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r254: added --ex-list and --ex-iter

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This commit is contained in:
Heng Li
2020-06-03 20:46:34 -04:00
parent e247c5f042
commit eddbc61952
6 changed files with 192 additions and 4 deletions
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Assembly.cpp
+5
View File
@@ -1159,10 +1159,15 @@ void ha_overlap_final(void)
int ha_assemble(void)
{
extern void ha_extract_print_list(const All_reads *rs, int n_rounds, const char *o);
int r, hom_cov = -1, ovlp_loaded = 0;
if (asm_opt.load_index_from_disk && load_all_data_from_disk(&R_INF.paf, &R_INF.reverse_paf, asm_opt.output_file_name)) {
ovlp_loaded = 1;
fprintf(stderr, "[M::%s::%.3f*%.2f] ==> loaded corrected reads and overlaps from disk\n", __func__, yak_realtime(), yak_cpu_usage());
if (asm_opt.extract_list) {
ha_extract_print_list(&R_INF, asm_opt.extract_iter, asm_opt.extract_list);
exit(0);
}
if (!(asm_opt.flag & HA_F_SKIP_TRIOBIN) && !(asm_opt.flag & HA_F_VERBOSE_GFA)) ha_triobin(&asm_opt);
///if (!(asm_opt.flag & HA_F_SKIP_TRIOBIN)) ha_triobin(&asm_opt);
if (asm_opt.flag & HA_F_WRITE_EC) Output_corrected_reads();
CommandLines.cpp
+4
View File
@@ -17,6 +17,8 @@ static ko_longopt_t long_options[] = {
{ "skip-triobin", ko_no_argument, 304 },
{ "max-od-ec", ko_no_argument, 305 },
{ "max-od-final", ko_no_argument, 306 },
{ "ex-list", ko_required_argument, 307 },
{ "ex-iter", ko_required_argument, 308 },
{ 0, 0, 0 }
};
@@ -400,6 +402,8 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
else if (c == 304) asm_opt->flag |= HA_F_SKIP_TRIOBIN;
else if (c == 305) asm_opt->max_ov_diff_ec = atof(opt.arg);
else if (c == 306) asm_opt->max_ov_diff_final = atof(opt.arg);
else if (c == 307) asm_opt->extract_list = opt.arg;
else if (c == 308) asm_opt->extract_iter = atoi(opt.arg);
else if (c == 'l')
{ ///0: disable purge_dup; 1: purge containment; 2: purge overlap
asm_opt->purge_level_primary = asm_opt->purge_level_trio = atoi(opt.arg);
CommandLines.h
+3 -1
View File
@@ -3,7 +3,7 @@
#include <pthread.h>
#define HA_VERSION "0.7-dirty-r253"
#define HA_VERSION "0.7-dirty-r254"
#define VERBOSE 0
@@ -26,6 +26,8 @@ typedef struct {
char* required_read_name;
char *fn_bin_yak[2];
char *fn_bin_list[2];
char *extract_list;
int extract_iter;
int thread_num;
int k_mer_length;
int mz_win;
Makefile
+4 -2
View File
@@ -4,7 +4,7 @@ CPPFLAGS=
INCLUDES=
OBJS= CommandLines.o Process_Read.o Assembly.o Hash_Table.o \
POA.o Correct.o Levenshtein_distance.o Overlaps.o Trio.o kthread.o Purge_Dups.o \
htab.o hist.o sketch.o anchor.o sys.o
htab.o hist.o sketch.o anchor.o extract.o sys.o
EXE= hifiasm
LIBS= -lz -lpthread -lm
@@ -51,10 +51,12 @@ Process_Read.o: Process_Read.h Overlaps.h kvec.h kdq.h CommandLines.h
Purge_Dups.o: ksort.h Purge_Dups.h kvec.h kdq.h Overlaps.h Hash_Table.h
Purge_Dups.o: htab.h Process_Read.h CommandLines.h Correct.h
Purge_Dups.o: Levenshtein_distance.h POA.h kthread.h
Trio.o: khashl.h kthread.h Process_Read.h Overlaps.h kvec.h kdq.h
Trio.o: khashl.h kthread.h kseq.h Process_Read.h Overlaps.h kvec.h kdq.h
Trio.o: CommandLines.h htab.h
anchor.o: htab.h Process_Read.h Overlaps.h kvec.h kdq.h CommandLines.h
anchor.o: ksort.h Hash_Table.h
extract.o: Process_Read.h Overlaps.h kvec.h kdq.h CommandLines.h khashl.h
extract.o: kseq.h
hist.o: htab.h Process_Read.h Overlaps.h kvec.h kdq.h CommandLines.h
htab.o: kthread.h khashl.h kseq.h ksort.h htab.h Process_Read.h Overlaps.h
htab.o: kvec.h kdq.h CommandLines.h
Overlaps.cpp
+1 -1
View File
@@ -10506,7 +10506,7 @@ long long miniedgeLen, R_to_U* ruIndex, uint32_t positive_flag, uint32_t negativ
{
to_replace = 1;
}
else if((cur_weight == max_weight))
else if (cur_weight == max_weight)
{
if(ll > base_maxLen)
{
extract.cpp
+175
View File
@@ -0,0 +1,175 @@
#include <zlib.h>
#include <string.h>
#include "Process_Read.h"
#include "khashl.h"
#include "kseq.h"
typedef const char *cstr_t;
KHASHL_CMAP_INIT(KH_LOCAL, strmap_t, ss, cstr_t, int, kh_hash_str, kh_eq_str)
KSTREAM_INIT(gzFile, gzread, 65536)
#define GFA_MALLOC(ptr, len) ((ptr) = (__typeof__(ptr))malloc((len) * sizeof(*(ptr))))
#define GFA_REALLOC(ptr, len) ((ptr) = (__typeof__(ptr))realloc((ptr), (len) * sizeof(*(ptr))))
char *gfa_strdup(const char *src)
{
int32_t len;
char *dst;
len = strlen(src);
GFA_MALLOC(dst, len + 1);
memcpy(dst, src, len + 1);
return dst;
}
char *gfa_strndup(const char *src, size_t n)
{
char *dst;
GFA_MALLOC(dst, n + 1);
strncpy(dst, src, n);
dst[n] = 0;
return dst;
}
char **gv_read_list(const char *o, int *n_)
{
int n = 0, m = 0;
char **s = 0;
*n_ = 0;
if (*o != '@') {
const char *q = o, *p;
for (p = q;; ++p) {
if (*p == ',' || *p == 0) {
if (n == m) {
m = m? m<<1 : 16;
GFA_REALLOC(s, m);
}
s[n++] = gfa_strndup(q, p - q);
if (*p == 0) break;
q = p + 1;
}
}
} else {
gzFile fp;
kstream_t *ks;
kstring_t str = {0,0,0};
int dret;
fp = gzopen(o + 1, "r");
if (fp == 0) return 0;
ks = ks_init(fp);
while (ks_getuntil(ks, KS_SEP_LINE, &str, &dret) >= 0) {
char *p;
for (p = str.s; *p && !isspace(*p); ++p);
if (n == m) {
m = m? m<<1 : 16;
GFA_REALLOC(s, m);
}
s[n++] = gfa_strndup(str.s, p - str.s);
}
ks_destroy(ks);
gzclose(fp);
}
if (s) s = (char**)realloc(s, n * sizeof(char*));
*n_ = n;
return s;
}
void ha_extract_print(const All_reads *rs, int n_rounds, int n, char **list)
{
strmap_t *h;
khint_t k;
int i, absent, m, l, max_len = 0;
uint64_t j;
char *s = 0;
const ma_hit_t_alloc *ov[2] = { rs->paf, rs->reverse_paf };
FILE *fp = stdout;
for (j = 0; j < rs->total_reads; ++j) {
if (max_len < (int)Get_NAME_LENGTH(*rs, j))
max_len = Get_NAME_LENGTH(*rs, j);
}
GFA_MALLOC(s, max_len + 1);
h = ss_init();
for (i = 0; i < n; ++i) {
k = ss_put(h, gfa_strdup(list[i]), &absent);
kh_val(h, k) = -1;
}
for (m = 0; m < n_rounds; ++m) {
for (j = 0; j < rs->total_reads; ++j) {
for (l = 0; l < 2; ++l) {
const ma_hit_t_alloc *o = &ov[l][j];
for (i = 0; i < (int)o->length; ++i) {
uint64_t q = Get_qn(o->buffer[i]);
uint64_t t = Get_tn(o->buffer[i]);
int q_hit = 0, t_hit = 0;
strncpy(s, Get_NAME(*rs, q), Get_NAME_LENGTH(*rs, q)); s[Get_NAME_LENGTH(*rs, q)] = 0;
k = ss_get(h, s);
q_hit = (k < kh_end(h) && kh_val(h, k) < m);
strncpy(s, Get_NAME(*rs, t), Get_NAME_LENGTH(*rs, t)); s[Get_NAME_LENGTH(*rs, t)] = 0;
k = ss_get(h, s);
t_hit = (k < kh_end(h) && kh_val(h, k) < m);
if ((!q_hit && !t_hit) || (q_hit && t_hit)) continue;
if (!q_hit) {
char *tmp = gfa_strndup(Get_NAME(*rs, q), Get_NAME_LENGTH(*rs, q));
k = ss_put(h, tmp, &absent);
if (absent) kh_val(h, k) = m;
else free(tmp);
}
if (!t_hit) {
char *tmp = gfa_strndup(Get_NAME(*rs, t), Get_NAME_LENGTH(*rs, t));
k = ss_put(h, tmp, &absent);
if (absent) kh_val(h, k) = m;
else free(tmp);
}
}
}
}
}
for (j = 0; j < rs->total_reads; ++j) {
for (l = 0; l < 2; ++l) {
const ma_hit_t_alloc *o = &ov[l][j];
for (i = 0; i < (int)o->length; ++i) {
uint64_t q = Get_qn(o->buffer[i]);
uint64_t t = Get_tn(o->buffer[i]);
int q_hit = 0, t_hit = 0;
strncpy(s, Get_NAME(*rs, q), Get_NAME_LENGTH(*rs, q)); s[Get_NAME_LENGTH(*rs, q)] = 0;
k = ss_get(h, s);
q_hit = (k < kh_end(h));
strncpy(s, Get_NAME(*rs, t), Get_NAME_LENGTH(*rs, t)); s[Get_NAME_LENGTH(*rs, t)] = 0;
k = ss_get(h, s);
t_hit = (k < kh_end(h));
if (!q_hit && !t_hit) continue;
fwrite(Get_NAME(*rs, q), 1, Get_NAME_LENGTH(*rs, q), fp);
fwrite("\t", 1, 1, fp);
fprintf(fp, "%lu\t", (unsigned long)Get_READ_LENGTH(*rs, q));
fprintf(fp, "%d\t", Get_qs(o->buffer[i]));
fprintf(fp, "%d\t", Get_qe(o->buffer[i]));
fputs(o->buffer[i].rev? "-\t" : "+\t", fp);
fwrite(Get_NAME(*rs, t), 1, Get_NAME_LENGTH(*rs, t), fp);
fwrite("\t", 1, 1, fp);
fprintf(fp, "%lu\t", (unsigned long)Get_READ_LENGTH(*rs, t));
fprintf(fp, "%d\t", Get_ts(o->buffer[i]));
fprintf(fp, "%d\t%d\t%d\t%d\n", Get_te(o->buffer[i]), o->buffer[i].ml, o->buffer[i].bl, !l);
}
}
}
for (k = 0; k != kh_end(h); ++k)
if (kh_exist(h, k))
free((char*)kh_key(h, k));
ss_destroy(h);
free(s);
}
void ha_extract_print_list(const All_reads *rs, int n_rounds, const char *o)
{
int i, n;
char **list;
list = gv_read_list(o, &n);
ha_extract_print(rs, n_rounds, n, list);
for (i = 0; i < n; ++i) free(list[i]);
free(list);
}