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Bugfix in calculating max diff for per base sequence content #91

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Merged
andrewdavidsmith merged 3 commits into from
Mar 20, 2026
Merged

Bugfix in calculating max diff for per base sequence content #91

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928c419
src/Module.hpp: silencing a compiler warning for unused arg
andrewdavidsmith Mar 20, 2026
75b5a26
src/Module.cpp: fixing a bug when calculating the maximum difference …
andrewdavidsmith Mar 20, 2026
37a012c
test/md5sum.txt: updating test output file hashes for bugfix in calcu…
andrewdavidsmith Mar 20, 2026
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30 changes: 9 additions & 21 deletions src/Module.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -772,7 +772,8 @@ ModulePerBaseSequenceQuality::make_html_data() {
}

void
ModulePerBaseSequenceQuality::read_data_line(const std::string &line) {}
ModulePerBaseSequenceQuality::read_data_line(
[[maybe_unused]] const std::string &line) {}

/************** PER TILE SEQUENCE QUALITY ********************/
const std::string ModulePerTileSequenceQuality::module_name =
Expand Down Expand Up @@ -1116,28 +1117,15 @@ ModulePerBaseSequenceContent::summarize_module(FastqStats &stats) {
t_pos =
100.0 * t_pos / std::max(std::numeric_limits<double>::min(), total_pos);

// for WGBS, we only test non-bisulfite treated bases
if (!is_reverse_complement)
max_diff = std::max(max_diff, std::fabs(a_pos - g_pos));
else
max_diff = std::max(max_diff, std::fabs(c_pos - t_pos));

if (!is_bisulfite) {
max_diff = std::max(max_diff, std::fabs(a_pos - c_pos));
max_diff = std::max(max_diff, std::fabs(a_pos - t_pos));
max_diff = std::max(max_diff, std::fabs(c_pos - g_pos));
max_diff = std::max(max_diff, std::fabs(t_pos - g_pos));

if (!is_reverse_complement)
max_diff = std::max(max_diff, std::fabs(c_pos - t_pos));
else
max_diff = std::max(max_diff, std::fabs(a_pos - g_pos));
}
// WGBS specific base content count
else {
if (is_bisulfite) {
// for WGBS, we only test non-bisulfite treated bases
max_diff =
std::max(max_diff, std::fabs((c_pos + t_pos) - (a_pos + g_pos)));
std::max(max_diff, is_reverse_complement ? std::fabs(c_pos - t_pos)
: std::fabs(a_pos - g_pos));
continue;
}
max_diff = std::max(
max_diff, std::max(std::fabs(a_pos - t_pos), std::fabs(c_pos - g_pos)));
}

// turns above values to percent
Expand Down
2 changes: 1 addition & 1 deletion src/Module.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -159,7 +159,7 @@ class ModulePerBaseSequenceQuality : public Module {
void
write_module(std::ostream &os);
void
read_data_line(const std::string &line);
read_data_line([[maybe_unused]] const std::string &line);
std::string
make_html_data();
};
Expand Down
4 changes: 2 additions & 2 deletions test/md5sum.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -2,8 +2,6 @@ fe1d421b95e1289f62d5f60157b8bed0 test_output/SRR1853178_1/fastqc_data.txt
36df1dcab539ba4ef885239fc8524636 test_output/SRR1853178_1/summary.txt
19c984bdddd5d656e8bb9f50bb08fc5a test_output/SRR3897196_2/fastqc_data.txt
80cd130958bcb2219f1e5a07d06a3b6e test_output/SRR3897196_2/summary.txt
eafecdffa8aa5357c70e3df61704d5c8 test_output/SRR9624732_1/fastqc_data.txt
a525d455b17eb6ba84cd2a60d281a2b0 test_output/SRR9624732_1/summary.txt
9bb60254ebbca76328a0fc5c7d35d38f test_output/SRR10143153_2/fastqc_data.txt
19f1811f324e4c44154f659bb6e22806 test_output/SRR10143153_2/summary.txt
b5b45d94670c42ddff565d53ff9b34e8 test_output/SRR1772703.lite.1/fastqc_data.txt
Expand All @@ -28,3 +26,5 @@ b736ee95d5c450ef5c0dda31957b6818 test_output/SRR3897196_1/summary.txt
9ad191925d47a57d4f8b12f21ba0a7c3 test_output/SRR10143153_1/summary.txt
255171890adc7117a5c4fae6d355091e test_output/SRR1853178_2/fastqc_data.txt
c331d0f7a6aa9d72be41ac531f9ba269 test_output/SRR1853178_2/summary.txt
c94f94bdfbed9b83f156c15ffea84127 test_output/SRR9624732_1/summary.txt
b433a0d30f3952f2f5f94cd90ecc6939 test_output/SRR9624732_1/fastqc_data.txt
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