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// Functions used to smaple kmers and get trusted kmers
#ifndef _MOURISL_GETKMERS
#define _MOURISL_GETKMERS
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <pthread.h>
#include "Reads.h"
#include "Store.h"
#include "KmerCode.h"
#include "utils.h"
// The pattern of sampling for each read.
// Marks the bits to indicate whether to sample the
// kmer end at that position.
#define SAMPLE_PATTERN_COUNT 65536
struct _SamplePattern
{
char tag[ MAX_READ_LENGTH / 8 ] ;
} ;
// Strcture for handling multi-threads
struct _SampleKmersThreadArg
{
int kmerLength ;
double alpha ;
//int batchSize ;
Store *kmers ;
Reads *reads ;
struct _SamplePattern *samplePatterns ;
pthread_mutex_t *lock ;
pthread_mutex_t *lockPut ;
} ;
struct _StoreKmersThreadArg
{
int kmerLength ;
//int batchSize ;
int *threshold ;
Store *kmers ;
Store *trustedKmers ;
Reads *reads ;
char goodQuality ;
char badQuality ;
pthread_mutex_t *lock ;
} ;
void *SampleKmers_Thread( void *arg ) ;
void SampleKmersInRead( char *read, char *qual, int kmerLength, double alpha, KmerCode &kmerCode, Store *kmers ) ;
void *StoreKmers_Thread( void *arg ) ;
void StoreTrustedKmers( char *read, char *qual, int kmerLength, char badQuality, int *threshold,
KmerCode &kmerCode, Store *kmers, Store *trustedKmers ) ;
#endif
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