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add an option to disable memory check
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Chenxi Zhou committed Jul 27, 2022
1 parent 17c18a8 commit d8a1fd7
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Showing 5 changed files with 41 additions and 18 deletions.
2 changes: 1 addition & 1 deletion Makefile
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
CFLAGS= -g -O3 -Wall -fno-strict-aliasing
CFLAGS= -g -O0 -Wall -fno-strict-aliasing
CPPFLAGS=
INCLUDES=
OBJS=
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2 changes: 1 addition & 1 deletion break.c
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Original file line number Diff line number Diff line change
Expand Up @@ -332,7 +332,7 @@ bp_t *detect_break_points_local_joint(link_mat_t *link_mat, uint32_t bin_size, d
seq = dict->s[i];
link = link_mat->link[i].link;
a = 0;
for (j = 1; j < seq.n; j++) {
for (j = 1; j < seq.n; ++j) {
seg = segs[seq.s + j];
s = (MAX(seg.a - MIN(flank_size, segs[seq.s + j - 1].y), 1) - 1) / bin_size;
e = (MAX(seg.a + MIN(flank_size, seg.y), 1) - 1) / bin_size;
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8 changes: 4 additions & 4 deletions enzyme.c
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Original file line number Diff line number Diff line change
Expand Up @@ -143,12 +143,12 @@ re_cuts_t *find_re_from_seqs(const char *f, uint32_t ml, char **enz_cs, int enz_

re_cuts->density = (double) n_re / genome_size;

fprintf(stderr, "[I::%s] NO. restriction enzyme cutting sites found in sequences: %ld\n", __func__, n_re);
fprintf(stderr, "[I::%s] number restriction enzyme cutting sites found in sequences: %ld\n", __func__, n_re);
fprintf(stderr, "[I::%s] restriction enzyme cutting sites density: %.6f\n", __func__, re_cuts->density);
#ifdef DEBUG_ENZ
fprintf(stderr, "[DEBUG_ENZ::%s] restriction enzyme cutting sites for individual sequences (n = %d)\n", __func__, n);
#ifdef DEBUG
fprintf(stderr, "[DEBUG::%s] restriction enzyme cutting sites for individual sequences (n = %d)\n", __func__, n);
for (i = 0; i < n; ++i)
fprintf(stderr, "[DEBUG_ENZ::%s] %s %u %u %.6f\n", __func__, sdict->s[i].name, sdict->s[i].len, re_cuts->re[i].n, (double) re_cuts->re[i].n / sdict->s[i].len);
fprintf(stderr, "[DEBUG::%s] %s %u %u %.6f\n", __func__, sdict->s[i].name, sdict->s[i].len, re_cuts->re[i].n, (double) re_cuts->re[i].n / sdict->s[i].len);
#endif

sd_destroy(sdict);
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12 changes: 12 additions & 0 deletions link.c
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Original file line number Diff line number Diff line change
Expand Up @@ -206,6 +206,10 @@ inter_link_mat_t *inter_link_mat_init(asm_dict_t *dict, re_cuts_t *re_cuts, uint
for (k = 0; k < 4; ++k) {
link->link[k] = (double *) calloc(p, sizeof(double));
link->linkb[k] = (double *) calloc(link->r, sizeof(double));
if (!link->link[k] || !link->linkb[k]) {
fprintf(stderr, "[E::%s] memory allocation failure\n", __func__);
exit(EXIT_FAILURE);
}
}

// calculate relative areas for each cell
Expand Down Expand Up @@ -314,6 +318,10 @@ intra_link_mat_t *intra_link_mat_init(asm_dict_t *dict, re_cuts_t *re_cuts, uint
a = ((double) dict->s[i].len - (double) (b - 1) * resolution) / resolution;
p = (long) b * (b + 1) / 2;
link->link = (double *) calloc(p, sizeof(double));
if (!link->link) {
fprintf(stderr, "[E::%s] memory allocation failure\n", __func__);
exit(EXIT_FAILURE);
}
if (re_dens) {
dens = re_dens[i];
for (j = 0; j < b; ++j) {
Expand Down Expand Up @@ -406,6 +414,10 @@ intra_link_mat_t *intra_link_mat_init_sdict(sdict_t *dict, re_cuts_t *re_cuts, u
a = ((double) dict->s[i].len - (double) (b - 1) * resolution) / resolution;
p = (long) b * (b + 1) / 2;
link->link = (double *) calloc(p, sizeof(double));
if (!link->link) {
fprintf(stderr, "[E::%s] memory allocation failure\n", __func__);
exit(EXIT_FAILURE);
}
if (re_dens) {
dens = re_dens[i];
for (j = 0; j < b; ++j) {
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35 changes: 23 additions & 12 deletions yahs.c
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Original file line number Diff line number Diff line change
Expand Up @@ -132,7 +132,7 @@ graph_t *build_graph_from_links(inter_link_mat_t *link_mat, asm_dict_t *dict, do
return g;
}

int run_scaffolding(char *fai, char *agp, char *link_file, uint32_t ml, uint8_t mq, re_cuts_t *re_cuts, char *out, int resolution, double *noise, long rss_limit)
int run_scaffolding(char *fai, char *agp, char *link_file, uint32_t ml, uint8_t mq, re_cuts_t *re_cuts, char *out, int resolution, double *noise, long rss_limit, int no_mem_check)
{
//TODO: adjust wt thres by resolution
sdict_t *sdict = make_sdict_from_index(fai, ml);
Expand All @@ -148,7 +148,7 @@ int run_scaffolding(char *fai, char *agp, char *link_file, uint32_t ml, uint8_t

long rss_intra, rss_inter;

rss_intra = estimate_intra_link_mat_init_rss(dict, resolution);
rss_intra = no_mem_check? 0 : estimate_intra_link_mat_init_rss(dict, resolution);
if ((rss_limit >= 0 && rss_intra > rss_limit) || rss_intra < 0) {
// no enough memory
fprintf(stderr, "[I::%s] No enough memory. Try higher resolutions... End of scaffolding round.\n", __func__);
Expand Down Expand Up @@ -177,7 +177,7 @@ int run_scaffolding(char *fai, char *agp, char *link_file, uint32_t ml, uint8_t
return ENOBND_ERR;
}

rss_inter = estimate_inter_link_mat_init_rss(dict, resolution, norm->r);
rss_inter = no_mem_check? 0 : estimate_inter_link_mat_init_rss(dict, resolution, norm->r);
if ((rss_limit >= 0 && rss_inter > rss_limit) || rss_inter < 0) {
// no enough memory
fprintf(stderr, "[I::%s] No enough memory. Try higher resolutions... End of scaffolding round.\n", __func__);
Expand Down Expand Up @@ -378,7 +378,7 @@ static void print_asm_stats(uint64_t *n_stats, uint32_t *l_stats, int all)
#endif
}

int run_yahs(char *fai, char *agp, char *link_file, uint32_t ml, uint8_t mq, char *out, int *resolutions, int nr, re_cuts_t *re_cuts, int no_contig_ec, int no_scaffold_ec)
int run_yahs(char *fai, char *agp, char *link_file, uint32_t ml, uint8_t mq, char *out, int *resolutions, int nr, re_cuts_t *re_cuts, int no_contig_ec, int no_scaffold_ec, int no_mem_check)
{
int ec_round, re, r, rc;
char *out_fn, *out_agp, *out_agp_break;
Expand All @@ -391,6 +391,8 @@ int run_yahs(char *fai, char *agp, char *link_file, uint32_t ml, uint8_t mq, cha
ram_limit(&rss_total, &rss_limit);
fprintf(stderr, "[I::%s] RAM total: %.3fGB\n", __func__, (double) rss_total / GB);
fprintf(stderr, "[I::%s] RAM limit: %.3fGB\n", __func__, (double) rss_limit / GB);
if (no_mem_check)
fprintf(stderr, "[I::%s] RAM check disabled\n", __func__);

sdict = make_sdict_from_index(fai, ml);
out_fn = (char *) malloc(strlen(out) + 35);
Expand Down Expand Up @@ -459,7 +461,7 @@ int run_yahs(char *fai, char *agp, char *link_file, uint32_t ml, uint8_t mq, cha

sprintf(out_fn, "%s_r%02d", out, r);
// noise per unit
re = run_scaffolding(fai, out_agp_break, link_file, ml, mq, re_cuts, out_fn, resolutions[r - 1], &noise, rss_limit);
re = run_scaffolding(fai, out_agp_break, link_file, ml, mq, re_cuts, out_fn, resolutions[r - 1], &noise, rss_limit, no_mem_check);
if (!re) {
sprintf(out_agp, "%s_r%02d.agp", out, r);
if (no_scaffold_ec == 0) {
Expand Down Expand Up @@ -580,6 +582,9 @@ static void print_help(FILE *fp_help)
fprintf(fp_help, " -e STR restriction enzyme cutting sites [none]\n");
fprintf(fp_help, " -l INT minimum length of a contig to scaffold [0]\n");
fprintf(fp_help, " -q INT minimum mapping quality [10]\n");
fprintf(fp_help, " --no-contig-ec do not do contig error correction\n");
fprintf(fp_help, " --no-scaffold-ec do not do scaffold error correction\n");
fprintf(fp_help, " --no-mem-check do not do memory check at runtime\n");
fprintf(fp_help, " -o STR prefix of output files [yahs.out]\n");
fprintf(fp_help, " -v INT verbose level [%d]\n", VERBOSE);
fprintf(fp_help, " --version show version number\n");
Expand All @@ -588,6 +593,7 @@ static void print_help(FILE *fp_help)
static ko_longopt_t long_options[] = {
{ "no-contig-ec", ko_no_argument, 301 },
{ "no-scaffold-ec", ko_no_argument, 302 },
{ "no-mem-check", ko_no_argument, 303 },
{ "help", ko_no_argument, 'h' },
{ "version", ko_no_argument, 'V' },
{ 0, 0, 0 }
Expand All @@ -606,15 +612,15 @@ int main(int argc, char *argv[])
ys_realtime0 = realtime();

char *fa, *fai, *agp, *link_file, *out, *restr, *ecstr, *ext, *link_bin_file, *agp_final, *fa_final;
int *resolutions, nr, mq, ml, no_contig_ec, no_scaffold_ec;
int *resolutions, nr, mq, ml, no_contig_ec, no_scaffold_ec, no_mem_check;

const char *opt_str = "a:e:r:o:l:q:Vv:h";
ketopt_t opt = KETOPT_INIT;

int c, ret;
FILE *fp_help = stderr;
fa = fai = agp = link_file = out = restr = link_bin_file = agp_final = fa_final = 0;
no_contig_ec = no_scaffold_ec = 0;
no_contig_ec = no_scaffold_ec = no_mem_check = 0;
mq = 10;
ml = 0;
ecstr = 0;
Expand All @@ -631,11 +637,14 @@ int main(int argc, char *argv[])
} else if (c == 'q') {
mq = atoi(opt.arg);
} else if (c == 'e') {
ecstr = opt.arg;
// make a copy of ecstr to make sure the CMD correct
ecstr = strdup(opt.arg);
} else if (c == 301) {
no_contig_ec = 1;
} else if (c == 302) {
no_scaffold_ec = 1;
} else if (c == 303 ) {
no_mem_check = 1;
} else if (c == 'v') {
VERBOSE = atoi(opt.arg);
} else if (c == 'V') {
Expand Down Expand Up @@ -744,17 +753,19 @@ int main(int argc, char *argv[])
}
pch = strtok(NULL, ",");
}
#ifdef DEBUG_ENZ
fprintf(stderr, "[DEBUG_ENZ::%s] list of restriction enzyme cutting sites (n = %ld)\n", __func__, enz_cs.n);
#ifdef DEBUG
fprintf(stderr, "[DEBUG::%s] list of restriction enzyme cutting sites (n = %ld)\n", __func__, enz_cs.n);
for (i = 0; i < enz_cs.n; ++i)
fprintf(stderr, "[DEBUG_ENZ::%s] %s\n", __func__, enz_cs.a[i]);
fprintf(stderr, "[DEBUG::%s] %s\n", __func__, enz_cs.a[i]);
#endif

re_cuts = find_re_from_seqs(fa, ml, enz_cs.a, enz_cs.n);

for (i = 0; i < enz_cs.n; ++i)
free(enz_cs.a[i]);
kv_destroy(enz_cs);

free(ecstr);
}

if (out == 0)
Expand Down Expand Up @@ -800,7 +811,7 @@ int main(int argc, char *argv[])
fprintf(stderr, "[DEBUG_OPTIONS::%s] ec[S]: %d\n", __func__, no_scaffold_ec);
#endif

ret = run_yahs(fai, agp, link_bin_file, ml, mq8, out, resolutions, nr, re_cuts, no_contig_ec, no_scaffold_ec);
ret = run_yahs(fai, agp, link_bin_file, ml, mq8, out, resolutions, nr, re_cuts, no_contig_ec, no_scaffold_ec, no_mem_check);

if (ret == 0) {
agp_final = (char *) malloc(strlen(out) + 35);
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