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brentp / fraguracy

overlapping bases in read-pairs from a fragment indicate accuracy and reveal error-prone sites
MIT License
31 stars 2 forks source link

combine-errors error #4

Closed atimms closed 1 year ago

atimms commented 1 year ago

Thanks for this interesting tool, I'm looking into some sequencer specific error profiles and had an issue when trying to combine the individual error files.

When I run combine-errors i.e. ./fraguracy combine-errors -f fraguracy-22-90139-1-errors.bed fraguracy-22-90140-1-errors.bed.

I get the error: thread 'main' panicked at 'Error reading first interval from file: ParseIntError { kind: InvalidDigit }', src/combine_errors.rs:74:37 note: run with RUST_BACKTRACE=1 environment variable to display a backtrace

brentp commented 1 year ago

Thanks for reporting! I botched that one. I haven't been using combine-errors, only combine-counts Will you give this a try? fraguracy.gz

Happy to hear anything that would be helpful for you.

brentp commented 1 year ago

BTW, if you only have a few samples, you can run fraguracy extract ... *.bam then it will make combine-errors and combine-counts unnecessary.

atimms commented 1 year ago

thanks for getting back to me so quickly

brentp commented 1 year ago

I also pushed a new release for this: https://github.com/brentp/fraguracy/releases/tag/v0.1.6 Thanks again for reporting. Might be a few more rough edges but should be easily fixed.

brentp commented 1 year ago

this was still broken in v0.1.6, I just pushed v0.1.8 that actually fixes it.