Question: Is overlap more tight in collision detection than contain ?

[kojix2]

I noticed a difference in behaviour when calling the contain and overlap functions.

First, adds the interval cr_add(cr, "chr1", 10, 10, 0);

overlap ("chr1", 10, 20) finds nothing.
contain ("chr1", 10, 20) finds this interval.

#include <stdio.h>
#include <stdlib.h>
#include "cgranges.h"

int main(void)
{
	cgranges_t *cr = cr_init();
	cr_add(cr, "chr1", 10, 10, 0);
	cr_index(cr);

	int64_t i, n, *b = 0, max_b = 0;
	n = cr_overlap(cr, "chr1", 10, 11, &b, &max_b);
	for (i = 0; i < n; ++i)
		printf("%d\t%d\t%d\n", cr_start(cr, b[i]), cr_end(cr, b[i]), cr_label(cr, b[i]));
	free(b);

	cr_destroy(cr);
	return 0;
}

# no output

#include <stdio.h>
#include <stdlib.h>
#include "cgranges.h"

int main(void)
{
	cgranges_t *cr = cr_init();
	cr_add(cr, "chr1", 10, 10, 0);
	cr_index(cr);

	int64_t i, n, *b = 0, max_b = 0;
	n = cr_contain(cr, "chr1", 10, 11, &b, &max_b);
	for (i = 0; i < n; ++i)
		printf("%d\t%d\t%d\n", cr_start(cr, b[i]), cr_end(cr, b[i]), cr_label(cr, b[i]));
	free(b);

	cr_destroy(cr);
	return 0;
}

10	10	0

This behaviour was somewhat surprising. Is this normal behaviour? I'm not very familiar with genomics, so I don't know exactly how it should behave.

[lh3]

This is really caused by 0-length intervals. [10,10) is zero-length. cr_overlap effectively filters out all such intervals. cr_contain uses a different algorithm and doesn't have the issue. I need to address this.