5 #include "sam_header.h"
9 static void replace_cigar(bam1_t *b, int n, uint32_t *cigar)
11 if (n != b->core.n_cigar) {
12 int o = b->core.l_qname + b->core.n_cigar * 4;
13 if (b->data_len + (n - b->core.n_cigar) * 4 > b->m_data) {
14 b->m_data = b->data_len + (n - b->core.n_cigar) * 4;
15 kroundup32(b->m_data);
16 b->data = (uint8_t*)realloc(b->data, b->m_data);
18 memmove(b->data + b->core.l_qname + n * 4, b->data + o, b->data_len - o);
19 memcpy(b->data + b->core.l_qname, cigar, n * 4);
20 b->data_len += (n - b->core.n_cigar) * 4;
22 } else memcpy(b->data + b->core.l_qname, cigar, n * 4);
25 #define write_cigar(_c, _n, _m, _v) do { \
28 _c = (uint32_t*)realloc(_c, _m * 4); \
33 static void unpad_seq(bam1_t *b, kstring_t *s)
37 uint32_t *cigar = bam1_cigar(b);
38 uint8_t *seq = bam1_seq(b);
39 // b->core.l_qseq gives length of the SEQ entry (including soft clips, S)
40 // We need the padded length after alignment from the CIGAR (excluding
41 // soft clips S, but including pads from CIGAR D operations)
43 for (k = 0; k < b->core.n_cigar; ++k) {
45 op= bam_cigar_op(cigar[k]);
46 ol = bam_cigar_oplen(cigar[k]);
47 if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF || op == BAM_CDEL)
51 for (k = 0, s->l = 0, j = 0; k < b->core.n_cigar; ++k) {
53 op = bam_cigar_op(cigar[k]);
54 ol = bam_cigar_oplen(cigar[k]);
55 if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
56 for (i = 0; i < ol; ++i, ++j) s->s[s->l++] = bam1_seqi(seq, j);
57 } else if (op == BAM_CSOFT_CLIP) {
59 } else if (op == BAM_CHARD_CLIP) {
61 } else if (op == BAM_CDEL) {
62 for (i = 0; i < ol; ++i) s->s[s->l++] = 0;
64 fprintf(stderr, "[depad] ERROR: Didn't expect CIGAR op %c in read %s\n", BAM_CIGAR_STR[op], bam1_qname(b));
68 assert(length == s->l);
71 int bam_pad2unpad(samfile_t *in, samfile_t *out)
78 int ret = 0, n2 = 0, m2 = 0, *posmap = 0;
81 r.l = r.m = q.l = q.m = 0; r.s = q.s = 0;
84 while ((read_ret = samread(in, b)) >= 0) { // read one alignment from `in'
85 uint32_t *cigar = bam1_cigar(b);
87 if (b->core.pos == 0 && b->core.tid >= 0 && strcmp(bam1_qname(b), h->target_name[b->core.tid]) == 0) {
90 fprintf(stderr, "[depad] Found embedded reference %s\n", bam1_qname(b));
94 if (h->target_len[r_tid] != r.l) {
95 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);
98 write_cigar(cigar2, n2, m2, bam_cigar_gen(b->core.l_qseq, BAM_CMATCH));
99 replace_cigar(b, n2, cigar2);
100 posmap = realloc(posmap, r.m * sizeof(int));
101 for (i = k = 0; i < r.l; ++i) {
105 } else if (b->core.n_cigar > 0) {
107 if (b->core.tid < 0) {
108 fprintf(stderr, "[depad] ERROR: Read %s has CIGAR but no RNAME\n", bam1_qname(b));
110 } else if (b->core.tid != r_tid) {
111 fprintf(stderr, "[depad] ERROR: Missing %s embedded reference sequence\n", h->target_name[b->core.tid]);
115 if (bam_cigar_op(cigar[0]) == BAM_CSOFT_CLIP) {
116 write_cigar(cigar2, n2, m2, cigar[0]);
117 } else if (bam_cigar_op(cigar[0]) == BAM_CHARD_CLIP) {
118 write_cigar(cigar2, n2, m2, cigar[0]);
119 if (b->core.n_cigar > 2 && bam_cigar_op(cigar[1]) == BAM_CSOFT_CLIP) {
120 write_cigar(cigar2, n2, m2, cigar[1]);
123 /* Determine CIGAR operator for each base in the aligned read */
124 for (i = 0, k = b->core.pos; i < q.l; ++i, ++k)
125 q.s[i] = q.s[i]? (r.s[k]? BAM_CMATCH : BAM_CINS) : (r.s[k]? BAM_CDEL : BAM_CPAD);
126 /* Include any pads if starts with an insert */
127 if (q.s[0] == BAM_CINS) {
128 for (k = 0; k+1 < b->core.pos && !r.s[b->core.pos - k - 1]; ++k);
129 if (k) write_cigar(cigar2, n2, m2, bam_cigar_gen(k, BAM_CPAD));
131 /* Count consecutive CIGAR operators to turn into a CIGAR string */
132 for (i = k = 1, op = q.s[0]; i < q.l; ++i) {
134 write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op));
138 write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op));
139 if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CSOFT_CLIP) {
140 write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
141 } else if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CHARD_CLIP) {
142 if (b->core.n_cigar > 2 && bam_cigar_op(cigar[b->core.n_cigar-2]) == BAM_CSOFT_CLIP) {
143 write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-2]);
145 write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
147 /* Remove redundant P operators between M/X/=/D operators, e.g. 5M2P10M -> 15M */
149 for (i = 2; i < n2; ++i)
150 if (bam_cigar_op(cigar2[i-1]) == BAM_CPAD) {
151 pre_op = bam_cigar_op(cigar2[i-2]);
152 post_op = bam_cigar_op(cigar2[i]);
153 /* Note don't need to check for X/= as code above will use M only */
154 if ((pre_op == BAM_CMATCH || pre_op == BAM_CDEL) && (post_op == BAM_CMATCH || post_op == BAM_CDEL)) {
155 /* This is a redundant P operator */
156 cigar2[i-1] = 0; // i.e. 0M
157 /* If had same operator either side, combine them in post_op */
158 if (pre_op == post_op) {
159 /* If CIGAR M, could treat as simple integers since BAM_CMATCH is zero*/
160 cigar2[i] = bam_cigar_gen(bam_cigar_oplen(cigar2[i-2]) + bam_cigar_oplen(cigar2[i]), post_op);
161 cigar2[i-2] = 0; // i.e. 0M
165 /* Remove the zero'd operators (0M) */
166 for (i = k = 0; i < n2; ++i)
167 if (cigar2[i]) cigar2[k++] = cigar2[i];
169 replace_cigar(b, n2, cigar2);
170 b->core.pos = posmap[b->core.pos];
175 fprintf(stderr, "[depad] truncated file.\n");
178 free(r.s); free(q.s); free(posmap);
183 static int usage(int is_long_help);
185 int main_pad2unpad(int argc, char *argv[])
187 samfile_t *in = 0, *out = 0;
188 int c, is_bamin = 1, compress_level = -1, is_bamout = 1, is_long_help = 0;
189 char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0;
192 /* parse command-line options */
193 strcpy(in_mode, "r"); strcpy(out_mode, "w");
194 while ((c = getopt(argc, argv, "Sso:u1?")) >= 0) {
196 case 'S': is_bamin = 0; break;
197 case 's': assert(compress_level == -1); is_bamout = 0; break;
198 case 'o': fn_out = strdup(optarg); break;
199 case 'u': assert(is_bamout == 1); compress_level = 0; break;
200 case '1': assert(is_bamout == 1); compress_level = 1; break;
201 case '?': is_long_help = 1; break;
202 default: return usage(is_long_help);
205 if (argc == optind) return usage(is_long_help);
207 if (is_bamin) strcat(in_mode, "b");
208 if (is_bamout) strcat(out_mode, "b");
209 strcat(out_mode, "h");
210 if (compress_level >= 0) {
212 tmp[0] = compress_level + '0'; tmp[1] = '\0';
213 strcat(out_mode, tmp);
216 // open file handlers
217 if ((in = samopen(argv[optind], in_mode, fn_list)) == 0) {
218 fprintf(stderr, "[depad] fail to open \"%s\" for reading.\n", argv[optind]);
222 if (in->header == 0) {
223 fprintf(stderr, "[depad] fail to read the header from \"%s\".\n", argv[optind]);
227 /* TODO - The reference sequence lengths in the BAM + SAM headers should be updated */
228 if ((out = samopen(fn_out? fn_out : "-", out_mode, in->header)) == 0) {
229 fprintf(stderr, "[depad] fail to open \"%s\" for writing.\n", fn_out? fn_out : "standard output");
235 ret = bam_pad2unpad(in, out);
238 // close files, free and return
239 free(fn_list); free(fn_out);
245 static int usage(int is_long_help)
247 fprintf(stderr, "\n");
248 fprintf(stderr, "Usage: samtools depad <in.bam>\n\n");
249 fprintf(stderr, "Options: -s output is SAM (default is BAM)\n");
250 fprintf(stderr, " -S input is SAM (default is BAM)\n");
251 fprintf(stderr, " -u uncompressed BAM output (can't use with -s)\n");
252 fprintf(stderr, " -1 fast compression BAM output (can't use with -s)\n");
253 //TODO - These are the arguments I think make sense to support:
254 //fprintf(stderr, " -@ INT number of BAM compression threads [0]\n");
255 //fprintf(stderr, " -T FILE reference sequence file (force -S) [null]\n");
256 fprintf(stderr, " -o FILE output file name [stdout]\n");
257 fprintf(stderr, " -? longer help\n");
258 fprintf(stderr, "\n");
260 fprintf(stderr, "Notes:\n\
262 1. Requires embedded reference sequences (before the reads for that reference).\n\
264 2. The input padded alignment read's CIGAR strings must not use P or I operators.\n\