simple_pileup_common.hpp File Reference

#include "genesis/population/format/simple_pileup_reader.hpp"
#include "genesis/sequence/functions/quality.hpp"
#include <string>
#include <vector>

Go to the source code of this file.

Namespaces
	genesis
	Container namespace for all symbols of genesis in order to keep them separate when used as a library.
	genesis::population

Functions
SampleCounts	convert_to_sample_counts (SimplePileupReader::Sample const &sample, unsigned char min_phred_score)
Variant	convert_to_variant (SimplePileupReader::Record const &record, unsigned char min_phred_score)
genesis::sequence::QualityEncoding	guess_pileup_quality_encoding (std::shared_ptr< utils::BaseInputSource > source, size_t max_lines=0)
	Guess the quality score encoding for an (m)pileup input, based on counts of how often each char appeared in the quality string (of the input pileup file for example). More...