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Report both total reads and alignments; version bump #86

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Apr 21, 2024
Merged

Report both total reads and alignments; version bump #86

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6 changes: 4 additions & 2 deletions src/Metrics.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -344,7 +344,6 @@ std::ofstream& operator<<(std::ofstream &stream, rnaseqc::Metrics &counter)
std::vector<std::string> keys = {
//"Alternative Alignments",
//"Chimeric Reads",
"Duplicate Reads",
"End 1 Antisense",
"End 2 Antisense",
"End 1 Bases",
Expand Down Expand Up @@ -375,11 +374,14 @@ std::ofstream& operator<<(std::ofstream &stream, rnaseqc::Metrics &counter)
"Split Reads",
"Total Bases",
"Total Mapped Pairs",
"Total Reads",
// "Total Reads",
"Unique Mapping, Vendor QC Passed Reads",
"Unpaired Reads"
};
stream << "Total Alignments\t" << counter.get("Total Alignments") << std::endl;
stream << "Alternative Alignments\t" << counter.get("Alternative Alignments") << std::endl;
stream << "Supplementary Alignments\t" << counter.get("Supplementary Alignments") << std::endl;
stream << "Total Reads\t" << counter.get("Total Alignments") - counter.get("Alternative Alignments") - counter.get("Supplementary Alignments") << std::endl;
stream << "Chimeric Fragments\t";
if (counter.get("Chimeric Fragments_tag"))
{
Expand Down
7 changes: 4 additions & 3 deletions src/RNASeQC.cpp
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Expand Up @@ -22,7 +22,7 @@ using namespace args;
using namespace rnaseqc;

const string NM = "NM";
const string VERSION = "RNASeQC 2.4.2";
const string VERSION = "RNASeQC 2.4.3";
const double MAD_FACTOR = 1.4826;
const unsigned int LEGACY_MAX_READ_LENGTH = 100000u;
const int LEGACY_SPLIT_DISTANCE = 100;
Expand Down Expand Up @@ -89,7 +89,7 @@ int main(int argc, char* argv[])
const unsigned int BASE_MISMATCH_THRESHOLD = baseMismatchThreshold ? baseMismatchThreshold.Get() : 6u;
const unsigned int MAPPING_QUALITY_THRESHOLD = mappingQualityThreshold ? mappingQualityThreshold.Get() : (LegacyMode.Get() ? 4u : 255u);
const unsigned int COVERAGE_MASK = coverageMaskSize ? coverageMaskSize.Get() : 500u;
// const int SPLIT_DISTANCE = 100;
// const int SPLIT_DISTANCE = 100;
const int VERBOSITY = verbosity ? verbosity.Get() : 0;
const int BIAS_OFFSET = biasOffset ? biasOffset.Get() : 0;
const int BIAS_WINDOW = biasWindow ? biasWindow.Get() : 100;
Expand Down Expand Up @@ -252,6 +252,7 @@ int main(int argc, char* argv[])
}
//count metrics based on basic read data
if (alignment.SecondaryFlag()) counter.increment("Alternative Alignments");
if (alignment.SupplementaryFlag()) counter.increment("Supplementary Alignments");
else if (alignment.QCFailFlag()) counter.increment("Failed Vendor QC");
else if (alignment.MapQuality() < MAPPING_QUALITY_THRESHOLD) counter.increment("Low Mapping Quality");
if (alignment.SupplementaryFlag() && !(LegacyMode.Get() || readStringTag(alignment, chimeric_tag, trash)))
Expand Down Expand Up @@ -393,7 +394,7 @@ int main(int argc, char* argv[])
if (VERBOSITY > 1) cout << "Average Reads/Sec: " << static_cast<double>(alignmentCount) / difftime(t2, t1) << endl;
cout << "Estimating library complexity..." << endl;
}
counter.increment("Total Reads", alignmentCount);
counter.increment("Total Alignments", alignmentCount);
double duplicates = static_cast<double>(counter.get("Duplicate Pairs"));
double unique = static_cast<double>(counter.get("Unique Fragments"));
double numReads = duplicates + unique;
Expand Down
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