TODO: 0. Add consolidation and vacuum to Hich engine
- Remove limit-chroms in write DNA methylation section.
- Validate download.sh and index.sh test setup scripts
- Allow filtering output write and statistics input separately
- Test: interleaved, single-end alignment
- Test: aligner combinations
- Restriction fragment filtering
- Dockerize, distribute
- Test suite
cat input.bed | \
sort -k1,1 -k2,2n | \
bedtools genomecov -bg -i stdin -g chrom.sizes | \
bedGraphToBigWig stdin chrom.sizes output.bw