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Updating numerical format for sequence quality (base and tile) #93

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Merged
andrewdavidsmith merged 2 commits into from
Mar 25, 2026
+46 −35
Merged

Updating numerical format for sequence quality (base and tile) #93

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cd18cde
src/Module.cpp: updating output precision for the per base sequence q…
andrewdavidsmith Mar 25, 2026
3d80372
test/md5sum.txt: updating test output file hashes for updated numeric…
andrewdavidsmith Mar 25, 2026
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33 changes: 22 additions & 11 deletions src/Module.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -736,14 +736,22 @@ ModulePerBaseSequenceQuality::make_grade() {

void
ModulePerBaseSequenceQuality::write_module(std::ostream &os) {
constexpr auto max_precision{std::numeric_limits<double>::digits10};
const auto default_precision{os.precision()};
os << "#Base\tMean\tMedian\tLower Quartile\tUpper Quartile"
<< "\t10th Percentile\t90th Percentile\n";

// GS: TODO make base groups
for (std::size_t i = 0; i < num_groups; ++i) {
os << base_groups[i] << "\t" << group_mean[i] << "\t" << group_median[i]
<< "\t" << group_lquartile[i] << "\t" << group_uquartile[i] << "\t"
<< group_ldecile[i] << "\t" << group_udecile[i] << "\n";
// clang-format off
os << base_groups[i] << "\t"
<< std::setprecision(max_precision) << group_mean[i] << "\t"
<< std::fixed << std::setprecision(1) << group_median[i] << "\t"
<< std::fixed << std::setprecision(1) << group_lquartile[i] << "\t"
<< std::fixed << std::setprecision(1) << group_uquartile[i] << "\t"
<< std::fixed << std::setprecision(1) << group_ldecile[i] << "\t"
<< std::fixed << std::setprecision(1) << group_udecile[i] << "\n"
<< std::defaultfloat << std::setprecision(default_precision);
// clang-format on
}
}

Expand Down Expand Up @@ -869,16 +877,17 @@ ModulePerTileSequenceQuality::make_grade() {

void
ModulePerTileSequenceQuality::write_module(std::ostream &os) {

constexpr auto max_precision{std::numeric_limits<double>::digits10};
const auto default_precision{os.precision()};
// prints tiles sorted by value
os << "#Tile\tBase\tMean\n";
for (std::size_t i = 0; i < std::size(tiles_sorted); ++i) {
for (std::size_t j = 0; j < max_read_length; ++j) {

if (std::size(tile_position_quality[tiles_sorted[i]]) >= j) {
os << tiles_sorted[i] << "\t" << j + 1 << "\t"
<< tile_position_quality[tiles_sorted[i]][j];
os << "\n";
<< std::setprecision(max_precision)
<< tile_position_quality[tiles_sorted[i]][j]
<< std::setprecision(default_precision) << "\n";
}
}
}
Expand Down Expand Up @@ -1294,7 +1303,8 @@ ModulePerBaseSequenceContent::make_html_data() {
const std::string ModulePerSequenceGCContent::module_name =
"Per sequence GC content";
ModulePerSequenceGCContent::ModulePerSequenceGCContent(
const FalcoConfig &config) : Module(ModulePerSequenceGCContent::module_name) {
const FalcoConfig &config) :
Module(ModulePerSequenceGCContent::module_name) {
auto gc_vars = config.limits.find("gc_sequence")->second;
gc_warn = gc_vars.find("warn")->second;
gc_error = gc_vars.find("error")->second;
Expand Down Expand Up @@ -2152,8 +2162,9 @@ ModuleKmerContent::write_module(std::ostream &os) {
const std::size_t kmer = kmers_to_report[i].first;
os << size_t_to_seq(kmer, kmer_size) << "\t" << total_kmer_counts[kmer]
<< "\t"
<< "0.0" << "\t" << obs_exp_max[kmer] << "\t"
<< where_obs_exp_is_max[kmer] << "\n";
<< "0.0"
<< "\t" << obs_exp_max[kmer] << "\t" << where_obs_exp_is_max[kmer]
<< "\n";
}
}

Expand Down
48 changes: 24 additions & 24 deletions test/md5sum.txt
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Original file line number Diff line number Diff line change
@@ -1,30 +1,30 @@
37014d8b6e5338c54f6e39a9a65448da test_output/SRR1853178_1/fastqc_data.txt
36df1dcab539ba4ef885239fc8524636 test_output/SRR1853178_1/summary.txt
ce1121532724dbfc9f75408f3b6bb1b8 test_output/SRR3897196_2/fastqc_data.txt
80cd130958bcb2219f1e5a07d06a3b6e test_output/SRR3897196_2/summary.txt
189608afba8bc88f237259a8801417c4 test_output/SRR9624732_1/fastqc_data.txt
3dedc28a43582799ca5c2de6853e3b67 test_output/SRR10143153_1/fastqc_data.txt
9ad191925d47a57d4f8b12f21ba0a7c3 test_output/SRR10143153_1/summary.txt
10a3ea6bdc7e89f7c554060987300a74 test_output/SRR9624732_1/fastqc_data.txt
c94f94bdfbed9b83f156c15ffea84127 test_output/SRR9624732_1/summary.txt
a96c16a6ac4cce541f745b25d5b04fef test_output/SRR10143153_2/fastqc_data.txt
19f1811f324e4c44154f659bb6e22806 test_output/SRR10143153_2/summary.txt
1991f6ba435c23642d3141856864ad99 test_output/SRR1772703.lite.1/fastqc_data.txt
f3247224a624ef3e715251881cbb92d6 test_output/SRR3897196_2/fastqc_data.txt
80cd130958bcb2219f1e5a07d06a3b6e test_output/SRR3897196_2/summary.txt
efe57274c57b831a35ece02a55b10b44 test_output/SRR10124060/fastqc_data.txt
776f7d1b53bbed8683de9ca1d2529f1e test_output/SRR10124060/summary.txt
00499da31b38353a64b3fbf865134f44 test_output/SRR3897196_1/fastqc_data.txt
b736ee95d5c450ef5c0dda31957b6818 test_output/SRR3897196_1/summary.txt
f40ed230afd94501978ae4e5b4b723af test_output/SRR6387347/fastqc_data.txt
a61f65047e76f93300967cf399d044de test_output/SRR6387347/summary.txt
b5b45572ad129a4306d4c1cfdea9a394 test_output/SRR1772703.lite.1/fastqc_data.txt
ad5727295e7c8de6eb6874837bf1518f test_output/SRR1772703.lite.1/summary.txt
657b3a5b77d8a7b9d5e8ff3c08dae765 test_output/SRR9624732_2/fastqc_data.txt
8241ed3eef4e21c6bc9ab6d55905c45e test_output/SRR9878537.lite.1/fastqc_data.txt
e5c40997d4993c07e164ee5598c39cf9 test_output/SRR9878537.lite.1/summary.txt
b513012ef040d0cb53f311d860326704 test_output/SRR9624732_2/fastqc_data.txt
fefc5d746f853c14b5e00421ad1ec260 test_output/SRR9624732_2/summary.txt
e4df74ec74cf5ee69dd76d08825d1b2c test_output/SRR10124060/fastqc_data.txt
776f7d1b53bbed8683de9ca1d2529f1e test_output/SRR10124060/summary.txt
e5e62fbaefdf730452e0133eca248f69 test_output/SRR891268_2/fastqc_data.txt
6583ae57d3bb86621ad8dcca23372f81 test_output/SRR1853178_2/fastqc_data.txt
c331d0f7a6aa9d72be41ac531f9ba269 test_output/SRR1853178_2/summary.txt
4d1ef8e0aad4027b5e59ef869cd9d196 test_output/SRR1853178_1/fastqc_data.txt
36df1dcab539ba4ef885239fc8524636 test_output/SRR1853178_1/summary.txt
b45e9f0c7840b539470d065b4bf2797c test_output/SRR10143153_2/fastqc_data.txt
19f1811f324e4c44154f659bb6e22806 test_output/SRR10143153_2/summary.txt
88b9fabb6c5e41326b5fe93e94875893 test_output/SRR891268_2/fastqc_data.txt
20a8e50baace4c672622793874a3d7de test_output/SRR891268_2/summary.txt
401d183c10a50bdf0eac497c63630918 test_output/SRR9878537.lite.1/fastqc_data.txt
e5c40997d4993c07e164ee5598c39cf9 test_output/SRR9878537.lite.1/summary.txt
8334959b07f8baa92548ad939aff5df0 test_output/SRR891268_1/fastqc_data.txt
3177a87258f3a9edd6a02a740a207b34 test_output/SRR891268_1/fastqc_data.txt
69e7d0c53cd2e67117637c408b65333a test_output/SRR891268_1/summary.txt
985da7c31b11a4cb40686bf20d0df9cd test_output/SRR6059706.lite.1/fastqc_data.txt
dbd6ffc33ab0c131f70db7be3398ddae test_output/SRR6059706.lite.1/fastqc_data.txt
e348e4bcc7fc6f05e989ac7858d2b287 test_output/SRR6059706.lite.1/summary.txt
2eb1acd772bf29031455cb38072a396f test_output/SRR6387347/fastqc_data.txt
a61f65047e76f93300967cf399d044de test_output/SRR6387347/summary.txt
d79d49f81677f19247bbd9cd6021f903 test_output/SRR3897196_1/fastqc_data.txt
b736ee95d5c450ef5c0dda31957b6818 test_output/SRR3897196_1/summary.txt
c93b8e4f2f14664419f57fb33edf5b64 test_output/SRR10143153_1/fastqc_data.txt
9ad191925d47a57d4f8b12f21ba0a7c3 test_output/SRR10143153_1/summary.txt
940b43bfbddd9d22cac65895c6d37ae8 test_output/SRR1853178_2/fastqc_data.txt
c331d0f7a6aa9d72be41ac531f9ba269 test_output/SRR1853178_2/summary.txt
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