Foreword
Introduction
1 Scope
2 Normative references
3 Terms and definitions
4 Abbreviated terms
5 Conventions
5.1 General
5.2 Arithmetic operators
5.3 Logical operators
5.4 Relational operators
5.5 Bit-wise operators
5.6 Assignment operators
5.7 Range notation
5.8 Mathematical functions
5.9 Order of operation precedence
5.10 Variables, syntax elements and tables
5.11 Text description of logical operators
5.12 Processes
6 Syntax and semantics
6.1 Method of specifying syntax in tabular form
6.2 Bit ordering
6.3 Specification of syntax functions and data types
6.4 Semantics
7 Data structures
7.1 General
7.2 Data unit
7.3 Raw reference
7.3.1 General
7.3.2 Syntax and semantics
7.4 Parameter set
7.4.1 Syntax and semantics
7.4.2 Encoding parameters
7.5 Access unit
7.5.1 Syntax and semantics
7.5.2 Access unit types
8 Descriptors
9 Sequencing reads
9.1 General
9.2 Supported symbols
9.3 Paired-end reads
9.4 Reverse-complement reads
9.5 Data classes
9.6 Aligned data
9.7 Unaligned data
10 Decoding process
10.1 General
10.2 dataset_type = 0 or 1
10.2.1 General
10.2.2 References padding
10.2.3 Type 1 AU (Class P)
10.2.4 Type 2 AU (Class N)
10.2.5 Type 3 AU (Class M)
10.2.6 Type 4 AU (Class I)
10.2.7 Type 5 AU (Class HM)
10.2.8 Type 6 AU (Class U)
10.3 dataset_type = 2
10.3.1 General
10.3.2 Type 1 AU
10.3.3 Type 2 AU
10.3.4 Type 3 AU
10.3.5 Type 4 AU
10.3.6 Type 6 AU
10.4 Genomic descriptors
10.4.1 General
10.4.2 pos
10.4.3 rcomp
10.4.4 flags
10.4.5 mmpos
10.4.6 mmtype
10.4.7 clips
10.4.8 ureads
10.4.9 rlen
10.4.10 pair
10.4.11 mscore
10.4.12 mmap
10.4.13 msar
10.4.14 rtype
10.4.15 rgroup
10.4.16 qv
10.4.17 rname
10.4.18 rftp
10.4.19 rftt
10.4.20 tokentype descriptors
10.5 sequence
10.5.1 General
10.5.2 Aligned reads (Classes P, N, M, I, HM)
10.5.3 Unmapped reads (Class HM, U)
10.6 e-cigar
10.6.1 Syntax
10.6.2 Decoding process for the first alignment
10.6.3 Decoding process for other alignments
10.6.4 Reference transformation
11 Representation of reference sequences
11.1 External reference
11.2 Embedded reference
11.3 Computed reference
11.3.1 General
11.3.2 Supported Algorithms
11.3.3 Reference transformation
11.3.4 PushIn
11.3.5 Local assembly
11.3.6 Global assembly
12 Block payload parsing process
12.1 General
12.2 Inverse binarizations
12.2.1 General
12.2.2 Binary (BI)
12.2.3 Truncated unary (TU)
12.2.4 Exponential golomb (EG)
12.2.5 If the output of step 2 is 1, symVal= -1*symValTruncated exponential golomb (TEG)
12.2.6 Signed truncated exponential golomb (STEG)
12.2.7 Split unit-wise truncated unary (SUTU)
12.2.8 Signed split unit-wise truncated unary (SSUTU)
12.2.9 Double truncated unary (DTU)
12.2.10 Signed double truncated unary (SDTU)
12.3 Decoder configuration
12.3.1 Sequences and quality values
12.3.2 Support values
12.3.3 CABAC binarizations
12.3.4 Transformation parameters
12.3.5 Msar descriptor and read identifiers
12.3.6 State variables
12.4 Initialization process for context variables
12.5 Arithmetic decoding engine
12.5.1 Initialization
12.5.2 Arithmetic decoding process
12.6 Decoding process for sequence descriptors
12.6.1 General
12.6.2 Block payload decoding process
13 Output format
13.1 General
13.2 MPEG-G record
13.2.1 General
13.2.2 number_of_template_segments
13.2.3 number_of_record_segments
13.2.4 number_of_alignments
13.2.5 class_ID
13.2.6 read_group_len
13.2.7 reserved
13.2.8 read_1_first
13.2.9 seq_ID
13.2.10 as_depth
13.2.11 read_len
13.2.12 qv_depth
13.2.13 read_name_len
13.2.14 read_name
13.2.15 read_group
13.2.16 sequence
13.2.17 quality_values
13.2.18 mapping_pos
13.2.19 ecigar_len
13.2.20 ecigar_string
13.2.21 reverse_comp
13.2.22 mapping_score
13.2.23 split_alignment
13.2.24 delta
13.2.25 split_pos
13.2.26 split_seq_ID
13.2.27 flags
13.2.28 more_alignments
13.2.29 next_pos
13.2.30 next_seq_ID
13.3 Initialization process
Annex A (informative) Tokenization of reads identifiers
Annex B (informative) Mapping quality
Annex C (informative) Inverse binarization examples
