static int calcuIS (STACK * intStack)
{
long long sum = 0;
int avg = 0;
int *item;
int num = intStack->item_c;
if (num < 100)
{
return avg;
}
stackBackup (intStack);
while ((item = (int *) stackPop (intStack)) != NULL)
{
sum += *item;
}
stackRecover (intStack);
num = intStack->item_c;
avg = sum / num;
sum = 0;
stackBackup (intStack);
while ((item = (int *) stackPop (intStack)) != NULL)
{
sum += (*item - avg) * (*item - avg);
}
int SD = sqrt (sum / (num - 1));
if (SD == 0)
{
printf ("SD=%d, ", SD);
return avg;
}
stackRecover (intStack);
sum = num = 0;
while ((item = (int *) stackPop (intStack)) != NULL)
if (abs (*item - avg) < 3 * SD)
{
sum += *item;
num++;
}
if(num == 0) avg = 0;
else avg = sum / num;
printf ("SD=%d, ", SD);
return avg;
}
//search linear structure starting with the root of a tree
static int startEdgeFromNode ( kmer_t * node1, FILE * fp )
{
int node_c, palindrome;
unsigned char flag;
KMER_PT * ite_pt, *temp_pt;
Kmer word1, bal_word1;
char ch1;
if ( node1->linear || node1->deleted )
{ return 0; }
// ignore floating loop
word1 = node1->seq;
bal_word1 = reverseComplement ( word1, overlaplen );
// linear structure
for ( ch1 = 0; ch1 < 4; ch1++ ) // for every node on outgoing list
{
flag = get_kmer_right_cov ( *node1, ch1 );
if ( !flag )
{ continue; }
emptyStack ( nodeStack );
temp_pt = ( KMER_PT * ) stackPush ( nodeStack );
temp_pt->node = node1;
temp_pt->isSmaller = 1;
temp_pt->kmer = word1;
stringBeads ( temp_pt, ch1, &node_c );
//printf("%d nodes\n",node_c);
if ( node_c < 2 )
{ printf ( "%d nodes in this line!!!!!!!!!!!\n", node_c ); }
else
{
//make a reverse complement node list
stackBackup ( nodeStack );
emptyStack ( bal_nodeStack );
while ( ( ite_pt = ( KMER_PT * ) stackPop ( nodeStack ) ) != NULL )
{
temp_pt = ( KMER_PT * ) stackPush ( bal_nodeStack );
temp_pt->kmer = reverseComplement ( ite_pt->kmer, overlaplen );
}
stackRecover ( nodeStack );
palindrome = check_iden_kmerList ( nodeStack, bal_nodeStack );
stackRecover ( nodeStack );
if ( palindrome )
{
merge_linearV2 ( 0, nodeStack, node_c, fp );
}
else
{ merge_linearV2 ( 1, nodeStack, node_c, fp ); }
}
} //every possible outgoing edges
for ( ch1 = 0; ch1 < 4; ch1++ ) // for every node on incoming list
{
flag = get_kmer_left_cov ( *node1, ch1 );
if ( !flag )
{ continue; }
emptyStack ( nodeStack );
temp_pt = ( KMER_PT * ) stackPush ( nodeStack );
temp_pt->node = node1;
temp_pt->isSmaller = 0;
temp_pt->kmer = bal_word1;
stringBeads ( temp_pt, int_comp ( ch1 ), &node_c );
if ( node_c < 2 )
{ printf ( "%d nodes in this line!!!!!!!!!!!\n", node_c ); }
else
{
//make a reverse complement node list
stackBackup ( nodeStack );
emptyStack ( bal_nodeStack );
while ( ( ite_pt = ( KMER_PT * ) stackPop ( nodeStack ) ) != NULL )
{
temp_pt = ( KMER_PT * ) stackPush ( bal_nodeStack );
temp_pt->kmer = reverseComplement ( ite_pt->kmer, overlaplen );
}
stackRecover ( nodeStack );
palindrome = check_iden_kmerList ( nodeStack, bal_nodeStack );
stackRecover ( nodeStack );
if ( palindrome )
{
merge_linearV2 ( 0, nodeStack, node_c, fp );
//printf("edge is palindrome with length %d\n",temp_edge.length);
}
else
{ merge_linearV2 ( 1, nodeStack, node_c, fp ); }
}
} //every possible incoming edges
return 0;
}
