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Draft:BGZF

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  • Comment: At least one reference shows a basic misunderstanding of referencing, and you need to check them all. a reference must be about the subject nor merely a mention that it has been used in research. Each reference must meet the following tough criteria"
    We require references from significant coverage about the topic of the article, and independent of it, in multiple secondary sources which are WP:RS please. See WP:42. Please also see WP:PRIMARY which details the limited permitted usage of primary sources and WP:SELFPUB which has clear limitations on self published sources. Providing sufficient references, ideally one per fact referred to, that meet these tough criteria is likely to allow this article to remain. Lack of them or an inability to find them is likely to mean that the topic is not suitable for inclusion, certainly today. 🇵🇸‍🇺🇦 FiddleTimtrent FaddleTalk to me 🇺🇦‍🇵🇸 00:05, 14 June 2025 (UTC)
  • Comment: There are no changes since last submission — please see my helpdesk post for discussion of sources regarding notability and context around submission. Thank you! Rare Moon (talk) 17:18, 13 June 2025 (UTC)
  • Comment: Please see my helpdesk post for discussion of sources regarding notability. Thank you! Rare Moon (talk) 17:18, 13 June 2025 (UTC)
  • Comment: Re: previous review(s) — I have added additional citations that discuss BGZF and build upon the features of algorithsm. The GNG comment appears more generic and reflects a lack of WP:AFCPURPOSE – please note that this is a file format and algorithm (used widely in the field) as supported by citations. The key technical algorithm information obviously comes from the original spec, but that does not mean it's not notable. The use of file format / algorithm is discussed in many contexts and those manuscripts do not need to provide algorithm discussion again (as is the norm, to cite the original manuscript). Consider for example gzip article. Thank you! Rare Moon (talk) 20:49, 8 June 2025 (UTC)
  • Comment: Sources lack qualifying WP:GNG. ☮️Counter-Strike:Mention 269🕉️(🗨️ ● ✉️ ● 📔) 06:31, 4 June 2025 (UTC)
  • Comment: The article uses a large amount of technical jargon and does not provide a general introduction to the subject. I am not sure if the topic meets GNG. Caleb Stanford (talk) 20:40, 10 May 2025 (UTC)
  • Comment: Publications by the developers of BGZF are not independent. jlwoodwa (talk) 23:28, 1 April 2025 (UTC)


BGZF (Blocked GNU Zip Format)
Filename extension
.gz
Internet media type
application/gzip
Magic number`\x1f\x8b\x08\x04` (initial bytes, standard Gzip magic. BGZF adds specific extra fields in the header of each block.)
Developed bySAMtools project / HTSlib
Initial releasec. 2009 (along with SAM/BAM format specification)
Type of formatCompressed file format, Indexed file format
Container forCommonly used for bioinformatics data like SAM, BAM, VCF records
Extended fromGzip
Standardhttps://samtools.github.io/hts-specs/SAMv1.pdf#page=13.12
Websitewww.htslib.org/doc/bgzip.html

Blocked GNU Zip Format (BGZF) is a variant of gzip file format that uses block compression, a method that compresses data in independent blocks of content—each of which is a valid gzip file. This design is utilized widely in bioinformatics for genomic data compression.[1] The block-based design provides efficient storage, random access with indexed queries,[2][3] and parallel processing; allowing large-scale data processing.[4]

The format was developed as part of SAM/BAM specification and SAMtools.[5] It is a core component of the common BAM format (the binary version of the Sequence Alignment Map format) and is also used to compress and index Variant Call Format (VCF), FASTA, and BED files.[6] Because each block is a standard gzip block, a BGZF file can be decompressed by any standard gzip-compatible tool, ensuring backward compatibility.[7] A general purpose compression utility bgzf is distributed with HTSlib software library.[6]

Uses

[edit]

BGZF is widely utilized in bioinformatics for the compression of large datasets where efficient random access is a crucial requirement.[1] Due to large sizes of next-generation sequencing data formats like SAM files,[8] they are compressed into binary BAM format utilizing BGZF compression.[4][9]

For random access, an index file is created for a BGZF-compressed file, typically using Tabix.[10] This index stores the file offsets of the compressed blocks alongside the corresponding genomic coordinates, thus allowing a program to seek directly to the block containing the data queried, decompress only them, and retrieve the requested information, avoiding the need to process the entire file.[10]

The format is also extensively employed for compressing variant call files (VCF) along with their associated Tabix indexes,[10] and similarly for other substantial genomic data files such as BED, GFF/GTF, and occasionally FASTQ when indexed access is necessary.[6] A broad range of bioinformatics software packages are equipped to read and write BGZF-compressed files; these include well-known tools like SAMtools, HTSlib, BCF/VCFtools,[11] Picard tools, the GATK, and libraries such as Biopython.[12][13] The standard command-line utility for creating BGZF-compressed files and their corresponding .gzi indexes is bgzip, which is distributed as part of HTSlib.[7]

BGZF has been adapted for development of more efficient data-specific compression methods and algorithms leveraging its block based design.[14]

Design schema

[edit]

A BGZF file consists of a series of concatenated BGZF blocks. Each block, whether in its compressed or uncompressed state, is limited to a maximum size of 64 kilobytes. Each BGZF block is itself a fully compliant gzip archive, adhering to the specifications outlined in RFC 1952.[15]

Schema of a single compressed block that constitutes the basic unit of a BGZF compressed file.

Each BGZF block contains a standard gzip file header with the following standard-compliant extensions:

  1. The F.EXTRA bit in the header is set to indicate that extra fields are present.
  2. The extra field used by BGZF uses the two subfield ID values 66 and 67 (ASCII ‘BC’).
  3. The length of the BGZF extra field payload (field LEN in the gzip specification) is 2 (two bytes of payload).
  4. The payload of the BGZF extra field is a 16-bit unsigned integer in little-endian format. This integer gives the size of the containing BGZF block minus one.

This block design allows use of an associated index file (storing offsets of each BGZF block) to fetch and decompress only the block of data that pertains to the query, thus avoiding the computational overhead of reading and decompressing all BGZF blocks.[10]

Random access

[edit]

EOF marker

[edit]

End-of-file marker for BGZF enables detection of erroneously truncated files and generate warnings or errors for the user. The EOF marker block is an empty (data block of length zero) BGZF block encoded with the default zlib compression level settings, and consists of the following 28 hexadecimal bytes: 

1f 8b 08 04 00 00 00 00 00 ff 06 00 42 43 02 00 1b 00 03 00 00 00 00 00 00 00 00 00

The presence of an EOF marker by itself does not signal an end of the file, however, an EOF marker present at the end of a BGZF file indicates that the immediately following physical EOF is the end of the file as intended by the program that wrote it.[15]

See also

[edit]

References

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  1. ^ a b Lan, Divon; Tobler, Ray; Souilmi, Yassine; Llamas, Bastien (2021-08-25). "Genozip: a universal extensible genomic data compressor". Bioinformatics (Oxford, England). 37 (16): 2225–2230. doi:10.1093/bioinformatics/btab102. ISSN 1367-4811. PMC 8388020. PMID 33585897. BGZF-block level indexing that is common in standard indexes of genomic file formats
  2. ^ Yamada, Taiju (2020-04-01). "7bgzf: Replacing samtools bgzip deflation for archiving and real-time compression". Computational Biology and Chemistry. 85: 107207. doi:10.1016/j.compbiolchem.2020.107207. ISSN 1476-9271. PMID 32092548.
  3. ^ Danecek, Petr; Bonfield, James K; Liddle, Jennifer; Marshall, John; Ohan, Valeriu; Pollard, Martin O; Whitwham, Andrew; Keane, Thomas; McCarthy, Shane A; Davies, Robert M; Li, Heng (2021-02-01). "Twelve years of SAMtools and BCFtools". GigaScience. 10 (2): giab008. doi:10.1093/gigascience/giab008. ISSN 2047-217X. PMC 7931819. PMID 33590861. [..] both formats can be either plain (uncompressed) or block-compressed with BGZF for random access and compact size.
  4. ^ a b Hernaez, Mikel; Pavlichin, Dmitri; Weissman, Tsachy; Ochoa, Idoia (2019-07-20). "Genomic Data Compression". Annual Review of Biomedical Data Science. 2: 19–37. doi:10.1146/annurev-biodatasci-072018-021229. ISSN 2574-3414.
  5. ^ Li, Heng; Handsaker, Bob; Wysoker, Alec; Fennell, Tim; Ruan, Jue; Homer, Nils; Marth, Gabor; Abecasis, Goncalo; Durbin, Richard; et al. (1000 Genome Project Data Processing Subgroup) (15 August 2009). "The Sequence Alignment/Map format and SAMtools". Bioinformatics. 25 (16): 2078–2079. doi:10.1093/bioinformatics/btp352. ISSN 1367-4803. PMC 2723002. PMID 19505943.
  6. ^ a b c Bonfield, James K; Marshall, John; Danecek, Petr; Li, Heng; Ohan, Valeriu; Whitwham, Andrew; Keane, Thomas; Davies, Robert M (2021-02-01). "HTSlib: C library for reading/writing high-throughput sequencing data". GigaScience. 10 (2): giab007. doi:10.1093/gigascience/giab007. ISSN 2047-217X. PMC 7931820. PMID 33594436.
  7. ^ a b "bgzip(1) manual page". www.htslib.org. Retrieved 2025-06-03.
  8. ^ Weeks, N. T. (2018). "Openmp task parallelism for faster genomic data processing" (PDF). Reading, decoding, sorting, encoding, and writing large sequence alignment files (tens or hundreds of GBs) can be time-consuming and resource intensive.
  9. ^ Sadikin, Rifki; Arisal, Andria; Omar, Rofithah; Mazni, Nur Hidayah (November 2017). "Processing next generation sequencing data in map-reduce framework using hadoop-BAM in a computer cluster". 2017 2nd International conferences on Information Technology, Information Systems and Electrical Engineering (ICITISEE). pp. 421–425. doi:10.1109/ICITISEE.2017.8285542. ISBN 978-1-5386-0658-2.
  10. ^ a b c d Li, Heng (2011-03-01). "Tabix: fast retrieval of sequence features from generic TAB-delimited files". Bioinformatics. 27 (5): 718–719. doi:10.1093/bioinformatics/btq671. ISSN 1367-4803. PMC 3042176. PMID 21208982.
  11. ^ Danecek, Petr; Bonfield, James K; Liddle, Jennifer; Marshall, John; Ohan, Valeriu; Pollard, Martin O; Whitwham, Andrew; Keane, Thomas; McCarthy, Shane A; Davies, Robert M; Li, Heng (1 February 2021). "Twelve years of SAMtools and BCFtools". GigaScience. 10 (2). doi:10.1093/gigascience/giab008. ISSN 2047-217X. PMC 7931819. PMID 33590861.
  12. ^ "Bio.bgzf module — Biopython 1.85 documentation". Biopython. Retrieved 3 June 2025.
  13. ^ "BlockCompressedOutputStream (htsjdk 2.8.1 API)". SAMtools/HTSlib. Retrieved 3 June 2025.
  14. ^ Li, Miaoxin; Li, Jiang; Li, Mulin Jun; Pan, Zhicheng; Hsu, Jacob Shujui; Liu, Dajiang J.; Zhan, Xiaowei; Wang, Junwen; Song, Youqiang; Sham, Pak Chung (2017-05-19). "Robust and rapid algorithms facilitate large-scale whole genome sequencing downstream analysis in an integrative framework". Nucleic Acids Research. 45 (9): e75. doi:10.1093/nar/gkx019. ISSN 1362-4962. PMC 5435951. PMID 28115622.
  15. ^ a b "HTS format specifications". samtools.github.io. Retrieved 2025-04-01.
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