delete_utils.h

// read distribution of insert length, etc
#define SEQAN_HAS_ZLIB 1
#include "utils.h"
#ifndef DELETE_UTILS_H
#define DELETE_UTILS_H

struct ParametersAluDelete: public ParametersAlu
{
	int minLen_alu_del, coverage_high;
	ParametersAluDelete(): minLen_alu_del(200),
	coverage_high(90)
	{}
};

class GetIOPathDelete : public GetIOPath{
	public:
		string path0_;
		GetIOPathDelete(string config_file);
};

enum T_READ
{useless_read, unknow_read, mid_read, clip_read}; // used for deletions

bool get_align_pos(int aluBegin, int aluEnd, int beginPos, int endPos, int &ref_a, int &ref_b, int &read_a, int &read_b, seqan::BamAlignmentRecord &record);
bool split_global_align(seqan::CharString &fa_seq, seqan::BamAlignmentRecord &record, int read_a, int read_b, int &score, int &align_len);
T_READ classify_read(seqan::BamAlignmentRecord & record, int aluBegin, int aluEnd, FastaFileHandler *fasta_fh, bool debug = false);

bool combine_pns_vcf(string path0, string f_in_suffix, string f_out, vector <string> &pns, vector <string> & chrns, map <string, std::set<int> > & chrn_aluBegin, float llh_th, string ref_name);

string tread_toStr(T_READ td);

#endif