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Added barcode support

This commit is contained in:
Heng Li 2011-01-15 15:35:39 -05:00
parent 10721ca602
commit 51d354cd28
7 changed files with 45 additions and 21 deletions
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1
.gitignore vendored
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@ -1,3 +1,4 @@
*.[oa] *.[oa]
bwa bwa
test test
.*.swp

11
bwape.c
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@ -645,13 +645,13 @@ ubyte_t *bwa_paired_sw(const bntseq_t *bns, const ubyte_t *_pacseq, int n_seqs,
void bwa_sai2sam_pe_core(const char *prefix, char *const fn_sa[2], char *const fn_fa[2], pe_opt_t *popt) void bwa_sai2sam_pe_core(const char *prefix, char *const fn_sa[2], char *const fn_fa[2], pe_opt_t *popt)
{ {
extern bwa_seqio_t *bwa_open_reads(int mode, const char *fn_fa); extern bwa_seqio_t *bwa_open_reads(int mode, const char *fn_fa);
int i, j, n_seqs, tot_seqs = 0, read_flag = 0; int i, j, n_seqs, tot_seqs = 0;
bwa_seq_t *seqs[2]; bwa_seq_t *seqs[2];
bwa_seqio_t *ks[2]; bwa_seqio_t *ks[2];
clock_t t; clock_t t;
bntseq_t *bns, *ntbns = 0; bntseq_t *bns, *ntbns = 0;
FILE *fp_sa[2]; FILE *fp_sa[2];
gap_opt_t opt; gap_opt_t opt, opt0;
khint_t iter; khint_t iter;
isize_info_t last_ii; // this is for the last batch of reads isize_info_t last_ii; // this is for the last batch of reads
char str[1024]; char str[1024];
@ -671,6 +671,7 @@ void bwa_sai2sam_pe_core(const char *prefix, char *const fn_sa[2], char *const f
fread(&opt, sizeof(gap_opt_t), 1, fp_sa[0]); fread(&opt, sizeof(gap_opt_t), 1, fp_sa[0]);
ks[0] = bwa_open_reads(opt.mode, fn_fa[0]); ks[0] = bwa_open_reads(opt.mode, fn_fa[0]);
opt0 = opt;
fread(&opt, sizeof(gap_opt_t), 1, fp_sa[1]); // overwritten! fread(&opt, sizeof(gap_opt_t), 1, fp_sa[1]); // overwritten!
ks[1] = bwa_open_reads(opt.mode, fn_fa[1]); ks[1] = bwa_open_reads(opt.mode, fn_fa[1]);
if (!(opt.mode & BWA_MODE_COMPREAD)) { if (!(opt.mode & BWA_MODE_COMPREAD)) {
@ -691,14 +692,12 @@ void bwa_sai2sam_pe_core(const char *prefix, char *const fn_sa[2], char *const f
// core loop // core loop
bwa_print_sam_SQ(bns); bwa_print_sam_SQ(bns);
bwa_print_sam_PG(); bwa_print_sam_PG();
read_flag |= (opt.mode & BWA_MODE_COMPREAD)? 1 : 0; while ((seqs[0] = bwa_read_seq(ks[0], 0x40000, &n_seqs, opt0.mode, opt0.trim_qual)) != 0) {
read_flag |= ((opt.mode & BWA_MODE_IL13)? 1 : 0)<<1;
while ((seqs[0] = bwa_read_seq(ks[0], 0x40000, &n_seqs, read_flag, opt.trim_qual)) != 0) {
int cnt_chg; int cnt_chg;
isize_info_t ii; isize_info_t ii;
ubyte_t *pacseq; ubyte_t *pacseq;
seqs[1] = bwa_read_seq(ks[1], 0x40000, &n_seqs, read_flag, opt.trim_qual); seqs[1] = bwa_read_seq(ks[1], 0x40000, &n_seqs, opt.mode, opt.trim_qual);
tot_seqs += n_seqs; tot_seqs += n_seqs;
t = clock(); t = clock();

8
bwase.c
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@ -472,6 +472,7 @@ void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, in
} else printf("*"); } else printf("*");
if (bwa_rg_id) printf("\tRG:Z:%s", bwa_rg_id); if (bwa_rg_id) printf("\tRG:Z:%s", bwa_rg_id);
if (p->bc[0]) printf("\tBC:Z:%s", p->bc);
if (p->clip_len < p->full_len) printf("\tXC:i:%d", p->clip_len); if (p->clip_len < p->full_len) printf("\tXC:i:%d", p->clip_len);
if (p->type != BWA_TYPE_NO_MATCH) { if (p->type != BWA_TYPE_NO_MATCH) {
int i; int i;
@ -519,6 +520,7 @@ void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, in
printf("%s", p->qual); printf("%s", p->qual);
} else printf("*"); } else printf("*");
if (bwa_rg_id) printf("\tRG:Z:%s", bwa_rg_id); if (bwa_rg_id) printf("\tRG:Z:%s", bwa_rg_id);
if (p->bc[0]) printf("\tBC:Z:%s", p->bc);
if (p->clip_len < p->full_len) printf("\tXC:i:%d", p->clip_len); if (p->clip_len < p->full_len) printf("\tXC:i:%d", p->clip_len);
putchar('\n'); putchar('\n');
} }
@ -587,7 +589,7 @@ int bwa_set_rg(const char *s)
void bwa_sai2sam_se_core(const char *prefix, const char *fn_sa, const char *fn_fa, int n_occ) void bwa_sai2sam_se_core(const char *prefix, const char *fn_sa, const char *fn_fa, int n_occ)
{ {
extern bwa_seqio_t *bwa_open_reads(int mode, const char *fn_fa); extern bwa_seqio_t *bwa_open_reads(int mode, const char *fn_fa);
int i, n_seqs, tot_seqs = 0, m_aln, read_flag = 0; int i, n_seqs, tot_seqs = 0, m_aln;
bwt_aln1_t *aln = 0; bwt_aln1_t *aln = 0;
bwa_seq_t *seqs; bwa_seq_t *seqs;
bwa_seqio_t *ks; bwa_seqio_t *ks;
@ -611,9 +613,7 @@ void bwa_sai2sam_se_core(const char *prefix, const char *fn_sa, const char *fn_f
// set ks // set ks
ks = bwa_open_reads(opt.mode, fn_fa); ks = bwa_open_reads(opt.mode, fn_fa);
// core loop // core loop
read_flag |= (opt.mode & BWA_MODE_COMPREAD)? 1 : 0; while ((seqs = bwa_read_seq(ks, 0x40000, &n_seqs, opt.mode, opt.trim_qual)) != 0) {
read_flag |= ((opt.mode & BWA_MODE_IL13)? 1 : 0)<<1;
while ((seqs = bwa_read_seq(ks, 0x40000, &n_seqs, read_flag, opt.trim_qual)) != 0) {
tot_seqs += n_seqs; tot_seqs += n_seqs;
t = clock(); t = clock();

28
bwaseqio.c
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@ -1,4 +1,5 @@
#include <zlib.h> #include <zlib.h>
#include <ctype.h>
#include "bwtaln.h" #include "bwtaln.h"
#include "utils.h" #include "utils.h"
#include "bamlite.h" #include "bamlite.h"
@ -139,20 +140,41 @@ static bwa_seq_t *bwa_read_bam(bwa_seqio_t *bs, int n_needed, int *n, int is_com
return seqs; return seqs;
} }
bwa_seq_t *bwa_read_seq(bwa_seqio_t *bs, int n_needed, int *n, int flag, int trim_qual) #define BARCODE_LOW_QUAL 13
bwa_seq_t *bwa_read_seq(bwa_seqio_t *bs, int n_needed, int *n, int mode, int trim_qual)
{ {
bwa_seq_t *seqs, *p; bwa_seq_t *seqs, *p;
kseq_t *seq = bs->ks; kseq_t *seq = bs->ks;
int n_seqs, l, i, is_comp = flag&1, is_64 = flag&2; int n_seqs, l, i, is_comp = mode&BWA_MODE_COMPREAD, is_64 = mode&BWA_MODE_IL13, l_bc = mode>>24;
long n_trimmed = 0, n_tot = 0; long n_trimmed = 0, n_tot = 0;
if (bs->is_bam) return bwa_read_bam(bs, n_needed, n, is_comp, trim_qual); if (l_bc > 15) {
fprintf(stderr, "[%s] the maximum barcode length is 15.\n", __func__);
return 0;
}
if (bs->is_bam) return bwa_read_bam(bs, n_needed, n, is_comp, trim_qual); // l_bc has no effect for BAM input
n_seqs = 0; n_seqs = 0;
seqs = (bwa_seq_t*)calloc(n_needed, sizeof(bwa_seq_t)); seqs = (bwa_seq_t*)calloc(n_needed, sizeof(bwa_seq_t));
while ((l = kseq_read(seq)) >= 0) { while ((l = kseq_read(seq)) >= 0) {
if (is_64 && seq->qual.l) if (is_64 && seq->qual.l)
for (i = 0; i < seq->qual.l; ++i) seq->qual.s[i] -= 31; for (i = 0; i < seq->qual.l; ++i) seq->qual.s[i] -= 31;
if (seq->seq.l <= l_bc) continue; // sequence length equals or smaller than the barcode length
p = &seqs[n_seqs++]; p = &seqs[n_seqs++];
if (l_bc) { // then trim barcode
for (i = 0; i < l_bc; ++i)
p->bc[i] = (seq->qual.l && seq->qual.s[i]-33 < BARCODE_LOW_QUAL)? tolower(seq->seq.s[i]) : toupper(seq->seq.s[i]);
p->bc[i] = 0;
for (; i < seq->seq.l; ++i)
seq->seq.s[i - l_bc] = seq->seq.s[i];
seq->seq.l -= l_bc; seq->seq.s[seq->seq.l] = 0;
if (seq->qual.l) {
for (i = l_bc; i < seq->qual.l; ++i)
seq->qual.s[i - l_bc] = seq->qual.s[i];
seq->qual.l -= l_bc; seq->qual.s[seq->qual.l] = 0;
}
l = seq->seq.l;
} else p->bc[0] = 0;
p->tid = -1; // no assigned to a thread p->tid = -1; // no assigned to a thread
p->qual = 0; p->qual = 0;
p->full_len = p->clip_len = p->len = l; p->full_len = p->clip_len = p->len = l;

10
bwtaln.c
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@ -172,7 +172,7 @@ bwa_seqio_t *bwa_open_reads(int mode, const char *fn_fa)
void bwa_aln_core(const char *prefix, const char *fn_fa, const gap_opt_t *opt) void bwa_aln_core(const char *prefix, const char *fn_fa, const gap_opt_t *opt)
{ {
int i, n_seqs, tot_seqs = 0, read_flag = 0; int i, n_seqs, tot_seqs = 0;
bwa_seq_t *seqs; bwa_seq_t *seqs;
bwa_seqio_t *ks; bwa_seqio_t *ks;
clock_t t; clock_t t;
@ -190,9 +190,7 @@ void bwa_aln_core(const char *prefix, const char *fn_fa, const gap_opt_t *opt)
// core loop // core loop
fwrite(opt, sizeof(gap_opt_t), 1, stdout); fwrite(opt, sizeof(gap_opt_t), 1, stdout);
read_flag |= (opt->mode & BWA_MODE_COMPREAD)? 1 : 0; while ((seqs = bwa_read_seq(ks, 0x40000, &n_seqs, opt->mode, opt->trim_qual)) != 0) {
read_flag |= ((opt->mode & BWA_MODE_IL13)? 1 : 0)<<1;
while ((seqs = bwa_read_seq(ks, 0x40000, &n_seqs, read_flag, opt->trim_qual)) != 0) {
tot_seqs += n_seqs; tot_seqs += n_seqs;
t = clock(); t = clock();
@ -248,7 +246,7 @@ int bwa_aln(int argc, char *argv[])
gap_opt_t *opt; gap_opt_t *opt;
opt = gap_init_opt(); opt = gap_init_opt();
while ((c = getopt(argc, argv, "n:o:e:i:d:l:k:cLR:m:t:NM:O:E:q:f:b012I")) >= 0) { while ((c = getopt(argc, argv, "n:o:e:i:d:l:k:cLR:m:t:NM:O:E:q:f:b012IB:")) >= 0) {
switch (c) { switch (c) {
case 'n': case 'n':
if (strstr(optarg, ".")) opt->fnr = atof(optarg), opt->max_diff = -1; if (strstr(optarg, ".")) opt->fnr = atof(optarg), opt->max_diff = -1;
@ -276,6 +274,7 @@ int bwa_aln(int argc, char *argv[])
case '1': opt->mode |= BWA_MODE_BAM_READ1; break; case '1': opt->mode |= BWA_MODE_BAM_READ1; break;
case '2': opt->mode |= BWA_MODE_BAM_READ2; break; case '2': opt->mode |= BWA_MODE_BAM_READ2; break;
case 'I': opt->mode |= BWA_MODE_IL13; break; case 'I': opt->mode |= BWA_MODE_IL13; break;
case 'B': opt->mode |= atoi(optarg) << 24; break;
default: return 1; default: return 1;
} }
} }
@ -303,6 +302,7 @@ int bwa_aln(int argc, char *argv[])
fprintf(stderr, " -R INT stop searching when there are >INT equally best hits [%d]\n", opt->max_top2); fprintf(stderr, " -R INT stop searching when there are >INT equally best hits [%d]\n", opt->max_top2);
fprintf(stderr, " -q INT quality threshold for read trimming down to %dbp [%d]\n", BWA_MIN_RDLEN, opt->trim_qual); fprintf(stderr, " -q INT quality threshold for read trimming down to %dbp [%d]\n", BWA_MIN_RDLEN, opt->trim_qual);
fprintf(stderr, " -f FILE file to write output to instead of stdout\n"); fprintf(stderr, " -f FILE file to write output to instead of stdout\n");
fprintf(stderr, " -B INT length of barcode\n");
fprintf(stderr, " -c input sequences are in the color space\n"); fprintf(stderr, " -c input sequences are in the color space\n");
fprintf(stderr, " -L log-scaled gap penalty for long deletions\n"); fprintf(stderr, " -L log-scaled gap penalty for long deletions\n");
fprintf(stderr, " -N non-iterative mode: search for all n-difference hits (slooow)\n"); fprintf(stderr, " -N non-iterative mode: search for all n-difference hits (slooow)\n");

6
bwtaln.h
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@ -74,6 +74,8 @@ typedef struct {
bwa_cigar_t *cigar; bwa_cigar_t *cigar;
// for multi-threading only // for multi-threading only
int tid; int tid;
// barcode
char bc[16]; // null terminated; up to 15 bases
// NM and MD tags // NM and MD tags
uint32_t full_len:20, nm:12; uint32_t full_len:20, nm:12;
char *md; char *md;
@ -91,7 +93,7 @@ typedef struct {
typedef struct { typedef struct {
int s_mm, s_gapo, s_gape; int s_mm, s_gapo, s_gape;
int mode; int mode; // bit 24-31 are the barcode length
int indel_end_skip, max_del_occ, max_entries; int indel_end_skip, max_del_occ, max_entries;
float fnr; float fnr;
int max_diff, max_gapo, max_gape; int max_diff, max_gapo, max_gape;
@ -126,7 +128,7 @@ extern "C" {
bwa_seqio_t *bwa_bam_open(const char *fn, int which); bwa_seqio_t *bwa_bam_open(const char *fn, int which);
void bwa_seq_close(bwa_seqio_t *bs); void bwa_seq_close(bwa_seqio_t *bs);
void seq_reverse(int len, ubyte_t *seq, int is_comp); void seq_reverse(int len, ubyte_t *seq, int is_comp);
bwa_seq_t *bwa_read_seq(bwa_seqio_t *seq, int n_needed, int *n, int is_comp, int trim_qual); bwa_seq_t *bwa_read_seq(bwa_seqio_t *seq, int n_needed, int *n, int mode, int trim_qual);
void bwa_free_read_seq(int n_seqs, bwa_seq_t *seqs); void bwa_free_read_seq(int n_seqs, bwa_seq_t *seqs);
int bwa_cal_maxdiff(int l, double err, double thres); int bwa_cal_maxdiff(int l, double err, double thres);

2
main.c
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@ -3,7 +3,7 @@
#include "main.h" #include "main.h"
#ifndef PACKAGE_VERSION #ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.5.9rc1-r10" #define PACKAGE_VERSION "0.5.9rc1-r11"
#endif #endif
static int usage() static int usage()