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Add back REF/ALT to csv output in addition to resolved GT fields #83

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Merged
merged 1 commit into from
Mar 13, 2025
Merged

Add back REF/ALT to csv output in addition to resolved GT fields #83

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13 changes: 12 additions & 1 deletion src/genomicsdb_processor.h
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Original file line number Diff line number Diff line change
Expand Up @@ -92,15 +92,26 @@ class ColumnarVariantCallProcessor : public GenomicsDBVariantCallProcessor {
const int64_t* coordinates,
const genomic_interval_t& genomic_interval,
const std::vector<genomic_field_t>& genomic_fields);
void process_str_field(const std::string& field_name, PyObject *calls, int dims, npy_intp *sizes) {
auto found = std::find(m_field_names.begin(), m_field_names.end(), field_name);
if (found != m_field_names.end()) {
PyDict_SetItem(calls, PyUnicode_FromString(field_name.c_str()),
PyArray_SimpleNewFromData(dims, sizes, NPY_OBJECT, m_string_fields[field_name].data()));
}
}
PyObject* construct_data_frame() {
int dims = 1;
npy_intp sizes[1] = { static_cast<npy_intp>(m_sample_names.size()) };
PyObject *calls = PyDict_New();
PyDict_SetItem(calls, PyUnicode_FromString("Sample"), PyArray_SimpleNewFromData(dims, sizes, NPY_OBJECT, m_sample_names.data()));
PyDict_SetItem(calls, PyUnicode_FromString("CHR"), PyArray_SimpleNewFromData(dims, sizes, NPY_OBJECT, m_chrom.data()));
PyDict_SetItem(calls, PyUnicode_FromString("POS"), PyArray_SimpleNewFromData(dims, sizes, NPY_INT64, m_pos.data()));

// Process REF, ALT and GT first.
process_str_field("REF", calls, dims, sizes);
process_str_field("ALT", calls, dims, sizes);
process_str_field("GT", calls, dims, sizes);
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Naive question: can you tell me why we process REF, ALT, GT first instead of in the loop?

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They could be in any order based on how GenomicsDB processes them. We could let the loop handle it, but sometimes, the order is ALT,REF,..,GT. I just thought it nicer to have REF before ALT, guess it does not matter for GT as much.. But, I can process them in the loop if that is OK too. Let me know.

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Yeah, can't decide. My initial concern was that this bit of code gets invoked for each variant so trying to minimize any extraneous code. But that's probably micro-optimization...thoughts?

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@nalinigans nalinigans Mar 13, 2025 •
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This bit of code is not invoked per variant call, it happens only once per query - see. The calls themselves are already populated as m_string_fields in the dictionary backed by std::map<std::string, std::vector<PyObject *>> m_string_fields as part of the code here. That said, I could probably order them at initialization.

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Ah - thanks for that clarification, I misread this as being part of process somehow. I think this is good to merge the way it is if you want.

for (auto field_name: m_field_names) {
if (field_name == "REF" || field_name == "ALT" || field_name == "GT") continue;
if (m_string_fields.find(field_name) != m_string_fields.end()) {
PyDict_SetItem(calls, PyUnicode_FromString(field_name.c_str()),
PyArray_SimpleNewFromData(dims, sizes, NPY_OBJECT, m_string_fields[field_name].data()));
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2 changes: 1 addition & 1 deletion src/genomicsdb_processor_columnar.cpp
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Expand Up @@ -41,7 +41,7 @@ void ColumnarVariantCallProcessor::process(const interval_t& interval) {
for (auto& field_type_pair : *genomic_field_types) {
std::string field_name = field_type_pair.first;
genomic_field_type_t field_type = field_type_pair.second;
if (!field_name.compare("END") || !field_name.compare("REF") || !field_name.compare("ALT")) {
if (!field_name.compare("END")) {
continue;
}
m_field_names.push_back(field_name);
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