bin_reads.h

#ifndef MGEMS_ASSIGN_READS_H
#define MGEMS_ASSIGN_READS_H

#include <fstream>
#include <vector>
#include <string>

#include "Matrix.hpp"

#include "mGEMS_alignment.hpp"

namespace mGEMS {
void FilterTargetGroups(const std::vector<std::string> &group_names,
			const std::vector<double> &abundances,
			const double min_abundance,
			std::vector<std::string> *target_groups);
// mGEMS::ReadAbundances
//   Reads in the `_abundances.txt` file from mSWEEP.
//   Input:
//     `stream`: Stream pointing to the `_abundances.txt` file.
//   Output:
//     `abundances`: The relative abundances (2nd column in the file).
//     `groups`: Names of the reference lineages (1st column).
void ReadAbundances(std::istream &stream, std::vector<double> *abundances,
		    std::vector<std::string> *groups);

// mGEMS::WriteBin
//   Writes the ids (i. e. line numbers divided by 4) of the reads in the bin.
//   Input:
//     `binned_reads`: The bin.
//     `of`: Stream for the output.
void WriteBin(const std::vector<uint32_t> &binned_reads, std::ostream &of);

// mGEMS::WriteAssignments
//   Writes the boolean read to group assignments matrix in tab-separated format.
//   Input:
//     `assignments_mat`: The matrix from mGEMS::Bin.
//     `aln`: Themisto pseudoalignments.
//     `of`: Stream for the output.
void WriteAssignments(const std::vector<std::vector<bool>> &assignments_mat,
		      const mGEMS::Alignment &aln, std::ostream &of);

// mGEMS::Bin
//   Returns a 2D vector that contains the ids (line numbers in the
//   .fastq files divided by 4) of reads assigned to the groups
//   that were requested.
//   Input:
//     `aln`: Pseudoalignments from Themisto.
//     `abundances`: Relative abundances from mSWEEP.
//     `theta_frac`: Tuning parameter for the thresholds..
//     `single_only`: Only assign reads that are assigned to just a single lineage.
//     `probs_file`: Read probability matrix (.probs file) from mSWEEP.
//     `*target_groups`: Names of the groups that bins will be created for.
//   Output:
//     `*target_groups`: The names will be reordered to match the order of the bins.
//      `*unassigned_bin`: Vector containing the ids of reads that were not assigned to any bin.
//      `out_bins`: Vector containing the bins for the groups given in `*target_groups`.
//      `*assignments_mat`: The read assignment matrix from AssignProbs.
std::vector<std::vector<uint32_t>> Bin(const mGEMS::Alignment &aln,
				       const std::vector<double> &abundances,
				       const long double theta_frac,
				       const bool single_only,
				       std::istream &probs_file,
				       std::vector<std::string> *target_groups,
				       std::vector<uint32_t> *unassigned_bin,
				       std::vector<std::vector<bool>> *assignments_mat);
// mGEMS::BinFromMatrix
//   Same as above but perform the binning on a probability
//   matrix that has already been read into memory.
std::vector<std::vector<uint32_t>> BinFromMatrix(const std::vector<std::vector<uint32_t>> &reads_to_ecs,
						 const std::vector<double> &abundances,
						 const seamat::Matrix<double> &probs_mat,
						 const std::vector<std::string> &all_group_names,
						 std::vector<std::string> *target_groups);
}

#endif