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prepare to ditch stdaln.{h,c}

This commit is contained in:
Heng Li 2013-03-04 10:32:33 -05:00
parent d35f33b513
commit 1a451df800
1 changed files with 1 additions and 24 deletions
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25
bwtsw2_pair.c
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@ -7,11 +7,7 @@
#include "bwtsw2.h"
#include "kstring.h"
#include "utils.h"
#ifndef _NO_SSE2
#include "ksw.h"
#else
#include "stdaln.h"
#endif
#define MIN_RATIO 0.8
#define OUTLIER_BOUND 2.0
@ -126,8 +122,7 @@ void bsw2_pair1(const bsw2opt_t *opt, int64_t l_pac, const uint8_t *pac, const b
for (i = 0; i < l_mseq; ++i) // on the forward strand
seq[i] = nst_nt4_table[(int)mseq[i]];
}
#ifndef _NO_SSE2
{ // FIXME!!! The following block has not been tested since the update of the ksw library
{
int flag = KSW_XSUBO | KSW_XSTART | (l_mseq * g_mat[0] < 250? KSW_XBYTE : 0) | opt->t;
kswr_t aln;
aln = ksw_align(l_mseq, seq, end - beg, ref, 5, g_mat, opt->q, opt->r, flag, 0);
@ -146,24 +141,6 @@ void bsw2_pair1(const bsw2opt_t *opt, int64_t l_pac, const uint8_t *pac, const b
printf("G=%d,G2=%d,beg=%d,end=%d,k=%lld,len=%d\n", a->G, a->G2, a->beg, a->end, a->k, a->len);
*/
}
#else
{
AlnParam ap;
path_t path[2];
int matrix[25];
for (i = 0; i < 25; ++i) matrix[i] = g_mat[i];
ap.gap_open = opt->q; ap.gap_ext = opt->r; ap.gap_end = opt->r;
ap.matrix = matrix; ap.row = 5; ap.band_width = 50;
a->G = aln_local_core(ref, end - beg, seq, l_mseq, &ap, path, 0, opt->t, &a->G2);
if (a->G < opt->t) a->G = 0;
if (a->G2 < opt->t) a->G2 = 0;
if (a->G2) a->flag |= BSW2_FLAG_TANDEM;
a->k = beg + path[0].i - 1;
a->len = path[1].i - path[0].i + 1;
a->beg = path[0].j - 1;
a->end = path[1].j;
}
#endif
if (a->is_rev) i = a->beg, a->beg = l_mseq - a->end, a->end = l_mseq - i;
free(seq);
}