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#include <stdlib.h>
/*
Author: Ian N Schenck
Version: 7/21/2006
Most of this was ripped out of James Taylor's never-released code,
and plugged in here for use in Python. Slight modifications were
made where I saw fit.
It looks as if CpG's are typically not next to gaps.
*/
static inline int is_cpg( char * sp1, char * sp2, int pos)
{
if ( pos < 1 ) return 0;
if ( sp1[pos + 1] == '\0' ) return 0;
if ( sp1[pos - 1] != 'C' && sp2[pos - 1] != 'C' &&
sp1[pos + 1] == 'G' && sp2[pos + 1] == 'G' &&
(sp1[pos] == 'C' || sp2[pos] == 'C') ) return 1;
if ( sp1[pos + 1] != 'G' && sp2[pos + 1] != 'G' &&
sp1[pos - 1] == 'C' && sp2[pos - 1] == 'C' &&
(sp1[pos] == 'G' || sp2[pos] == 'G') ) return 1;
return 0;
}
static inline int is_non_cpg( char * sp1, char * sp2, int pos)
{
// first one can't assuredly be cpg
if ( pos < 1 ) return 1;
if ( sp1[pos + 1] == '\0' ) return 0;
return
( sp1[pos - 1] != 'C' && sp2[pos - 1] != 'C' &&
sp1[pos + 1] != 'G' && sp2[pos + 1] != 'G' );
}
static inline int is_cpg_restricted( char * sp1, char * sp2, int pos )
{
return !is_non_cpg( sp1, sp2, pos );
}
int next( char * sp1, char * sp2, int start, int (*func)(char*,char*,int))
{
while( sp1[start+1] != '\0')
{
if( func(sp1, sp2, start) )
return start;
start++;
}
// nothing found
return -1;
}
int next_cpg( char * sp1, char * sp2, int start)
{
return next( sp1, sp2, start, &is_cpg);
}
int next_cpg_restricted( char * sp1, char *sp2, int start)
{
return next( sp1, sp2, start, &is_cpg_restricted );
}
int next_non_cpg( char * sp1, char * sp2, int start)
{
return next( sp1, sp2, start, &is_non_cpg);
}
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