We are using Conpair as part of a pipeline for a large project to ensure that samples from the same patient are properly paired. The tool is working well for us and we especially appreciate the integration with multiqc. However, to improve the visualization of samples with no overlapping markers in multiqc, we need an output file to be created for these files, instead of just a warning.
At the moment, no output file is created for samples with 0 overlapping markers, so the sample pair does not get included in the multiqc report. Including these sample pairs with concordance = 0.00% in the multiqc output would make it easier for us to spot problematic samples, which might otherwise be missed.
I realize that not everyone would want this behavior, so an option to toggle this on and off could be added. Let me know if you'd consider including this as a feature or option in a future release, happy to develop further a create a PR.
Hi!
We are using Conpair as part of a pipeline for a large project to ensure that samples from the same patient are properly paired. The tool is working well for us and we especially appreciate the integration with multiqc. However, to improve the visualization of samples with no overlapping markers in multiqc, we need an output file to be created for these files, instead of just a warning.
At the moment, no output file is created for samples with 0 overlapping markers, so the sample pair does not get included in the multiqc report. Including these sample pairs with concordance = 0.00% in the multiqc output would make it easier for us to spot problematic samples, which might otherwise be missed.
I've forked the repository and added a commit that solves this issue for our purposes: https://github.com/MareikeJaniak/Conpair/commit/7bc3908b7279a6de70b1089f0713ff02c16cb6bd
I realize that not everyone would want this behavior, so an option to toggle this on and off could be added. Let me know if you'd consider including this as a feature or option in a future release, happy to develop further a create a PR.
Best, Mareike