Fixes
- [bedmethyl, merge] Merge and write concurrently, improves memory usage and runtime massively.
- [dmr] Don't fail an entire section (i.e. batch) when one sample does not have a particular contig.
- [modbam, check-tags] Fix counter so that records that fail reading are counted.
- [pileup, sampler] Don't use non-primary alignments when calculating pass thresholds.