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kmer_count_map.cpp
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kmer_count_map.cpp
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#include "config.h"
#include "kmer.h"
#include "kmer_count_map.h"
#include "utils.h"
#include "contig_store.h"
#include "kmer_ext_map.h"
#define FILTER_ON 0
KmerCountMap::KmerCountMap(k_t k)
: k(k),
sb_filter(INITIAL_CAPACITY, 0.001, 0,
(bloom_filter_hash_func_t) kmer_hash_K),
hash_map(INITIAL_CAPACITY, 0,
(hash_map_hash_func_t) kmer_hash_K,
(hash_map_eq_func_t) kmer_eq_K, kmer_size(k))
{
}
void KmerCountMap::insert(qekmer_t* qekmer)
{
#if FILTER_ON
if (!sb_filter.check(qekmer->kmer)) {
sb_filter.add(qekmer->kmer);
} else {
#endif
hash_map.try_insert(qekmer->kmer);
if (qekmer->lqual > Config::Q_MIN)
hash_map.map[qekmer->kmer].lquals[qekmer->exts.left]++;
if (qekmer->rqual > Config::Q_MIN)
hash_map.map[qekmer->kmer].rquals[qekmer->exts.right]++;
#if FILTER_ON
}
#endif
}
void KmerCountMap::trim(KmerExtMap& kmer_ext_map)
{
for (map_type_t::iterator it = hash_map.map.begin();
it != hash_map.map.end();
it++) {
kmer_t kmer = it->first;
ext_map_t ext_map = it->second.ext_map(Config::D_MIN);
if (ext_map.valid())
kmer_ext_map.insert(kmer, ext_map);
else
free(kmer);
}
}