5 #include "sam_header.h"
10 static void replace_cigar(bam1_t *b, int n, uint32_t *cigar)
12 if (n != b->core.n_cigar) {
13 int o = b->core.l_qname + b->core.n_cigar * 4;
14 if (b->data_len + (n - b->core.n_cigar) * 4 > b->m_data) {
15 b->m_data = b->data_len + (n - b->core.n_cigar) * 4;
16 kroundup32(b->m_data);
17 b->data = (uint8_t*)realloc(b->data, b->m_data);
19 memmove(b->data + b->core.l_qname + n * 4, b->data + o, b->data_len - o);
20 memcpy(b->data + b->core.l_qname, cigar, n * 4);
21 b->data_len += (n - b->core.n_cigar) * 4;
23 } else memcpy(b->data + b->core.l_qname, cigar, n * 4);
26 #define write_cigar(_c, _n, _m, _v) do { \
29 _c = (uint32_t*)realloc(_c, _m * 4); \
34 static void unpad_seq(bam1_t *b, kstring_t *s)
38 uint32_t *cigar = bam1_cigar(b);
39 uint8_t *seq = bam1_seq(b);
40 // b->core.l_qseq gives length of the SEQ entry (including soft clips, S)
41 // We need the padded length after alignment from the CIGAR (excluding
42 // soft clips S, but including pads from CIGAR D operations)
44 for (k = 0; k < b->core.n_cigar; ++k) {
46 op= bam_cigar_op(cigar[k]);
47 ol = bam_cigar_oplen(cigar[k]);
48 if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF || op == BAM_CDEL)
52 for (k = 0, s->l = 0, j = 0; k < b->core.n_cigar; ++k) {
54 op = bam_cigar_op(cigar[k]);
55 ol = bam_cigar_oplen(cigar[k]);
56 if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
57 for (i = 0; i < ol; ++i, ++j) s->s[s->l++] = bam1_seqi(seq, j);
58 } else if (op == BAM_CSOFT_CLIP) {
60 } else if (op == BAM_CHARD_CLIP) {
62 } else if (op == BAM_CDEL) {
63 for (i = 0; i < ol; ++i) s->s[s->l++] = 0;
65 fprintf(stderr, "[depad] ERROR: Didn't expect CIGAR op %c in read %s\n", BAM_CIGAR_STR[op], bam1_qname(b));
69 assert(length == s->l);
72 int bam_pad2unpad(samfile_t *in, samfile_t *out, faidx_t *fai)
79 int ret = 0, n2 = 0, m2 = 0, *posmap = 0;
82 r.l = r.m = q.l = q.m = 0; r.s = q.s = 0;
85 while ((read_ret = samread(in, b)) >= 0) { // read one alignment from `in'
86 uint32_t *cigar = bam1_cigar(b);
88 if (b->core.pos == 0 && b->core.tid >= 0 && strcmp(bam1_qname(b), h->target_name[b->core.tid]) == 0) {
91 fprintf(stderr, "[depad] Found embedded reference %s\n", bam1_qname(b));
95 if (h->target_len[r_tid] != r.l) {
96 fprintf(stderr, "[depad] ERROR: (Padded) length of %s is %i in BAM header, but %ld in embedded reference\n", bam1_qname(b), h->target_len[r_tid], r.l);
99 write_cigar(cigar2, n2, m2, bam_cigar_gen(b->core.l_qseq, BAM_CMATCH));
100 replace_cigar(b, n2, cigar2);
101 posmap = realloc(posmap, r.m * sizeof(int));
102 for (i = k = 0; i < r.l; ++i) {
106 } else if (b->core.n_cigar > 0) {
108 if (b->core.tid < 0) {
109 fprintf(stderr, "[depad] ERROR: Read %s has CIGAR but no RNAME\n", bam1_qname(b));
111 } else if (b->core.tid != r_tid) {
112 fprintf(stderr, "[depad] ERROR: Missing %s embedded reference sequence\n", h->target_name[b->core.tid]);
116 if (bam_cigar_op(cigar[0]) == BAM_CSOFT_CLIP) {
117 write_cigar(cigar2, n2, m2, cigar[0]);
118 } else if (bam_cigar_op(cigar[0]) == BAM_CHARD_CLIP) {
119 write_cigar(cigar2, n2, m2, cigar[0]);
120 if (b->core.n_cigar > 2 && bam_cigar_op(cigar[1]) == BAM_CSOFT_CLIP) {
121 write_cigar(cigar2, n2, m2, cigar[1]);
124 /* Determine CIGAR operator for each base in the aligned read */
125 for (i = 0, k = b->core.pos; i < q.l; ++i, ++k)
126 q.s[i] = q.s[i]? (r.s[k]? BAM_CMATCH : BAM_CINS) : (r.s[k]? BAM_CDEL : BAM_CPAD);
127 /* Include any pads if starts with an insert */
128 if (q.s[0] == BAM_CINS) {
129 for (k = 0; k+1 < b->core.pos && !r.s[b->core.pos - k - 1]; ++k);
130 if (k) write_cigar(cigar2, n2, m2, bam_cigar_gen(k, BAM_CPAD));
132 /* Count consecutive CIGAR operators to turn into a CIGAR string */
133 for (i = k = 1, op = q.s[0]; i < q.l; ++i) {
135 write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op));
139 write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op));
140 if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CSOFT_CLIP) {
141 write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
142 } else if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CHARD_CLIP) {
143 if (b->core.n_cigar > 2 && bam_cigar_op(cigar[b->core.n_cigar-2]) == BAM_CSOFT_CLIP) {
144 write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-2]);
146 write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
148 /* Remove redundant P operators between M/X/=/D operators, e.g. 5M2P10M -> 15M */
150 for (i = 2; i < n2; ++i)
151 if (bam_cigar_op(cigar2[i-1]) == BAM_CPAD) {
152 pre_op = bam_cigar_op(cigar2[i-2]);
153 post_op = bam_cigar_op(cigar2[i]);
154 /* Note don't need to check for X/= as code above will use M only */
155 if ((pre_op == BAM_CMATCH || pre_op == BAM_CDEL) && (post_op == BAM_CMATCH || post_op == BAM_CDEL)) {
156 /* This is a redundant P operator */
157 cigar2[i-1] = 0; // i.e. 0M
158 /* If had same operator either side, combine them in post_op */
159 if (pre_op == post_op) {
160 /* If CIGAR M, could treat as simple integers since BAM_CMATCH is zero*/
161 cigar2[i] = bam_cigar_gen(bam_cigar_oplen(cigar2[i-2]) + bam_cigar_oplen(cigar2[i]), post_op);
162 cigar2[i-2] = 0; // i.e. 0M
166 /* Remove the zero'd operators (0M) */
167 for (i = k = 0; i < n2; ++i)
168 if (cigar2[i]) cigar2[k++] = cigar2[i];
170 replace_cigar(b, n2, cigar2);
171 b->core.pos = posmap[b->core.pos];
176 fprintf(stderr, "[depad] truncated file.\n");
179 free(r.s); free(q.s); free(posmap);
184 static int usage(int is_long_help);
186 int main_pad2unpad(int argc, char *argv[])
188 samfile_t *in = 0, *out = 0;
190 int c, is_bamin = 1, compress_level = -1, is_bamout = 1, is_long_help = 0;
191 char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0, *fn_ref = 0;
194 /* parse command-line options */
195 strcpy(in_mode, "r"); strcpy(out_mode, "w");
196 while ((c = getopt(argc, argv, "Sso:u1T:?")) >= 0) {
198 case 'S': is_bamin = 0; break;
199 case 's': assert(compress_level == -1); is_bamout = 0; break;
200 case 'o': fn_out = strdup(optarg); break;
201 case 'u': assert(is_bamout == 1); compress_level = 0; break;
202 case '1': assert(is_bamout == 1); compress_level = 1; break;
203 case 'T': fn_ref = strdup(optarg); is_bamin = 0; break;
204 case '?': is_long_help = 1; break;
205 default: return usage(is_long_help);
208 if (argc == optind) return usage(is_long_help);
210 if (is_bamin) strcat(in_mode, "b");
211 if (is_bamout) strcat(out_mode, "b");
212 strcat(out_mode, "h");
213 if (compress_level >= 0) {
215 tmp[0] = compress_level + '0'; tmp[1] = '\0';
216 strcat(out_mode, tmp);
219 // Load FASTA reference (also needed for SAM -> BAM if missing header)
221 fn_list = samfaipath(fn_ref);
222 fai = fai_load(fn_ref);
224 // open file handlers
225 if ((in = samopen(argv[optind], in_mode, fn_list)) == 0) {
226 fprintf(stderr, "[depad] fail to open \"%s\" for reading.\n", argv[optind]);
230 if (in->header == 0) {
231 fprintf(stderr, "[depad] fail to read the header from \"%s\".\n", argv[optind]);
235 /* TODO - The reference sequence lengths in the BAM + SAM headers should be updated */
236 if ((out = samopen(fn_out? fn_out : "-", out_mode, in->header)) == 0) {
237 fprintf(stderr, "[depad] fail to open \"%s\" for writing.\n", fn_out? fn_out : "standard output");
243 ret = bam_pad2unpad(in, out, fai);
246 // close files, free and return
247 free(fn_list); free(fn_out);
254 static int usage(int is_long_help)
256 fprintf(stderr, "\n");
257 fprintf(stderr, "Usage: samtools depad <in.bam>\n\n");
258 fprintf(stderr, "Options: -s output is SAM (default is BAM)\n");
259 fprintf(stderr, " -S input is SAM (default is BAM)\n");
260 fprintf(stderr, " -u uncompressed BAM output (can't use with -s)\n");
261 fprintf(stderr, " -1 fast compression BAM output (can't use with -s)\n");
262 fprintf(stderr, " -T FILE reference sequence file [null]\n");
263 fprintf(stderr, " -o FILE output file name [stdout]\n");
264 fprintf(stderr, " -? longer help\n");
265 fprintf(stderr, "\n");
267 fprintf(stderr, "Notes:\n\
269 1. Requires embedded reference sequences (before the reads for that reference),\n\
270 with the future aim to also support a FASTA padded reference sequence file.\n\
272 2. The input padded alignment read's CIGAR strings must not use P or I operators.\n\