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Updates including fix for roi on counts-nano output and move to strict SAM as assumed in format command
- #299
#299
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andrewdavidsmith
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uniq-bsrate-stats-accumulation
smithlabcode/dnmtools:uniq-bsrate-stats-accumulation
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Oct 7, 2025
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Updates including fix for roi on counts-nano output and move to strict SAM as assumed in format command
#299
andrewdavidsmith
merged 11 commits into
master
smithlabcode/dnmtools:master
from
uniq-bsrate-stats-accumulation
smithlabcode/dnmtools:uniq-bsrate-stats-accumulation
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Commits
Commits on Sep 27, 2025
src/utils/uniq.cpp: computing the derived values when they are printed and only keeping track of the fundamental counts; this is so the db will be in normal form
andrewdavidsmith
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2708965
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src/analysis/bsrate.cpp: computing the derived values when they are printed and only keeping track of the fundamental counts; this is so the db will be in normal form
andrewdavidsmith
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Commits on Oct 7, 2025
src/common/LevelsCounter.hcpp: made functions for mean_depth, mean_depth_covered and sites_covered_fraction
andrewdavidsmith
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src/abismal: updating submodule
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src/common/LevelsCounter.hcpp: renamed sites_covered_fraction to sites_covered_frac to match the colname in the view in methbase db
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src/analysis/hmr.cpp: cleanup
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src/utils/format-reads.cpp: now requiring that the input be given as strict SAM format
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src/utils/format-reads.cpp: fixing a bug of negative of negative
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src/common/LevelsCounter.cpp: cleanup
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src/analysis/roimethstat.cpp: allowing an option for extra cols in output, which is useful for current counts format output by counts-nano
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data/md5sum.txt: updates for changes to abismal submodule and very minor change to a tag in the output of levels. Might break.
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