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C++ compiler compat #1

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bc226b7
C++ compiler compat
f0t1h Jun 15, 2025
6971bce
Fix some warnings
f0t1h Jun 15, 2025
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4 changes: 2 additions & 2 deletions Makefile
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Expand Up @@ -6,8 +6,8 @@ OBJS := $(SRCS:.c=.o)
# directories
CURRENT_DIR := $(shell pwd)

GXX := gcc
CXXFLAGS = -O3 -Wall -Wextra -Wpedantic
GXX ?= gcc
CXXFLAGS = -O3 -Wall -Wextra -Wpedantic -march=native

# object files that need lcptools
LCPTOOLS_CXXFLAGS := -I$(CURRENT_DIR)/lcptools/include
Expand Down
3 changes: 2 additions & 1 deletion fa_parser.c
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Expand Up @@ -399,4 +399,5 @@ void print_ref_seqs(const struct ref_seq *seqs, int is_rgfa, FILE *out) {
fprintf(out, "\t*\n");
}
}
}
}

3 changes: 2 additions & 1 deletion fa_parser.h
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Expand Up @@ -46,4 +46,5 @@ void read_fasta(struct opt_arg *args, struct ref_seq *seqs);
*/
void print_ref_seqs(const struct ref_seq *seqs, int is_rgfa, FILE *out);

#endif
#endif

3 changes: 2 additions & 1 deletion lbdg.c
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Expand Up @@ -86,4 +86,5 @@ void lbdg_print_ref_seq(struct ref_seq *seqs, FILE *out) {
}

free(bit_arr);
}
}

3 changes: 2 additions & 1 deletion lbdg.h
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Expand Up @@ -21,4 +21,5 @@
*/
void lbdg_print_ref_seq(struct ref_seq *seqs, FILE *out);

#endif
#endif

3 changes: 2 additions & 1 deletion lcpan.c
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Expand Up @@ -72,4 +72,5 @@ int main(int argc, char* argv[]) {
free_ref_seq(&seqs);

return 0;
}
}

12 changes: 6 additions & 6 deletions opt_parser.c
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Expand Up @@ -30,7 +30,7 @@ int summarize(struct opt_arg *args) {
return 1;
}

void printOptions() {
void printOptions(void) {
fprintf(stderr, "[Options]:\n");
fprintf(stderr, "\t--ref | -r Reference FASTA File. (.fai should be present)\n");
fprintf(stderr, "\t--vcf | -v VCF File.\n");
Expand All @@ -44,7 +44,7 @@ void printOptions() {
fprintf(stderr, "\t--verbose Verbose [Default: false]\n");
}

void printUsage() {
void printUsage(void) {
fprintf(stderr, "Usage: ./lcpan [PROGRAM] [OPTIONS]\n\n");
fprintf(stderr, "[PROGRAM]: \n");
fprintf(stderr, "\t-vg: Uses a variation graph-based approach.\n");
Expand Down Expand Up @@ -207,7 +207,7 @@ void parse_opts(int argc, char* argv[], struct opt_arg *args) {
validate_file(args->vcf_path, "vcf");
}

char *fai_path = malloc(strlen(args->fasta_path)+5);
char *fai_path = (char *) malloc(strlen(args->fasta_path)+5);
if (fai_path == NULL) {
fprintf(stderr, "[ERROR] Memory allocation failed\n");
exit(EXIT_FAILURE);
Expand All @@ -225,14 +225,14 @@ void parse_opts(int argc, char* argv[], struct opt_arg *args) {
}
} else {
if (args->is_rgfa) {
args->gfa_path = malloc(strlen(args->prefix)+6);
args->gfa_path = (char *) malloc(strlen(args->prefix)+6);
if (!args->gfa_path) {
fprintf(stderr, "[ERROR] malloc failed");
exit(EXIT_FAILURE);
}
snprintf(args->gfa_path, strlen(args->prefix)+6, "%s.rgfa", args->prefix);
} else {
args->gfa_path = malloc(strlen(args->prefix)+5);
args->gfa_path = (char *) malloc(strlen(args->prefix)+5);
if (!args->gfa_path) {
fprintf(stderr, "[ERROR] malloc failed");
exit(EXIT_FAILURE);
Expand All @@ -246,4 +246,4 @@ void parse_opts(int argc, char* argv[], struct opt_arg *args) {
}

(void)(args->verbose && summarize(args));
}
}
3 changes: 2 additions & 1 deletion struct_def.h
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Expand Up @@ -126,4 +126,5 @@ struct t_arg {
int *exit_signal;
};

#endif
#endif

6 changes: 3 additions & 3 deletions tpool.c
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Expand Up @@ -13,7 +13,7 @@ struct tpool_work *tpool_work_create(thread_func_t func, void *arg) {
if (func == NULL)
return NULL;

work = malloc(sizeof(struct tpool_work));
work = (struct tpool_work *) malloc(sizeof(struct tpool_work));
work->func = func;
work->arg = arg;
work->next = NULL;
Expand Down Expand Up @@ -63,7 +63,7 @@ struct tpool_work *tpool_work_get(struct tpool *tm) {
* @param arg Pointer to the thread pool structure.
*/
void* tpool_worker(void *arg) {
struct tpool *tm = arg;
struct tpool *tm = (struct tpool *) arg;
struct tpool_work *work;

while (1) {
Expand Down Expand Up @@ -106,7 +106,7 @@ struct tpool *tpool_create(size_t num) {
if (num == 0)
num = 1;

tm = calloc(1, sizeof(*tm));
tm = (struct tpool *) calloc(1, sizeof(*tm));
tm->thread_cnt = num;

pthread_mutex_init(&(tm->work_mutex), NULL);
Expand Down
8 changes: 7 additions & 1 deletion utils.h
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Expand Up @@ -8,6 +8,12 @@
#include <string.h>
#include <pthread.h>

#if defined (__cplusplus)
#define COLITERAL(type) type
#else
#define COLITERAL(type) (struct type)
#endif

#define MIN(a,b) (((a)<(b))?(a):(b))
#define MAX(a,b) (((a)>(b))?(a):(b))

Expand Down Expand Up @@ -182,4 +188,4 @@ void refine_seq(struct lps *str, int no_overlap);
*/
void print_path(const struct ref_seq *seqs, FILE *out);

#endif
#endif
38 changes: 18 additions & 20 deletions vg.c
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Expand Up @@ -164,7 +164,7 @@ int add_elem_2_vgd(struct vg_data *vgd, uint64_t *arr, int size, uint64_t start,
}
while (i < size && (uint32_t)(arr[i]) < end) {
check_vg_data(vgd); // check if there is a space to add element
vgd->data[vgd->size] = (struct vg_data_element){INCOMING, arr[i] >> 32, 0xFFFFFFFFFFFFFFFF, 0xFFFFFFFF & arr[i], NULL, NULL, 0}; // order not matter here
vgd->data[vgd->size] = COLITERAL(vg_data_element){INCOMING, arr[i] >> 32, 0xFFFFFFFFFFFFFFFF, 0xFFFFFFFF & arr[i], NULL, NULL, 0}; // order not matter here
vgd->size++;
i++;
}
Expand Down Expand Up @@ -302,21 +302,21 @@ void vg_read_vcf_thd(void *args) {
uint64_t prev_segment_id = vgd->prev_id;
for (int k=0; k<segment_count-1; k++) {
uint64_t segment_id = set_id(vgd, split_points[k+1], &(t_args->core_id_index));
segments[k] = (struct simple_core){segment_id, split_points[k], split_points[k+1]};
segments[k] = COLITERAL(simple_core){segment_id, split_points[k], split_points[k+1]};
print_seq(segment_id, seq+split_points[k], split_points[k+1]-split_points[k], seq_name, split_points[k], 0, t_args->is_rgfa, t_args->out1);
print_link(prev_segment_id, '+', segment_id, '+', 0, t_args->out2);
prev_segment_id = segment_id;
t_args->seqs->chrs[vgd->chr_idx].ids[vgd->core_idx][k] = segment_id;
}
segments[segment_count-1] = (struct simple_core){vgd->curr_id, split_points[segment_count-1], curr_core->end};
segments[segment_count-1] = COLITERAL(simple_core){vgd->curr_id, split_points[segment_count-1], curr_core->end};
print_seq(vgd->curr_id, seq+split_points[segment_count-1], curr_core->end-split_points[segment_count-1], seq_name, split_points[segment_count-1], 0, t_args->is_rgfa, t_args->out1);
print_link(prev_segment_id, '+', vgd->curr_id, '+', 0, t_args->out2);
t_args->seqs->chrs[vgd->chr_idx].ids[vgd->core_idx][segment_count-1] = 0;
} else {
const char *seq = t_args->seqs->chrs[vgd->chr_idx].seq;
const char *seq_name = t_args->seqs->chrs[vgd->chr_idx].seq_name;
const struct simple_core *curr_core = &(t_args->seqs->chrs[vgd->chr_idx].cores[vgd->core_idx]);
segments[0] = (struct simple_core){vgd->curr_id, curr_core->start, curr_core->end};
segments[0] = COLITERAL(simple_core){vgd->curr_id, curr_core->start, curr_core->end};
print_seq(vgd->curr_id, seq+curr_core->start, curr_core->end-curr_core->start, seq_name, curr_core->start, 0, t_args->is_rgfa, t_args->out1);
print_link(vgd->prev_id, '+', vgd->curr_id, '+', 0, t_args->out2);
t_args->seqs->chrs[vgd->chr_idx].ids[vgd->core_idx] = NULL;
Expand Down Expand Up @@ -499,8 +499,6 @@ void vg_read_vcf(struct opt_arg *args, struct ref_seq *seqs) {
exit(EXIT_FAILURE);
}

int line_count = 0;

int rem_vars_capacity = 256;
int rem_vars_size = 0;
uint64_t *rem_vars = (uint64_t *)malloc(rem_vars_capacity * sizeof(uint64_t)); // id+end
Expand Down Expand Up @@ -532,7 +530,6 @@ void vg_read_vcf(struct opt_arg *args, struct ref_seq *seqs) {
// validate `line`
if (skip_line || len < 2 || line[0] == '#') continue;
if (line[len - 1] == '\n') { line[len - 1] = '\0'; len--; }
line_count++;

// parse the `line`
char *chrom, *index, *id, *ref, *alt;
Expand Down Expand Up @@ -665,12 +662,12 @@ void vg_read_vcf(struct opt_arg *args, struct ref_seq *seqs) {
uint64_t ref_token_len = strlen(ref_token);
if (check_vg_data(vgd)) {
if (offset + ref_token_len < curr_chr->cores[core_idx].end) { // DEL inside
vgd->data[vgd->size] = (struct vg_data_element){IN_DEL, 0, offset+1, offset+ref_token_len, NULL, NULL, order};
vgd->data[vgd->size] = COLITERAL(vg_data_element){IN_DEL, 0, offset+1, offset+ref_token_len, NULL, NULL, order};
vgd->size++;
} else if (offset + 1 < curr_chr->cores[core_idx].end) { // it starts inside
rem_vars_size = add_elem_2_rem_arr(&rem_vars, rem_vars_size, rem_vars_capacity, args->core_id_index, offset+ref_token_len);
if (rem_vars_size > rem_vars_capacity) rem_vars_capacity *= 2;
vgd->data[vgd->size] = (struct vg_data_element){OUT_DEL, args->core_id_index, offset+1, 0xFFFFFFFFFFFFFFFF, NULL, NULL, order};
vgd->data[vgd->size] = COLITERAL(vg_data_element){OUT_DEL, args->core_id_index, offset+1, 0xFFFFFFFFFFFFFFFF, NULL, NULL, order};
vgd->size++;
args->core_id_index++;
} else {
Expand All @@ -691,12 +688,12 @@ void vg_read_vcf(struct opt_arg *args, struct ref_seq *seqs) {
if (1 == ref_len && 1 == alt_token_len) { // SNP
if (offset + 1 < curr_chr->cores[core_idx].end) {
print_seq_vg(args->core_id_index, alt_token, 1, id, order, offset, 1, args->is_rgfa, out_segment);
vgd->data[vgd->size] = (struct vg_data_element){IN_SNP, args->core_id_index, offset, offset+1, NULL, NULL, order}; // id assigned for segment
vgd->data[vgd->size] = COLITERAL(vg_data_element){IN_SNP, args->core_id_index, offset, offset+1, NULL, NULL, order}; // id assigned for segment
} else {
rem_vars_size = add_elem_2_rem_arr(&rem_vars, rem_vars_size, rem_vars_capacity, args->core_id_index, offset+1);
if (rem_vars_size > rem_vars_capacity) rem_vars_capacity *= 2;
print_seq_vg(args->core_id_index, alt_token, 1, id, order, offset, 1, args->is_rgfa, out_segment);
vgd->data[vgd->size] = (struct vg_data_element){OUT_SNP, args->core_id_index, offset, 0xFFFFFFFFFFFFFFFF, NULL, NULL, order}; // id assigned for segment
vgd->data[vgd->size] = COLITERAL(vg_data_element){OUT_SNP, args->core_id_index, offset, 0xFFFFFFFFFFFFFFFF, NULL, NULL, order}; // id assigned for segment
}
vgd->size++;
args->core_id_index++;
Expand All @@ -705,23 +702,23 @@ void vg_read_vcf(struct opt_arg *args, struct ref_seq *seqs) {
if (alt_token_len / 2 < curr_chr->cores[core_idx].end - curr_chr->cores[core_idx].start) {
print_seq_vg(args->core_id_index, alt_token+1, alt_token_len-1, id, order, offset, 1, args->is_rgfa, out_segment);
if (offset + 1 < curr_chr->cores[core_idx].end) {
vgd->data[vgd->size] = (struct vg_data_element){IN_INS, args->core_id_index, offset+1, offset+1, NULL, NULL, order}; // id assigned for segment
vgd->data[vgd->size] = COLITERAL(vg_data_element){IN_INS, args->core_id_index, offset+1, offset+1, NULL, NULL, order}; // id assigned for segment
} else {
rem_vars_size = add_elem_2_rem_arr(&rem_vars, rem_vars_size, rem_vars_capacity, args->core_id_index, offset+1);
if (rem_vars_size > rem_vars_capacity) rem_vars_capacity *= 2;
vgd->data[vgd->size] = (struct vg_data_element){OUT_INS, args->core_id_index, offset+1, 0xFFFFFFFFFFFFFFFF, NULL, NULL, order}; // id assigned for segment
vgd->data[vgd->size] = COLITERAL(vg_data_element){OUT_INS, args->core_id_index, offset+1, 0xFFFFFFFFFFFFFFFF, NULL, NULL, order}; // id assigned for segment
}
vgd->size++;
args->core_id_index++;
} else { // Large INS, to be processed with LCP
char *alt_token_copy = strdup(alt_token);
char *seq_id = strdup(id);
if (offset + 1 < curr_chr->cores[core_idx].end) { // if inside of the lcp core
vgd->data[vgd->size] = (struct vg_data_element){IN_INS_SV, args->core_id_index, offset+1, offset+1, alt_token_copy, seq_id, order};
vgd->data[vgd->size] = COLITERAL(vg_data_element){IN_INS_SV, args->core_id_index, offset+1, offset+1, alt_token_copy, seq_id, order};
} else { // if in the edge of the end of the lcp core
rem_vars_size = add_elem_2_rem_arr(&rem_vars, rem_vars_size, rem_vars_capacity, args->core_id_index, offset+1);
if (rem_vars_size > rem_vars_capacity) rem_vars_capacity *= 2;
vgd->data[vgd->size] = (struct vg_data_element){OUT_INS_SV, args->core_id_index, offset+1, 0xFFFFFFFFFFFFFFFF, alt_token_copy, seq_id, order};
vgd->data[vgd->size] = COLITERAL(vg_data_element){OUT_INS_SV, args->core_id_index, offset+1, 0xFFFFFFFFFFFFFFFF, alt_token_copy, seq_id, order};
}
vgd->size++;
args->core_id_index++;
Expand All @@ -730,23 +727,23 @@ void vg_read_vcf(struct opt_arg *args, struct ref_seq *seqs) {
if (alt_token_len / 2 < curr_chr->cores[core_idx].end - curr_chr->cores[core_idx].start) { // alteration, simply print the underling string
print_seq_vg(args->core_id_index, alt_token, alt_token_len, id, order, offset, 1, args->is_rgfa, out_segment);
if (offset + ref_len < curr_chr->cores[core_idx].end) {
vgd->data[vgd->size] = (struct vg_data_element){IN_ALT, args->core_id_index, offset, offset+ref_len, NULL, NULL, order};
vgd->data[vgd->size] = COLITERAL(vg_data_element){IN_ALT, args->core_id_index, offset, offset+ref_len, NULL, NULL, order};
} else {
rem_vars_size = add_elem_2_rem_arr(&rem_vars, rem_vars_size, rem_vars_capacity, args->core_id_index, offset+ref_len);
if (rem_vars_size > rem_vars_capacity) rem_vars_capacity *= 2;
vgd->data[vgd->size] = (struct vg_data_element){OUT_ALT, args->core_id_index, offset, 0xFFFFFFFFFFFFFFFF, NULL, NULL, order};
vgd->data[vgd->size] = COLITERAL(vg_data_element){OUT_ALT, args->core_id_index, offset, 0xFFFFFFFFFFFFFFFF, NULL, NULL, order};
}
vgd->size++;
args->core_id_index++;
} else { // check if it the alt_token requires LCP processing
char *alt_token_copy = strdup(alt_token);
char *seq_id = strdup(id);
if (offset + ref_len < curr_chr->cores[core_idx].end) {
vgd->data[vgd->size] = (struct vg_data_element){IN_ALT_SV, args->core_id_index, offset, offset+ref_len, alt_token_copy, seq_id, order};
vgd->data[vgd->size] = COLITERAL(vg_data_element){IN_ALT_SV, args->core_id_index, offset, offset+ref_len, alt_token_copy, seq_id, order};
} else {
rem_vars_size = add_elem_2_rem_arr(&rem_vars, rem_vars_size, rem_vars_capacity, args->core_id_index, offset+ref_len);
if (rem_vars_size > rem_vars_capacity) rem_vars_capacity *= 2;
vgd->data[vgd->size] = (struct vg_data_element){OUT_ALT_SV, args->core_id_index, offset, 0xFFFFFFFFFFFFFFFF, alt_token_copy, seq_id, order};
vgd->data[vgd->size] = COLITERAL(vg_data_element){OUT_ALT_SV, args->core_id_index, offset, 0xFFFFFFFFFFFFFFFF, alt_token_copy, seq_id, order};
}
vgd->size++;
args->core_id_index++;
Expand Down Expand Up @@ -856,4 +853,5 @@ void vg_read_vcf(struct opt_arg *args, struct ref_seq *seqs) {
fclose(out_path);
fclose(out_segment);
fclose(out_link);
}
}

3 changes: 2 additions & 1 deletion vg.h
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Expand Up @@ -25,4 +25,5 @@
*/
void vg_read_vcf(struct opt_arg *args, struct ref_seq *seqs);

#endif
#endif

3 changes: 2 additions & 1 deletion vgx.c
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Expand Up @@ -414,4 +414,5 @@ void vgx_read_vcf(struct opt_arg *args, struct ref_seq *seqs) {
fclose(out_log);

printf("[INFO] Ended processing %d lines. \n", line_count);
}
}

3 changes: 2 additions & 1 deletion vgx.h
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Expand Up @@ -23,4 +23,5 @@
*/
void vgx_read_vcf(struct opt_arg *args, struct ref_seq *seqs);

#endif
#endif