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Giraffe paired end fragment length #4438

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Giraffe paired end fragment length #4438

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64ad504
Make distance between a pair of alignments in giraffe be the distance…
xchang1 Nov 6, 2024
786805a
make default distance limit 1.5x the read length
xchang1 Nov 12, 2024
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6 changes: 3 additions & 3 deletions src/minimizer_mapper.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -3291,10 +3291,10 @@ int64_t MinimizerMapper::distance_between(const Alignment& aln1, const Alignment
crash_unless(aln1.path().mapping_size() != 0);
crash_unless(aln2.path().mapping_size() != 0);

pos_t pos1 = initial_position(aln1.path());
pos_t pos2 = final_position(aln2.path());
pos_t pos1 = final_position(aln1.path());
pos_t pos2 = initial_position(aln2.path());

return distance_between(pos1, pos2);
return SnarlDistanceIndex::sum(distance_between(pos1, pos2), aln1.sequence().size() + aln2.sequence().size());
}

void MinimizerMapper::extension_to_alignment(const GaplessExtension& extension, Alignment& alignment) const {
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4 changes: 2 additions & 2 deletions src/minimizer_mapper.hpp
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Expand Up @@ -293,7 +293,7 @@ class MinimizerMapper : public AlignerClient {

static constexpr size_t default_max_multimaps = 1;
size_t max_multimaps = default_max_multimaps;
static constexpr size_t default_distance_limit = 200;
static constexpr size_t default_distance_limit = 0;
size_t distance_limit = default_distance_limit;

/// If false, skip computing base-level alignments.
Expand Down Expand Up @@ -381,7 +381,7 @@ class MinimizerMapper : public AlignerClient {
* Get the distance limit for the given read length
*/
size_t get_distance_limit(size_t read_length) const {
return max(distance_limit, read_length + 50);
return max(distance_limit, (size_t) ((int)read_length * 1.5));
}

/// The information we store for each seed.
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