ssize_t
qes_seqfile_write (struct qes_seqfile *seqfile, struct qes_seq *seq)
{
#define sf_putc_check(c) ret = QES_ZFPUTC(seqfile->qf->fp, c); \
if (ret != c) {return -2;} \
else res_len += 1; \
ret = 0
#define sf_puts_check(s) ret = QES_ZFPUTS(seqfile->qf->fp, s); \
if (ret < 0) {return -2;} \
else res_len += ret; \
ret = 0
int ret = 0;
ssize_t res_len = 0;
if (!qes_seqfile_ok(seqfile) || !qes_seq_ok(seq)) {
return -2;
}
switch (seqfile->format) {
case FASTA_FMT:
sf_putc_check(FASTA_DELIM);
sf_puts_check(seq->name.str);
if (qes_seq_has_comment(seq)) {
sf_putc_check(' ');
sf_puts_check(seq->comment.str);
}
sf_putc_check('\n');
sf_puts_check(seq->seq.str);
sf_putc_check('\n');
break;
case FASTQ_FMT:
sf_putc_check(FASTQ_DELIM);
sf_puts_check(seq->name.str);
if (qes_seq_has_comment(seq)) {
sf_putc_check(' ');
sf_puts_check(seq->comment.str);
}
sf_putc_check('\n');
sf_puts_check(seq->seq.str);
sf_putc_check('\n');
if (qes_seq_has_qual(seq)) {
sf_putc_check('+');
sf_putc_check('\n');
sf_puts_check(seq->qual.str);
sf_putc_check('\n');
}
break;
case UNKNOWN_FMT:
default:
return -2;
break;
}
return res_len;
#undef sf_putc_check
#undef sf_puts_check
}
/*******************************************************************************
* MAIN *
*******************************************************************************/
int
trunc_main(int argc, char *argv[])
{
int c = 0;
size_t truncat = 0;
float truncprop = 0.;
const char *filename = NULL;
/* Parse CLI options */
while ((c = getopt(argc, argv, trunc_optstr)) >= 0) {
switch (c) {
case 'p':
truncprop = atof(optarg);
break;
case 'l':
truncat = atoi(optarg);
break;
case 'h':
trunc_usage(stdout);
return EXIT_SUCCESS;
break;
case '?':
trunc_usage(stderr);
return EXIT_FAILURE;
break;
}
}
if (optind >= argc || (truncat == 0 && truncprop == 0.0)) {
trunc_usage(stderr);
return EXIT_FAILURE;
}
filename = argv[optind];
struct qes_seq *seq = qes_seq_create();
struct qes_seqfile *sf = qes_seqfile_create(filename, "r");
ssize_t res;
while ((res = qes_seqfile_read(sf, seq)) > 0) {
if (truncprop != 0.0) {
truncat = truncprop * seq->seq.len;
}
qes_seq_truncate(seq, truncat);
qes_seq_print(seq, stdout, !qes_seq_has_qual(seq), 0);
}
qes_seqfile_destroy(sf);
qes_seq_destroy(seq);
return EXIT_SUCCESS;
}
