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         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) {
  37                 int op, ol;
  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) {
  43                         j += ol;
  44                 } else if (op == BAM_CHARD_CLIP) {
  45                         /* do nothing */
  46                 } else if (op == BAM_CDEL || op == BAM_CPAD) {
  47                         for (i = 0; i < ol; ++i) s->s[s->l++] = 0;
  48                 } else {
  49                         fprintf(stderr, "[depad] ERROR: Didn't expect CIGAR op %c in read %s\n", BAM_CIGAR_STR[op], bam1_qname(b));
  50                         assert(-1);
  51                 }
  52         }
  53 }
  54
  55 int bam_pad2unpad(bamFile in, bamFile out)
  56 {
  57         bam_header_t *h;
  58         bam1_t *b;
  59         kstring_t r, q;
  60         int r_tid = -1;
  61         uint32_t *cigar2 = 0;
  62         int n2 = 0, m2 = 0, *posmap = 0;
  63
  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);
  67         b = bam_init1();
  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);
  71                 n2 = 0;
  72                 if (b->core.pos == 0 && b->core.tid >= 0 && strcmp(bam1_qname(b), h->target_name[b->core.tid]) == 0) {
  73                         int i, k;
  74                         /*
  75                         fprintf(stderr, "[depad] Found embedded reference %s\n", bam1_qname(b));
  76                         */
  77                         r_tid = b->core.tid;
  78                         unpad_seq(b, &r);
  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);
  81                                 return -1;
  82                         }
  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) {
  87                                 posmap[i] = k;
  88                                 if (r.s[i]) ++k;
  89                         }
  90                 } else if (b->core.n_cigar > 0) {
  91                         int i, k, op;
  92                         if (b->core.tid < 0) {
  93                                 fprintf(stderr, "[depad] ERROR: Read %s has CIGAR but no RNAME\n", bam1_qname(b));
  94                                 return -1;
  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]);
  97                                 return -1;
  98                         }
  99                         unpad_seq(b, &q);
 100                         if (bam_cigar_op(cigar[0]) == BAM_CSOFT_CLIP) {
 101                                 write_cigar(cigar2, n2, m2, cigar[0]);
 102                         } else if (bam_cigar_op(cigar[0]) == BAM_CHARD_CLIP) {
 103                                 write_cigar(cigar2, n2, m2, cigar[0]);
 104                                 if (b->core.n_cigar > 2 && bam_cigar_op(cigar[1]) == BAM_CSOFT_CLIP) {
 105                                         write_cigar(cigar2, n2, m2, cigar[1]);
 106                                 }
 107                         } else {
 108                                 /* Insert a dummy 0M entry to let use remove superfluous leading P ops */
 109                                 write_cigar(cigar2, n2, m2, 0);
 110                         }
 111                         /* Include any pads if starts with an insert */
 112                         for (k = 0; k+1 < b->core.pos && !r.s[b->core.pos - k - 1]; ++k);
 113                         if (k) write_cigar(cigar2, n2, m2, bam_cigar_gen(k, BAM_CPAD));
 114                         /* Determine CIGAR operator for each base in the aligned read */
 115                         for (i = 0, k = b->core.pos; i < q.l; ++i, ++k)
 116                                 q.s[i] = q.s[i]? (r.s[k]? BAM_CMATCH : BAM_CINS) : (r.s[k]? BAM_CDEL : BAM_CPAD);
 117                         /* Count consecutive CIGAR operators to turn into a CIGAR string */
 118                         for (i = k = 1, op = q.s[0]; i < q.l; ++i) {
 119                                 if (op != q.s[i]) {
 120                                         write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op));
 121                                         op = q.s[i]; k = 1;
 122                                 } else ++k;
 123                         }
 124                         write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op));
 125                         if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CSOFT_CLIP) {
 126                                 write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
 127                         } else if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CHARD_CLIP) {
 128                                 if (b->core.n_cigar > 2 && bam_cigar_op(cigar[b->core.n_cigar-2]) == BAM_CSOFT_CLIP) {
 129                                         write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-2]);
 130                                 }
 131                                 write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
 132                         }
 133                         /* Remove redundant P operators between M/X/=/D operators, e.g. 5M2P10M -> 15M */
 134                         /* or right at the start before M/X/=/D */
 135                         int pre_op, post_op;
 136                         for (i = 2; i < n2; ++i)
 137                                 if (bam_cigar_op(cigar2[i-1]) == BAM_CPAD) {
 138                                         pre_op = bam_cigar_op(cigar2[i-2]);
 139                                         post_op = bam_cigar_op(cigar2[i]);
 140                                         /* Note don't need to check for X/= as code above will use M only */
 141                                         if ((pre_op == BAM_CMATCH || pre_op == BAM_CDIFF || pre_op == BAM_CSOFT_CLIP || pre_op == BAM_CHARD_CLIP) || (post_op == BAM_CMATCH || post_op == BAM_CDIFF)) {
 142                                                 /* This is a redundant P operator */
 143                                                 cigar2[i-1] = 0; // i.e. 0M
 144                                                 /* If had same operator either side, combine them in post_op */
 145                                                 if (pre_op == post_op) {
 146                                                         /* If CIGAR M, could treat as simple integers since BAM_CMATCH is zero*/
 147                                                         cigar2[i] = bam_cigar_gen(bam_cigar_oplen(cigar2[i-2]) + bam_cigar_oplen(cigar2[i]), post_op);
 148                                                         cigar2[i-2] = 0; // i.e. 0M
 149                                                 }
 150                                         }
 151                                 }
 152                         /* Remove the zero'd operators (0M) */
 153                         for (i = k = 0; i < n2; ++i)
 154                                 if (cigar2[i]) cigar2[k++] = cigar2[i];
 155                         n2 = k;
 156                         replace_cigar(b, n2, cigar2);
 157                         b->core.pos = posmap[b->core.pos];
 158                 }
 159                 bam_write1(out, b);
 160         }
 161         free(r.s); free(q.s); free(posmap);
 162         bam_destroy1(b);
 163         bam_header_destroy(h);
 164         return 0;
 165 }
 166
 167 int main_pad2unpad(int argc, char *argv[])
 168 {
 169         bamFile in, out;
 170         int result=0;
 171         if (argc == 1) {
 172                 fprintf(stderr, "Usage: samtools depad <in.bam>\n");
 173                 return 1;
 174         }
 175         in = strcmp(argv[1], "-")? bam_open(argv[1], "r") : bam_dopen(fileno(stdin), "r");
 176         out = bam_dopen(fileno(stdout), "w");
 177         result = bam_pad2unpad(in, out);
 178         bam_close(in); bam_close(out);
 179         return result;
 180 }