int main(int argc, char** argv)
{
if(argc < 3 || argc > 4)
{
print_usage();
}
char* in_path = argv[1];
char* out_path = argv[2];
unsigned long line_wrap = 0;
if(argc == 4)
{
char *line_wrap_str = argv[3];
char *endptr;
line_wrap = strtoul(line_wrap_str, &endptr, 10);
if((unsigned)(endptr-line_wrap_str) != strlen(line_wrap_str))
{
print_usage();
}
}
SeqFileType out_file_type = SEQ_UNKNOWN;
char out_zipped = 0;
seq_guess_filetype_from_path(out_path, &out_file_type, &out_zipped);
if(out_file_type == SEQ_UNKNOWN)
{
fprintf(stderr, "%s:%i: Sorry, I cannot identify the output file's format "
"from its path [file: %s]\n", __FILE__, __LINE__, out_path);
exit(EXIT_FAILURE);
}
SeqFile* in_file = seq_file_open(in_path);
SeqFile* out_file = seq_file_open_write(out_path, out_file_type,
out_zipped, line_wrap);
if(in_file == NULL)
{
fprintf(stderr, "%s:%i: Couldn't open input file: %s\n",
__FILE__, __LINE__, in_path);
exit(EXIT_FAILURE);
}
if(out_file == NULL)
{
fprintf(stderr, "%s:%i: Couldn't open output file: %s\n",
__FILE__, __LINE__, out_path);
exit(EXIT_FAILURE);
}
printf(" In : %s [%s]\n", in_path, seq_file_get_type_str(in_file));
printf(" Out: %s [%s]\n", out_path, seq_file_get_type_str(out_file));
// Start converting
size_t bytes_written = 0;
char c[2] = ".";
if(out_file_type == SEQ_PLAIN)
{
// Example reading in an entire entry at a time using seq_read_all_bases()
StrBuf *bases = strbuf_new();
while(seq_next_read(in_file))
{
while(seq_read_all_bases(in_file, bases))
{
bytes_written += seq_file_write_seq(out_file, bases->buff);
}
}
}
else
{
// Example reading in a char at a time using seq_read_base()
while(seq_next_read(in_file))
{
const char* read_name = seq_get_read_name(in_file);
bytes_written += seq_file_write_name(out_file, read_name);
unsigned long seq_length = 0;
while(seq_read_base(in_file, c))
{
seq_length++;
if(!(bytes_written += seq_file_write_seq(out_file, c)))
{
fprintf(stderr, "%s:%i: Couldn't write base to file "
"[file: %s; line: %lu]\n",
__FILE__, __LINE__,
seq_get_path(out_file), seq_curr_line_number(in_file));
exit(EXIT_FAILURE);
}
}
if(seq_has_quality_scores(out_file))
{
size_t bytes_written_before_qual = bytes_written;
while(seq_read_qual(in_file, c))
{
if(!(bytes_written += seq_file_write_qual(out_file, c)))
{
fprintf(stderr, "%s:%i: Couldn't write quality score to file "
"[file: %s; line: %lu]\n",
__FILE__, __LINE__, seq_get_path(out_file),
seq_curr_line_number(in_file));
exit(EXIT_FAILURE);
}
}
if(bytes_written == bytes_written_before_qual)
{
// No quality scores were read - fill in
unsigned long i;
*c = '?';
for(i = 0; i < seq_length; i++)
bytes_written += seq_file_write_qual(out_file, c);
}
}
}
}
unsigned long seq_total_bases_read = seq_total_bases_passed(in_file);
unsigned long total_entries = seq_get_read_index(in_file);
seq_file_close(in_file);
bytes_written += seq_file_close(out_file);
printf("%lu entries read\n", total_entries);
printf("%lu bases read\n", seq_total_bases_read);
printf("%lu bytes written\n", bytes_written);
printf("Done. \n");
return EXIT_SUCCESS;
}
// If seq2 is NULL, read pair of entries from first file
// Otherwise read an entry from each
void align_from_file(const char *path1, const char *path2,
void (align)(StrBuf*, StrBuf*, const char*, const char*))
{
SeqFile *sf1 = seq_file_open(path1);
SeqFile *sf2;
if(sf1 == NULL)
{
fprintf(stderr, "Alignment Error: couldn't open file %s\n", path1);
fflush(stderr);
return;
}
if(path2 != NULL)
{
sf2 = seq_file_open(path2);
if(sf2 == NULL)
{
fprintf(stderr, "Alignment Error: couldn't open file %s\n", path1);
fflush(stderr);
return;
}
}
else
{
sf2 = sf1;
}
StrBuf *entry1_title = strbuf_new();
StrBuf *entry2_title = strbuf_new();
StrBuf *entry1_seq = strbuf_new();
StrBuf *entry2_seq = strbuf_new();
char *title1 = NULL, *title2 = NULL;
// Loop while we can read a sequence from the first file
while(seq_next_read(sf1))
{
seq_read_all_bases(sf1, entry1_seq);
if(seq_file_get_type(sf1) != SEQ_PLAIN)
{
strbuf_set(entry1_title, seq_get_read_name(sf1));
title1 = entry1_title->buff;
}
if(!seq_next_read(sf2))
{
fprintf(stderr, "Alignment Error: Odd number of sequences - "
"I read in pairs!\n");
fflush(stderr);
break;
}
seq_read_all_bases(sf2, entry2_seq);
if(seq_file_get_type(sf2) != SEQ_PLAIN)
{
strbuf_set(entry2_title, seq_get_read_name(sf2));
title2 = entry2_title->buff;
}
(align)(entry1_seq, entry2_seq, title1, title2);
}
// warn if no bases read
if(seq_total_bases_passed(sf1) == 0)
{
fprintf(stderr, "Alignment Warning: empty input\n");
fflush(stderr);
}
// Close files
seq_file_close(sf1);
if(path2 != NULL)
seq_file_close(sf2);
// Free memory
strbuf_free(entry1_title);
strbuf_free(entry2_title);
strbuf_free(entry1_seq);
strbuf_free(entry2_seq);
}
