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Merged
nh13 merged 1 commit into from
Nov 24, 2025
Merged

feat: the -M option now specifies the output type (reads, variants, o… #85

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48 changes: 27 additions & 21 deletions src/dwgsim.c
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Original file line number Diff line number Diff line change
Expand Up @@ -498,7 +498,7 @@ void dwgsim_core(dwgsim_opt_t * opt)
contigs = NULL;
}

if(0 == opt->muts_only) {
if(opt->output_type != OUTPUT_TYPE_MUTS) {
fprintf(stderr, "[dwgsim_core] Currently on: \n0");
}
else {
Expand All @@ -508,8 +508,8 @@ void dwgsim_core(dwgsim_opt_t * opt)
while ((l = seq_read_fasta(opt->fp_fa, &seq, name, 0)) >= 0) {
int64_t n_pairs = 0;
n_ref--;
if(1 == opt->muts_only) {

if(opt->output_type == OUTPUT_TYPE_MUTS) {
fprintf(stderr, "\r[dwgsim_core] Currently on: %s", name);
if(name_len_max < strlen(name)) {
name_len_max = strlen(name);
Expand Down Expand Up @@ -616,9 +616,11 @@ void dwgsim_core(dwgsim_opt_t * opt)
// generate mutations and print them out
mutseq[0] = mutseq_init(); mutseq[1] = mutseq_init();
mut_diref(opt, &seq, mutseq[0], mutseq[1], contig_i, muts_input);
mut_print(name, &seq, mutseq[0], mutseq[1], opt->fp_mut, opt->fp_vcf);
if(opt->output_type != OUTPUT_TYPE_READS) {
mut_print(name, &seq, mutseq[0], mutseq[1], opt->fp_mut, opt->fp_vcf);
}

if(0 == opt->muts_only) {
if(opt->output_type != OUTPUT_TYPE_MUTS) {
int num_failed = 0;
for (ii = 0; ii != n_pairs; ++ii, ++ctr) { // the core loop
if(0 == (ctr % 10000)) {
Expand Down Expand Up @@ -1113,16 +1115,18 @@ int main(int argc, char *argv[])
opt->fp_fa = xopen(argv[optind+0], "r");
snprintf(fn_fai, sizeof(fn_fai), "%s.fai", argv[optind+0]);
opt->fp_fai = fopen(fn_fai, "r"); // NB: depends on returning NULL;
snprintf(fn_tmp, sizeof(fn_tmp), "%s.mutations.txt", argv[optind+1]);
opt->fp_mut = xopen(fn_tmp, "w");
snprintf(fn_tmp, sizeof(fn_tmp), "%s.mutations.vcf", argv[optind+1]);
opt->fp_vcf = xopen(fn_tmp, "w");
if(0 == opt->muts_only) {
if (opt->output_type != OUTPUT_TYPE_BWA) {
if(opt->output_type != OUTPUT_TYPE_READS) {
snprintf(fn_tmp, sizeof(fn_tmp), "%s.mutations.txt", argv[optind+1]);
opt->fp_mut = xopen(fn_tmp, "w");
snprintf(fn_tmp, sizeof(fn_tmp), "%s.mutations.vcf", argv[optind+1]);
opt->fp_vcf = xopen(fn_tmp, "w");
}
if(opt->output_type != OUTPUT_TYPE_MUTS) {
if (opt->reads_output_type != READS_OUTPUT_TYPE_BWA) {
snprintf(fn_tmp, sizeof(fn_tmp), "%s.bfast.fastq.gz", argv[optind+1]);
opt->fp_bfast = gzopen(fn_tmp, "w");
}
if (opt->output_type != OUTPUT_TYPE_BFAST) {
if (opt->reads_output_type != READS_OUTPUT_TYPE_BFAST) {
snprintf(fn_tmp, sizeof(fn_tmp), "%s.bwa.read1.fastq.gz", argv[optind+1]);
opt->fp_bwa1 = gzopen(fn_tmp, "w");
snprintf(fn_tmp, sizeof(fn_tmp), "%s.bwa.read2.fastq.gz", argv[optind+1]);
Expand All @@ -1134,18 +1138,20 @@ int main(int argc, char *argv[])
dwgsim_core(opt);

// Close files
if(0 == opt->muts_only) {
if (opt->output_type != OUTPUT_TYPE_BWA) {
gzclose(opt->fp_bfast);
if(NULL != opt->fp_fai) fclose(opt->fp_fai);
if(opt->output_type != OUTPUT_TYPE_READS) {
fclose(opt->fp_mut);
fclose(opt->fp_vcf);
}
if(opt->output_type != OUTPUT_TYPE_MUTS) {
if (opt->reads_output_type != READS_OUTPUT_TYPE_BWA) {
gzclose(opt->fp_bfast);
}
if (opt->output_type != OUTPUT_TYPE_BFAST) {
gzclose(opt->fp_bwa1); gzclose(opt->fp_bwa2);
if (opt->reads_output_type != READS_OUTPUT_TYPE_BFAST) {
gzclose(opt->fp_bwa1); gzclose(opt->fp_bwa2);
}
fclose(opt->fp_fa);
fclose(opt->fp_fa);
}
if(NULL != opt->fp_fai) fclose(opt->fp_fai);
fclose(opt->fp_mut);
fclose(opt->fp_vcf);

dwgsim_opt_destroy(opt);

Expand Down
20 changes: 12 additions & 8 deletions src/dwgsim_opt.c
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Original file line number Diff line number Diff line change
Expand Up @@ -63,7 +63,6 @@ dwgsim_opt_t* dwgsim_opt_init()
opt->flow_order_len = 0;
opt->use_base_error = 0;
opt->seed = -1;
opt->muts_only = 0;
opt->fixed_quality = NULL;
opt->quality_std = 2.0;
opt->fn_muts_input = NULL;
Expand All @@ -73,6 +72,8 @@ dwgsim_opt_t* dwgsim_opt_init()
opt->fp_bfast = opt->fp_bwa1 = opt->fp_bwa2 = NULL;
opt->fp_fa = opt->fp_fai = NULL;
opt->read_prefix = NULL;
opt->reads_output_type = READS_OUTPUT_TYPE_ALL;
opt->output_type = OUTPUT_TYPE_ALL;
opt->amplicons = 0;

return opt;
Expand Down Expand Up @@ -132,15 +133,18 @@ int dwgsim_opt_usage(dwgsim_opt_t *opt)
fprintf(stderr, " -B use a per-base error rate for Ion Torrent data [%s]\n", __IS_TRUE(opt->use_base_error));
fprintf(stderr, " -H haploid mode [%s]\n", __IS_TRUE(opt->is_hap));
fprintf(stderr, " -z INT random seed (-1 uses the current time) [%d]\n", opt->seed);
fprintf(stderr, " -M generate a mutations file only [%s]\n", __IS_TRUE(opt->muts_only));
fprintf(stderr, " -M output files to generate [%d]:\n", opt->output_type);
fprintf(stderr, " 0: both reads and mutation files\n");
fprintf(stderr, " 1: reads only\n");
fprintf(stderr, " 2: mutations only\n");
fprintf(stderr, " -m FILE the mutations txt file to re-create [%s]\n", (MUT_INPUT_TXT != opt->fn_muts_input_type) ? "not using" : opt->fn_muts_input);
fprintf(stderr, " -b FILE the bed-like file set of candidate mutations [%s]\n", (MUT_INPUT_BED == opt->fn_muts_input_type) ? "not using" : opt->fn_muts_input);
fprintf(stderr, " -v FILE the vcf file set of candidate mutations (use pl tag for strand) [%s]\n", (MUT_INPUT_VCF == opt->fn_muts_input_type) ? "not using" : opt->fn_muts_input);
fprintf(stderr, " -x FILE the bed of regions to cover [%s]\n", (NULL == opt->fn_regions_bed) ? "not using" : opt->fn_regions_bed);
fprintf(stderr, " -P STRING a read prefix to prepend to each read name [%s]\n", (NULL == opt->read_prefix) ? "not using" : opt->read_prefix);
fprintf(stderr, " -q STRING a fixed base quality to apply (single character) [%s]\n", (NULL == opt->fixed_quality) ? "not using" : opt->fixed_quality);
fprintf(stderr, " -Q FLOAT standard deviation of the base quality scores [%.2lf]\n", (NULL == opt->fixed_quality) ? opt->quality_std : 0.0);
fprintf(stderr, " -o INT output type for the FASTQ files [%d]:\n", opt->output_type);
fprintf(stderr, " -o INT output type for the FASTQ files [%d]:\n", opt->reads_output_type);
fprintf(stderr, " 0: interleaved (bfast) and per-read-end (bwa)\n");
fprintf(stderr, " 1: per-read-end (bwa) only\n");
fprintf(stderr, " 2: interleaved (bfast) only\n");
Expand Down Expand Up @@ -204,7 +208,7 @@ dwgsim_opt_parse(dwgsim_opt_t *opt, int argc, char *argv[])
int c;
int muts_input_type = 0;

while ((c = getopt(argc, argv, "id:s:N:C:1:2:e:E:r:F:R:X:I:c:S:A:n:y:BHf:z:Mm:b:v:x:P:q:Q:o:ah")) >= 0) {
while ((c = getopt(argc, argv, "id:s:N:C:1:2:e:E:r:F:R:X:I:c:S:A:n:y:BHf:z:M:m:b:v:x:P:q:Q:o:ah")) >= 0) {
switch (c) {
case 'i': opt->is_inner = 1; break;
case 'd': opt->dist = dwgsim_atoi(optarg, 'd', 0); break;
Expand Down Expand Up @@ -237,7 +241,7 @@ dwgsim_opt_parse(dwgsim_opt_t *opt, int argc, char *argv[])
case 'H': opt->is_hap = 1; break;
case 'h': return 0;
case 'z': opt->seed = dwgsim_atoi(optarg, 'z', 1); break;
case 'M': opt->muts_only = 1; break;
case 'M': opt->output_type = dwgsim_atoi(optarg, 'M', 0); break;
case 'm':
free(opt->fn_muts_input);
opt->fn_muts_input = strdup(optarg);
Expand Down Expand Up @@ -293,7 +297,7 @@ dwgsim_opt_parse(dwgsim_opt_t *opt, int argc, char *argv[])
}
break;
case 'Q': opt->quality_std = atof(optarg); break;
case 'o': opt->output_type = atoi(optarg); break;
case 'o': opt->reads_output_type = atoi(optarg); break;
case 'a': opt->amplicons = 1; break;
default: fprintf(stderr, "Unrecognized option: -%c\n", c); return 0;
}
Expand Down Expand Up @@ -364,7 +368,7 @@ dwgsim_opt_parse(dwgsim_opt_t *opt, int argc, char *argv[])
fprintf(stderr, "Warning: remember to use the -P option with dwgsim_eval\n");
}

__check_option(opt->output_type, 0, 2, "-o");
__check_option(opt->reads_output_type, 0, 2, "-o");

switch(muts_input_type) {
case 0x0:
Expand Down Expand Up @@ -448,7 +452,7 @@ dwgsim_opt_parse(dwgsim_opt_t *opt, int argc, char *argv[])
opt->e[1].by = (opt->e[1].end - opt->e[1].start) / opt->length[1];
}

__check_option(opt->muts_only, 0, 1, "-M");
__check_option(opt->output_type, OUTPUT_TYPE_ALL, OUTPUT_TYPE_MUTS, "-M");
__check_option(opt->amplicons, 0, 1, "-a");

if (opt->amplicons == 1 && opt->fn_regions_bed != NULL) {
Expand Down
10 changes: 7 additions & 3 deletions src/dwgsim_opt.h
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Original file line number Diff line number Diff line change
Expand Up @@ -5,9 +5,13 @@

#define ERROR_RATE_NUM_RANDOM_READS 1000000

#define READS_OUTPUT_TYPE_ALL 0
#define READS_OUTPUT_TYPE_BWA 1
#define READS_OUTPUT_TYPE_BFAST 2

#define OUTPUT_TYPE_ALL 0
#define OUTPUT_TYPE_BWA 1
#define OUTPUT_TYPE_BFAST 2
#define OUTPUT_TYPE_READS 1
#define OUTPUT_TYPE_MUTS 2


typedef struct {
Expand Down Expand Up @@ -37,7 +41,6 @@ typedef struct {
int32_t use_base_error;
int32_t is_hap;
int32_t seed;
int32_t muts_only;
char *fixed_quality;
double quality_std;
char *fn_muts_input;
Expand All @@ -51,6 +54,7 @@ typedef struct {
FILE *fp_fa;
FILE *fp_fai;
char *read_prefix;
int32_t reads_output_type;
int32_t output_type;
int32_t amplicons;
} dwgsim_opt_t;
Expand Down