why alignment results are 16 characters shorter than input sequences?

[chenying2016]

In bench.c, we make sequences a and b identical sequences and both of length 10000. And we then add a statement
printf("m(%lld)\n", m);
after line 3674 of file gaba.c.
When we compile and run bench.c, it always output
m(9984)
while the normal output should be
m(10000).
Is there something going wrong?

[ocxtal]

First of all, I'm sorry the bench.c being incorrect in calling the libgaba APIs. The correct one will be the following:

/* root coordinates; align from the heads */
uint32_t asp = 0, bsp = 0;

/* margin */
char const m[96] = {0};

/* build section structs */
gaba_section_t asec = gaba_build_section(0, a, strlen(a));
gaba_section_t bsec = gaba_build_section(2, b, strlen(b));
gaba_section_t msec = gaba_build_section(4, &m[32], 32);

/* keep current pointers in ap and bp */
gaba_section_t const *ap = &asec, *bp = &bsec;

/* fill the body of the banded matrix */
gaba_fill_t *f = gaba_dp_fill_root(
	dp, ap, asp, bp, bsp);

/* keep section with the maximum cell value in m */
gaba_fill_t *m = f;

/* fill-in the tail of the banded matrix */
uint32_t flag = GABA_STATUS_TERM;
do {
	if (f->status & GABA_STATUS_UPDATE_A) {
		ap = &msec;
	}
	if (f->status & GABA_STATUS_UPDATE_B) {
		bp = &msec;
	}
	flag |= f->status & (
		GABA_STATUS_UPDATE_A | GABA_STATUS_UPDATE_B
	);
	f = gaba_dp_fill(dp, f, ap, bp);
	m = (f->max > m->max)? f : m;
} while (!(flag & f->status));

/* fill-in is done, m holds block with the maximum */
printf("score(%lld)\n", m->max);

The behavior of the library comes from its design principle to handle each input sequence as a concatenation of sequence segments. The library forwards the front of the band (or ``extends the band'') till 32-base-long subsequence pair is available (see Fig in https://github.com/ocxtal/libgaba#sequences). So, to align toward the tips of two sequences we have to pass margin or dummy sequences after the sequences of interest.

Thanks,

Hajime Suzuki