7 static void replace_cigar(bam1_t *b, int n, uint32_t *cigar)
9 if (n != b->core.n_cigar) {
10 int o = b->core.l_qname + b->core.n_cigar * 4;
11 if (b->data_len + (n - b->core.n_cigar) * 4 > b->m_data) {
12 b->m_data = b->data_len + (n - b->core.n_cigar) * 4;
13 kroundup32(b->m_data);
14 b->data = (uint8_t*)realloc(b->data, b->m_data);
16 memmove(b->data + b->core.l_qname + n * 4, b->data + o, b->data_len - o);
17 memcpy(b->data + b->core.l_qname, cigar, n * 4);
18 b->data_len += (n - b->core.n_cigar) * 4;
20 } else memcpy(b->data + b->core.l_qname, cigar, n * 4);
23 #define write_cigar(_c, _n, _m, _v) do { \
26 _c = (uint32_t*)realloc(_c, _m * 4); \
31 static void unpad_seq(bam1_t *b, kstring_t *s)
35 uint32_t *cigar = bam1_cigar(b);
36 uint8_t *seq = bam1_seq(b);
37 // b->core.l_qseq gives length of the SEQ entry (including soft clips, S)
38 // We need the padded length after alignment from the CIGAR (excluding
39 // soft clips S, but including pads from CIGAR D operations)
41 for (k = 0; k < b->core.n_cigar; ++k) {
43 op= bam_cigar_op(cigar[k]);
44 ol = bam_cigar_oplen(cigar[k]);
45 if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF || op == BAM_CDEL)
49 for (k = 0, s->l = 0, j = 0; k < b->core.n_cigar; ++k) {
51 op = bam_cigar_op(cigar[k]);
52 ol = bam_cigar_oplen(cigar[k]);
53 if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
54 for (i = 0; i < ol; ++i, ++j) s->s[s->l++] = bam1_seqi(seq, j);
55 } else if (op == BAM_CSOFT_CLIP) {
57 } else if (op == BAM_CHARD_CLIP) {
59 } else if (op == BAM_CDEL) {
60 for (i = 0; i < ol; ++i) s->s[s->l++] = 0;
62 fprintf(stderr, "[depad] ERROR: Didn't expect CIGAR op %c in read %s\n", BAM_CIGAR_STR[op], bam1_qname(b));
66 assert(length == s->l);
69 int bam_pad2unpad(bamFile in, bamFile out)
76 int n2 = 0, m2 = 0, *posmap = 0;
78 h = bam_header_read(in);
79 /* TODO - The reference sequence lengths in the BAM + SAM headers should be updated */
80 bam_header_write(out, h);
82 r.l = r.m = q.l = q.m = 0; r.s = q.s = 0;
83 while (bam_read1(in, b) >= 0) {
84 uint32_t *cigar = bam1_cigar(b);
86 if (b->core.pos == 0 && b->core.tid >= 0 && strcmp(bam1_qname(b), h->target_name[b->core.tid]) == 0) {
89 fprintf(stderr, "[depad] Found embedded reference %s\n", bam1_qname(b));
93 if (h->target_len[r_tid] != r.l) {
94 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);
97 write_cigar(cigar2, n2, m2, bam_cigar_gen(b->core.l_qseq, BAM_CMATCH));
98 replace_cigar(b, n2, cigar2);
99 posmap = realloc(posmap, r.m * sizeof(int));
100 for (i = k = 0; i < r.l; ++i) {
104 } else if (b->core.n_cigar > 0) {
106 if (b->core.tid < 0) {
107 fprintf(stderr, "[depad] ERROR: Read %s has CIGAR but no RNAME\n", bam1_qname(b));
109 } else if (b->core.tid != r_tid) {
110 fprintf(stderr, "[depad] ERROR: Missing %s embedded reference sequence\n", h->target_name[b->core.tid]);
114 if (bam_cigar_op(cigar[0]) == BAM_CSOFT_CLIP) {
115 write_cigar(cigar2, n2, m2, cigar[0]);
116 } else if (bam_cigar_op(cigar[0]) == BAM_CHARD_CLIP) {
117 write_cigar(cigar2, n2, m2, cigar[0]);
118 if (b->core.n_cigar > 2 && bam_cigar_op(cigar[1]) == BAM_CSOFT_CLIP) {
119 write_cigar(cigar2, n2, m2, cigar[1]);
122 /* Determine CIGAR operator for each base in the aligned read */
123 for (i = 0, k = b->core.pos; i < q.l; ++i, ++k)
124 q.s[i] = q.s[i]? (r.s[k]? BAM_CMATCH : BAM_CINS) : (r.s[k]? BAM_CDEL : BAM_CPAD);
125 /* Include any pads if starts with an insert */
126 if (q.s[0] == BAM_CINS) {
127 for (k = 0; k+1 < b->core.pos && !r.s[b->core.pos - k - 1]; ++k);
128 if (k) write_cigar(cigar2, n2, m2, bam_cigar_gen(k, BAM_CPAD));
130 /* Count consecutive CIGAR operators to turn into a CIGAR string */
131 for (i = k = 1, op = q.s[0]; i < q.l; ++i) {
133 write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op));
137 write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op));
138 if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CSOFT_CLIP) {
139 write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
140 } else if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CHARD_CLIP) {
141 if (b->core.n_cigar > 2 && bam_cigar_op(cigar[b->core.n_cigar-2]) == BAM_CSOFT_CLIP) {
142 write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-2]);
144 write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
146 /* Remove redundant P operators between M/X/=/D operators, e.g. 5M2P10M -> 15M */
148 for (i = 2; i < n2; ++i)
149 if (bam_cigar_op(cigar2[i-1]) == BAM_CPAD) {
150 pre_op = bam_cigar_op(cigar2[i-2]);
151 post_op = bam_cigar_op(cigar2[i]);
152 /* Note don't need to check for X/= as code above will use M only */
153 if ((pre_op == BAM_CMATCH || pre_op == BAM_CDEL) && (post_op == BAM_CMATCH || post_op == BAM_CDEL)) {
154 /* This is a redundant P operator */
155 cigar2[i-1] = 0; // i.e. 0M
156 /* If had same operator either side, combine them in post_op */
157 if (pre_op == post_op) {
158 /* If CIGAR M, could treat as simple integers since BAM_CMATCH is zero*/
159 cigar2[i] = bam_cigar_gen(bam_cigar_oplen(cigar2[i-2]) + bam_cigar_oplen(cigar2[i]), post_op);
160 cigar2[i-2] = 0; // i.e. 0M
164 /* Remove the zero'd operators (0M) */
165 for (i = k = 0; i < n2; ++i)
166 if (cigar2[i]) cigar2[k++] = cigar2[i];
168 replace_cigar(b, n2, cigar2);
169 b->core.pos = posmap[b->core.pos];
173 free(r.s); free(q.s); free(posmap);
175 bam_header_destroy(h);
179 static int usage(int is_long_help);
181 int main_pad2unpad(int argc, char *argv[])
184 int c, is_long_help = 0;
187 /* parse command-line options */
188 while ((c = getopt(argc, argv, "?")) >= 0) {
190 case '?': is_long_help = 1; break;
191 default: return usage(is_long_help);
194 if (argc == optind) return usage(is_long_help);
196 in = strcmp(argv[1], "-")? bam_open(argv[1], "r") : bam_dopen(fileno(stdin), "r");
197 out = bam_dopen(fileno(stdout), "w");
198 result = bam_pad2unpad(in, out);
199 bam_close(in); bam_close(out);
203 static int usage(int is_long_help)
205 fprintf(stderr, "\n");
206 fprintf(stderr, "Usage: samtools depad <in.bam>\n\n");
207 fprintf(stderr, "Options: -? longer help\n");
208 //TODO - These are the arguments I think make sense to support:
209 //fprintf(stderr, "Usage: samtools depad [options] <in.bam>|<in.sam>\n\n");
210 //fprintf(stderr, "Options: -b output BAM\n");
211 //fprintf(stderr, " -S input is SAM\n");
212 //fprintf(stderr, " -u uncompressed BAM output (force -b)\n");
213 //fprintf(stderr, " -1 fast compression (force -b)\n");
214 //fprintf(stderr, " -@ INT number of BAM compression threads [0]\n");
215 //fprintf(stderr, " -T FILE reference sequence file (force -S) [null]\n");
216 //fprintf(stderr, " -o FILE output file name [stdout]\n");
217 //fprintf(stderr, " -? longer help\n");
218 fprintf(stderr, "\n");
220 fprintf(stderr, "Notes:\n\
222 1. Requires embedded reference sequences (before the reads for that reference).\n\
224 2. The input padded alignment read's CIGAR strings must not use P or I operators.\n\