Bede Constantinides
Bede Constantinides
Hi @sureman, base quality is not considered currently. I agree that this coud be a useful feature, athough it is not something I currently plan to implement. I do have...
Hi @mdshw5 : ) Does Simplesam have operation-specific functionality? Or does it simply parse CIGAR ops as single char strings at face value? If the latter, it should be fine....
Sorry for not being clearer – yes it only means that the MD is redundant for some applications.
Ah yes. At least we can now count indels *and* substitutions without the MD this way. Thanks again for making Simplesam.
Plotting functionality needs removal
Would probably make sense to infer from a user-supplied reference rather than work this put directly from bam See https://github.com/bede/kindel/issues/13
Use minimap2 mappy bindings? https://github.com/lh3/minimap2/tree/master/python
Hi : ) Could you be more specific about what you mean by 'the' reference?
Thanks for clarifying Miquel. At the moment this tool infers consensus using the SAM/BAM alone, meaning that to do this I would either have to rely on the SAM/BAM `MD`...