PandaNextSeq panda_trim_overhangs(
PandaNextSeq inner,
void *inner_data,
PandaDestroy inner_destroy,
PandaLogProxy logger,
panda_nt *forward,
size_t forward_length,
panda_nt *reverse,
size_t reverse_length,
bool skip,
double threshold,
void **next_data,
PandaDestroy *next_destroy) {
struct hang_data *data = malloc(sizeof(struct hang_data));
size_t it;
data->next = inner;
data->next_data = inner_data;
data->next_destroy = inner_destroy;
data->skip = skip;
data->threshold = threshold;
for (it = 0; it < forward_length; it++)
data->forward[forward_length - it - 1] = forward[it];
for (it = 0; it < reverse_length; it++)
data->reverse[reverse_length - it - 1] = reverse[it];
data->forward_length = forward_length;
data->reverse_length = reverse_length;
data->logger = panda_log_proxy_ref(logger);
*next_data = data;
*next_destroy = hang_free;
return hang_next;
}
PandaMux panda_mux_new(
PandaNextSeq next,
void *next_data,
PandaDestroy next_destroy,
PandaLogProxy logger) {
PandaMux mux = malloc(sizeof(struct panda_mux));
mux->refcnt = 1;
mux->next = next;
mux->next_data = next_data;
mux->next_destroy = next_destroy;
mux->logger = panda_log_proxy_ref(logger);
mux->noalgn = NULL;
mux->noalgn_data = NULL;
mux->noalgn_destroy = NULL;
mux->child_count = 0;
pthread_mutex_init(&mux->mutex, NULL);
pthread_mutex_init(&mux->next_mutex, NULL);
pthread_rwlock_init(&mux->noalgn_rwlock, NULL);
return mux;
}
PandaAssembler panda_assembler_new_kmer(
PandaNextSeq next,
void *next_data,
PandaDestroy next_destroy,
PandaLogProxy logger,
size_t num_kmers) {
PandaAssembler assembler = malloc(sizeof(struct panda_assembler));
if (assembler == NULL) {
if (next_destroy != NULL) {
next_destroy(next_data);
}
return NULL;
}
assembler->refcnt = 1;
assembler->name[0] = '\0';
assembler->next = next;
assembler->next_data = next_data;
assembler->next_destroy = next_destroy;
assembler->noalgn = NULL;
assembler->noalgn_data = NULL;
assembler->noalgn_destroy = NULL;
assembler->rejected = NULL;
assembler->modules = NULL;
assembler->modules_length = 0;
assembler->modules_size = 0;
assembler->result.forward = NULL;
assembler->forward_primer_length = 0;
assembler->result.reverse = NULL;
assembler->result.sequence = assembler->result_seq;
assembler->reverse_primer_length = 0;
assembler->forward_trim = 0;
assembler->reverse_trim = 0;
assembler->nofpcount = 0;
assembler->norpcount = 0;
assembler->okcount = 0;
assembler->lowqcount = 0;
assembler->noalgncount = 0;
assembler->badreadcount = 0;
assembler->slowcount = 0;
assembler->count = 0;
assembler->post_primers = false;
assembler->threshold = log(0.6);
assembler->algo = panda_algorithm_simple_bayes_new();
memset(assembler->overlapcount, 0, 2 * PANDA_MAX_LEN * sizeof(long));
assembler->longest_overlap = 0;
assembler->num_kmers = num_kmers;
assert(1 << (8 * sizeof(seqindex)) > PANDA_MAX_LEN);
assembler->kmerseen = malloc(KMERSEEN_SIZE(num_kmers));
if (assembler->kmerseen == NULL) {
if (next_destroy != NULL) {
next_destroy(next_data);
}
free(assembler);
return NULL;
}
assembler->logger = panda_log_proxy_ref(logger);
#ifdef HAVE_PTHREAD
pthread_mutex_init(&assembler->mutex, NULL);
#endif
memset(assembler->kmerseen, 0, KMERSEEN_SIZE(num_kmers));
panda_assembler_set_maximum_overlap(assembler, 0);
panda_assembler_set_minimum_overlap(assembler, 2);
panda_assembler_set_primer_penalty(assembler, 0);
return assembler;
}
