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Merged
asl merged 1 commit into from
May 26, 2026
+27 −27
Merged

Silence some warnings #1574

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30 changes: 15 additions & 15 deletions src/common/io/graph/cigar.inl
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Original file line number Diff line number Diff line change
Expand Up @@ -35,13 +35,13 @@ namespace cigar::grammar {
auto integer = dsl::if_(dsl::lit_c < '-' > ) + dsl::digits<>.no_leading_zero();
auto fraction = dsl::lit_c < '.' > >> dsl::digits<>;
auto exp_char = dsl::lit_c < 'e' > | dsl::lit_c<'E'>;
auto exponent = exp_char >> (dsl::lit_c < '+' > | dsl::lit_c < '-' > ) + dsl::digits<>;
auto exponent = exp_char >> ((dsl::lit_c < '+' > | dsl::lit_c < '-' > ) + dsl::digits<>);
return dsl::peek(dsl::lit_c < '-' > / dsl::digit<>) >>
dsl::position +
(dsl::position +
integer +
dsl::if_(fraction) +
dsl::if_(exponent) +
dsl::position;
dsl::position);
}();

static constexpr auto value = lexy::callback<float>(
Expand All @@ -64,17 +64,17 @@ namespace cigar::grammar {

static constexpr auto rule = [] {
auto colon = dsl::lit_c<':'>;
return dsl::p<tag_name> >> colon +
(
dsl::capture(LEXY_LIT("A")) >> colon + dsl::p < tag_character > |
dsl::capture(LEXY_LIT("i")) >> colon + dsl::p < tag_integer > |
dsl::capture(LEXY_LIT("f")) >> colon + dsl::p < tag_float > |
dsl::capture(LEXY_LIT("Z")) >> colon + dsl::p < tag_string > |
dsl::capture(LEXY_LIT("J")) >> colon + dsl::p < tag_string > |
dsl::capture(LEXY_LIT("H")) >> colon + dsl::p < tag_string > |
dsl::capture(LEXY_LIT("B")) >> colon + dsl::p < tag_string > |
return dsl::p<tag_name> >> (
colon + (
dsl::capture(LEXY_LIT("A")) >> (colon + dsl::p < tag_character >) |
dsl::capture(LEXY_LIT("i")) >> (colon + dsl::p < tag_integer >) |
dsl::capture(LEXY_LIT("f")) >> (colon + dsl::p < tag_float >) |
dsl::capture(LEXY_LIT("Z")) >> (colon + dsl::p < tag_string >) |
dsl::capture(LEXY_LIT("J")) >> (colon + dsl::p < tag_string >) |
dsl::capture(LEXY_LIT("H")) >> (colon + dsl::p < tag_string >) |
dsl::capture(LEXY_LIT("B")) >> (colon + dsl::p < tag_string >) |
dsl::error<invalid_tag_type>
);
));
}();

static constexpr auto value = lexy::callback<cigar::tag>(
Expand All @@ -101,7 +101,7 @@ namespace cigar::grammar {
static constexpr auto value = lexy::callback<cigar::cigarop>(
[]() { return cigar::cigarop{0, 0}; },
[](std::uint32_t cnt, auto lexeme) {
return cigar::cigarop{cnt, lexeme[0]};
return cigar::cigarop{cnt & 0xFFFFFF, lexeme[0]};
});
};

Expand All @@ -116,7 +116,7 @@ namespace cigar::grammar {

static constexpr auto rule = [] {
auto tags = dsl::list(dsl::p<tag>, dsl::trailing_sep(tab));
return dsl::eof | (tab >> tags + dsl::eof);
return dsl::eof | (tab >> (tags + dsl::eof));
}();
static constexpr auto value = lexy::as_list<std::vector<cigar::tag>>;
};
Expand Down
22 changes: 11 additions & 11 deletions src/common/io/graph/gfa.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -80,11 +80,11 @@ struct segment {
static constexpr auto name = "GFA segment";

static constexpr auto rule =
LEXY_LIT("S") >>
LEXY_LIT("S") >> (
tab + dsl::p<segment_name> +
tab + (LEXY_LIT("*") |
dsl::identifier(dsl::ascii::alpha)) +
dsl::p<opt_tags>;
dsl::p<opt_tags>);
static constexpr auto value = lexy::construct<gfa::segment>;
};

Expand All @@ -103,13 +103,13 @@ struct link {
static constexpr auto name = "GFA link line";

static constexpr auto rule =
LEXY_LIT("L") >>
LEXY_LIT("L") >> (
tab + dsl::p<segment_name> +
tab + dsl::p<segment_orientation> +
tab + dsl::p<segment_name> +
tab + dsl::p<segment_orientation> +
tab + (LEXY_LIT("*") | dsl::p<cigar_string>) +
dsl::p<opt_tags>;
dsl::p<opt_tags>);
static constexpr auto value = lexy::construct<gfa::link>;
};

Expand All @@ -127,13 +127,13 @@ struct gaplink {
static constexpr auto name = "GFA jump line";

static constexpr auto rule =
LEXY_LIT("J") >>
LEXY_LIT("J") >> (
tab + dsl::p<segment_name> +
tab + dsl::p<segment_orientation> +
tab + dsl::p<segment_name> +
tab + dsl::p<segment_orientation> +
tab + (LEXY_LIT("*") | (dsl::else_ >> dsl::p<segment_distance>)) +
dsl::p<opt_tags>;
dsl::p<opt_tags>);
static constexpr auto value = lexy::construct<gfa::gaplink>;
};

Expand All @@ -159,11 +159,11 @@ struct path {
};

static constexpr auto rule =
LEXY_LIT("P") >>
LEXY_LIT("P") >> (
tab + dsl::p<segment_name> +
tab + dsl::p<segments> +
tab + (LEXY_LIT("*") | dsl::p<overlaps>) +
dsl::p<opt_tags>;
dsl::p<opt_tags>);
static constexpr auto value = lexy::construct<gfa::path>;
};

Expand Down Expand Up @@ -209,14 +209,14 @@ struct walk {
};

static constexpr auto rule =
LEXY_LIT("W") >>
LEXY_LIT("W") >> (
tab + dsl::p<sample_id> + // SampleId
tab + dsl::integer<unsigned> + // HapIndex
tab + dsl::p<sequence_id> + // SeqId
tab + dsl::p<opt_uint64_t> + // SeqStart
tab + dsl::p<opt_uint64_t> + // SeqEnd
tab + dsl::p<wsegments> + // Walk
dsl::p<opt_tags>;
dsl::p<opt_tags>);
static constexpr auto value = lexy::construct<gfa::walk>;
};

Expand All @@ -241,7 +241,7 @@ struct record {
dsl::p<walk> |
comment |
// Explicitly ignore all other records (though require proper tab-delimited format)
dsl::ascii::alpha >> tab + dsl::until(dsl::newline).or_eof() |
dsl::ascii::alpha >> (tab + dsl::until(dsl::newline).or_eof()) |
dsl::error<expected_gfa_record>;
}();

Expand Down
2 changes: 1 addition & 1 deletion src/common/modules/genome_consistance_checker.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -432,7 +432,7 @@ void GenomeConsistenceChecker::Fill() {
}

vector<size_t> theoretic_lens;
for (const auto &prefix: vector<std::string>{"0_", "1_"}) {
for (auto prefix: {"0_", "1_"}) {
for (const auto &chr: genome.GetChromosomes()) {
string label = prefix + chr.name;
INFO("Spelling label " << label);
Expand Down
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