void output_updated_edges ( char * outfile )
{
FILE * fp;
char name[256];
unsigned int i, validCounter = 0;
EDGE * edge;
sprintf ( name, "%s.updated.edge", outfile );
fp = ckopen ( name, "w" );
for ( i = 1; i <= num_ed; i++ )
{ validCounter++; }
fprintf ( fp, "EDGEs %d\n", validCounter );
validCounter = 0;
for ( i = 1; i <= num_ed; i++ )
{
edge = &edge_array[i];
fprintf ( fp, ">length %d,", edge->length );
print_kmer ( fp, vt_array[edge->from_vt].kmer, ',' );
print_kmer ( fp, vt_array[edge->to_vt].kmer, ',' );
if ( EdSmallerThanTwin ( i ) )
{ fprintf ( fp, "1," ); }
else if ( EdLargerThanTwin ( i ) )
{ fprintf ( fp, "-1," ); }
else
{ fprintf ( fp, "0," ); }
fprintf ( fp, "%d\n", edge->cvg );
}
fclose ( fp );
}
void output_1edge ( preEDGE * edge, FILE * fp )
{
int i;
fprintf ( fp, ">length %d,", edge->length );
print_kmer ( fp, edge->from_node, ',' );
print_kmer ( fp, edge->to_node, ',' );
fprintf ( fp, "cvg %d, %d\n", edge->cvg, edge->bal_edge );
for ( i = 0; i < edge->length; i++ )
{
fprintf ( fp, "%c", int2base ( ( int ) edge->seq[i] ) );
if ( ( i + 1 ) % 100 == 0 )
{ fprintf ( fp, "\n" ); }
}
fprintf ( fp, "\n" );
}
//after this LINKFLAGFILTER in the Kmer is destroyed
static void output1vt ( kmer_t * node1, FILE * fp )
{
if ( !node1 )
{ return; }
if ( ! ( node1->linear ) && ! ( node1->deleted ) )
{
outvCounter++;
print_kmer ( fp, node1->seq, ' ' );
//printKmerSeq(stdout,node1->seq);
//printf("\n");
if ( outvCounter % 8 == 0 )
{ fprintf ( fp, "\n" ); }
}
}
int main(int argc, char **argv) {
char *fn = NULL;
FILE *fh = NULL;
unsigned int kmer = 0;
bool nonzero = false;
bool label = false;
bool kmer_set = false;
bool count_compliment = false;
bool force_sparse = false;
static struct option long_options[] = {
{"input", required_argument, 0, 'i'},
{"kmer", required_argument, 0, 'k'},
{"compliment", required_argument, 0, 'c'},
{"nonzero", no_argument, 0, 'n'},
{"label", no_argument, 0, 'l'},
{"sparse", no_argument, 0, 's'},
{"help", no_argument, 0, 'h'},
{0, 0, 0, 0}
};
while (1) {
int option_index = 0;
int c = 0;
c = getopt_long (argc, argv, "i:k:cnslvh", long_options, &option_index);
if (c == -1)
break;
switch (c) {
case 'i':
fn = optarg;
break;
case 'k':
kmer = atoi(optarg);
kmer_set = true;
break;
case 'c':
count_compliment = true;
break;
case 'n':
nonzero = true;
break;
case 'l':
label = true;
break;
case 's':
force_sparse = true;
break;
case 'h':
help();
exit(EXIT_SUCCESS);
break;
case 'v':
printf("dna-utils version " VERSION "\n");
exit(EXIT_SUCCESS);
break;
default:
break;
}
}
if(argc == 1) {
help();
exit(EXIT_FAILURE);
}
if(fn == NULL) {
fprintf(stderr, "no input file specified with -i, reading from stdin\n");
fh = stdin;
}
else {
fh = fopen(fn, "r");
if(fh == NULL) {
fprintf(stderr, "Could not open %s - %s\n", fn, strerror(errno));
exit(EXIT_FAILURE);
}
}
if(!kmer_set) {
fprintf(stderr, "Error: kmer (-k) must be supplied\n");
exit(EXIT_FAILURE);
}
if(kmer == 0) {
fprintf(stderr, "Error: invalid kmer - '%d'.\n", kmer);
exit(EXIT_FAILURE);
}
if(kmer > 12 || force_sparse) {
kmer_map *counts = NULL;
kmer_map *res = get_kmer_counts_from_file(counts, fh, kmer, count_compliment);
print_kmer(res, label, nonzero, kmer);
}
else {
unsigned long long *counts = NULL;
unsigned long long *res = get_kmer_counts_from_file(counts, fh, kmer, count_compliment);
print_kmer(res, label, nonzero, kmer);
}
return EXIT_SUCCESS;
}
