6 static void replace_cigar(bam1_t *b, int n, uint32_t *cigar)
8 if (n != b->core.n_cigar) {
9 int o = b->core.l_qname + b->core.n_cigar * 4;
10 if (b->data_len + (n - b->core.n_cigar) * 4 > b->m_data) {
11 b->m_data = b->data_len + (n - b->core.n_cigar) * 4;
12 kroundup32(b->m_data);
13 b->data = (uint8_t*)realloc(b->data, b->m_data);
15 memmove(b->data + b->core.l_qname + n * 4, b->data + o, b->data_len - o);
16 memcpy(b->data + b->core.l_qname, cigar, n * 4);
17 b->data_len += (n - b->core.n_cigar) * 4;
19 } else memcpy(b->data + b->core.l_qname, cigar, n * 4);
22 #define write_cigar(_c, _n, _m, _v) do { \
25 _c = (uint32_t*)realloc(_c, _m * 4); \
30 static void unpad_seq(bam1_t *b, kstring_t *s)
33 uint32_t *cigar = bam1_cigar(b);
34 uint8_t *seq = bam1_seq(b);
35 ks_resize(s, b->core.l_qseq);
36 for (k = 0, s->l = 0, j = 0; k < b->core.n_cigar; ++k) {
38 op = bam_cigar_op(cigar[k]);
39 ol = bam_cigar_oplen(cigar[k]);
40 if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
41 for (i = 0; i < ol; ++i, ++j) s->s[s->l++] = bam1_seqi(seq, j);
42 } else if (op == BAM_CSOFT_CLIP) {
44 } else if (op == BAM_CHARD_CLIP) {
46 } else if (op == BAM_CDEL || op == BAM_CPAD) {
47 for (i = 0; i < ol; ++i) s->s[s->l++] = 0;
49 fprintf(stderr, "[depad] ERROR: Didn't expect CIGAR op %c in read %s\n", BAM_CIGAR_STR[op], bam1_qname(b));
55 int bam_pad2unpad(bamFile in, bamFile out)
62 int n2 = 0, m2 = 0, *posmap = 0;
64 h = bam_header_read(in);
65 /* TODO - The reference sequence lengths in the BAM + SAM headers should be updated */
66 bam_header_write(out, h);
68 r.l = r.m = q.l = q.m = 0; r.s = q.s = 0;
69 while (bam_read1(in, b) >= 0) {
70 uint32_t *cigar = bam1_cigar(b);
72 if (b->core.pos == 0 && b->core.tid >= 0 && strcmp(bam1_qname(b), h->target_name[b->core.tid]) == 0) {
75 fprintf(stderr, "[depad] Found embedded reference %s\n", bam1_qname(b));
79 if (h->target_len[r_tid] != r.l) {
80 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);
83 write_cigar(cigar2, n2, m2, bam_cigar_gen(b->core.l_qseq, BAM_CMATCH));
84 replace_cigar(b, n2, cigar2);
85 posmap = realloc(posmap, r.m * sizeof(int));
86 for (i = k = 0; i < r.l; ++i) {
90 } else if (b->core.n_cigar > 0) {
92 if (b->core.tid < 0) {
93 fprintf(stderr, "[depad] ERROR: Read %s has CIGAR but no RNAME\n", bam1_qname(b));
95 } else if (b->core.tid != r_tid) {
96 fprintf(stderr, "[depad] ERROR: Missing %s embedded reference sequence\n", h->target_name[b->core.tid]);
100 if (bam_cigar_op(cigar[0]) == BAM_CSOFT_CLIP) write_cigar(cigar2, n2, m2, cigar[0]);
101 if (bam_cigar_op(cigar[0]) == BAM_CHARD_CLIP) {
102 write_cigar(cigar2, n2, m2, cigar[0]);
103 if (b->core.n_cigar > 2 && bam_cigar_op(cigar[1]) == BAM_CSOFT_CLIP) {
104 write_cigar(cigar2, n2, m2, cigar[1]);
107 /* Include any pads if starts with an insert */
108 for (k = 0; k+1 < b->core.pos && !r.s[b->core.pos - k - 1]; ++k);
109 if (k) write_cigar(cigar2, n2, m2, bam_cigar_gen(k, BAM_CPAD));
110 /* Determine CIGAR operator for each base in the aligned read */
111 for (i = 0, k = b->core.pos; i < q.l; ++i, ++k)
112 q.s[i] = q.s[i]? (r.s[k]? BAM_CMATCH : BAM_CINS) : (r.s[k]? BAM_CDEL : BAM_CPAD);
113 /* Count consecutive CIGAR operators to turn into a CIGAR string */
114 for (i = k = 1, op = q.s[0]; i < q.l; ++i) {
116 write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op));
120 write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op));
121 if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CSOFT_CLIP) write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
122 if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CHARD_CLIP) {
123 if (b->core.n_cigar > 2 && bam_cigar_op(cigar[b->core.n_cigar-2]) == BAM_CSOFT_CLIP) {
124 write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-2]);
126 write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
128 /* Remove redundant P operators between M operators, e.g. 5M2P10M -> 15M */
129 for (i = 2; i < n2; ++i)
130 if (bam_cigar_op(cigar2[i]) == BAM_CMATCH && bam_cigar_op(cigar2[i-1]) == BAM_CPAD && bam_cigar_op(cigar2[i-2]) == BAM_CMATCH)
131 cigar2[i] += cigar2[i-2], cigar2[i-2] = cigar2[i-1] = 0;
132 for (i = k = 0; i < n2; ++i)
133 if (cigar2[i]) cigar2[k++] = cigar2[i];
135 replace_cigar(b, n2, cigar2);
136 b->core.pos = posmap[b->core.pos];
140 free(r.s); free(q.s); free(posmap);
142 bam_header_destroy(h);
146 int main_pad2unpad(int argc, char *argv[])
151 fprintf(stderr, "Usage: samtools depad <in.bam>\n");
154 in = strcmp(argv[1], "-")? bam_open(argv[1], "r") : bam_dopen(fileno(stdin), "r");
155 out = bam_dopen(fileno(stdout), "w");
156 result = bam_pad2unpad(in, out);
157 bam_close(in); bam_close(out);