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[IO] BAM index support
Platform
- SeqAn version: 3.0
- Operating system:
Linux kaya 5.17.9-arch1-1 #1 SMP PREEMPT Wed, 18 May 2022 17:30:11 +0000 x86_64 GNU/Linux - Compiler:
gcc (GCC) 12.1.0
Question
Is there a way to use *.bam.bai files to use as an index? The documentation on your site covers generating arbitrary indexes, but can it also be used to (auto-)load the companion index file when loading the BAM file? I currently use seqan3::sam_file_input in{file}; to load the input file.
Thank you!
Hi @jay-tux,
unfortunately we do not support BAM indexing yet in seqan3. I can't give a good time estimate on when we will be able to implement this feature. I know of a external draft bai support though. I'll ask the authors and come back to you.
Alright! Thank you!
If it's not implemented yet, no worries. I think I can do without.
Hi @smehringer, I also have a use case in which BAM indexing would help. (In the end, I would like to be able to do pileup like in pysam.) If there is an implementation available, I would be interested.
I'm very sorry for the late reply!
@Irallia Could you point them to the bam index library of Josh you are using in IgenVar?
@Irallia Could you point them to the bam index library of Josh you are using in IgenVar?
https://github.com/joshuak94/BAMIntervalTree
This is just to cast my vote for this feature. I switched back to htslib for all the bamIO and I guess you know that no one ever really wants to do that... Thanks for the link above. Will have a look.
