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dev-450: support diff ins/del penalties. NO TEST!!
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@lh3
lh3 committed Mar 28, 2014
1 parent 578bb55 commit 9ce50a4
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Showing 7 changed files with 81 additions and 49 deletions.
24 changes: 18 additions & 6 deletions bwa.c
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Original file line number Diff line number Diff line change
Expand Up @@ -86,7 +86,7 @@ void bwa_fill_scmat(int a, int b, int8_t mat[25])
}

// Generate CIGAR when the alignment end points are known
uint32_t *bwa_gen_cigar(const int8_t mat[25], int q, int r, int w_, int64_t l_pac, const uint8_t *pac, int l_query, uint8_t *query, int64_t rb, int64_t re, int *score, int *n_cigar, int *NM)
uint32_t *bwa_gen_cigar2(const int8_t mat[25], int o_del, int e_del, int o_ins, int e_ins, int w_, int64_t l_pac, const uint8_t *pac, int l_query, uint8_t *query, int64_t rb, int64_t re, int *score, int *n_cigar, int *NM)
{
uint32_t *cigar = 0;
uint8_t tmp, *rseq;
Expand All @@ -113,9 +113,11 @@ uint32_t *bwa_gen_cigar(const int8_t mat[25], int q, int r, int w_, int64_t l_pa
for (i = 0, *score = 0; i < l_query; ++i)
*score += mat[rseq[i]*5 + query[i]];
} else {
int w, max_gap, min_w;
int w, max_gap, max_ins, max_del, min_w;
// set the band-width
max_gap = (int)((double)(((l_query+1)>>1) * mat[0] - q) / r + 1.);
max_ins = (int)((double)(((l_query+1)>>1) * mat[0] - o_ins) / e_ins + 1.);
max_del = (int)((double)(((l_query+1)>>1) * mat[0] - o_del) / e_del + 1.);
max_gap = max_ins > max_del? max_ins : max_del;
max_gap = max_gap > 1? max_gap : 1;
w = (max_gap + abs(rlen - l_query) + 1) >> 1;
w = w < w_? w : w_;
Expand All @@ -127,7 +129,7 @@ uint32_t *bwa_gen_cigar(const int8_t mat[25], int q, int r, int w_, int64_t l_pa
printf("* Global ref: "); for (i = 0; i < rlen; ++i) putchar("ACGTN"[(int)rseq[i]]); putchar('\n');
printf("* Global query: "); for (i = 0; i < l_query; ++i) putchar("ACGTN"[(int)query[i]]); putchar('\n');
}
*score = ksw_global(l_query, query, rlen, rseq, 5, mat, q, r, w, n_cigar, &cigar);
*score = ksw_global2(l_query, query, rlen, rseq, 5, mat, o_del, e_del, o_ins, e_ins, w, n_cigar, &cigar);
}
{// compute NM and MD
int k, x, y, u, n_mm = 0, n_gap = 0;
Expand Down Expand Up @@ -169,7 +171,12 @@ uint32_t *bwa_gen_cigar(const int8_t mat[25], int q, int r, int w_, int64_t l_pa
return cigar;
}

int bwa_fix_xref(const int8_t mat[25], int q, int r, int w, const bntseq_t *bns, const uint8_t *pac, uint8_t *query, int *qb, int *qe, int64_t *rb, int64_t *re)
uint32_t *bwa_gen_cigar(const int8_t mat[25], int q, int r, int w_, int64_t l_pac, const uint8_t *pac, int l_query, uint8_t *query, int64_t rb, int64_t re, int *score, int *n_cigar, int *NM)
{
return bwa_gen_cigar2(mat, q, r, q, r, w_, l_pac, pac, l_query, query, rb, re, score, n_cigar, NM);
}

int bwa_fix_xref2(const int8_t mat[25], int o_del, int e_del, int o_ins, int e_ins, int w, const bntseq_t *bns, const uint8_t *pac, uint8_t *query, int *qb, int *qe, int64_t *rb, int64_t *re)
{
int is_rev;
int64_t cb, ce, fm;
Expand All @@ -188,7 +195,7 @@ int bwa_fix_xref(const int8_t mat[25], int q, int r, int w, const bntseq_t *bns,
int64_t x;
cb = cb > *rb? cb : *rb;
ce = ce < *re? ce : *re;
cigar = bwa_gen_cigar(mat, q, r, w, bns->l_pac, pac, *qe - *qb, query + *qb, *rb, *re, &score, &n_cigar, &NM);
cigar = bwa_gen_cigar2(mat, o_del, e_del, o_ins, e_ins, w, bns->l_pac, pac, *qe - *qb, query + *qb, *rb, *re, &score, &n_cigar, &NM);
for (i = 0, x = *rb, y = *qb; i < n_cigar; ++i) {
int op = cigar[i]&0xf, len = cigar[i]>>4;
if (op == 0) {
Expand All @@ -214,6 +221,11 @@ int bwa_fix_xref(const int8_t mat[25], int q, int r, int w, const bntseq_t *bns,
return (*qb == *qe || *rb == *re)? -2 : 0;
}

int bwa_fix_xref(const int8_t mat[25], int q, int r, int w, const bntseq_t *bns, const uint8_t *pac, uint8_t *query, int *qb, int *qe, int64_t *rb, int64_t *re)
{
return bwa_fix_xref2(mat, q, r, q, r, w, bns, pac, query, qb, qe, rb, re);
}

/*********************
* Full index reader *
*********************/
Expand Down
2 changes: 2 additions & 0 deletions bwa.h
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Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,9 @@ extern "C" {

void bwa_fill_scmat(int a, int b, int8_t mat[25]);
uint32_t *bwa_gen_cigar(const int8_t mat[25], int q, int r, int w_, int64_t l_pac, const uint8_t *pac, int l_query, uint8_t *query, int64_t rb, int64_t re, int *score, int *n_cigar, int *NM);
uint32_t *bwa_gen_cigar2(const int8_t mat[25], int o_del, int e_del, int o_ins, int e_ins, int w_, int64_t l_pac, const uint8_t *pac, int l_query, uint8_t *query, int64_t rb, int64_t re, int *score, int *n_cigar, int *NM);
int bwa_fix_xref(const int8_t mat[25], int q, int r, int w, const bntseq_t *bns, const uint8_t *pac, uint8_t *query, int *qb, int *qe, int64_t *rb, int64_t *re);
int bwa_fix_xref2(const int8_t mat[25], int o_del, int e_del, int o_ins, int e_ins, int w, const bntseq_t *bns, const uint8_t *pac, uint8_t *query, int *qb, int *qe, int64_t *rb, int64_t *re);

char *bwa_idx_infer_prefix(const char *hint);
bwt_t *bwa_idx_load_bwt(const char *hint);
Expand Down
29 changes: 19 additions & 10 deletions bwamem.c
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Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,10 @@ mem_opt_t *mem_opt_init()
mem_opt_t *o;
o = calloc(1, sizeof(mem_opt_t));
o->flag = 0;
o->a = 1; o->b = 4; o->q = 6; o->r = 1; o->w = 100;
o->a = 1; o->b = 4;
o->o_del = o->o_ins = 6;
o->e_del = o->e_ins = 1;
o->w = 100;
o->T = 30;
o->zdrop = 100;
o->pen_unpaired = 17;
Expand Down Expand Up @@ -446,7 +449,9 @@ void mem_mark_primary_se(const mem_opt_t *opt, int n, mem_alnreg_t *a, int64_t i
kv_init(z);
for (i = 0; i < n; ++i) a[i].sub = 0, a[i].secondary = -1, a[i].hash = hash_64(id+i);
ks_introsort(mem_ars_hash, n, a);
tmp = opt->a + opt->b > opt->q + opt->r? opt->a + opt->b : opt->q + opt->r;
tmp = opt->a + opt->b;
tmp = opt->o_del + opt->e_del > tmp? opt->o_del + opt->e_del : tmp;
tmp = opt->o_ins + opt->e_ins > tmp? opt->o_ins + opt->e_ins : tmp;
kv_push(int, z, 0);
for (i = 1; i < n; ++i) {
for (k = 0; k < z.n; ++k) {
Expand Down Expand Up @@ -522,7 +527,7 @@ int mem_chain2aln_short(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac,
rseq = bns_get_seq(l_pac, pac, rb, re, &rlen);
assert(rlen == re - rb);
xtra = KSW_XSUBO | KSW_XSTART | ((qe - qb) * opt->a < 250? KSW_XBYTE : 0) | (opt->min_seed_len * opt->a);
x = ksw_align(qe - qb, (uint8_t*)query + qb, re - rb, rseq, 5, opt->mat, opt->q, opt->r, xtra, 0);
x = ksw_align2(qe - qb, (uint8_t*)query + qb, re - rb, rseq, 5, opt->mat, opt->o_del, opt->e_del, opt->o_ins, opt->e_ins, xtra, 0);
free(rseq);
if (x.tb < MEM_SHORT_EXT>>1 || x.te > re - rb - (MEM_SHORT_EXT>>1)) return 1;

Expand All @@ -537,7 +542,9 @@ int mem_chain2aln_short(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac,

static inline int cal_max_gap(const mem_opt_t *opt, int qlen)
{
int l = (int)((double)(qlen * opt->a - opt->q) / opt->r + 1.);
int l_del = (int)((double)(qlen * opt->a - opt->o_del) / opt->e_del + 1.);
int l_ins = (int)((double)(qlen * opt->a - opt->o_ins) / opt->e_ins + 1.);
int l = l_del > l_ins? l_del : l_ins;
l = l > 1? l : 1;
return l < opt->w<<1? l : opt->w<<1;
}
Expand Down Expand Up @@ -638,7 +645,7 @@ void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int
printf("*** Left ref: "); for (j = 0; j < tmp; ++j) putchar("ACGTN"[(int)rs[j]]); putchar('\n');
printf("*** Left query: "); for (j = 0; j < s->qbeg; ++j) putchar("ACGTN"[(int)qs[j]]); putchar('\n');
}
a->score = ksw_extend(s->qbeg, qs, tmp, rs, 5, opt->mat, opt->q, opt->r, aw[0], opt->pen_clip5, opt->zdrop, s->len * opt->a, &qle, &tle, &gtle, &gscore, &max_off[0]);
a->score = ksw_extend2(s->qbeg, qs, tmp, rs, 5, opt->mat, opt->o_del, opt->e_del, opt->o_ins, opt->e_ins, aw[0], opt->pen_clip5, opt->zdrop, s->len * opt->a, &qle, &tle, &gtle, &gscore, &max_off[0]);
if (bwa_verbose >= 4) { printf("*** Left extension: prev_score=%d; score=%d; bandwidth=%d; max_off_diagonal_dist=%d\n", prev, a->score, aw[0], max_off[0]); fflush(stdout); }
if (a->score == prev || max_off[0] < (aw[0]>>1) + (aw[0]>>2)) break;
}
Expand Down Expand Up @@ -666,7 +673,7 @@ void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int
printf("*** Right ref: "); for (j = 0; j < rmax[1] - rmax[0] - re; ++j) putchar("ACGTN"[(int)rseq[re+j]]); putchar('\n');
printf("*** Right query: "); for (j = 0; j < l_query - qe; ++j) putchar("ACGTN"[(int)query[qe+j]]); putchar('\n');
}
a->score = ksw_extend(l_query - qe, query + qe, rmax[1] - rmax[0] - re, rseq + re, 5, opt->mat, opt->q, opt->r, aw[1], opt->pen_clip3, opt->zdrop, sc0, &qle, &tle, &gtle, &gscore, &max_off[1]);
a->score = ksw_extend2(l_query - qe, query + qe, rmax[1] - rmax[0] - re, rseq + re, 5, opt->mat, opt->o_del, opt->e_del, opt->o_ins, opt->e_ins, aw[1], opt->pen_clip3, opt->zdrop, sc0, &qle, &tle, &gtle, &gscore, &max_off[1]);
if (bwa_verbose >= 4) { printf("*** Right extension: prev_score=%d; score=%d; bandwidth=%d; max_off_diagonal_dist=%d\n", prev, a->score, aw[1], max_off[1]); fflush(stdout); }
if (a->score == prev || max_off[1] < (aw[1]>>1) + (aw[1]>>2)) break;
}
Expand Down Expand Up @@ -942,7 +949,7 @@ mem_alnreg_v mem_align1(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *
mem_aln_t mem_reg2aln(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, int l_query, const char *query_, const mem_alnreg_t *ar)
{
mem_aln_t a;
int i, w2, qb, qe, NM, score, is_rev, last_sc = -(1<<30), l_MD;
int i, w2, tmp, qb, qe, NM, score, is_rev, last_sc = -(1<<30), l_MD;
int64_t pos, rb, re;
uint8_t *query;

Expand All @@ -958,18 +965,20 @@ mem_aln_t mem_reg2aln(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *
query[i] = query_[i] < 5? query_[i] : nst_nt4_table[(int)query_[i]];
a.mapq = ar->secondary < 0? mem_approx_mapq_se(opt, ar) : 0;
if (ar->secondary >= 0) a.flag |= 0x100; // secondary alignment
if (bwa_fix_xref(opt->mat, opt->q, opt->r, opt->w, bns, pac, (uint8_t*)query, &qb, &qe, &rb, &re) < 0) {
if (bwa_fix_xref2(opt->mat, opt->o_del, opt->e_del, opt->o_ins, opt->e_ins, opt->w, bns, pac, (uint8_t*)query, &qb, &qe, &rb, &re) < 0) {
fprintf(stderr, "[E::%s] If you see this message, please let the developer know. Abort. Sorry.\n", __func__);
exit(1);
}
w2 = infer_bw(qe - qb, re - rb, ar->truesc, opt->a, opt->q, opt->r);
tmp = infer_bw(qe - qb, re - rb, ar->truesc, opt->a, opt->o_del, opt->e_del);
w2 = infer_bw(qe - qb, re - rb, ar->truesc, opt->a, opt->o_ins, opt->e_ins);
w2 = w2 > tmp? w2 : tmp;
if (bwa_verbose >= 4) printf("* Band width: inferred=%d, cmd_opt=%d, alnreg=%d\n", w2, opt->w, ar->w);
if (w2 > opt->w) w2 = w2 < ar->w? w2 : ar->w;
// else w2 = opt->w; // TODO: check if we need this line on long reads. On 1-800bp reads, it does not matter and it should be.
i = 0; a.cigar = 0;
do {
free(a.cigar);
a.cigar = bwa_gen_cigar(opt->mat, opt->q, opt->r, w2, bns->l_pac, pac, qe - qb, (uint8_t*)&query[qb], rb, re, &score, &a.n_cigar, &NM);
a.cigar = bwa_gen_cigar2(opt->mat, opt->o_del, opt->e_del, opt->o_ins, opt->e_ins, w2, bns->l_pac, pac, qe - qb, (uint8_t*)&query[qb], rb, re, &score, &a.n_cigar, &NM);
if (bwa_verbose >= 4) printf("* Final alignment: w2=%d, global_sc=%d, local_sc=%d\n", w2, score, ar->truesc);
if (score == last_sc) break; // it is possible that global alignment and local alignment give different scores
last_sc = score;
Expand Down
4 changes: 3 additions & 1 deletion bwamem.h
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,9 @@ typedef struct __smem_i smem_i;
#define MEM_F_NO_EXACT 0x40

typedef struct {
int a, b, q, r; // match score, mismatch penalty and gap open/extension penalty. A gap of size k costs q+k*r
int a, b; // match score and mismatch penalty
int o_del, e_del;
int o_ins, e_ins;
int pen_unpaired; // phred-scaled penalty for unpaired reads
int pen_clip5,pen_clip3;// clipping penalty. This score is not deducted from the DP score.
int w; // band width
Expand Down
6 changes: 4 additions & 2 deletions bwamem_pair.c
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Original file line number Diff line number Diff line change
Expand Up @@ -145,7 +145,7 @@ int mem_matesw(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, const me
kswr_t aln;
mem_alnreg_t b;
int tmp, xtra = KSW_XSUBO | KSW_XSTART | (l_ms * opt->a < 250? KSW_XBYTE : 0) | opt->min_seed_len;
aln = ksw_align(l_ms, seq, len, ref, 5, opt->mat, opt->q, opt->r, xtra, 0);
aln = ksw_align2(l_ms, seq, len, ref, 5, opt->mat, opt->o_del, opt->e_del, opt->o_ins, opt->e_ins, xtra, 0);
memset(&b, 0, sizeof(mem_alnreg_t));
if (aln.score >= opt->min_seed_len && aln.qb >= 0) { // something goes wrong if aln.qb < 0
b.qb = is_rev? l_ms - (aln.qe + 1) : aln.qb;
Expand Down Expand Up @@ -219,7 +219,9 @@ int mem_pair(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, const mem_
y[v.a[i].y&3] = i;
}
if (u.n) { // found at least one proper pair
int tmp = opt->a + opt->b > opt->q + opt->r? opt->a + opt->b : opt->q + opt->r;
int tmp = opt->a + opt->b;
tmp = tmp > opt->o_del + opt->e_del? tmp : opt->o_del + opt->e_del;
tmp = tmp > opt->o_ins + opt->e_ins? tmp : opt->o_ins + opt->e_ins;
ks_introsort_128(u.n, u.a);
i = u.a[u.n-1].y >> 32; k = u.a[u.n-1].y << 32 >> 32;
z[v.a[i].y&1] = v.a[i].y<<32>>34; // index of the best pair
Expand Down
63 changes: 34 additions & 29 deletions fastmap.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ int main_mem(int argc, char *argv[])
kseq_t *ks, *ks2 = 0;
bseq1_t *seqs;
bwaidx_t *idx;
char *rg_line = 0;
char *p, *rg_line = 0;
void *ko = 0, *ko2 = 0;
int64_t n_processed = 0;

Expand All @@ -35,8 +35,6 @@ int main_mem(int argc, char *argv[])
else if (c == 'w') opt->w = atoi(optarg);
else if (c == 'A') opt->a = atoi(optarg);
else if (c == 'B') opt->b = atoi(optarg);
else if (c == 'O') opt->q = atoi(optarg);
else if (c == 'E') opt->r = atoi(optarg);
else if (c == 'T') opt->T = atoi(optarg);
else if (c == 'U') opt->pen_unpaired = atoi(optarg);
else if (c == 't') opt->n_threads = atoi(optarg), opt->n_threads = opt->n_threads > 1? opt->n_threads : 1;
Expand All @@ -56,8 +54,15 @@ int main_mem(int argc, char *argv[])
else if (c == 'Q') {
opt->mapQ_coef_len = atoi(optarg);
opt->mapQ_coef_fac = opt->mapQ_coef_len > 0? log(opt->mapQ_coef_len) : 0;
} else if (c == 'O') {
opt->o_del = opt->o_ins = strtol(optarg, &p, 10);
if (*p != 0 && ispunct(*p) && isdigit(p[1]))
opt->o_ins = strtol(p+1, &p, 10);
} else if (c == 'E') {
opt->e_del = opt->e_ins = strtol(optarg, &p, 10);
if (*p != 0 && ispunct(*p) && isdigit(p[1]))
opt->e_ins = strtol(p+1, &p, 10);
} else if (c == 'L') {
char *p;
opt->pen_clip5 = opt->pen_clip3 = strtol(optarg, &p, 10);
if (*p != 0 && ispunct(*p) && isdigit(p[1]))
opt->pen_clip3 = strtol(p+1, &p, 10);
Expand All @@ -71,33 +76,33 @@ int main_mem(int argc, char *argv[])
fprintf(stderr, "\n");
fprintf(stderr, "Usage: bwa mem [options] <idxbase> <in1.fq> [in2.fq]\n\n");
fprintf(stderr, "Algorithm options:\n\n");
fprintf(stderr, " -t INT number of threads [%d]\n", opt->n_threads);
fprintf(stderr, " -k INT minimum seed length [%d]\n", opt->min_seed_len);
fprintf(stderr, " -w INT band width for banded alignment [%d]\n", opt->w);
fprintf(stderr, " -d INT off-diagonal X-dropoff [%d]\n", opt->zdrop);
fprintf(stderr, " -r FLOAT look for internal seeds inside a seed longer than {-k} * FLOAT [%g]\n", opt->split_factor);
// fprintf(stderr, " -s INT look for internal seeds inside a seed with less than INT occ [%d]\n", opt->split_width);
fprintf(stderr, " -c INT skip seeds with more than INT occurrences [%d]\n", opt->max_occ);
fprintf(stderr, " -D FLOAT drop chains shorter than FLOAT fraction of the longest overlapping chain [%.2f]\n", opt->chain_drop_ratio);
fprintf(stderr, " -m INT perform at most INT rounds of mate rescues for each read [%d]\n", opt->max_matesw);
fprintf(stderr, " -S skip mate rescue\n");
fprintf(stderr, " -P skip pairing; mate rescue performed unless -S also in use\n");
fprintf(stderr, " -e discard full-length exact matches\n");
fprintf(stderr, " -A INT score for a sequence match [%d]\n", opt->a);
fprintf(stderr, " -B INT penalty for a mismatch [%d]\n", opt->b);
fprintf(stderr, " -O INT gap open penalty [%d]\n", opt->q);
fprintf(stderr, " -E INT gap extension penalty; a gap of size k cost {-O} + {-E}*k [%d]\n", opt->r);
fprintf(stderr, " -L INT penalty for clipping [%d]\n", opt->pen_clip5);
fprintf(stderr, " -U INT penalty for an unpaired read pair [%d]\n", opt->pen_unpaired);
fprintf(stderr, " -t INT number of threads [%d]\n", opt->n_threads);
fprintf(stderr, " -k INT minimum seed length [%d]\n", opt->min_seed_len);
fprintf(stderr, " -w INT band width for banded alignment [%d]\n", opt->w);
fprintf(stderr, " -d INT off-diagonal X-dropoff [%d]\n", opt->zdrop);
fprintf(stderr, " -r FLOAT look for internal seeds inside a seed longer than {-k} * FLOAT [%g]\n", opt->split_factor);
// fprintf(stderr, " -s INT look for internal seeds inside a seed with less than INT occ [%d]\n", opt->split_width);
fprintf(stderr, " -c INT skip seeds with more than INT occurrences [%d]\n", opt->max_occ);
fprintf(stderr, " -D FLOAT drop chains shorter than FLOAT fraction of the longest overlapping chain [%.2f]\n", opt->chain_drop_ratio);
fprintf(stderr, " -m INT perform at most INT rounds of mate rescues for each read [%d]\n", opt->max_matesw);
fprintf(stderr, " -S skip mate rescue\n");
fprintf(stderr, " -P skip pairing; mate rescue performed unless -S also in use\n");
fprintf(stderr, " -e discard full-length exact matches\n");
fprintf(stderr, " -A INT score for a sequence match [%d]\n", opt->a);
fprintf(stderr, " -B INT penalty for a mismatch [%d]\n", opt->b);
fprintf(stderr, " -O INT[,INT] gap open penalties for deletions and insertions [%d,%d]\n", opt->o_del, opt->o_ins);
fprintf(stderr, " -E INT[,INT] gap extension penalty; a gap of size k cost '{-O} + {-E}*k' [%d,%d]\n", opt->e_del, opt->e_ins);
fprintf(stderr, " -L INT[,INT] penalty for 5'- and 3'-end clipping [%d,%d]\n", opt->pen_clip5, opt->pen_clip3);
fprintf(stderr, " -U INT penalty for an unpaired read pair [%d]\n", opt->pen_unpaired);
fprintf(stderr, "\nInput/output options:\n\n");
fprintf(stderr, " -p first query file consists of interleaved paired-end sequences\n");
fprintf(stderr, " -R STR read group header line such as '@RG\\tID:foo\\tSM:bar' [null]\n");
fprintf(stderr, " -p first query file consists of interleaved paired-end sequences\n");
fprintf(stderr, " -R STR read group header line such as '@RG\\tID:foo\\tSM:bar' [null]\n");
fprintf(stderr, "\n");
fprintf(stderr, " -v INT verbose level: 1=error, 2=warning, 3=message, 4+=debugging [%d]\n", bwa_verbose);
fprintf(stderr, " -T INT minimum score to output [%d]\n", opt->T);
fprintf(stderr, " -a output all alignments for SE or unpaired PE\n");
fprintf(stderr, " -C append FASTA/FASTQ comment to SAM output\n");
fprintf(stderr, " -M mark shorter split hits as secondary (for Picard/GATK compatibility)\n");
fprintf(stderr, " -v INT verbose level: 1=error, 2=warning, 3=message, 4+=debugging [%d]\n", bwa_verbose);
fprintf(stderr, " -T INT minimum score to output [%d]\n", opt->T);
fprintf(stderr, " -a output all alignments for SE or unpaired PE\n");
fprintf(stderr, " -C append FASTA/FASTQ comment to SAM output\n");
fprintf(stderr, " -M mark shorter split hits as secondary (for Picard/GATK compatibility)\n");
fprintf(stderr, "\nNote: Please read the man page for detailed description of the command line and options.\n");
fprintf(stderr, "\n");
free(opt);
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2 changes: 1 addition & 1 deletion main.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
#include "utils.h"

#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.7+dev-r449"
#define PACKAGE_VERSION "0.7.7+dev-r450"
#endif

int bwa_fa2pac(int argc, char *argv[]);
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