Talk:Binary Alignment Map

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Hi all, I just added a reference to Genozip in this article, a tool of which I am the author. Per Wikipedia rules, I have declared a "conflict of interest". I added it because I think it genuinely relevant for this article and adds value to the readers. If you agree, please kindly remove the template message. Divon lan (talk) 21:48, 21 February 2021 (UTC)[reply]

Requested move 9 April 2025

It has been proposed in this section that Binary Alignment Map be renamed and moved to BAM (file format).

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Binary Alignment Map → BAM (file format) – Redirect exists at the preferred title and move is contested by @Pppery: but unclear why — Vivek Rai (talk) 22:59, 8 April 2025 (UTC) This is a contested technical request (permalink). Vivek Rai (talk) 23:54, 9 April 2025 (UTC)[reply]

The change would make it WP:CONSISTENT with SAM (file format) and CRAM (file format) which are currently existing pages capturing similar information. Also, in the field, this file format is rarely, if ever, called a "binary alignment map" file. BAM is the colloquial and popular way to refer it and would not make sense if SAM (file format) or CRAM (file format) exist as such at the moment. Move was initiated by @Intrisit: but later reverted. Vivek Rai (talk) 23:55, 9 April 2025 (UTC)[reply]

Oppose per WP:Article titles#Avoid ambiguous abbreviations/WP:NATURALDIS. * Pppery * _{it has begun...} 23:59, 9 April 2025 (UTC)[reply]

I appreciate that you re-stated your reasoning and citing WP:TITLE#Avoid ambiguous abbreviations and WP:NATURALDIS. I understand the general preference for unambiguous, natural titles; however, there are strong factors to consider here for the proposed move (esp. considering the further context and examples I have included in my reply above). So, if could you elaborate on the following below, that'd be a constructive path forward:

Wikipedia:Common name The term "BAM" is overwhelmingly the primary and most recognizable name for this file format within the relevant scientific community (bioinformatics, genomics). "Binary Alignment Map" is rarely, if ever, used in practice, documentation, or software. WP:TITLE guidance often prioritizes recognizability and common usage. How should the near-universal usage of "BAM" be weighed against the general avoidance of abbreviations?
WP:CONSISTENT: The proposed title BAM (file format) aligns directly with the existing, established titles for its companion formats, SAM (file format) and CRAM (file format). Maintaining consistency among these closely related topics seems crucial for user navigation and understanding. Does the preference for natural disambiguation override the benefit of consistency in this established set of articles?

Given these points, the parenthetical "(file format)" seems to effectively address the ambiguity concern, specifically targeting the correct subject, much like it does for SAM and CRAM. Vivek Rai (talk) 01:52, 10 April 2025 (UTC)[reply]

Support per WP:CONSISTENT as noted above. I appreciate we should avoid ambiguous abbreviations but in my experience 'BAM' is by far the most common way to refer to these files. Amkilpatrick (talk) 09:14, 10 April 2025 (UTC)[reply]

Support any variety with BAM + disambiguation w/ preference for naturalness. My searching shows that it is common to refer to these as BAM files much like any other file format. Though, I find it hard to decipher what exactly 'common name' means for such a niche topic. There are some other varieties to consider too: .BAM, .bam file, BAM format, etc. These too are more natural disambiguations from other articles at BAM.

Consistency is a weak argument here as you could equally validly argue SAM (file format) and CRAM (file format) should be at Sequence alignment map and Compressed reference-oriented alignment map to match Binary Alignment Map on the basis of consistency. You could also look to the titling of other biology-related file formats and see that neither proposed title is consistent with all others listed there. ⇌ Synpath 17:01, 10 April 2025 (UTC)[reply]