Replacing GenomicRegion from smithlab_cpp#327

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andrewdavidsmith merged 6 commits intomasterfrom

replacing-genomic-region

Dec 22, 2025

Commits on Dec 22, 2025

multiple sources: replacing GenomicRegion and SimpleGenomicRegion with Interval6 and Interval
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multiple sources: making output file a required argument
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src/utils/selectsites.cpp: using Interval instead of Interval6
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src/common/Interval.cpp: fixing a bug that filed when the end of a line was just after the stop site
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src/analysis/roimethstat.cpp: reverting to local function for formatting levels counter because the format used by roi has been slightly different from the general format. Also reading the input in…
andrewdavidsmith
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src/analysis/pmd.cpp: fixing a bug initializing transition matrix
andrewdavidsmith
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