padding.c

   1 #include <string.h>
   2 #include <assert.h>
   3 #include <unistd.h>
   4 #include "kstring.h"
   5 #include "bam.h"
   6
   7 static void replace_cigar(bam1_t *b, int n, uint32_t *cigar)
   8 {
   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);
  15                 }
  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;
  19                 b->core.n_cigar = n;
  20         } else memcpy(b->data + b->core.l_qname, cigar, n * 4);
  21 }
  22
  23 #define write_cigar(_c, _n, _m, _v) do { \
  24                 if (_n == _m) { \
  25                         _m = _m? _m<<1 : 4; \
  26                         _c = (uint32_t*)realloc(_c, _m * 4); \
  27                 } \
  28                 _c[_n++] = (_v); \
  29         } while (0)
  30
  31 static void unpad_seq(bam1_t *b, kstring_t *s)
  32 {
  33         int k, j, i;
  34         int length;
  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)
  40         length = 0;
  41         for (k = 0; k < b->core.n_cigar; ++k) {
  42                 int op, ol;
  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)
  46                         length += ol;
  47         }
  48         ks_resize(s, length);
  49         for (k = 0, s->l = 0, j = 0; k < b->core.n_cigar; ++k) {
  50                 int op, ol;
  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) {
  56                         j += ol;
  57                 } else if (op == BAM_CHARD_CLIP) {
  58                         /* do nothing */
  59                 } else if (op == BAM_CDEL) {
  60                         for (i = 0; i < ol; ++i) s->s[s->l++] = 0;
  61                 } else {
  62                         fprintf(stderr, "[depad] ERROR: Didn't expect CIGAR op %c in read %s\n", BAM_CIGAR_STR[op], bam1_qname(b));
  63                         assert(-1);
  64                 }
  65         }
  66         assert(length == s->l);
  67 }
  68
  69 int bam_pad2unpad(bamFile in, bamFile out)
  70 {
  71         bam_header_t *h;
  72         bam1_t *b;
  73         kstring_t r, q;
  74         int r_tid = -1;
  75         uint32_t *cigar2 = 0;
  76         int n2 = 0, m2 = 0, *posmap = 0;
  77
  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);
  81         b = bam_init1();
  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);
  85                 n2 = 0;
  86                 if (b->core.pos == 0 && b->core.tid >= 0 && strcmp(bam1_qname(b), h->target_name[b->core.tid]) == 0) {
  87                         int i, k;
  88                         /*
  89                         fprintf(stderr, "[depad] Found embedded reference %s\n", bam1_qname(b));
  90                         */
  91                         r_tid = b->core.tid;
  92                         unpad_seq(b, &r);
  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);
  95                                 return -1;
  96                         }
  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) {
 101                                 posmap[i] = k;
 102                                 if (r.s[i]) ++k;
 103                         }
 104                 } else if (b->core.n_cigar > 0) {
 105                         int i, k, op;
 106                         if (b->core.tid < 0) {
 107                                 fprintf(stderr, "[depad] ERROR: Read %s has CIGAR but no RNAME\n", bam1_qname(b));
 108                                 return -1;
 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]);
 111                                 return -1;
 112                         }
 113                         unpad_seq(b, &q);
 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]);
 120                                 }
 121                         }
 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));
 129                         }
 130                         /* Count consecutive CIGAR operators to turn into a CIGAR string */
 131                         for (i = k = 1, op = q.s[0]; i < q.l; ++i) {
 132                                 if (op != q.s[i]) {
 133                                         write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op));
 134                                         op = q.s[i]; k = 1;
 135                                 } else ++k;
 136                         }
 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]);
 143                                 }
 144                                 write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
 145                         }
 146                         /* Remove redundant P operators between M/X/=/D operators, e.g. 5M2P10M -> 15M */
 147                         int pre_op, post_op;
 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
 161                                                 }
 162                                         }
 163                                 }
 164                         /* Remove the zero'd operators (0M) */
 165                         for (i = k = 0; i < n2; ++i)
 166                                 if (cigar2[i]) cigar2[k++] = cigar2[i];
 167                         n2 = k;
 168                         replace_cigar(b, n2, cigar2);
 169                         b->core.pos = posmap[b->core.pos];
 170                 }
 171                 bam_write1(out, b);
 172         }
 173         free(r.s); free(q.s); free(posmap);
 174         bam_destroy1(b);
 175         bam_header_destroy(h);
 176         return 0;
 177 }
 178
 179 static int usage(int is_long_help);
 180
 181 int main_pad2unpad(int argc, char *argv[])
 182 {
 183         bamFile in, out;
 184         int c, is_long_help = 0;
 185         int result=0;
 186
 187         /* parse command-line options */
 188         while ((c = getopt(argc, argv, "?")) >= 0) {
 189                 switch (c) {
 190                 case '?': is_long_help = 1; break;
 191                 default: return usage(is_long_help);
 192                 }
 193         }
 194         if (argc == optind) return usage(is_long_help);
 195
 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);
 200         return result;
 201 }
 202
 203 static int usage(int is_long_help)
 204 {
 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");
 219         if (is_long_help)
 220                 fprintf(stderr, "Notes:\n\
 221 \n\
 222   1. Requires embedded reference sequences (before the reads for that reference).\n\
 223 \n\
 224   2. The input padded alignment read's CIGAR strings must not use P or I operators.\n\
 225 \n");
 226         return 1;
 227 }