brentp / pbr Goto Github PK

It has bothered me for years that there is no useful tool to pileup mutation at strand-specific mode, which is particularly important for analyzing RNA libraries. I have written a tool (https://github.com/y9c/cpup) to parse the samtools mpileup result to achive this, but the performance is bad. I am curious if future releases of pbr will incorporate support for this feature. If that is the case, I am willing to submit a pull request to contribute to its development.

Hello,

Thank you for your effort and for this tool!
I was trying to install it as sh build.sh but I got this error build.sh: line 5: cross: command not found.

I am not sure if this is because of the cross compiler? I have already installed perbase.

Am I missing something?

Thank you in advance!

perbase already supports this, we need a flag to switch behavior.

it might already work, but need to check this.

Will it be useful to add filter for tags, such as "[NH]>1" to filter reads of multiple hits? Will the same grammar as --input-fmt-option of samtools help?

Thank you.

lua performance can be improved quite a bit by using methods:

read:mapping_quality() < 0.5

instead of properties:

read.mapping_quality < 0.5

I prefer the former syntax, but the performance difference might be enough to warrant a change.

It would be great if the reference base of the site can be ouput into the pileup table, which would make it easy to call and filter mutation ratio of each site.

https://docs.rs/mlua/latest/mlua/struct.Chunk.html#method.into_function

and here: https://github.com/khvzak/script-bench-rs/blob/main/benches/mlua.rs.t#L35-L44

this should be faster than .load()