Use unsorted BAM

[lachlancoin]

It would be great to support unsorted BAM without a BAI file, to stream the records

[cmdcolin]

interesting idea. is this for use in the browser? or is it node.js? for full size bam files?

just as extra random info: I stumbled across a random project that is focused on streaming whole files in js
https://github.com/nrminor/genotype

Also, writing custom rust-htslib code can be pretty not too bad, and fast, so might be preferable compared to paying the javascript slowness task on large bam files (we've tried to optimize this library as much as we can but still gonna be slower than native code:))

[lachlancoin]

Thanks, thats a good suggestion, thank you. This was for browser since my application doesn't require sorted and indexed bam. Also some applications its useful to work with bam sorted by read id rather than genomic location. I was using rshiny before so javascript seems fairly quick but I appreciate rust wasm would be quicker

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On Thu, 12 Feb 2026, 1:27 pm Colin Diesh, ***@***.***> wrote: *cmdcolin* left a comment (GMOD/bam-js#125) <#125 (comment)> interesting idea. is this for use in the browser? or is it node.js? for full size bam files? just as extra random info: I stumbled across a random project that is focused on streaming whole files in js https://github.com/nrminor/genotype Also, writing custom rust-htslib code can be pretty not too bad, and fast, so might be preferable compared to paying the javascript slowness task on large bam files (we've tried to optimize this library as much as we can but still gonna be slower than native code:)) — Reply to this email directly, view it on GitHub <#125 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AA6TKZGDLCNUQOH7Q3ECRTD4LPQHTAVCNFSM6AAAAACU2K7V7CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTQOBYGMYTQOBRG4> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[cmdcolin]

just to ask again, are you trying to stream large bam files e.g. gigabytes of data?

or do you have a 'read name index' like https://github.com/jts/bri ?

just curious

regarding the rust-htslib recommendation, i haven't actually tried compiling rust-htslib to wasm, that is likely actually not trivial (though i should test it out) i only referred to rust-htslib in case you were doing work on the command line rather than in the browser. Another option for the wasm is https://biowasm.com but it cross compiled samtols rather than just htslib, we evaluated it and it was faster to use @gmod/bam-js over the samtools cross compilation (since with the samtools emscripten browser compilation, you have to parse its text output rather than use a lower level binary interface. @gmod/bam (this library) is actually faster since it gives you low level binary interfaces, and we do use wasm to some extent already in @gmod/bam to decompress bgzip blocks)

[lachlancoin]

Up to 1Gb. Large but not too large. I'd like to keep it in the order they come off the machine. I don't have a read name index, but they come ordered according to read-name off the machine. I implemented a simple biowasm based approach for sorting and indexing a bam as a work around (see https://tb.unevenly.org/bam.html) . We are doing a project in a resource limited setting so trying to make it as easy as possible to get resistance SNPS from the BAM that is generated by the Nanopore sequencer. It would be great to have a single step, since my application just processes each read (just looking for drug resistance mutations at a read level). I was initially hoping I could use a null baiFilehandler with gmod bam-js and it would work fine with a streamRecords function, but I think you only have a streamRecordsForRange function . I also haven't tried using rust in wasm yet, but it was on the list of things to try.. Thanks!

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On Fri, 13 Feb 2026 at 13:54, Colin Diesh ***@***.***> wrote: *cmdcolin* left a comment (GMOD/bam-js#125) <#125 (comment)> just to ask again, are you trying to stream large bam files e.g. gigabytes of data? or do you have a 'read name index' like https://github.com/jts/bri ? just curious regarding the rust-htslib recommendation, i haven't actually tried compiling rust-htslib to wasm, that is likely actually not trivial (though i should test it out) i only referred to rust-htslib in case you were doing work on the command line rather than in the browser. Another option for the wasm is https://biowasm.com but it cross compiled samtols rather than just htslib, we evaluated it and it was faster to use @gmod/bam-js over the samtools cross compilation (since with the samtools emscripten browser compilation, you have to parse its text output rather than use a lower level binary interface. @gmod/bam (this library) is actually faster since it gives you low level binary interfaces, and we do use wasm to some extent already in @gmod/bam to decompress bgzip blocks) — Reply to this email directly, view it on GitHub <#125 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AA6TKZBKLIP6SGZXY76LDT34LU4FNAVCNFSM6AAAAACU2K7V7CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTQOJUGUZDSNRUGY> . You are receiving this because you authored the thread.Message ID: ***@***.***>