Counts for nanopore reads with both 5mC and 5hmC#263

Merged

andrewdavidsmith merged 13 commits intomasterfrom

nanopore-counts

Jun 9, 2025

Commits on Jun 7, 2025

src/analysis/nanopore.cpp: reworking code for efficiency and to cross-check CpG site locations with the indicated sites of modifications
andrewdavidsmith
committed

Commits on Jun 8, 2025

src/utils/symmetric-cpgs.cpp: adding a flag to allow extra fields in the input, which are ignored, when making symmetric CpG counts files. This is for nanopore, which currently has extra fields in …
andrewdavidsmith
committed
src/dnmtools.cpp: the command for counts from nanopore data is now nanocount
andrewdavidsmith
committed
src/common/MSite.hcpp: adding a static bool member to the MSite class that when set allows parsing of MSite / counts files that have extra fields that are to be ignored. The 'add' function for maki…
andrewdavidsmith
committed
src/analysis/nanopore.cpp: added functionality to deal separately with methyl and hydroxy, both of which are assumed present in the BAM file. Also performance improvements, stats output to file, an…
andrewdavidsmith
committed