Counts for nanopore reads with both 5mC and 5hmC#263
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andrewdavidsmith merged 13 commits intomasterfrom Jun 9, 2025
Merged
Counts for nanopore reads with both 5mC and 5hmC#263andrewdavidsmith merged 13 commits intomasterfrom
andrewdavidsmith merged 13 commits intomasterfrom
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…as counts but with nanopore data
…likely will be changed
…-check CpG site locations with the indicated sites of modifications
…the input, which are ignored, when making symmetric CpG counts files. This is for nanopore, which currently has extra fields in the counts files by default
… that when set allows parsing of MSite / counts files that have extra fields that are to be ignored. The 'add' function for making symmetric CpGs by adding info from both strands now also does not assume integer values for the amount of methylation. Also code formatting.
…h methyl and hydroxy, both of which are assumed present in the BAM file. Also performance improvements, stats output to file, and a debug option to use only reads from a specified strand (which will probably be removed soon)
…ved file writing speed
…sym and roi test files which have changed after incorporating a different rounding in sym that works for nanopore
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Added the counts-nano command to process BAM files from nanopore with a default check on the base caller and updated the sym command to work with methylation levels that don't correspond to integers relative to the total number of reads