hmr checks if entries in a methcounts file are sorted, but this also involves checking chromosomes for alphabetical ordering. This means that HMR will fail on the following lines which are very common in most input datasets:
chr9 150616189 + CpG 0 0
chr10 2124 + CpG 0 0
we need to allow it to be flexible to any combination of chromosomes as long as they are grouped together.
guilhermesena1
commented
2 years ago
hmrchecks if entries in a methcounts file are sorted, but this also involves checking chromosomes for alphabetical ordering. This means that HMR will fail on the following lines which are very common in most input datasets:we need to allow it to be flexible to any combination of chromosomes as long as they are grouped together.