static void output_1contig ( int id, EDGE * edge, FILE * fp, boolean tip )
{
int i;
Kmer kmer;
char ch;
fprintf ( fp, ">%d length %d cvg_%.1f_tip_%d\n", id, edge->length + overlaplen, ( double ) edge->cvg / 10, tip );
//fprintf(fp,">%d\n",id);
kmer = vt_array[edge->from_vt].kmer;
for ( i = overlaplen - 1; i >= 0; i-- )
{
ch = kmer & 3;
kmer >>= 2;
kmerSeq[i] = ch;
}
for ( i = 0; i < overlaplen; i++ )
{ fprintf ( fp, "%c", int2base ( ( int ) kmerSeq[i] ) ); }
for ( i = 0; i < edge->length; i++ )
{
fprintf ( fp, "%c", int2base ( ( int ) getCharInTightString ( edge->seq, i ) ) );
if ( ( i + overlaplen + 1 ) % 100 == 0 )
{ fprintf ( fp, "\n" ); }
}
fprintf ( fp, "\n" );
}
int EdgeEqual ( unsigned int prev, unsigned int next )
{
int i = 0;
int length = edge_array[prev].length;
char ch1, ch2;
int equal = 0;
for ( i = 0; i < length; ++i )
{
ch1 = int2base ( ( int ) getCharInTightString ( edge_array[prev].seq, i ) );
ch2 = int2base ( ( int ) getCharInTightString ( edge_array[next].seq, i ) );
if ( ( equal = BaseEqual ( ch1, ch2 ) ) )
{
return equal;
}
}
return 0;
};
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++);
}
}
/*
void print_kmer(FILE *fp,Kmer kmer,char c)
{
fprintf(fp,"%llx %llx %llx %llx",kmer.high1,kmer.low1,kmer.high2,kmer.low2);
fprintf(fp,"%c",c);
}*/
void printTightString (char *tightSeq, int len)
{
int i;
for (i = 0; i < len; i++)
{
printf ("%c", int2base ((int) getCharInTightString (tightSeq, i)));
if ((i + 1) % 100 == 0)
{
printf ("\n");
}
}
printf ("\n");
}
static void printEdgeSeq (FILE * fp, char *tightSeq, int len)
{
int i;
for (i = 0; i < len; i++)
{
fprintf (fp, "%c", int2base ((int) getCharInTightString (tightSeq, i)));
if ((i + overlaplen + 1) % 100 == 0)
{
fprintf (fp, "\n");
}
}
fprintf (fp, "\n");
}
void output_1contig (int id, EDGE * edge, FILE * fp, boolean tip)
{
int i;
Kmer kmer;
fprintf (fp, ">%d length %d cvg_%.1f_tip_%d\n", id, edge->length + overlaplen, (double) edge->cvg / 10, tip);
kmer = vt_array[edge->from_vt].kmer;
printKmerSeq ( fp, kmer );
for (i = 0; i < edge->length; i++)
{
fprintf (fp, "%c", int2base ((int) getCharInTightString (edge->seq, i)));
if ((i + overlaplen + 1) % 100 == 0)
{
fprintf (fp, "\n");
}
}
fprintf (fp, "\n");
}
static int cmp_seq ( const void * a, const void * b )
{
EDGE * A, *B;
A = ( EDGE * ) a;
B = ( EDGE * ) b;
if ( KmerLarger ( vt_array[A->from_vt].kmer, vt_array[B->from_vt].kmer ) )
{
return 1;
}
else if ( KmerSmaller ( vt_array[A->from_vt].kmer , vt_array[B->from_vt].kmer ) )
{
return -1;
}
else
{
if ( A->seq[0] > B->seq[0] )
{
return 1;
}
else if ( A->seq[0] == B->seq[0] )
{
int i = 0;
for ( i = 1; i < A->length && i < B->length; i++ )
{
if ( getCharInTightString ( A->seq, i ) > getCharInTightString ( B->seq, i ) )
{ return 1; }
else if ( getCharInTightString ( A->seq, i ) < getCharInTightString ( B->seq, i ) )
{ return -1; }
}
if ( i == A->length && i < B->length )
{ return -1; }
else if ( i < A->length && i == B->length )
{ return 1; }
else
{
printKmerSeq ( stderr , vt_array[A->from_vt].kmer );
fprintf ( stderr , "\n" );
printKmerSeq ( stderr , vt_array[B->from_vt].kmer );
fprintf ( stderr , "\n" );
for ( i = 0; i < A->length; i++ )
{
printf( "%c", int2base ( ( int ) getCharInTightString ( A->seq, i ) ) );
}
printf( "\n" );
for ( i = 0; i < B->length; i++ )
{
printf( "%c", int2base ( ( int ) getCharInTightString ( B->seq, i ) ) );
}
printf( "\n" );
printf( "cmp_seq:\terr\n" );
exit ( 0 );
return 0;
}
}
else
{
return -1;
}
}
};