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Cache Phred error probabilities during BAM QC #66

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Merged
kaichop merged 1 commit into from
Oct 1, 2026
Merged

Cache Phred error probabilities during BAM QC #66

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12 changes: 11 additions & 1 deletion src/hts_reader.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@ Class for reading a set number of records from a BAM file. Used for multi-thread
#include <sstream>
#include <fstream>
#include <math.h>
#include <array>
#include <algorithm> // std::find
#include <random>
#include <htslib/sam.h>
Expand Down Expand Up @@ -38,6 +39,15 @@ HTSReader::~HTSReader(){
// Update read and base counts
int HTSReader::updateReadAndBaseCounts(bam1_t* record, Basic_Seq_Statistics& basic_qc, Basic_Seq_Quality_Statistics& seq_quality_info, bool is_primary) {

// BAM qualities are bytes, so calculate each error probability once.
static const std::array<double, 256> base_quality_probabilities = [] {
std::array<double, 256> probabilities;
for (int quality = 0; quality < 256; quality++) {
probabilities[quality] = pow(10, -quality / 10.0);
}
return probabilities;
}();

// Update read QC
basic_qc.total_num_reads++; // Update the total number of reads
int read_length = (int) record->core.l_qseq;
Expand All @@ -55,7 +65,7 @@ int HTSReader::updateReadAndBaseCounts(bam1_t* record, Basic_Seq_Statistics& bas
seq_quality_info.base_quality_distribution[(uint64_t)base_quality]++;

// Convert the Phred quality value to a probability
double base_quality_prob = pow(10, -base_quality / 10.0);
double base_quality_prob = base_quality_probabilities[base_quality];
cumulative_base_prob += base_quality_prob;

// Get the base and update the base count
Expand Down
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