 i = 0; i < rec_count; ++i)
{
if (records[i].sequence_breaks)
{
for (uint32 j = 0; j < records[i].sequence_breaks->size(); ++j)
{
if ((*records[i].sequence_breaks)[j] > (int32) max_line_break_len)
{
max_line_break_len = (*records[i].sequence_breaks)[j];
}
}
}
if (records[i].quality_breaks)
{
for (uint32 j = 0; j < records[i].quality_breaks->size(); ++j)
{
if ((*records[i].quality_breaks)[j] > (int32) max_line_break_len)
{
max_line_break_len = (*records[i].quality_breaks)[j];
}
}
}
}
uint32 line_breaks_bits = BitStream::BitLength(max_line_break_len);
bit_stream.PutBits(line_breaks_bits, 5);
for (uint32 i = 0; i < rec_count; ++i)
{
if (records[i].sequence_breaks)
{
for (uint32 j = 0; j < records[i].sequence_breaks->size(); ++j)
{
bit_stream.PutBits((*records[i].sequence_breaks)[j], line_breaks_bits);
}
}
bit_stream.PutBits(0, line_breaks_bits);
if (records[i].quality_breaks)
{
for (uint32 j = 0; j < records[i].quality_breaks->size(); ++j)
{
bit_stream.PutBits((*records[i].quality_breaks)[j], line_breaks_bits);
}
}
bit_stream.PutBits(0, line_breaks_bits);
}
}
bit_stream.FlushPartialWordBuffer();
bool is_num_field_constant = (fastq_flags & FLAG_CONST_NUM_FIELDS) != 0;
StoreTitle(bit_stream, fields, block_no, is_num_field_constant);
if (_quality_stats_mode == QUALITY_RLE)
{
StoreQualityRLE(bit_stream, qua_code, qua_huf_codes, run_huf_codes, n_qualities);
}
else
{
bool use_trunc_hash = _quality_stats_mode == QUALITY_PLAIN_TRUNC;
StoreQualityPlain(bit_stream, qua_code, qua_huf_codes, n_qualities, use_trunc_hash);
}
bool try_lz = (fastq_flags & FLAG_TRY_LZ) != 0;
if ((fastq_flags & FLAG_DNA_PLAIN) != 0)
{
StoreDNAPlain(bit_stream, lz_matcher, sym_code, try_lz);
}
else
{
StoreDNAHuf(bit_stream, lz_matcher, sym_code, sym_huf_codes, try_lz);
}
#if (D_COMPUTE_RECORDS_CRC_PER_BLOCK)
uint32 hash = ComputeRecordsCrc32();
bit_stream.PutWord(hash);
#endif
}