r815: optionally output ref fasta header
Also fixed a bug in reading .ann files
This commit is contained in:
Heng Li
parent
1e611b235c
commit
35ac99b4f7
6
bntseq.c
6
bntseq.c
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@ -94,7 +94,7 @@ void bns_dump(const bntseq_t *bns, const char *prefix)
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bntseq_t *bns_restore_core(const char *ann_filename, const char* amb_filename, const char* pac_filename)
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{
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char str[1024];
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char str[8192];
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FILE *fp;
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const char *fname;
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bntseq_t *bns;
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@ -117,14 +117,14 @@ bntseq_t *bns_restore_core(const char *ann_filename, const char* amb_filename, c
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if (scanres != 2) goto badread;
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p->name = strdup(str);
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// read fasta comments
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while (str - q < sizeof(str) - 1 && (c = fgetc(fp)) != '\n' && c != EOF) *q++ = c;
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while (q - str < sizeof(str) - 1 && (c = fgetc(fp)) != '\n' && c != EOF) *q++ = c;
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while (c != '\n' && c != EOF) c = fgetc(fp);
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if (c == EOF) {
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scanres = EOF;
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goto badread;
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}
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*q = 0;
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if (q - str > 1) p->anno = strdup(str + 1); // skip leading space
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if (q - str > 1 && strcmp(str, " (null)") != 0) p->anno = strdup(str + 1); // skip leading space
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else p->anno = strdup("");
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// read the rest
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scanres = fscanf(fp, "%lld%d%d", &xx, &p->len, &p->n_ambs);
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20
bwamem.c
20
bwamem.c
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@ -759,7 +759,7 @@ static inline int get_rlen(int n_cigar, const uint32_t *cigar)
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return l;
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}
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void mem_aln2sam(const bntseq_t *bns, kstring_t *str, bseq1_t *s, int n, const mem_aln_t *list, int which, const mem_aln_t *m_, int softclip_all)
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void mem_aln2sam(const mem_opt_t *opt, const bntseq_t *bns, kstring_t *str, bseq1_t *s, int n, const mem_aln_t *list, int which, const mem_aln_t *m_)
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{
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int i, l_name;
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mem_aln_t ptmp = list[which], *p = &ptmp, mtmp, *m = 0; // make a copy of the alignment to convert
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@ -788,7 +788,7 @@ void mem_aln2sam(const bntseq_t *bns, kstring_t *str, bseq1_t *s, int n, const m
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if (p->n_cigar) { // aligned
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for (i = 0; i < p->n_cigar; ++i) {
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int c = p->cigar[i]&0xf;
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if (!softclip_all && (c == 3 || c == 4))
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if (!(opt->flag&MEM_F_SOFTCLIP) && (c == 3 || c == 4))
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c = which? 4 : 3; // use hard clipping for supplementary alignments
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kputw(p->cigar[i]>>4, str); kputc("MIDSH"[c], str);
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}
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@ -816,7 +816,7 @@ void mem_aln2sam(const bntseq_t *bns, kstring_t *str, bseq1_t *s, int n, const m
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kputsn("*\t*", 3, str);
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} else if (!p->is_rev) { // the forward strand
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int i, qb = 0, qe = s->l_seq;
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if (p->n_cigar && which && !softclip_all) { // have cigar && not the primary alignment && not softclip all
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if (p->n_cigar && which && !(opt->flag&MEM_F_SOFTCLIP)) { // have cigar && not the primary alignment && not softclip all
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if ((p->cigar[0]&0xf) == 4 || (p->cigar[0]&0xf) == 3) qb += p->cigar[0]>>4;
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if ((p->cigar[p->n_cigar-1]&0xf) == 4 || (p->cigar[p->n_cigar-1]&0xf) == 3) qe -= p->cigar[p->n_cigar-1]>>4;
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}
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@ -830,7 +830,7 @@ void mem_aln2sam(const bntseq_t *bns, kstring_t *str, bseq1_t *s, int n, const m
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} else kputc('*', str);
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} else { // the reverse strand
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int i, qb = 0, qe = s->l_seq;
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if (p->n_cigar && which && !softclip_all) {
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if (p->n_cigar && which && !(opt->flag&MEM_F_SOFTCLIP)) {
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if ((p->cigar[0]&0xf) == 4 || (p->cigar[0]&0xf) == 3) qe -= p->cigar[0]>>4;
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if ((p->cigar[p->n_cigar-1]&0xf) == 4 || (p->cigar[p->n_cigar-1]&0xf) == 3) qb += p->cigar[p->n_cigar-1]>>4;
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}
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@ -875,6 +875,14 @@ void mem_aln2sam(const bntseq_t *bns, kstring_t *str, bseq1_t *s, int n, const m
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}
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if (p->XA) { kputsn("\tXA:Z:", 6, str); kputs(p->XA, str); }
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if (s->comment) { kputc('\t', str); kputs(s->comment, str); }
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if ((opt->flag&MEM_F_REF_HDR) && p->rid >= 0 && bns->anns[p->rid].anno != 0 && bns->anns[p->rid].anno[0] != 0) {
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int tmp;
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kputsn("\tXR:Z:", 6, str);
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tmp = str->l;
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kputs(bns->anns[p->rid].anno, str);
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for (i = tmp; i < str->l; ++i) // replace TAB in the comment to SPACE
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if (str->s[i] == '\t') str->s[i] = ' ';
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}
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kputc('\n', str);
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}
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@ -941,10 +949,10 @@ void mem_reg2sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pa
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mem_aln_t t;
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t = mem_reg2aln(opt, bns, pac, s->l_seq, s->seq, 0);
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t.flag |= extra_flag;
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mem_aln2sam(bns, &str, s, 1, &t, 0, m, opt->flag&MEM_F_SOFTCLIP);
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mem_aln2sam(opt, bns, &str, s, 1, &t, 0, m);
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} else {
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for (k = 0; k < aa.n; ++k)
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mem_aln2sam(bns, &str, s, aa.n, aa.a, k, m, opt->flag&MEM_F_SOFTCLIP);
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mem_aln2sam(opt, bns, &str, s, aa.n, aa.a, k, m);
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for (k = 0; k < aa.n; ++k) free(aa.a[k].cigar);
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free(aa.a);
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}
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1
bwamem.h
1
bwamem.h
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@ -18,6 +18,7 @@ typedef struct __smem_i smem_i;
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#define MEM_F_NO_RESCUE 0x20
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#define MEM_F_SELF_OVLP 0x40
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#define MEM_F_ALN_REG 0x80
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#define MEM_F_REF_HDR 0x100
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#define MEM_F_SOFTCLIP 0x200
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typedef struct {
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@ -247,7 +247,7 @@ int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
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extern void mem_mark_primary_se(const mem_opt_t *opt, int n, mem_alnreg_t *a, int64_t id);
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extern int mem_approx_mapq_se(const mem_opt_t *opt, const mem_alnreg_t *a);
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extern void mem_reg2sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, bseq1_t *s, mem_alnreg_v *a, int extra_flag, const mem_aln_t *m);
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extern void mem_aln2sam(const bntseq_t *bns, kstring_t *str, bseq1_t *s, int n, const mem_aln_t *list, int which, const mem_aln_t *m, int softclip_all);
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extern void mem_aln2sam(const mem_opt_t *opt, const bntseq_t *bns, kstring_t *str, bseq1_t *s, int n, const mem_aln_t *list, int which, const mem_aln_t *m);
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extern char **mem_gen_alt(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, const mem_alnreg_v *a, int l_query, const char *query);
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int n = 0, i, j, z[2], o, subo, n_sub, extra_flag = 1;
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@ -327,8 +327,8 @@ int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
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// write SAM
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h[0] = mem_reg2aln(opt, bns, pac, s[0].l_seq, s[0].seq, &a[0].a[z[0]]); h[0].mapq = q_se[0]; h[0].flag |= 0x40 | extra_flag; h[0].XA = XA[0]? XA[0][z[0]] : 0;
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h[1] = mem_reg2aln(opt, bns, pac, s[1].l_seq, s[1].seq, &a[1].a[z[1]]); h[1].mapq = q_se[1]; h[1].flag |= 0x80 | extra_flag; h[1].XA = XA[1]? XA[1][z[1]] : 0;
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mem_aln2sam(bns, &str, &s[0], 1, &h[0], 0, &h[1], opt->flag&MEM_F_SOFTCLIP); s[0].sam = strdup(str.s); str.l = 0;
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mem_aln2sam(bns, &str, &s[1], 1, &h[1], 0, &h[0], opt->flag&MEM_F_SOFTCLIP); s[1].sam = str.s;
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mem_aln2sam(opt, bns, &str, &s[0], 1, &h[0], 0, &h[1]); s[0].sam = strdup(str.s); str.l = 0;
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mem_aln2sam(opt, bns, &str, &s[1], 1, &h[1], 0, &h[0]); s[1].sam = str.s;
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if (strcmp(s[0].name, s[1].name) != 0) err_fatal(__func__, "paired reads have different names: \"%s\", \"%s\"\n", s[0].name, s[1].name);
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free(h[0].cigar); // h[0].XA will be freed in the following block
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free(h[1].cigar);
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@ -54,7 +54,7 @@ int main_mem(int argc, char *argv[])
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opt = mem_opt_init();
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memset(&opt0, 0, sizeof(mem_opt_t));
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while ((c = getopt(argc, argv, "epaFMCSPHYk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:W:x:G:h:y:")) >= 0) {
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while ((c = getopt(argc, argv, "epaFMCSPHVYk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:W:x:G:h:y:")) >= 0) {
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if (c == 'k') opt->min_seed_len = atoi(optarg), opt0.min_seed_len = 1;
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else if (c == 'x') mode = optarg;
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else if (c == 'w') opt->w = atoi(optarg), opt0.w = 1;
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@ -71,6 +71,7 @@ int main_mem(int argc, char *argv[])
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else if (c == 'e') opt->flag |= MEM_F_SELF_OVLP;
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else if (c == 'F') opt->flag |= MEM_F_ALN_REG;
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else if (c == 'Y') opt->flag |= MEM_F_SOFTCLIP;
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else if (c == 'V') opt->flag |= MEM_F_REF_HDR;
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else if (c == 'c') opt->max_occ = atoi(optarg), opt0.max_occ = 1;
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else if (c == 'd') opt->zdrop = atoi(optarg), opt0.zdrop = 1;
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else if (c == 'v') bwa_verbose = atoi(optarg);
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@ -163,6 +164,7 @@ int main_mem(int argc, char *argv[])
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fprintf(stderr, " -h INT if there are <INT hits with score >80%% of the max score, output all in XA [%d]\n", opt->max_hits);
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fprintf(stderr, " -a output all alignments for SE or unpaired PE\n");
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fprintf(stderr, " -C append FASTA/FASTQ comment to SAM output\n");
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fprintf(stderr, " -V output the reference FASTA header in the XR tag\n");
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fprintf(stderr, " -Y use soft clipping for supplementary alignments\n");
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fprintf(stderr, " -M mark shorter split hits as secondary\n\n");
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fprintf(stderr, " -I FLOAT[,FLOAT[,INT[,INT]]]\n");
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