bits_extend

bMACS.c

#include <stdio.h>
#include <stdlib.h>
#define SHIFT 4
#define MSK 0x0F
#define UNT 1
#define N 300000000
#define print(X) for (i=1;i<1+N;i++) {printf("%d\t%d\n",i,(X)[i]);}


unsigned char aln[1+N];
unsigned char pileup[1+N];

void set(unsigned long i)
{
	if ((aln[i] & MSK) != MSK ) {
		aln[i] += UNT;
	}
}


void nset(unsigned long i)
{
	if ((aln[i] & ~MSK) != ~MSK) {
		aln[i] += UNT << SHIFT;
	}
}

inline int get(unsigned long i) { return aln[i] & MSK; }
inline int nget(unsigned long i) { return aln[i] >> SHIFT; }

unsigned long before(unsigned long i, int shift, unsigned long start)
{
	if (start < i - shift)
		return i - shift;
	else
		return start;
}

unsigned long after(unsigned long i, int shift, unsigned long end)
{
	if (i+shift < end)
		return i + shift;
	else
		return end;
}
       
int ext(unsigned long pos, int shift, int seed)
{
	unsigned long left;
	unsigned long right;
	int sum;
	unsigned long i;

	left = before(pos, shift, 1);
	right = after(pos, shift, N+1);
	if (seed == 0) {
		sum = 0;
		for (i=left; i<pos; i++)
			sum += get(i);
		for (i=pos; i<right; i++)
			sum += nget(i);
		return sum;
	} else {
		return get(pos) - get(left) + nget(right) - nget(pos);
	}
}

int main(void)
{
	unsigned long i;
	int shiftsize = 200;
	for (i=1; i < N+1; i++)
		aln[i] = 0;

	set(10); set(10); set(11); set(12); nset(29); nset(20);

	for (i=1; i < N+1; i++)
		pileup[i] = 0;

	pileup[1] = ext(1, shiftsize, 0);
	for (i=2; i<N+1; i++) {
		pileup[i] = pileup[i-1] + ext(i, shiftsize, 1);
	}
}