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Use ksw2 to align soft-clipped ends from ungapped alignment #382

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Use ksw2 to align soft-clipped ends from ungapped alignment #382

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02ea196
Update ksw2 to the most recent upstream version
marcelm Feb 15, 2023
4f6d50a
Move ksw2 files to a subdirectory and add license
marcelm Feb 15, 2023
237cb91
Implement Aligner::ksw_extend()
marcelm Feb 17, 2023
a90d697
Add operator<< for ksw_extz_t
marcelm Mar 13, 2023
b89e3d7
Turn the ref parameter of some functions into string_view
marcelm Dec 14, 2023
36513bc
Add operator<< for AlignmentInfo
marcelm Dec 15, 2023
92d221b
Explicitly set a wildcard score in the ksw score matrix
marcelm Dec 15, 2023
13938c5
Pass ref as a string_view
marcelm Dec 15, 2023
9d72201
Make ksw actually use the score matrix
marcelm Dec 15, 2023
c36cc0a
Return empty alignment if query is empty
marcelm Dec 15, 2023
7d23a81
Add soft clipping to CIGAR if necessary
marcelm Dec 15, 2023
26b472e
If ungapped alignment is softclipped, ksw_extend soft-clipped ends
marcelm Dec 15, 2023
83edcf2
Update baseline commit
marcelm Dec 17, 2023
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Add soft clipping to CIGAR if necessary
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@marcelm
marcelm committed Feb 22, 2024
commit 7d23a81e91fb8390bd19f87e9f3525837ed21b11
2 changes: 2 additions & 0 deletions src/aligner.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -317,7 +317,9 @@ AlignmentInfo Aligner::ksw_extend(const std::string& query, const std::string_vi
info.ref_end = ez.max_t + 1;
info.query_end = ez.max_q + 1;
info.sw_score = ez.max;
info.cigar.push(CIGAR_SOFTCLIP, query.length() - info.query_end);
}
assert(info.cigar.derived_sequence_length() == query.length());

kfree(km, ez.cigar);
return info;
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12 changes: 12 additions & 0 deletions src/cigar.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -77,6 +77,18 @@ class Cigar {
return dist;
}

size_t derived_sequence_length() const {
size_t length = 0;
for (auto op_len : m_ops) {
auto op = op_len & 0xf;
auto len = op_len >> 4;
if (op == CIGAR_MATCH || op == CIGAR_EQ || op == CIGAR_X || op == CIGAR_INS || op == CIGAR_SOFTCLIP) {
length += len;
}
}
return length;
}

void reverse() {
std::reverse(m_ops.begin(), m_ops.end());
}
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