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Accepting reads without mod info for nanopore analysis #329

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Merged
andrewdavidsmith merged 2 commits into from
Dec 23, 2025
+8 −6
Merged

Accepting reads without mod info for nanopore analysis #329

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e3c0da6
src/analysis/nanopore.cpp: allowing for no modifications within a rea…
andrewdavidsmith Dec 22, 2025
531ff8c
release workflows: enabling htslib mods
andrewdavidsmith Dec 23, 2025
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2 changes: 1 addition & 1 deletion .github/workflows/dnmtools_release_linux.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -59,7 +59,7 @@ jobs:
cd /workspace && \
autoreconf -i && \
mkdir build && cd build && \
../configure --with-libdeflate && \
../configure --with-libdeflate --with-htsmods && \
../data/make_full_license_info_header.sh ../data/LICENSE > license.h && \
echo "#define INCLUDE_FULL_LICENSE_INFO 1" >> config.h && \
make -j4 LDFLAGS="-static-libgcc -static-libstdc++ -s" && \
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2 changes: 1 addition & 1 deletion .github/workflows/dnmtools_release_macos.yml
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Expand Up @@ -54,7 +54,7 @@ jobs:
run: |
./autogen.sh
mkdir build && cd build
../configure --with-libdeflate \
../configure --with-libdeflate --with-htsmods \
CXX=g++-14 \
LDFLAGS="-L/opt/dnmtools/lib -static-libgcc -static-libstdc++ -Wl,-dead_strip" \
CPPFLAGS="-I/opt/dnmtools/include"
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10 changes: 6 additions & 4 deletions src/analysis/nanopore.cpp
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Expand Up @@ -942,14 +942,16 @@ valid_modification_types(const std::string &infile,
// ADS: or bam_parse_basemod2(aln.b, m, HTS_MOD_REPORT_UNCHECKED)
int n_types{};
const auto types = bam_mods_recorded(m.get(), &n_types);
valid_types = (n_types == 1 && types[0] == 'C') ||
(n_types >= 2 && types[0] == 'h' && types[1] == 'm');
// clang-format off
valid_types = ((n_types == 0) ||
(n_types == 1 && types[0] == 'C') ||
(n_types >= 2 && types[0] == 'h' && types[1] == 'm'));
// clang-format on
if (!valid_types) {
message = "n_types: " + std::to_string(n_types) + "\n";
for (auto i = 0; i < n_types; ++i) {
for (auto i = 0; i < n_types; ++i)
message += "type[" + std::to_string(i) +
"]=" + std::to_string(static_cast<char>(types[i])) + "\n";
}
}
}
return std::make_pair(valid_types, message);
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