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r215: binning with external list (NOT TESTED!!)

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This commit is contained in:
Heng Li
2020-04-10 01:06:43 -04:00
parent f32bfc904a
commit 71328f7423
2 changed files with 60 additions and 2 deletions
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Trio.cpp
+59 -1
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@@ -3,8 +3,10 @@
#include <stdarg.h>
#include <string.h>
#include <assert.h>
#include <zlib.h>
#include "khashl.h" // hash table
#include "kthread.h"
#include "kseq.h"
#include "Process_Read.h"
#include "htab.h"
#include "CommandLines.h"
@@ -27,6 +29,8 @@ KHASHL_SET_INIT(static klib_unused, yak_ht_t, yak_ht, uint64_t, yak_ch_hash, yak
typedef const char *ha_cstr_t;
KHASHL_MAP_INIT(static klib_unused, cstr_ht_t, cstr_ht, ha_cstr_t, int64_t, kh_hash_str, kh_eq_str)
KSTREAM_INIT(gzFile, gzread, 65536)
typedef struct {
struct yak_ht_t *h;
} yak_ch1_t;
@@ -284,8 +288,62 @@ static void ha_triobin_yak(const hifiasm_opt_t *opt)
fprintf(stderr, "[M::%s::%.3f*%.2f] ==> partitioned reads using yak dumps\n", __func__, yak_realtime(), yak_cpu_usage());
}
static int ha_triobin_set_list(const cstr_ht_t *h, const char *fn, int flag)
{
gzFile fp;
kstream_t *ks;
kstring_t str = {0,0,0};
int dret;
int64_t n_tot = 0, n_bin = 0;
fp = gzopen(fn, "r");
if (fp == 0) {
fprintf(stderr, "ERROR: failed to open file '%s'\n", fn);
return -1;
}
ks = ks_init(fp);
while (ks_getuntil(ks, KS_SEP_LINE, &str, &dret) >= 0) {
char *p;
khint_t k;
++n_tot;
for (p = str.s; *p; ++p)
if (*p == '\t' || *p == ' ')
*p = 0;
k = cstr_ht_get(h, str.s);
if (k != kh_end(h)) {
R_INF.trio_flag[kh_val(h, k)] = flag;
++n_bin;
}
}
free(str.s);
ks_destroy(ks);
gzclose(fp);
fprintf(stderr, "[M::%s::%.3f*%.2f] flagged %ld reads, out of %ld lines in file '%s'\n",
__func__, yak_realtime(), yak_cpu_usage(), (long)n_bin, (long)n_tot, fn);
return 0;
}
static void ha_triobin_list(const hifiasm_opt_t *opt)
{
int64_t i;
khint_t k;
cstr_ht_t *h;
assert(R_INF.total_reads < (uint32_t)-1);
h = cstr_ht_init();
for (i = 0; i < (int64_t)R_INF.total_reads; ++i) {
int absent;
char *str = (char*)calloc(Get_NAME_LENGTH(R_INF, i) + 1, 1);
strncpy(str, Get_NAME(R_INF, i), Get_NAME_LENGTH(R_INF, i));
k = cstr_ht_put(h, str, &absent);
if (absent) kh_val(h, k) = i;
}
fprintf(stderr, "[M::%s::%.3f*%.2f] created the hash table for read names\n", __func__, yak_realtime(), yak_cpu_usage());
ha_triobin_set_list(h, opt->fn_bin_list[0], FATHER);
ha_triobin_set_list(h, opt->fn_bin_list[1], MOTHER);
for (k = 0; k < kh_end(h); ++k)
if (kh_exist(h, k))
free((char*)kh_key(h, k));
cstr_ht_destroy(h);
fprintf(stderr, "[M::%s::%.3f*%.2f] ==> partitioned reads with external lists\n", __func__, yak_realtime(), yak_cpu_usage());
}
void ha_triobin(const hifiasm_opt_t *opt)
@@ -293,6 +351,6 @@ void ha_triobin(const hifiasm_opt_t *opt)
memset(R_INF.trio_flag, AMBIGU, R_INF.total_reads * sizeof(uint8_t));
if (opt->fn_bin_list[0] && opt->fn_bin_list[1])
ha_triobin_list(opt);
else if (opt->fn_bin_yak[0] && opt->fn_bin_yak[1])
if (opt->fn_bin_yak[0] && opt->fn_bin_yak[1])
ha_triobin_yak(opt);
}