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chhylp123
2021-02-02 13:09:29 -05:00
parent b2b4624cea
commit 167f880377
3 changed files with 45 additions and 1 deletions
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3
Assembly.cpp
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@@ -848,7 +848,8 @@ void ha_overlap_and_correct(int round)
b[i] = ha_ovec_init(0, (round == asm_opt.number_of_round - 1));
if(ha_idx) hom_cov = asm_opt.hom_cov;
if(ha_idx == NULL) ha_idx = ha_pt_gen(&asm_opt, ha_flt_tab, round == 0? 0 : 1, 0, &R_INF, &hom_cov, &het_cov); // build the index
if (round == 0 && ha_flt_tab == 0) // then asm_opt.hom_cov hasn't been updated
debug_adapter(&asm_opt, &R_INF);
if (round == 0 && ha_flt_tab == 0) // then asm_opt.hom_cov hasn't been updated
ha_opt_update_cov(&asm_opt, hom_cov);
if (asm_opt.required_read_name)
kt_for(asm_opt.thread_num, worker_ovec_related_reads, b, R_INF.total_reads);

42
htab.cpp
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@@ -720,6 +720,48 @@ static void *worker_count(void *data, int step, void *in) // callback for kt_pip
return 0;
}
void debug_adapter(const hifiasm_opt_t *asm_opt, All_reads *rs)
{
int ret;
uint32_t i, m, pass, unpass;
gzFile fp = 0;
kseq_t *ks = NULL;
UC_Read ucr;
init_UC_Read(&ucr);
for (i = m = pass = unpass = 0; i < (uint32_t)asm_opt->num_reads; ++i)
{
if ((fp = gzopen(asm_opt->read_file_names[i], "r")) == 0) continue;
ks = kseq_init(fp);
while ((ret = kseq_read(ks)) >= 0)
{
int l = ks->seq.l;
if((l - asm_opt->adapterLen*2) <= 0) continue;
recover_UC_Read(&ucr, rs, m);
fprintf(stderr, "l: %d, ucr.length: %lld, asm_opt->adapterLen: %d\n",
l, ucr.length, asm_opt->adapterLen);
if(memcmp(ucr.seq, ks->seq.s+asm_opt->adapterLen, ucr.length) == 0)
{
pass++;
}
else
{
unpass++;
}
m++;
}
kseq_destroy(ks);
gzclose(fp);
ks = NULL;
fp = 0;
}
destory_UC_Read(&ucr);
fprintf(stderr, "[M::%s::# reads: %u, # pass: %u, # unpass: %u\n]", __func__, m, pass, unpass);
exit(1);
}
static ha_ct_t *yak_count(const yak_copt_t *opt, const char *fn, int flag, ha_pt_t *p0, ha_ct_t *c0, const void *flt_tab, All_reads *rs, int64_t *n_seq)
{
///for 0-th counting, flag = HAF_COUNT_ALL|HAF_RS_WRITE_LEN|HAF_CREATE_NEW

1
htab.h
View File

@@ -62,6 +62,7 @@ void ha_triobin(const hifiasm_opt_t *opt);
void ha_sketch(const char *str, int len, int w, int k, uint32_t rid, int is_hpc, ha_mz1_v *p, const void *hf);
void ha_sketch_query(const char *str, int len, int w, int k, uint32_t rid, int is_hpc, ha_mz1_v *p, const void *hf, kvec_t_u8_warp* k_flag, kvec_t_u64_warp* dbg_ct);
int ha_analyze_count(int n_cnt, const int64_t *cnt, int *peak_het);
void debug_adapter(const hifiasm_opt_t *asm_opt, All_reads *rs);
static inline uint64_t yak_hash64(uint64_t key, uint64_t mask) // invertible integer hash function
{