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Fix IUPAC bug #78

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Merged
hannespetur merged 2 commits into from
Jun 1, 2021
Merged

Fix IUPAC bug #78

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f5648a8
assume non ACGT are N for skyr
hannespetur May 28, 2021
0d4cf84
fixes iupac bug
hannespetur Jun 1, 2021
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2 changes: 1 addition & 1 deletion include/graphtyper/typer/variant.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -98,7 +98,7 @@ std::vector<Variant> break_down_variant(Variant && variant,
std::vector<Variant> break_down_skyr(Variant && var, long const reach);
std::vector<Variant> extract_sequences_from_aligned_variant(Variant const && variant, std::size_t const THRESHOLD);
std::vector<Variant> simplify_complex_haplotype(Variant && variant, std::size_t const THRESHOLD);
std::vector<Variant> break_multi_snps(Variant const && var);
std::vector<Variant> break_multi_snps(Variant && var);
SampleCall bin_phred(Variant const & new_var,
Variant const & old_var,
SampleCall const & old_call,
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27 changes: 10 additions & 17 deletions src/typer/variant.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1044,9 +1044,6 @@ void Variant::trim_sequences(bool const keep_one_match)

bool Variant::add_base_in_front(bool const add_N)
{
// uint32_t abs_pos_copy = abs_pos - graph.genomic_region.get_absolute_begin_position() + 1;
// uint32_t abs_pos_copy = abs_pos - graph.genomic_region.get_absolute_begin_position() + 1;
// //graph.genomic_region.abs_pos;
uint32_t contig_pos = absolute_pos.get_contig_position(abs_pos, graph.contigs).second;
uint32_t contig_pos_cp = contig_pos;
uint32_t new_contig_pos = contig_pos - 1;
Expand All @@ -1055,9 +1052,14 @@ bool Variant::add_base_in_front(bool const add_N)
if (first_base.size() != 1 || contig_pos_cp != contig_pos || new_contig_pos != contig_pos - 1)
return false; // The base in front could not be extracted

if (!add_N && first_base[0] == 'N')
bool const is_not_ACGT = first_base[0] != 'A' && first_base[0] != 'C' && first_base[0] != 'G' && first_base[0] != 'T';

if (!add_N && is_not_ACGT)
return false;

if (add_N && is_not_ACGT)
first_base[0] = 'N'; // make sure it's N then

// Insert the new first base in front of all the sequences
for (auto & seq : seqs)
{
Expand Down Expand Up @@ -1589,17 +1591,9 @@ std::vector<Variant> break_down_variant(Variant && var,
{
// We need to make sure there is a matching first base
if (not var.is_with_matching_first_bases())
{
if (!var.add_base_in_front())
{
// Could not add a first base. Add N
for (auto & seq : var.seqs)
seq.insert(seq.begin(), 'N');
}
}
var.add_base_in_front(true); // Add N

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@hannespetur hannespetur Jun 1, 2021

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This is the actual bugfix, rest is some clang-tidy warnings.

std::vector<Variant> new_broken_down_snps = break_multi_snps(std::move(var));

std::move(new_broken_down_snps.begin(), new_broken_down_snps.end(), std::back_inserter(broken_down_vars));
}
else if (!is_no_variant_overlapping)
Expand All @@ -1621,9 +1615,9 @@ std::vector<Variant> break_down_variant(Variant && var,
// Make everything biallelic
std::vector<Variant> broken_down_vars2;

for (auto && var : broken_down_vars)
for (auto && broken_var : broken_down_vars)
{
auto new_vars = make_biallelic(std::move(var));
auto new_vars = make_biallelic(std::move(broken_var));
std::move(new_vars.begin(), new_vars.end(), std::back_inserter(broken_down_vars2));
}

Expand Down Expand Up @@ -1914,12 +1908,11 @@ void find_variant_sequences(gyper::Variant & new_var, gyper::Variant const & old
new_var.seqs = std::move(new_seqs);
}

std::vector<Variant> break_multi_snps(Variant const && var)
std::vector<Variant> break_multi_snps(Variant && var)
{
uint32_t const pos = var.abs_pos;
std::vector<std::vector<char>> const & seqs = var.seqs;
std::vector<Variant> new_vars;
// assert(var.infos.count("SBF1") == 1);

for (long j = 0; j < static_cast<long>(seqs[0].size()); ++j)
{
Expand Down