0
|
1 #include <zlib.h>
|
|
2 #include <ctype.h>
|
|
3 #include "bwtaln.h"
|
|
4 #include "utils.h"
|
|
5 #include "bamlite.h"
|
|
6
|
|
7 #include "kseq.h"
|
|
8 KSEQ_INIT(gzFile, gzread)
|
|
9
|
|
10 extern unsigned char nst_nt4_table[256];
|
|
11 static char bam_nt16_nt4_table[] = { 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4 };
|
|
12
|
|
13 struct __bwa_seqio_t {
|
|
14 // for BAM input
|
|
15 int is_bam, which; // 1st bit: read1, 2nd bit: read2, 3rd: SE
|
|
16 bamFile fp;
|
|
17 // for fastq input
|
|
18 kseq_t *ks;
|
|
19 };
|
|
20
|
|
21 bwa_seqio_t *bwa_bam_open(const char *fn, int which)
|
|
22 {
|
|
23 bwa_seqio_t *bs;
|
|
24 bam_header_t *h;
|
|
25 bs = (bwa_seqio_t*)calloc(1, sizeof(bwa_seqio_t));
|
|
26 bs->is_bam = 1;
|
|
27 bs->which = which;
|
|
28 bs->fp = bam_open(fn, "r");
|
|
29 h = bam_header_read(bs->fp);
|
|
30 bam_header_destroy(h);
|
|
31 return bs;
|
|
32 }
|
|
33
|
|
34 bwa_seqio_t *bwa_seq_open(const char *fn)
|
|
35 {
|
|
36 gzFile fp;
|
|
37 bwa_seqio_t *bs;
|
|
38 bs = (bwa_seqio_t*)calloc(1, sizeof(bwa_seqio_t));
|
|
39 fp = xzopen(fn, "r");
|
|
40 bs->ks = kseq_init(fp);
|
|
41 return bs;
|
|
42 }
|
|
43
|
|
44 void bwa_seq_close(bwa_seqio_t *bs)
|
|
45 {
|
|
46 if (bs == 0) return;
|
|
47 if (bs->is_bam) bam_close(bs->fp);
|
|
48 else {
|
|
49 gzclose(bs->ks->f->f);
|
|
50 kseq_destroy(bs->ks);
|
|
51 }
|
|
52 free(bs);
|
|
53 }
|
|
54
|
|
55 void seq_reverse(int len, ubyte_t *seq, int is_comp)
|
|
56 {
|
|
57 int i;
|
|
58 if (is_comp) {
|
|
59 for (i = 0; i < len>>1; ++i) {
|
|
60 char tmp = seq[len-1-i];
|
|
61 if (tmp < 4) tmp = 3 - tmp;
|
|
62 seq[len-1-i] = (seq[i] >= 4)? seq[i] : 3 - seq[i];
|
|
63 seq[i] = tmp;
|
|
64 }
|
|
65 if (len&1) seq[i] = (seq[i] >= 4)? seq[i] : 3 - seq[i];
|
|
66 } else {
|
|
67 for (i = 0; i < len>>1; ++i) {
|
|
68 char tmp = seq[len-1-i];
|
|
69 seq[len-1-i] = seq[i]; seq[i] = tmp;
|
|
70 }
|
|
71 }
|
|
72 }
|
|
73
|
|
74 int bwa_trim_read(int trim_qual, bwa_seq_t *p)
|
|
75 {
|
|
76 int s = 0, l, max = 0, max_l = p->len;
|
|
77 if (trim_qual < 1 || p->qual == 0) return 0;
|
|
78 for (l = p->len - 1; l >= BWA_MIN_RDLEN; --l) {
|
|
79 s += trim_qual - (p->qual[l] - 33);
|
|
80 if (s < 0) break;
|
|
81 if (s > max) max = s, max_l = l;
|
|
82 }
|
|
83 p->clip_len = p->len = max_l;
|
|
84 return p->full_len - p->len;
|
|
85 }
|
|
86
|
|
87 static bwa_seq_t *bwa_read_bam(bwa_seqio_t *bs, int n_needed, int *n, int is_comp, int trim_qual)
|
|
88 {
|
|
89 bwa_seq_t *seqs, *p;
|
|
90 int n_seqs, l, i;
|
|
91 long n_trimmed = 0, n_tot = 0;
|
|
92 bam1_t *b;
|
|
93
|
|
94 b = bam_init1();
|
|
95 n_seqs = 0;
|
|
96 seqs = (bwa_seq_t*)calloc(n_needed, sizeof(bwa_seq_t));
|
|
97 while (bam_read1(bs->fp, b) >= 0) {
|
|
98 uint8_t *s, *q;
|
|
99 int go = 0;
|
|
100 if ((bs->which & 1) && (b->core.flag & BAM_FREAD1)) go = 1;
|
|
101 if ((bs->which & 2) && (b->core.flag & BAM_FREAD2)) go = 1;
|
|
102 if ((bs->which & 4) && !(b->core.flag& BAM_FREAD1) && !(b->core.flag& BAM_FREAD2))go = 1;
|
|
103 if (go == 0) continue;
|
|
104 l = b->core.l_qseq;
|
|
105 p = &seqs[n_seqs++];
|
|
106 p->tid = -1; // no assigned to a thread
|
|
107 p->qual = 0;
|
|
108 p->full_len = p->clip_len = p->len = l;
|
|
109 n_tot += p->full_len;
|
|
110 s = bam1_seq(b); q = bam1_qual(b);
|
|
111 p->seq = (ubyte_t*)calloc(p->len + 1, 1);
|
|
112 p->qual = (ubyte_t*)calloc(p->len + 1, 1);
|
|
113 for (i = 0; i != p->full_len; ++i) {
|
|
114 p->seq[i] = bam_nt16_nt4_table[(int)bam1_seqi(s, i)];
|
|
115 p->qual[i] = q[i] + 33 < 126? q[i] + 33 : 126;
|
|
116 }
|
|
117 if (bam1_strand(b)) { // then reverse
|
|
118 seq_reverse(p->len, p->seq, 1);
|
|
119 seq_reverse(p->len, p->qual, 0);
|
|
120 }
|
|
121 if (trim_qual >= 1) n_trimmed += bwa_trim_read(trim_qual, p);
|
|
122 p->rseq = (ubyte_t*)calloc(p->full_len, 1);
|
|
123 memcpy(p->rseq, p->seq, p->len);
|
|
124 seq_reverse(p->len, p->seq, 0); // *IMPORTANT*: will be reversed back in bwa_refine_gapped()
|
|
125 seq_reverse(p->len, p->rseq, is_comp);
|
|
126 p->name = strdup((const char*)bam1_qname(b));
|
|
127 if (n_seqs == n_needed) break;
|
|
128 }
|
|
129 *n = n_seqs;
|
|
130 if (n_seqs && trim_qual >= 1)
|
|
131 fprintf(stderr, "[bwa_read_seq] %.1f%% bases are trimmed.\n", 100.0f * n_trimmed/n_tot);
|
|
132 if (n_seqs == 0) {
|
|
133 free(seqs);
|
|
134 bam_destroy1(b);
|
|
135 return 0;
|
|
136 }
|
|
137 bam_destroy1(b);
|
|
138 return seqs;
|
|
139 }
|
|
140
|
|
141 #define BARCODE_LOW_QUAL 13
|
|
142
|
|
143 bwa_seq_t *bwa_read_seq(bwa_seqio_t *bs, int n_needed, int *n, int mode, int trim_qual)
|
|
144 {
|
|
145 bwa_seq_t *seqs, *p;
|
|
146 kseq_t *seq = bs->ks;
|
|
147 int n_seqs, l, i, is_comp = mode&BWA_MODE_COMPREAD, is_64 = mode&BWA_MODE_IL13, l_bc = mode>>24;
|
|
148 long n_trimmed = 0, n_tot = 0;
|
|
149
|
|
150 if (l_bc > BWA_MAX_BCLEN) {
|
|
151 fprintf(stderr, "[%s] the maximum barcode length is %d.\n", __func__, BWA_MAX_BCLEN);
|
|
152 return 0;
|
|
153 }
|
|
154 if (bs->is_bam) return bwa_read_bam(bs, n_needed, n, is_comp, trim_qual); // l_bc has no effect for BAM input
|
|
155 n_seqs = 0;
|
|
156 seqs = (bwa_seq_t*)calloc(n_needed, sizeof(bwa_seq_t));
|
|
157 while ((l = kseq_read(seq)) >= 0) {
|
|
158 if ((mode & BWA_MODE_CFY) && (seq->comment.l != 0)) {
|
|
159 // skip reads that are marked to be filtered by Casava
|
|
160 char *s = index(seq->comment.s, ':');
|
|
161 if (s && *(++s) == 'Y') {
|
|
162 continue;
|
|
163 }
|
|
164 }
|
|
165 if (is_64 && seq->qual.l)
|
|
166 for (i = 0; i < seq->qual.l; ++i) seq->qual.s[i] -= 31;
|
|
167 if (seq->seq.l <= l_bc) continue; // sequence length equals or smaller than the barcode length
|
|
168 p = &seqs[n_seqs++];
|
|
169 if (l_bc) { // then trim barcode
|
|
170 for (i = 0; i < l_bc; ++i)
|
|
171 p->bc[i] = (seq->qual.l && seq->qual.s[i]-33 < BARCODE_LOW_QUAL)? tolower(seq->seq.s[i]) : toupper(seq->seq.s[i]);
|
|
172 p->bc[i] = 0;
|
|
173 for (; i < seq->seq.l; ++i)
|
|
174 seq->seq.s[i - l_bc] = seq->seq.s[i];
|
|
175 seq->seq.l -= l_bc; seq->seq.s[seq->seq.l] = 0;
|
|
176 if (seq->qual.l) {
|
|
177 for (i = l_bc; i < seq->qual.l; ++i)
|
|
178 seq->qual.s[i - l_bc] = seq->qual.s[i];
|
|
179 seq->qual.l -= l_bc; seq->qual.s[seq->qual.l] = 0;
|
|
180 }
|
|
181 l = seq->seq.l;
|
|
182 } else p->bc[0] = 0;
|
|
183 p->tid = -1; // no assigned to a thread
|
|
184 p->qual = 0;
|
|
185 p->full_len = p->clip_len = p->len = l;
|
|
186 n_tot += p->full_len;
|
|
187 p->seq = (ubyte_t*)calloc(p->len, 1);
|
|
188 for (i = 0; i != p->full_len; ++i)
|
|
189 p->seq[i] = nst_nt4_table[(int)seq->seq.s[i]];
|
|
190 if (seq->qual.l) { // copy quality
|
|
191 p->qual = (ubyte_t*)strdup((char*)seq->qual.s);
|
|
192 if (trim_qual >= 1) n_trimmed += bwa_trim_read(trim_qual, p);
|
|
193 }
|
|
194 p->rseq = (ubyte_t*)calloc(p->full_len, 1);
|
|
195 memcpy(p->rseq, p->seq, p->len);
|
|
196 seq_reverse(p->len, p->seq, 0); // *IMPORTANT*: will be reversed back in bwa_refine_gapped()
|
|
197 seq_reverse(p->len, p->rseq, is_comp);
|
|
198 p->name = strdup((const char*)seq->name.s);
|
|
199 { // trim /[12]$
|
|
200 int t = strlen(p->name);
|
|
201 if (t > 2 && p->name[t-2] == '/' && (p->name[t-1] == '1' || p->name[t-1] == '2')) p->name[t-2] = '\0';
|
|
202 }
|
|
203 if (n_seqs == n_needed) break;
|
|
204 }
|
|
205 *n = n_seqs;
|
|
206 if (n_seqs && trim_qual >= 1)
|
|
207 fprintf(stderr, "[bwa_read_seq] %.1f%% bases are trimmed.\n", 100.0f * n_trimmed/n_tot);
|
|
208 if (n_seqs == 0) {
|
|
209 free(seqs);
|
|
210 return 0;
|
|
211 }
|
|
212 return seqs;
|
|
213 }
|
|
214
|
|
215 void bwa_free_read_seq(int n_seqs, bwa_seq_t *seqs)
|
|
216 {
|
|
217 int i, j;
|
|
218 for (i = 0; i != n_seqs; ++i) {
|
|
219 bwa_seq_t *p = seqs + i;
|
|
220 for (j = 0; j < p->n_multi; ++j)
|
|
221 if (p->multi[j].cigar) free(p->multi[j].cigar);
|
|
222 free(p->name);
|
|
223 free(p->seq); free(p->rseq); free(p->qual); free(p->aln); free(p->md); free(p->multi);
|
|
224 free(p->cigar);
|
|
225 }
|
|
226 free(seqs);
|
|
227 }
|