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bugfix: bug in the new ksw.c 

On my test data, one alignment is different, caused by polyA
This commit is contained in:
Heng Li 2013-02-12 17:48:46 -05:00
parent 28a7d501f2
commit 557daabf38
2 changed files with 12 additions and 6 deletions
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12
bwtsw2_pair.c
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@ -128,17 +128,23 @@ void bsw2_pair1(const bsw2opt_t *opt, int64_t l_pac, const uint8_t *pac, const b
} }
#ifndef _NO_SSE2 #ifndef _NO_SSE2
{ // FIXME!!! The following block has not been tested since the update of the ksw library { // FIXME!!! The following block has not been tested since the update of the ksw library
int flag = KSW_XSUBO | KSW_XSTOP | KSW_XSTART | (l_mseq * g_mat[0] < 250? KSW_XBYTE : 0); int flag = KSW_XSUBO | KSW_XSTART | (l_mseq * g_mat[0] < 250? KSW_XBYTE : 0) | opt->t;
kswr_t aln; kswr_t aln;
aln = ksw_align(l_mseq, seq, end - beg, ref, 5, g_mat, opt->q, opt->r, flag, 0); aln = ksw_align(l_mseq, seq, end - beg, ref, 5, g_mat, opt->q, opt->r, flag, 0);
a->G = aln.score; a->G = aln.score;
a->G2 = aln.score2; a->G2 = aln.score2;
if (a->G < opt->t) a->G = 0;
if (a->G2 < opt->t) a->G2 = 0; if (a->G2 < opt->t) a->G2 = 0;
if (a->G2) a->flag |= BSW2_FLAG_TANDEM; if (a->G2) a->flag |= BSW2_FLAG_TANDEM;
a->k = beg + aln.tb; a->k = beg + aln.tb;
a->len = aln.te - aln.tb; a->len = aln.te - aln.tb + 1;
a->beg = aln.qb; a->beg = aln.qb;
a->end = aln.qe; a->end = aln.qe + 1;
/*
printf("[Q] "); for (i = 0; i < l_mseq; ++i) putchar("ACGTN"[(int)seq[i]]); putchar('\n');
printf("[R] "); for (i = 0; i < end - beg; ++i) putchar("ACGTN"[(int)ref[i]]); putchar('\n');
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 #else
{ {

6
ksw.c
View File

@ -211,7 +211,7 @@ end_loop16:
low = te - i; high = te + i; low = te - i; high = te + i;
for (i = 0; i < n_b; ++i) { for (i = 0; i < n_b; ++i) {
int e = (int32_t)b[i]; int e = (int32_t)b[i];
if ((e < low || e > high) && b[i]>>32 > (uint32_t)r.score2) if ((e < low || e > high) && (int)(b[i]>>32) > r.score2)
r.score2 = b[i]>>32, r.te2 = e; r.score2 = b[i]>>32, r.te2 = e;
} }
} }
@ -311,7 +311,7 @@ end_loop8:
low = te - i; high = te + i; low = te - i; high = te + i;
for (i = 0; i < n_b; ++i) { for (i = 0; i < n_b; ++i) {
int e = (int32_t)b[i]; int e = (int32_t)b[i];
if ((e < low || e > high) && b[i]>>32 > (uint32_t)r.score2) if ((e < low || e > high) && (int)(b[i]>>32) > r.score2)
r.score2 = b[i]>>32, r.te2 = e; r.score2 = b[i]>>32, r.te2 = e;
} }
} }
@ -587,7 +587,7 @@ int main(int argc, char *argv[])
return 1; return 1;
} }
if (minsc > 0xffff) minsc = 0xffff; if (minsc > 0xffff) minsc = 0xffff;
if (minsc > 0) xtra |= KSW_XSUBO | minsc; xtra |= KSW_XSUBO | minsc;
// initialize scoring matrix // initialize scoring matrix
for (i = k = 0; i < 4; ++i) { for (i = k = 0; i < 4; ++i) {
for (j = 0; j < 4; ++j) for (j = 0; j < 4; ++j)