/*************************************************
Function:
loadContig
Description:
Loads contigs sequence.
Input:
1. graphfile: prefix of graph file
Output:
None.
Return:
None.
*************************************************/
void loadContig ( char * graphfile )
{
char c, name[256], line[1024], *tightSeq = NULL;
FILE * fp;
int n = 0, length, index = -1, edgeno;
unsigned int i;
unsigned int newIndex;
sprintf ( name, "%s.contig", graphfile );
fp = ckopen ( name, "r" );
while ( fgets ( line, sizeof ( line ), fp ) != NULL )
{
if ( line[0] == '>' )
{
if ( index >= 0 )
{
newIndex = index_array[edgeno];
contig_array[newIndex].seq = tightSeq;
}
n = 0;
index++;
sscanf ( line + 1, "%d %s %d", &edgeno, name, &length );
//printf("contig %d, length %d\n",edgeno,length);
tightSeq = ( char * ) ckalloc ( ( length / 4 + 1 ) * sizeof ( char ) );
}
else
{
for ( i = 0; i < strlen ( line ); i++ )
{
if ( line[i] >= 'a' && line[i] <= 'z' )
{
c = base2int ( line[i] - 'a' + 'A' );
writeChar2tightString ( c, tightSeq, n++ );
}
else if ( line[i] >= 'A' && line[i] <= 'Z' )
{
c = base2int ( line[i] );
writeChar2tightString ( c, tightSeq, n++ );
}
}
}
}
if ( index >= 0 )
{
newIndex = index_array[edgeno];
contig_array[newIndex].seq = tightSeq;
}
fprintf ( stderr, "%d contig(s) loaded.\n", index + 1 );
fclose ( fp );
//printf("the %dth contig with index 107\n",index);
}
void copySeq (char *targetS, char *sourceS, int pos, int length)
{
char ch;
int i, index;
index = pos;
for (i = 0; i < length; i++)
{
ch = getCharInTightString (sourceS, i);
writeChar2tightString (ch, targetS, index++);
}
}