padding.c

   1 #include <string.h>
   2 #include <assert.h>
   3 #include "kstring.h"
   4 #include "bam.h"
   5
   6 static void replace_cigar(bam1_t *b, int n, uint32_t *cigar)
   7 {
   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);
  14                 }
  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;
  18                 b->core.n_cigar = n;
  19         } else memcpy(b->data + b->core.l_qname, cigar, n * 4);
  20 }
  21
  22 #define write_cigar(_c, _n, _m, _v) do { \
  23                 if (_n == _m) { \
  24                         _m = _m? _m<<1 : 4; \
  25                         _c = (uint32_t*)realloc(_c, _m * 4); \
  26                 } \
  27                 _c[_n++] = (_v); \
  28         } while (0)
  29
  30 static void unpad_seq(bam1_t *b, kstring_t *s)
  31 {
  32         int k, j, i;
  33         int length;
  34         uint32_t *cigar = bam1_cigar(b);
  35         uint8_t *seq = bam1_seq(b);
  36         // b->core.l_qseq gives length of the SEQ entry (including soft clips, S)
  37         // We need the padded length after alignment from the CIGAR (excluding
  38         // soft clips S, but including pads from CIGAR D operations)
  39         length = 0;
  40         for (k = 0; k < b->core.n_cigar; ++k) {
  41                 int op, ol;
  42                 op= bam_cigar_op(cigar[k]);
  43                 ol = bam_cigar_oplen(cigar[k]);
  44                 if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF || op == BAM_CDEL)
  45                         length += ol;
  46         }
  47         ks_resize(s, length);
  48         for (k = 0, s->l = 0, j = 0; k < b->core.n_cigar; ++k) {
  49                 int op, ol;
  50                 op = bam_cigar_op(cigar[k]);
  51                 ol = bam_cigar_oplen(cigar[k]);
  52                 if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
  53                         for (i = 0; i < ol; ++i, ++j) s->s[s->l++] = bam1_seqi(seq, j);
  54                 } else if (op == BAM_CSOFT_CLIP) {
  55                         j += ol;
  56                 } else if (op == BAM_CHARD_CLIP) {
  57                         /* do nothing */
  58                 } else if (op == BAM_CDEL) {
  59                         for (i = 0; i < ol; ++i) s->s[s->l++] = 0;
  60                 } else {
  61                         fprintf(stderr, "[depad] ERROR: Didn't expect CIGAR op %c in read %s\n", BAM_CIGAR_STR[op], bam1_qname(b));
  62                         assert(-1);
  63                 }
  64         }
  65         assert(length == s->l);
  66 }
  67
  68 int bam_pad2unpad(bamFile in, bamFile out)
  69 {
  70         bam_header_t *h;
  71         bam1_t *b;
  72         kstring_t r, q;
  73         int r_tid = -1;
  74         uint32_t *cigar2 = 0;
  75         int n2 = 0, m2 = 0, *posmap = 0;
  76
  77         h = bam_header_read(in);
  78         /* TODO - The reference sequence lengths in the BAM + SAM headers should be updated */
  79         bam_header_write(out, h);
  80         b = bam_init1();
  81         r.l = r.m = q.l = q.m = 0; r.s = q.s = 0;
  82         while (bam_read1(in, b) >= 0) {
  83                 uint32_t *cigar = bam1_cigar(b);
  84                 n2 = 0;
  85                 if (b->core.pos == 0 && b->core.tid >= 0 && strcmp(bam1_qname(b), h->target_name[b->core.tid]) == 0) {
  86                         int i, k;
  87                         /*
  88                         fprintf(stderr, "[depad] Found embedded reference %s\n", bam1_qname(b));
  89                         */
  90                         r_tid = b->core.tid;
  91                         unpad_seq(b, &r);
  92                         if (h->target_len[r_tid] != r.l) {
  93                                 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);
  94                                 return -1;
  95                         }
  96                         write_cigar(cigar2, n2, m2, bam_cigar_gen(b->core.l_qseq, BAM_CMATCH));
  97                         replace_cigar(b, n2, cigar2);
  98                         posmap = realloc(posmap, r.m * sizeof(int));
  99                         for (i = k = 0; i < r.l; ++i) {
 100                                 posmap[i] = k;
 101                                 if (r.s[i]) ++k;
 102                         }
 103                 } else if (b->core.n_cigar > 0) {
 104                         int i, k, op;
 105                         if (b->core.tid < 0) {
 106                                 fprintf(stderr, "[depad] ERROR: Read %s has CIGAR but no RNAME\n", bam1_qname(b));
 107                                 return -1;
 108                         } else if (b->core.tid != r_tid) {
 109                                 fprintf(stderr, "[depad] ERROR: Missing %s embedded reference sequence\n", h->target_name[b->core.tid]);
 110                                 return -1;
 111                         }
 112                         unpad_seq(b, &q);
 113                         if (bam_cigar_op(cigar[0]) == BAM_CSOFT_CLIP) {
 114                                 write_cigar(cigar2, n2, m2, cigar[0]);
 115                         } else if (bam_cigar_op(cigar[0]) == BAM_CHARD_CLIP) {
 116                                 write_cigar(cigar2, n2, m2, cigar[0]);
 117                                 if (b->core.n_cigar > 2 && bam_cigar_op(cigar[1]) == BAM_CSOFT_CLIP) {
 118                                         write_cigar(cigar2, n2, m2, cigar[1]);
 119                                 }
 120                         }
 121                         /* Determine CIGAR operator for each base in the aligned read */
 122                         for (i = 0, k = b->core.pos; i < q.l; ++i, ++k)
 123                                 q.s[i] = q.s[i]? (r.s[k]? BAM_CMATCH : BAM_CINS) : (r.s[k]? BAM_CDEL : BAM_CPAD);
 124                         /* Include any pads if starts with an insert */
 125                         if (q.s[0] == BAM_CINS) {
 126                                 for (k = 0; k+1 < b->core.pos && !r.s[b->core.pos - k - 1]; ++k);
 127                                 if (k) write_cigar(cigar2, n2, m2, bam_cigar_gen(k, BAM_CPAD));
 128                         }
 129                         /* Count consecutive CIGAR operators to turn into a CIGAR string */
 130                         for (i = k = 1, op = q.s[0]; i < q.l; ++i) {
 131                                 if (op != q.s[i]) {
 132                                         write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op));
 133                                         op = q.s[i]; k = 1;
 134                                 } else ++k;
 135                         }
 136                         write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op));
 137                         if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CSOFT_CLIP) {
 138                                 write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
 139                         } else if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CHARD_CLIP) {
 140                                 if (b->core.n_cigar > 2 && bam_cigar_op(cigar[b->core.n_cigar-2]) == BAM_CSOFT_CLIP) {
 141                                         write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-2]);
 142                                 }
 143                                 write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
 144                         }
 145                         /* Remove redundant P operators between M/X/=/D operators, e.g. 5M2P10M -> 15M */
 146                         int pre_op, post_op;
 147                         for (i = 2; i < n2; ++i)
 148                                 if (bam_cigar_op(cigar2[i-1]) == BAM_CPAD) {
 149                                         pre_op = bam_cigar_op(cigar2[i-2]);
 150                                         post_op = bam_cigar_op(cigar2[i]);
 151                                         /* Note don't need to check for X/= as code above will use M only */
 152                                         if ((pre_op == BAM_CMATCH || pre_op == BAM_CDEL) && (post_op == BAM_CMATCH || post_op == BAM_CDEL)) {
 153                                                 /* This is a redundant P operator */
 154                                                 cigar2[i-1] = 0; // i.e. 0M
 155                                                 /* If had same operator either side, combine them in post_op */
 156                                                 if (pre_op == post_op) {
 157                                                         /* If CIGAR M, could treat as simple integers since BAM_CMATCH is zero*/
 158                                                         cigar2[i] = bam_cigar_gen(bam_cigar_oplen(cigar2[i-2]) + bam_cigar_oplen(cigar2[i]), post_op);
 159                                                         cigar2[i-2] = 0; // i.e. 0M
 160                                                 }
 161                                         }
 162                                 }
 163                         /* Remove the zero'd operators (0M) */
 164                         for (i = k = 0; i < n2; ++i)
 165                                 if (cigar2[i]) cigar2[k++] = cigar2[i];
 166                         n2 = k;
 167                         replace_cigar(b, n2, cigar2);
 168                         b->core.pos = posmap[b->core.pos];
 169                 }
 170                 bam_write1(out, b);
 171         }
 172         free(r.s); free(q.s); free(posmap);
 173         bam_destroy1(b);
 174         bam_header_destroy(h);
 175         return 0;
 176 }
 177
 178 int main_pad2unpad(int argc, char *argv[])
 179 {
 180         bamFile in, out;
 181         int result=0;
 182         if (argc == 1) {
 183                 fprintf(stderr, "Usage: samtools depad <in.bam>\n");
 184                 return 1;
 185         }
 186         in = strcmp(argv[1], "-")? bam_open(argv[1], "r") : bam_dopen(fileno(stdin), "r");
 187         out = bam_dopen(fileno(stdout), "w");
 188         result = bam_pad2unpad(in, out);
 189         bam_close(in); bam_close(out);
 190         return result;
 191 }