Mikkel Schubert

In that case you could probably just disable validation outright, since the tools used in the pipeline are unlikely to generate straight up invalid files. The easiest way to do...

After some consideration, I've decided to stop running ValidateSamFile as part of the pipeline going forward. The overhead is too large and it is very rare that problems are detected...

I haven't added it yet. I'll try to make a point release (v1.3.5) before the end of the week, that adds a "Validation" feature to the YAML file. Or maybe...

I couldn't think of anything else that needed to be fixed, so v1.3.5 is available now: # Validate everything with ValidateSamFile; this is the default behavior $ paleomix bam run...

Hi Vitali, The two files you mention (`.rmdup.collapsed.bam` and `.rmdup.normal.bam`) are intermediate files generated by the pipeline, prior to it filtering PCR duplicates. You should not be using these files...

Hi, What version of paleomix are you using? You can determine this by running `paleomix --version`. I am unfortunately not able to see the actual error from the snippet you...

Hi Zitian, Thank you very much! I've released a new version of paleomix (v1.3.3) that should fix this bug. But it is not terribly surprising that your BAM files are...

I am working on this now along with an overhaul of parts of the program. I realize that you would probably prefer a smaller update that just adds Python 3...

I've already replaced that copy with a dependency on ruamel.yaml in the development branch, based on your previous suggestions (see 433a33df9b34266db0341b284b6e8d9754d8915e). Is there a specific reason why you recommend PyYAML...

Python 3 development takes place in the py3x branch, but I've been too busy to work much on it recently. The releases I've made over the last few months have...