International IEC ISo Standard ISO/IEC 23092-2 Information technology Genomic Third edition information representation - 2024-03 Part 2: Coding of genomic information Technologies de I'information - Représentation des informations genomiques- Partie 2: Codage des informations génomiques Referencenumber ISO/IEC 23092-2:2024(en) @ISO/IEC 2024 IS0/IEC 23092-2:2024(en) COPYRIGHT PROTECTED DOCUMENT @IS0/IEC2024 All rights reserved. Unless otherwise specified, or required in the context of its implementation, no part of this publication may be reproduced or utilized otherwise in any form or by any means, electronic or mechanical, including photocopying, or posting on the internet or an intranet, without prior written permission. Permission can be requested from either ISO at the address below orIso's memberbody inthe countryofthe requester. ISO copyright office CP 40i:Ch.de Blandonnet 8 CH-1214 Vernier, Geneva Phone: +41 22 749 01 11 Email:[email protected] Website: www.iso.org Published in Switzerland @IS0/IEC2024-Allrightsreserved i IS0/IEC23092-2:2024(en) Contents Page Foreword. ..vii Introduction .viii 1 Scope. 1 2 Normative references .1 3 Terms and definitions .1 4 Abbreviated terms 6 5 Conventions 6 5.1 General 6 5.2 Arithmetic operators. 6 5.3 Logical operators.. 7 5.4 Relational operators 5.5 Bit-wise operators. 5.6 Assignment operators 8 5.7 Range notation 8 5.8 Mathematical functions. 8 5.9 Order of operation precedence 8 5.10 Variables, syntax elements and tables 9 5.11 Text description of logical operators .10 5.12 Processes. .11 6 Syntax and semantics 12 6.1 Method of specifying syntax in tabular form. 12 6.2 Bit ordering 13 6.3 Specification of syntax functions and data types 13 6.4 Semantics .14 7 Data structures. 14 7.1 General. .14 7.2 Data unit. 15 7.3 Raw reference .16 7.3.1 General .16 7.3.2 Syntax and semantics .16 7.4 Parameter set. .16 7.4.1 Syntax and semantics .16 7.4.2 Encoding parameters .17 7.5 Accessunit. 23 7.5.1 Syntax and semantics .24 7.5.2 Access unit types. .27 8 Descriptors 28 9 Sequencing reads. 31 9.1 General. .31 9.2 Supported symbols .31 9.3 Paired-endreads.. 33 9.4 Reverse-complement reads 33 9.5 Data classes 33 9.6 Aligned data 34 9.7 Unaligned data 35 10 Decoding process 35 10.1 General. 35 10.2 dataset_type = 0 or 1 36 10.2.1 General. 36 10.2.2 References padding 36 10.2.3 Type 1 AU (Class P) .37 IS0/IEC2024-Allrightsreserved iii IS0/IEC23092-2:2024(en) 10.2.4 Type 2 AU (Class N) 38 10.2.5 Type 3 AU (Class M) 38 10.2.6 Type 4 AU (Class I) 39 10.2.7 Type 5 AU (Class HM) 41 10.2.8 Type 6 AU (Class U) .41 10.3 dataset_type = 2. .42 10.3.1 General .42 10.3.2 Type 1 AU .43 10.3.3 Type 2 AU .43 10.3.4 Type 3 AU .43 10.3.5 Type 4 AU 44 10.3.6 Type 6 AU 44 10.4 Genomic descriptors 44 10.4.1 General 44 10.4.2 pos... .45 10.4.3 rcomp .45 10.4.4 flags. 46 10.4.5 mmpos. .47 10.4.6 mmtype. 49 10.4.7 clips 53 10.4.8 ureads. 55 10.4.9 rlen. 56 10.4.10 pair 57 10.4.11 mscore 64 10.4.12 mmap. 65 10.4.13msar 68 10.4.14 rtype 69 10.4.15 rgroup .71 10.4.16 qv. 71 10.4.17 rname 75 10.4.18 rftp 75 10.4.19rftt 76 10.4.20 tokentype descriptors 77 10.5 sequence 85 10.5.1 General 85 10.5.2 Aligned reads (Classes P, N, M, I, HM) 85 10.5.3 Unmapped reads (Class HM, U) 86 10.6 e-cigar. 86 10.6.1 Syntax.. 86 10.6.2 Decoding process for the first alignment. 88 10.6.3 Decoding process for other alignments 95 10.6.4 Reference transformation 95 11 Representation of reference sequences .96 11.1 External reference. 97 11.2 Embedded reference 97 11.3 Computed reference. 97 11.3.1 General 97 11.3.2 Supported Algorithms. 97 11.3.3 Reference transformation 98 11.3.4 PushIn.. 98 11.3.5 Local assembly 100 11.3.6 Global assembly 101 12 Block payload parsing process .101 12.1 General 101 12.2 Encoding Mode .. 102 12.3 Inverse binarizations 103 12.3.1 General 103 12.3.2 Binary (BI) 103 IS0/IEC2024-Allrightsreserved iv IS0/IEC23092-2:2024(en) 12.3.3 Truncated unary (TU) .104 12.3.4 Exponential golomb (EG) 104 12.3.5 Truncated expo