padding.c

   1 #include <string.h>
   2 #include <assert.h>
   3 #include <unistd.h>
   4 #include "kstring.h"
   5 #include "sam_header.h"
   6 #include "sam.h"
   7 #include "bam.h"
   8
   9 static void replace_cigar(bam1_t *b, int n, uint32_t *cigar)
  10 {
  11         if (n != b->core.n_cigar) {
  12                 int o = b->core.l_qname + b->core.n_cigar * 4;
  13                 if (b->data_len + (n - b->core.n_cigar) * 4 > b->m_data) {
  14                         b->m_data = b->data_len + (n - b->core.n_cigar) * 4;
  15                         kroundup32(b->m_data);
  16                         b->data = (uint8_t*)realloc(b->data, b->m_data);
  17                 }
  18                 memmove(b->data + b->core.l_qname + n * 4, b->data + o, b->data_len - o);
  19                 memcpy(b->data + b->core.l_qname, cigar, n * 4);
  20                 b->data_len += (n - b->core.n_cigar) * 4;
  21                 b->core.n_cigar = n;
  22         } else memcpy(b->data + b->core.l_qname, cigar, n * 4);
  23 }
  24
  25 #define write_cigar(_c, _n, _m, _v) do { \
  26                 if (_n == _m) { \
  27                         _m = _m? _m<<1 : 4; \
  28                         _c = (uint32_t*)realloc(_c, _m * 4); \
  29                 } \
  30                 _c[_n++] = (_v); \
  31         } while (0)
  32
  33 static void unpad_seq(bam1_t *b, kstring_t *s)
  34 {
  35         int k, j, i;
  36         int length;
  37         uint32_t *cigar = bam1_cigar(b);
  38         uint8_t *seq = bam1_seq(b);
  39         // b->core.l_qseq gives length of the SEQ entry (including soft clips, S)
  40         // We need the padded length after alignment from the CIGAR (excluding
  41         // soft clips S, but including pads from CIGAR D operations)
  42         length = 0;
  43         for (k = 0; k < b->core.n_cigar; ++k) {
  44                 int op, ol;
  45                 op= bam_cigar_op(cigar[k]);
  46                 ol = bam_cigar_oplen(cigar[k]);
  47                 if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF || op == BAM_CDEL)
  48                         length += ol;
  49         }
  50         ks_resize(s, length);
  51         for (k = 0, s->l = 0, j = 0; k < b->core.n_cigar; ++k) {
  52                 int op, ol;
  53                 op = bam_cigar_op(cigar[k]);
  54                 ol = bam_cigar_oplen(cigar[k]);
  55                 if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
  56                         for (i = 0; i < ol; ++i, ++j) s->s[s->l++] = bam1_seqi(seq, j);
  57                 } else if (op == BAM_CSOFT_CLIP) {
  58                         j += ol;
  59                 } else if (op == BAM_CHARD_CLIP) {
  60                         /* do nothing */
  61                 } else if (op == BAM_CDEL) {
  62                         for (i = 0; i < ol; ++i) s->s[s->l++] = 0;
  63                 } else {
  64                         fprintf(stderr, "[depad] ERROR: Didn't expect CIGAR op %c in read %s\n", BAM_CIGAR_STR[op], bam1_qname(b));
  65                         assert(-1);
  66                 }
  67         }
  68         assert(length == s->l);
  69 }
  70
  71 int bam_pad2unpad(samfile_t *in, samfile_t *out)
  72 {
  73         bam_header_t *h;
  74         bam1_t *b;
  75         kstring_t r, q;
  76         int r_tid = -1;
  77         uint32_t *cigar2 = 0;
  78         int ret = 0, n2 = 0, m2 = 0, *posmap = 0;
  79
  80         b = bam_init1();
  81         r.l = r.m = q.l = q.m = 0; r.s = q.s = 0;
  82         int read_ret;
  83         h = in->header;
  84         while ((read_ret = samread(in, b)) >= 0) { // read one alignment from `in'
  85                 uint32_t *cigar = bam1_cigar(b);
  86                 n2 = 0;
  87                 if (b->core.pos == 0 && b->core.tid >= 0 && strcmp(bam1_qname(b), h->target_name[b->core.tid]) == 0) {
  88                         int i, k;
  89                         /*
  90                         fprintf(stderr, "[depad] Found embedded reference %s\n", bam1_qname(b));
  91                         */
  92                         r_tid = b->core.tid;
  93                         unpad_seq(b, &r);
  94                         if (h->target_len[r_tid] != r.l) {
  95                                 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);
  96                                 return -1;
  97                         }
  98                         write_cigar(cigar2, n2, m2, bam_cigar_gen(b->core.l_qseq, BAM_CMATCH));
  99                         replace_cigar(b, n2, cigar2);
 100                         posmap = realloc(posmap, r.m * sizeof(int));
 101                         for (i = k = 0; i < r.l; ++i) {
 102                                 posmap[i] = k;
 103                                 if (r.s[i]) ++k;
 104                         }
 105                 } else if (b->core.n_cigar > 0) {
 106                         int i, k, op;
 107                         if (b->core.tid < 0) {
 108                                 fprintf(stderr, "[depad] ERROR: Read %s has CIGAR but no RNAME\n", bam1_qname(b));
 109                                 return -1;
 110                         } else if (b->core.tid != r_tid) {
 111                                 fprintf(stderr, "[depad] ERROR: Missing %s embedded reference sequence\n", h->target_name[b->core.tid]);
 112                                 return -1;
 113                         }
 114                         unpad_seq(b, &q);
 115                         if (bam_cigar_op(cigar[0]) == BAM_CSOFT_CLIP) {
 116                                 write_cigar(cigar2, n2, m2, cigar[0]);
 117                         } else if (bam_cigar_op(cigar[0]) == BAM_CHARD_CLIP) {
 118                                 write_cigar(cigar2, n2, m2, cigar[0]);
 119                                 if (b->core.n_cigar > 2 && bam_cigar_op(cigar[1]) == BAM_CSOFT_CLIP) {
 120                                         write_cigar(cigar2, n2, m2, cigar[1]);
 121                                 }
 122                         }
 123                         /* Determine CIGAR operator for each base in the aligned read */
 124                         for (i = 0, k = b->core.pos; i < q.l; ++i, ++k)
 125                                 q.s[i] = q.s[i]? (r.s[k]? BAM_CMATCH : BAM_CINS) : (r.s[k]? BAM_CDEL : BAM_CPAD);
 126                         /* Include any pads if starts with an insert */
 127                         if (q.s[0] == BAM_CINS) {
 128                                 for (k = 0; k+1 < b->core.pos && !r.s[b->core.pos - k - 1]; ++k);
 129                                 if (k) write_cigar(cigar2, n2, m2, bam_cigar_gen(k, BAM_CPAD));
 130                         }
 131                         /* Count consecutive CIGAR operators to turn into a CIGAR string */
 132                         for (i = k = 1, op = q.s[0]; i < q.l; ++i) {
 133                                 if (op != q.s[i]) {
 134                                         write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op));
 135                                         op = q.s[i]; k = 1;
 136                                 } else ++k;
 137                         }
 138                         write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op));
 139                         if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CSOFT_CLIP) {
 140                                 write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
 141                         } else if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CHARD_CLIP) {
 142                                 if (b->core.n_cigar > 2 && bam_cigar_op(cigar[b->core.n_cigar-2]) == BAM_CSOFT_CLIP) {
 143                                         write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-2]);
 144                                 }
 145                                 write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
 146                         }
 147                         /* Remove redundant P operators between M/X/=/D operators, e.g. 5M2P10M -> 15M */
 148                         int pre_op, post_op;
 149                         for (i = 2; i < n2; ++i)
 150                                 if (bam_cigar_op(cigar2[i-1]) == BAM_CPAD) {
 151                                         pre_op = bam_cigar_op(cigar2[i-2]);
 152                                         post_op = bam_cigar_op(cigar2[i]);
 153                                         /* Note don't need to check for X/= as code above will use M only */
 154                                         if ((pre_op == BAM_CMATCH || pre_op == BAM_CDEL) && (post_op == BAM_CMATCH || post_op == BAM_CDEL)) {
 155                                                 /* This is a redundant P operator */
 156                                                 cigar2[i-1] = 0; // i.e. 0M
 157                                                 /* If had same operator either side, combine them in post_op */
 158                                                 if (pre_op == post_op) {
 159                                                         /* If CIGAR M, could treat as simple integers since BAM_CMATCH is zero*/
 160                                                         cigar2[i] = bam_cigar_gen(bam_cigar_oplen(cigar2[i-2]) + bam_cigar_oplen(cigar2[i]), post_op);
 161                                                         cigar2[i-2] = 0; // i.e. 0M
 162                                                 }
 163                                         }
 164                                 }
 165                         /* Remove the zero'd operators (0M) */
 166                         for (i = k = 0; i < n2; ++i)
 167                                 if (cigar2[i]) cigar2[k++] = cigar2[i];
 168                         n2 = k;
 169                         replace_cigar(b, n2, cigar2);
 170                         b->core.pos = posmap[b->core.pos];
 171                 }
 172                 samwrite(out, b);
 173         }
 174         if (read_ret < -1) {
 175                 fprintf(stderr, "[depad] truncated file.\n");
 176                 ret = 1;
 177         }
 178         free(r.s); free(q.s); free(posmap);
 179         bam_destroy1(b);
 180         return ret;
 181 }
 182
 183 static int usage(int is_long_help);
 184
 185 int main_pad2unpad(int argc, char *argv[])
 186 {
 187         samfile_t *in = 0, *out = 0;
 188         int c, is_bamin = 1, compress_level = -1, is_bamout = 1, is_long_help = 0;
 189         char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0;
 190         int ret=0;
 191
 192         /* parse command-line options */
 193         strcpy(in_mode, "r"); strcpy(out_mode, "w");
 194         while ((c = getopt(argc, argv, "Sso:u1?")) >= 0) {
 195                 switch (c) {
 196                 case 'S': is_bamin = 0; break;
 197                 case 's': assert(compress_level == -1); is_bamout = 0; break;
 198                 case 'o': fn_out = strdup(optarg); break;
 199                 case 'u': assert(is_bamout == 1); compress_level = 0; break;
 200                 case '1': assert(is_bamout == 1); compress_level = 1; break;
 201                 case '?': is_long_help = 1; break;
 202                 default: return usage(is_long_help);
 203                 }
 204         }
 205         if (argc == optind) return usage(is_long_help);
 206
 207         if (is_bamin) strcat(in_mode, "b");
 208         if (is_bamout) strcat(out_mode, "b");
 209         strcat(out_mode, "h");
 210         if (compress_level >= 0) {
 211                 char tmp[2];
 212                 tmp[0] = compress_level + '0'; tmp[1] = '\0';
 213                 strcat(out_mode, tmp);
 214         }
 215
 216         // open file handlers
 217         if ((in = samopen(argv[optind], in_mode, fn_list)) == 0) {
 218                 fprintf(stderr, "[depad] fail to open \"%s\" for reading.\n", argv[optind]);
 219                 ret = 1;
 220                 goto depad_end;
 221         }
 222         if (in->header == 0) {
 223                 fprintf(stderr, "[depad] fail to read the header from \"%s\".\n", argv[optind]);
 224                 ret = 1;
 225                 goto depad_end;
 226         }
 227         /* TODO - The reference sequence lengths in the BAM + SAM headers should be updated */
 228         if ((out = samopen(fn_out? fn_out : "-", out_mode, in->header)) == 0) {
 229                 fprintf(stderr, "[depad] fail to open \"%s\" for writing.\n", fn_out? fn_out : "standard output");
 230                 ret = 1;
 231                 goto depad_end;
 232         }
 233
 234         // Do the depad
 235         ret = bam_pad2unpad(in, out);
 236
 237 depad_end:
 238         // close files, free and return
 239         free(fn_list); free(fn_out);
 240         samclose(in);
 241         samclose(out);
 242         return ret;
 243 }
 244
 245 static int usage(int is_long_help)
 246 {
 247         fprintf(stderr, "\n");
 248         fprintf(stderr, "Usage:   samtools depad <in.bam>\n\n");
 249         fprintf(stderr, "Options: -s       output is SAM (default is BAM)\n");
 250         fprintf(stderr, "         -S       input is SAM (default is BAM)\n");
 251         fprintf(stderr, "         -u       uncompressed BAM output (can't use with -s)\n");
 252         fprintf(stderr, "         -1       fast compression BAM output (can't use with -s)\n");
 253         //TODO - These are the arguments I think make sense to support:
 254         //fprintf(stderr, "         -@ INT   number of BAM compression threads [0]\n");
 255         //fprintf(stderr, "         -T FILE  reference sequence file (force -S) [null]\n");
 256         fprintf(stderr, "         -o FILE  output file name [stdout]\n");
 257         fprintf(stderr, "         -?       longer help\n");
 258         fprintf(stderr, "\n");
 259         if (is_long_help)
 260                 fprintf(stderr, "Notes:\n\
 261 \n\
 262   1. Requires embedded reference sequences (before the reads for that reference).\n\
 263 \n\
 264   2. The input padded alignment read's CIGAR strings must not use P or I operators.\n\
 265 \n");
 266         return 1;
 267 }