void add_arc(struct graph_adj *g, int id, int from, int to)
{
struct arc a;
a.id = id;
a.to = to;
ARRAY_PUSH(g->adj_list[from], a);
g->degree[from].dout++;
g->degree[to].din++;
g->n_arcs++;
}
int split_pe(int argc, char *argv[], char *progname)
{
int c, bc_len = -1, ret, i, j, bc_idx, only_count = 0;
unsigned num_mismatches = DEFAULT_NUM_MISMATCHES,
num_spacer_bases = DEFAULT_NUM_SPACER_BASES,
dna_alpha_len = strlen(DNA_ALPHA),
num_undetermined = 0;
char *out_prefix = NULL, *fn, **sptr,
bc_id[1024], bc_seq[1024], bc_seq_cpy[1024]; // hello, buffer overflow
clock_t t = clock();
BcRec bc;
ArrayBcRec bcs;
FILE *fp;
kseq_t *seq1, *seq2;
khash_t(str) *h = kh_init(str);
khint_t k, k2;
gzFile *fp1, *fp2;
ARRAY_INIT(&bcs, BcRec, 1000);
while ((c = getopt(argc, argv, "m:s:o:c")) >= 0) {
switch (c) {
case 'm': if (sscanf(optarg, "%u", &num_mismatches) != 1) {
fprintf(stderr, "Error: option -m expects unsigned int\n");
return -1;
}
break;
case 's': if (sscanf(optarg, "%u", &num_spacer_bases) != 1) {
fprintf(stderr, "Error: option -s expects unsigned int\n");
return -1;
}
break;
case 'o': out_prefix = strdup(optarg);
break;
case 'c': only_count = 1;
break;
}
}
if (optind + 3 != argc) {
print_pe_usage(progname);
return -1;
}
if (num_mismatches != 0 && num_mismatches != 1) {
fprintf(stderr, "Error: argument -m has to be 0 or 1\n");
return -1;
}
if (out_prefix == NULL) {
out_prefix = strdup(DEFAULT_OUTPUT_PREFIX);
}
for (sptr = argv+optind; sptr-argv<argc; sptr++) {
if (access(*sptr, F_OK) == -1) {
fprintf(stderr, "Error: file %s does not exist\n", *sptr);
return -1;
}
}
fprintf(stderr, "[barcode file: %s]\n", argv[optind]);
fprintf(stderr, "[fastq file1: %s]\n", argv[optind+1]);
fprintf(stderr, "[fastq file2: %s]\n", argv[optind+2]);
fprintf(stderr, "[number of mismatches allowed: %u]\n", num_mismatches);
fprintf(stderr, "[number of spacer bases: %u]\n", num_spacer_bases);
fprintf(stderr, "[output prefix: %s]\n", out_prefix);
fprintf(stderr, "[only count: %s]\n", only_count ? "true" : "false");
/* read barcode file */
if ((fp = fopen(argv[optind], "r")) == NULL) {
fprintf(stderr, "Error: cannot open barcode file %s\n", argv[optind]);
return -1;
}
while (fscanf(fp, "%s %s", bc_id, bc_seq) == 2) {
bc_len = strlen(bc_seq);
bc.id = strdup(bc_id);
bc.seq = strdup(bc_seq);
bc.num_found = 0;
if (!only_count) {
fn = (char*)calloc(strlen(out_prefix) + 3 + strlen(bc_id) + 6 + 1, sizeof(char));
strcpy(fn, out_prefix);
strcat(fn, "_1_");
strcat(fn, bc_id);
strcat(fn, ".fq.gz");
bc.fp1 = gzopen(fn, "w");
fn[strlen(out_prefix)+1] = '2';
bc.fp2 = gzopen(fn, "w");
free(fn);
} else {
bc.fp1 = NULL;
bc.fp2 = NULL;
}
ARRAY_PUSH(&bcs, BcRec, bc);
k = kh_put(str, h, strdup(bc_seq), &ret);
if (num_mismatches == 0) {
kh_val(h, k) = bcs.nextfree - 1;
//printf("setting %s to %lu (%s %s)\n", bc_seq, bcs.nextfree - 1, bcs.elems[bcs.nextfree - 1].seq, bcs.elems[bcs.nextfree - 1].id);
} else {
for (i=0; i<strlen(bc_seq); i++) {
strcpy(bc_seq_cpy, bc_seq);
for (j=0; j<dna_alpha_len; j++) {
bc_seq_cpy[i] = DNA_ALPHA[j];
k = kh_put(str, h, strdup(bc_seq_cpy), &ret);
kh_val(h, k) = bcs.nextfree - 1;
//printf("setting %s to %lu (%s %s)\n", bc_seq_cpy, bcs.nextfree - 1, bcs.elems[bcs.nextfree - 1].seq, bcs.elems[bcs.nextfree - 1].id);
}
}
}
}
fclose(fp);
if (bc_len == -1) {
fprintf(stderr, "Error: could not find any barcodes in file %s\n", argv[optind]);
return -1;
}
fp1 = gzopen(argv[optind+1], "r");
seq1 = kseq_init(fp1);
fp2 = gzopen(argv[optind+2], "r");
seq2 = kseq_init(fp2);
while (kseq_read(seq1) >= 0) {
strncpy(bc_seq, seq1->seq.s, bc_len);
k = kh_get(str, h, bc_seq);
kseq_read(seq2);
strncpy(bc_seq, seq2->seq.s, bc_len);
k2 = kh_get(str, h, bc_seq);
if (k != kh_end(h) || k2 != kh_end(h)) {
bc_idx = k2 != kh_end(h) ? kh_val(h, k2) : kh_val(h, k);
if (!only_count) {
gzprintf(bcs.elems[bc_idx].fp1, "@%s %s\n%s\n+\n%s\n"
, seq1->name.s
, seq1->comment.s
, seq1->seq.s+bc_len+num_spacer_bases
, seq1->qual.s+bc_len+num_spacer_bases);
gzprintf(bcs.elems[bc_idx].fp2, "@%s %s\n%s\n+\n%s\n"
, seq2->name.s
, seq2->comment.s
, seq2->seq.s+bc_len+num_spacer_bases
, seq2->qual.s+bc_len+num_spacer_bases);
}
bcs.elems[bc_idx].num_found += 2;
} else {
num_undetermined += 2;
}
}
gzclose(fp1);
gzclose(fp2);
kseq_destroy(seq1);
kseq_destroy(seq2);
for (i=0; i<bcs.nextfree; i++) {
printf("%s\t%s\t%u\n", bcs.elems[i].id, bcs.elems[i].seq, bcs.elems[i].num_found);
if (!only_count) {
gzclose(bcs.elems[i].fp1);
gzclose(bcs.elems[i].fp2);
}
}
printf("UNDETERMINED\tNONE\t%u\n", num_undetermined);
ARRAY_FREE(&bcs);
kh_destroy(str, h);
fprintf(stderr, "[CPU time: %.2f sec]\n", (float)(clock() - t) / CLOCKS_PER_SEC);
return 0;
}
