r329: ditch stdaln.{c,h}; no changes to bwa-mem
stdaln.{c,h} was written ten years ago. Its local and SW extension code are
actually buggy (though that rarely happens and usually does not affect the
results too much). ksw.{c,h} is more concise, potentially faster, less buggy,
and richer in features.
This commit is contained in:
Heng Li
parent
bb37e14d02
commit
98f8966750
6
Makefile
6
Makefile
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@ -4,7 +4,7 @@ CXXFLAGS= $(CFLAGS)
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AR= ar
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DFLAGS= -DHAVE_PTHREAD #-D_NO_SSE2 #-D_FILE_OFFSET_BITS=64
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LOBJS= utils.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o
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AOBJS= QSufSort.o bwt_gen.o stdaln.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \
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AOBJS= QSufSort.o bwt_gen.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \
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is.o bwtindex.o bwape.o kopen.o \
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bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o \
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bwtsw2_chain.o fastmap.o bwtsw2_pair.o
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@ -48,8 +48,8 @@ fastmap.o:bwt.h bwamem.h
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bwtaln.o:bwt.h bwtaln.h kseq.h
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bwtgap.o:bwtgap.h bwtaln.h bwt.h
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bwtsw2_core.o:bwtsw2.h bwt.h bwt_lite.h stdaln.h
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bwtsw2_aux.o:bwtsw2.h bwt.h bwt_lite.h stdaln.h
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bwtsw2_core.o:bwtsw2.h bwt.h bwt_lite.h
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bwtsw2_aux.o:bwtsw2.h bwt.h bwt_lite.h
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bwtsw2_main.o:bwtsw2.h
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clean:
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41
bwape.c
41
bwape.c
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@ -8,9 +8,9 @@
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#include "kvec.h"
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#include "bntseq.h"
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#include "utils.h"
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#include "stdaln.h"
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#include "bwase.h"
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#include "bwa.h"
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#include "ksw.h"
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typedef struct {
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int n;
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@ -397,16 +397,17 @@ int bwa_cal_pac_pos_pe(const bntseq_t *bns, const char *prefix, bwt_t *const _bw
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#define SW_MIN_MAPQ 17
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// cnt = n_mm<<16 | n_gapo<<8 | n_gape
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bwa_cigar_t *bwa_sw_core(bwtint_t l_pac, const ubyte_t *pacseq, int len, const ubyte_t *seq, int64_t *beg, int reglen,
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int *n_cigar, uint32_t *_cnt)
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bwa_cigar_t *bwa_sw_core(bwtint_t l_pac, const ubyte_t *pacseq, int len, const ubyte_t *seq, int64_t *beg, int reglen, int *n_cigar, uint32_t *_cnt)
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{
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kswr_t r;
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uint32_t *cigar32 = 0;
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bwa_cigar_t *cigar = 0;
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ubyte_t *ref_seq;
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bwtint_t k, x, y, l;
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int path_len, ret, subo;
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AlnParam ap = aln_param_bwa;
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path_t *path, *p;
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int xtra;
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int8_t mat[25];
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bwa_fill_scmat(1, 3, mat);
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// check whether there are too many N's
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if (reglen < SW_MIN_MATCH_LEN || (int64_t)l_pac - *beg < len) return 0;
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for (k = 0, x = 0; k < len; ++k)
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@ -417,15 +418,19 @@ bwa_cigar_t *bwa_sw_core(bwtint_t l_pac, const ubyte_t *pacseq, int len, const u
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ref_seq = (ubyte_t*)calloc(reglen, 1);
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for (k = *beg, l = 0; l < reglen && k < l_pac; ++k)
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ref_seq[l++] = pacseq[k>>2] >> ((~k&3)<<1) & 3;
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path = (path_t*)calloc(l+len, sizeof(path_t));
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// do alignment
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ret = aln_local_core(ref_seq, l, (ubyte_t*)seq, len, &ap, path, &path_len, 1, &subo);
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if (ret < 0 || subo == ret) { // no hit or tandem hits
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free(path); free(cigar); free(ref_seq); *n_cigar = 0;
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xtra = KSW_XSUBO | KSW_XSTART | (len < 250? KSW_XBYTE : 0);
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r = ksw_align(len, (uint8_t*)seq, l, ref_seq, 5, mat, 5, 1, xtra, 0);
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ksw_global(r.qe - r.qb + 1, &seq[r.qb], r.te - r.tb + 1, &ref_seq[r.tb], 5, mat, 5, 1, 50, n_cigar, &cigar32);
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cigar = (bwa_cigar_t*)cigar32;
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for (k = 0; k < *n_cigar; ++k)
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cigar[k] = __cigar_create((cigar32[k]&0xf), (cigar32[k]>>4));
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if (r.score < SW_MIN_MATCH_LEN || r.score2 == r.score) { // poor hit or tandem hits
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free(cigar); free(ref_seq); *n_cigar = 0;
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return 0;
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}
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cigar = bwa_aln_path2cigar(path, path_len, n_cigar);
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// check whether the alignment is good enough
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for (k = 0, x = y = 0; k < *n_cigar; ++k) {
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@ -435,17 +440,14 @@ bwa_cigar_t *bwa_sw_core(bwtint_t l_pac, const ubyte_t *pacseq, int len, const u
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else y += __cigar_len(c);
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}
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if (x < SW_MIN_MATCH_LEN || y < SW_MIN_MATCH_LEN) { // not good enough
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free(path); free(cigar); free(ref_seq);
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free(cigar); free(ref_seq);
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*n_cigar = 0;
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return 0;
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}
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{ // update cigar and coordinate;
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int start, end;
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p = path + path_len - 1;
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*beg += (p->i? p->i : 1) - 1;
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start = (p->j? p->j : 1) - 1;
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end = path->j;
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int start = r.qb, end = r.qe + 1;
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*beg += r.tb;
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cigar = (bwa_cigar_t*)realloc(cigar, sizeof(bwa_cigar_t) * (*n_cigar + 2));
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if (start) {
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memmove(cigar + 1, cigar, sizeof(bwa_cigar_t) * (*n_cigar));
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@ -462,8 +464,7 @@ bwa_cigar_t *bwa_sw_core(bwtint_t l_pac, const ubyte_t *pacseq, int len, const u
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{ // set *cnt
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int n_mm, n_gapo, n_gape;
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n_mm = n_gapo = n_gape = 0;
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p = path + path_len - 1;
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x = p->i? p->i - 1 : 0; y = p->j? p->j - 1 : 0;
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x = r.tb; y = r.qb;
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for (k = 0; k < *n_cigar; ++k) {
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bwa_cigar_t c = cigar[k];
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if (__cigar_op(c) == FROM_M) {
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@ -479,7 +480,7 @@ bwa_cigar_t *bwa_sw_core(bwtint_t l_pac, const ubyte_t *pacseq, int len, const u
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*_cnt = (uint32_t)n_mm<<16 | n_gapo<<8 | n_gape;
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}
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free(ref_seq); free(path);
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free(ref_seq);
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return cigar;
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}
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6
bwase.c
6
bwase.c
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@ -4,7 +4,6 @@
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#include <stdlib.h>
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#include <math.h>
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#include <time.h>
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#include "stdaln.h"
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#include "bwase.h"
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#include "bwtaln.h"
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#include "bntseq.h"
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@ -205,8 +204,8 @@ bwa_cigar_t *bwa_refine_gapped_core(bwtint_t l_pac, const ubyte_t *pacseq, int l
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if (__cigar_op(cigar[*n_cigar-1]) == FROM_D) --(*n_cigar); // deletion at the 3'-end
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// change "I" at either end of the read to S. just in case. This should rarely happen...
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if (__cigar_op(cigar[*n_cigar-1]) == FROM_I) cigar[*n_cigar-1] = __cigar_create(3, (__cigar_len(cigar[*n_cigar-1])));
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if (__cigar_op(cigar[0]) == FROM_I) cigar[0] = __cigar_create(3, (__cigar_len(cigar[0])));
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if (__cigar_op(cigar[*n_cigar-1]) == FROM_I) cigar[*n_cigar-1] = __cigar_create(FROM_S, (__cigar_len(cigar[*n_cigar-1])));
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if (__cigar_op(cigar[0]) == FROM_I) cigar[0] = __cigar_create(FROM_S, (__cigar_len(cigar[0])));
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*_pos = (bwtint_t)__pos;
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free(ref_seq);
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@ -589,5 +588,6 @@ int bwa_sai2sam_se(int argc, char *argv[])
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return 0;
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}
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bwa_sai2sam_se_core(prefix, argv[optind+1], argv[optind+2], n_occ, rg_line);
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free(prefix);
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return 0;
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}
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15
bwtaln.c
15
bwtaln.c
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@ -312,18 +312,3 @@ int bwa_aln(int argc, char *argv[])
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free(opt); free(prefix);
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return 0;
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}
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/* rgoya: Temporary clone of aln_path2cigar to accomodate for bwa_cigar_t,
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__cigar_op and __cigar_len while keeping stdaln stand alone */
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bwa_cigar_t *bwa_aln_path2cigar(const path_t *path, int path_len, int *n_cigar)
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{
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uint32_t *cigar32;
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bwa_cigar_t *cigar;
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int i;
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cigar32 = aln_path2cigar32((path_t*) path, path_len, n_cigar);
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cigar = (bwa_cigar_t*)cigar32;
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for (i = 0; i < *n_cigar; ++i)
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cigar[i] = __cigar_create( (cigar32[i]&0xf), (cigar32[i]>>4) );
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return cigar;
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}
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12
bwtaln.h
12
bwtaln.h
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@ -28,6 +28,11 @@
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#define bns_pac(pac, k) ((pac)[(k)>>2] >> ((~(k)&3)<<1) & 3)
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#endif
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#define FROM_M 0
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#define FROM_I 1
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#define FROM_D 2
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#define FROM_S 3
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typedef struct {
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bwtint_t w;
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int bid;
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@ -138,13 +143,6 @@ extern "C" {
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void bwa_cs2nt_core(bwa_seq_t *p, bwtint_t l_pac, ubyte_t *pac);
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/* rgoya: Temporary clone of aln_path2cigar to accomodate for bwa_cigar_t,
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__cigar_op and __cigar_len while keeping stdaln stand alone */
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#include "stdaln.h"
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bwa_cigar_t *bwa_aln_path2cigar(const path_t *path, int path_len, int *n_cigar);
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#ifdef __cplusplus
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}
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#endif
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2
main.c
2
main.c
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@ -4,7 +4,7 @@
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#include "utils.h"
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#ifndef PACKAGE_VERSION
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#define PACKAGE_VERSION "0.7.0-r324-beta"
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#define PACKAGE_VERSION "0.7.0-r329-beta"
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#endif
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static int usage()
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162
stdaln.h
162
stdaln.h
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@ -1,162 +0,0 @@
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/* The MIT License
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Copyright (c) 2003-2006, 2008, by Heng Li <lh3lh3@gmail.com>
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Permission is hereby granted, free of charge, to any person obtaining
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a copy of this software and associated documentation files (the
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"Software"), to deal in the Software without restriction, including
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without limitation the rights to use, copy, modify, merge, publish,
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distribute, sublicense, and/or sell copies of the Software, and to
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permit persons to whom the Software is furnished to do so, subject to
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the following conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
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BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
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ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
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CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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*/
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/*
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2009-07-23, 0.10.0
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- Use 32-bit to store CIGAR
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- Report suboptimal aligments
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- Implemented half-fixed-half-open DP
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2009-04-26, 0.9.10
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- Allow to set a threshold for local alignment
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2009-02-18, 0.9.9
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- Fixed a bug when no residue matches
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2008-08-04, 0.9.8
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- Fixed the wrong declaration of aln_stdaln_aux()
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- Avoid 0 coordinate for global alignment
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2008-08-01, 0.9.7
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- Change gap_end penalty to 5 in aln_param_bwa
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- Add function to convert path_t to the CIGAR format
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2008-08-01, 0.9.6
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- The first gap now costs (gap_open+gap_ext), instead of
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gap_open. Scoring systems are modified accordingly.
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- Gap end is now correctly handled. Previously it is not correct.
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- Change license to MIT.
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*/
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#ifndef LH3_STDALN_H_
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#define LH3_STDALN_H_
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#define STDALN_VERSION 0.11.0
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#include <stdint.h>
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#define FROM_M 0
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#define FROM_I 1
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#define FROM_D 2
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#define FROM_S 3
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#define ALN_TYPE_LOCAL 0
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#define ALN_TYPE_GLOBAL 1
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#define ALN_TYPE_EXTEND 2
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/* This is the smallest integer. It might be CPU-dependent in very RARE cases. */
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#define MINOR_INF -1073741823
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typedef struct
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{
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int gap_open;
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int gap_ext;
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int gap_end;
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int *matrix;
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int row;
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int band_width;
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} AlnParam;
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typedef struct
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{
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int i, j;
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unsigned char ctype;
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} path_t;
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typedef struct
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{
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path_t *path; /* for advanced users... :-) */
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int path_len; /* for advanced users... :-) */
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int start1, end1; /* start and end of the first sequence, coordinations are 1-based */
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int start2, end2; /* start and end of the second sequence, coordinations are 1-based */
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int score, subo; /* score */
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char *out1, *out2; /* print them, and then you will know */
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char *outm;
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int n_cigar;
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uint32_t *cigar32;
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} AlnAln;
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#ifdef __cplusplus
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extern "C" {
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#endif
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AlnAln *aln_stdaln_aux(const char *seq1, const char *seq2, const AlnParam *ap,
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int type, int do_align, int len1, int len2);
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AlnAln *aln_stdaln(const char *seq1, const char *seq2, const AlnParam *ap, int type, int do_align);
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void aln_free_AlnAln(AlnAln *aa);
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int aln_global_core(unsigned char *seq1, int len1, unsigned char *seq2, int len2, const AlnParam *ap,
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path_t *path, int *path_len);
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int aln_local_core(unsigned char *seq1, int len1, unsigned char *seq2, int len2, const AlnParam *ap,
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path_t *path, int *path_len, int _thres, int *_subo);
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int aln_extend_core(unsigned char *seq1, int len1, unsigned char *seq2, int len2, const AlnParam *ap,
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path_t *path, int *path_len, int G0, uint8_t *_mem);
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uint16_t *aln_path2cigar(const path_t *path, int path_len, int *n_cigar);
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uint32_t *aln_path2cigar32(const path_t *path, int path_len, int *n_cigar);
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#ifdef __cplusplus
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}
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#endif
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/********************
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* global variables *
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********************/
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extern AlnParam aln_param_bwa; /* = { 37, 9, 0, aln_sm_maq, 5, 50 }; */
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extern AlnParam aln_param_blast; /* = { 5, 2, 2, aln_sm_blast, 5, 50 }; */
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extern AlnParam aln_param_nt2nt; /* = { 10, 2, 2, aln_sm_nt, 16, 75 }; */
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extern AlnParam aln_param_aa2aa; /* = { 20, 19, 19, aln_sm_read, 16, 75 }; */
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extern AlnParam aln_param_rd2rd; /* = { 12, 2, 2, aln_sm_blosum62, 22, 50 }; */
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/* common nucleotide score matrix for 16 bases */
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extern int aln_sm_nt[], aln_sm_bwa[];
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/* BLOSUM62 and BLOSUM45 */
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extern int aln_sm_blosum62[], aln_sm_blosum45[];
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/* common read for 16 bases. note that read alignment is quite different from common nucleotide alignment */
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extern int aln_sm_read[];
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/* human-mouse score matrix for 4 bases */
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extern int aln_sm_hs[];
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#endif
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Reference in New Issue