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r207: multiple input files were not working

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Heng Li
2020-04-07 12:40:10 -04:00
parent a79fd0f360
commit 8efcdefcaf
2 changed files with 10 additions and 6 deletions
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CommandLines.h
+1 -1
View File
@@ -3,7 +3,7 @@
#include <pthread.h> #include <pthread.h>
#define HA_VERSION "0.3.0-dirty-r206" #define HA_VERSION "0.3.0-dirty-r207"
#define VERBOSE 0 #define VERBOSE 0
htab.cpp
+9 -5
View File
@@ -482,6 +482,7 @@ KSEQ_INIT(gzFile, gzread)
#define HAF_RS_WRITE_LEN 0x4 #define HAF_RS_WRITE_LEN 0x4
#define HAF_RS_WRITE_SEQ 0x8 #define HAF_RS_WRITE_SEQ 0x8
#define HAF_RS_READ 0x10 #define HAF_RS_READ 0x10
#define HAF_CREATE_NEW 0x20
typedef struct { // global data structure for kt_pipeline() typedef struct { // global data structure for kt_pipeline()
const yak_copt_t *opt; const yak_copt_t *opt;
@@ -665,12 +666,13 @@ static void *worker_count(void *data, int step, void *in) // callback for kt_pip
return 0; return 0;
} }
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) 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)
{ {
int read_rs = (rs && (flag & HAF_RS_READ)); int read_rs = (rs && (flag & HAF_RS_READ));
pl_data_t pl; pl_data_t pl;
gzFile fp = 0; gzFile fp = 0;
memset(&pl, 0, sizeof(pl_data_t)); memset(&pl, 0, sizeof(pl_data_t));
pl.n_seq = *n_seq;
if (read_rs) { if (read_rs) {
pl.rs_in = rs; pl.rs_in = rs;
init_UC_Read(&pl.ucr); init_UC_Read(&pl.ucr);
@@ -684,13 +686,13 @@ static ha_ct_t *yak_count(const yak_copt_t *opt, const char *fn, int flag, ha_pt
pl.opt = opt; pl.opt = opt;
pl.flag = flag; pl.flag = flag;
if (p0) { if (p0) {
pl.pt = p0, pl.create_new = 0; pl.pt = p0, pl.create_new = 0; // never create new elements in a position table
assert(p0->k == opt->k && p0->pre == opt->pre); assert(p0->k == opt->k && p0->pre == opt->pre);
} else if (c0) { } else if (c0) {
pl.ct = c0, pl.create_new = 0; pl.ct = c0, pl.create_new = !!(flag&HAF_CREATE_NEW);
assert(c0->k == opt->k && c0->pre == opt->pre); assert(c0->k == opt->k && c0->pre == opt->pre);
} else { } else {
pl.create_new = 1; pl.create_new = 1; // alware create new elements if the count table is empty
pl.ct = ha_ct_init(opt->k, opt->pre, opt->bf_n_hash, opt->bf_shift); pl.ct = ha_ct_init(opt->k, opt->pre, opt->bf_n_hash, opt->bf_shift);
} }
kt_pipeline(3, worker_count, &pl, 3); kt_pipeline(3, worker_count, &pl, 3);
@@ -700,12 +702,14 @@ static ha_ct_t *yak_count(const yak_copt_t *opt, const char *fn, int flag, ha_pt
kseq_destroy(pl.ks); kseq_destroy(pl.ks);
gzclose(fp); gzclose(fp);
} }
*n_seq = pl.n_seq;
return pl.ct; return pl.ct;
} }
ha_ct_t *ha_count(const hifiasm_opt_t *asm_opt, int flag, ha_pt_t *p0, const void *flt_tab, All_reads *rs) ha_ct_t *ha_count(const hifiasm_opt_t *asm_opt, int flag, ha_pt_t *p0, const void *flt_tab, All_reads *rs)
{ {
int i; int i;
int64_t n_seq = 0;
yak_copt_t opt; yak_copt_t opt;
ha_ct_t *h = 0; ha_ct_t *h = 0;
assert(!(flag & HAF_RS_WRITE_LEN) || !(flag & HAF_RS_WRITE_SEQ)); // not both assert(!(flag & HAF_RS_WRITE_LEN) || !(flag & HAF_RS_WRITE_SEQ)); // not both
@@ -722,7 +726,7 @@ ha_ct_t *ha_count(const hifiasm_opt_t *asm_opt, int flag, ha_pt_t *p0, const voi
opt.bf_shift = flag & HAF_COUNT_EXACT? 0 : asm_opt->bf_shift; opt.bf_shift = flag & HAF_COUNT_EXACT? 0 : asm_opt->bf_shift;
opt.n_thread = asm_opt->thread_num; opt.n_thread = asm_opt->thread_num;
for (i = 0; i < asm_opt->num_reads; ++i) for (i = 0; i < asm_opt->num_reads; ++i)
h = yak_count(&opt, asm_opt->read_file_names[i], flag, p0, h, flt_tab, rs); h = yak_count(&opt, asm_opt->read_file_names[i], flag|HAF_CREATE_NEW, p0, h, flt_tab, rs, &n_seq);
if (h && opt.bf_shift > 0) if (h && opt.bf_shift > 0)
ha_ct_destroy_bf(h); ha_ct_destroy_bf(h);
return h; return h;