NGSNGS_misc.h

#ifndef NGSNGS_MISC_H
#define NGSNGS_MISC_H
#include "fasta_sampler.h"
#include <htslib/kstring.h>
#include <htslib/faidx.h>
#include <htslib/sam.h>
#include <htslib/vcf.h>
#include <htslib/bgzf.h>

void ReversComplement(char* seq);

void Complement(char* seq);

void reverseChar(char* str,int length);

void Complement_k(kstring_t* seq);

void ReversComplement_k(kstring_t* seq);

void CreateSeqQualKString(bam1_t *aln, kstring_t *Sequence, kstring_t *Quality,int offset);

char* PrintCigarBamSet1(size_t n_cigar,const uint32_t *cigar);

BedEntry* readBedFile(const char* filename, int* entryCount); // Function to read BED file and store entries in an array of BedEntry

int compareBedEntries(const void* a, const void* b); // compare the entries

void sortBedEntries(BedEntry* entries, int entryCount); // sort the entries according to chromosome and coordinates

BedEntry* mergeOverlappingRegions(BedEntry* entries, int entryCount, int* mergedCount); //create the overlapping entries

BedEntry* checkbedentriesfasta(fasta_sampler *fs,BedEntry* entries,int entryCount,int* ReferenceCount);

BedEntry* maskbedentriesfasta(fasta_sampler *fs,BedEntry* entries,int entryCount,int* ReferenceCount);

BedEntry* vcftobedentries(const char* bcffilename, int id,const char* Name,size_t flanking, int* entryCount,int* ploidy);

void addVariant(BedEntry* entry, const char* variant,int position);

BedEntry* VCFLinkageDisequilibrium(BedEntry* entries, int entryCount, int* mergedCount,int ploidy,size_t flanking);

#endif