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 #include "faidx.h"
   9
  10 static void replace_cigar(bam1_t *b, int n, uint32_t *cigar)
  11 {
  12         if (n != b->core.n_cigar) {
  13                 int o = b->core.l_qname + b->core.n_cigar * 4;
  14                 if (b->data_len + (n - b->core.n_cigar) * 4 > b->m_data) {
  15                         b->m_data = b->data_len + (n - b->core.n_cigar) * 4;
  16                         kroundup32(b->m_data);
  17                         b->data = (uint8_t*)realloc(b->data, b->m_data);
  18                 }
  19                 memmove(b->data + b->core.l_qname + n * 4, b->data + o, b->data_len - o);
  20                 memcpy(b->data + b->core.l_qname, cigar, n * 4);
  21                 b->data_len += (n - b->core.n_cigar) * 4;
  22                 b->core.n_cigar = n;
  23         } else memcpy(b->data + b->core.l_qname, cigar, n * 4);
  24 }
  25
  26 #define write_cigar(_c, _n, _m, _v) do { \
  27                 if (_n == _m) { \
  28                         _m = _m? _m<<1 : 4; \
  29                         _c = (uint32_t*)realloc(_c, _m * 4); \
  30                 } \
  31                 _c[_n++] = (_v); \
  32         } while (0)
  33
  34 static void unpad_seq(bam1_t *b, kstring_t *s)
  35 {
  36         int k, j, i;
  37         int length;
  38         uint32_t *cigar = bam1_cigar(b);
  39         uint8_t *seq = bam1_seq(b);
  40         // b->core.l_qseq gives length of the SEQ entry (including soft clips, S)
  41         // We need the padded length after alignment from the CIGAR (excluding
  42         // soft clips S, but including pads from CIGAR D operations)
  43         length = 0;
  44         for (k = 0; k < b->core.n_cigar; ++k) {
  45                 int op, ol;
  46                 op= bam_cigar_op(cigar[k]);
  47                 ol = bam_cigar_oplen(cigar[k]);
  48                 if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF || op == BAM_CDEL)
  49                         length += ol;
  50         }
  51         ks_resize(s, length);
  52         for (k = 0, s->l = 0, j = 0; k < b->core.n_cigar; ++k) {
  53                 int op, ol;
  54                 op = bam_cigar_op(cigar[k]);
  55                 ol = bam_cigar_oplen(cigar[k]);
  56                 if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
  57                         for (i = 0; i < ol; ++i, ++j) s->s[s->l++] = bam1_seqi(seq, j);
  58                 } else if (op == BAM_CSOFT_CLIP) {
  59                         j += ol;
  60                 } else if (op == BAM_CHARD_CLIP) {
  61                         /* do nothing */
  62                 } else if (op == BAM_CDEL) {
  63                         for (i = 0; i < ol; ++i) s->s[s->l++] = 0;
  64                 } else {
  65                         fprintf(stderr, "[depad] ERROR: Didn't expect CIGAR op %c in read %s\n", BAM_CIGAR_STR[op], bam1_qname(b));
  66                         assert(-1);
  67                 }
  68         }
  69         assert(length == s->l);
  70 }
  71
  72 int load_unpadded_ref(faidx_t *fai, char *ref_name, int ref_len, kstring_t *seq)
  73 {
  74         char base;
  75         char *fai_ref = 0;
  76         int fai_ref_len = 0, k;
  77
  78         fai_ref = fai_fetch(fai, ref_name, &fai_ref_len);
  79         if (fai_ref_len != ref_len) {
  80                 fprintf(stderr, "[depad] ERROR: FASTA sequence %s length %i, expected %i\n", ref_name, fai_ref_len, ref_len);
  81                 free(fai_ref);
  82                 return -1;
  83         }
  84         ks_resize(seq, ref_len);
  85         seq->l = 0;
  86         for (k = 0; k < ref_len; ++k) {
  87                 base = fai_ref[k];
  88                 if (base == '-' || base == '*') {
  89                         // Map gaps to null to match unpad_seq function
  90                         seq->s[seq->l++] = 0;
  91                 } else {
  92                         // Want to map IUPAC bases to upper case, and reject other chars
  93                         int i = bam_nt16_table[(int)base];
  94                         if (i == 0 || i==16) { // Equals maps to 0, anything unexpected to 16
  95                                 fprintf(stderr, "[depad] ERROR: Invalid character %c (ASCII %i) in FASTA sequence %s\n", base, (int)base, ref_name);
  96                                 free(fai_ref);
  97                                 return -1;
  98                         }
  99                         seq->s[seq->l++] = bam_nt16_rev_table[i];
 100                 }
 101         }
 102         assert(ref_len == seq->l);
 103         free(fai_ref);
 104         return 0;
 105 }
 106
 107 inline int * update_posmap(int *posmap, kstring_t ref)
 108 {
 109         int i, k;
 110         posmap = realloc(posmap, ref.m * sizeof(int));
 111         for (i = k = 0; i < ref.l; ++i) {
 112                 posmap[i] = k;
 113                 if (ref.s[i]) ++k;
 114         }
 115         return posmap;
 116 }
 117
 118 int bam_pad2unpad(samfile_t *in, samfile_t *out, faidx_t *fai)
 119 {
 120         bam_header_t *h;
 121         bam1_t *b;
 122         kstring_t r, q;
 123         int r_tid = -1;
 124         uint32_t *cigar2 = 0;
 125         int ret = 0, n2 = 0, m2 = 0, *posmap = 0;
 126
 127         b = bam_init1();
 128         r.l = r.m = q.l = q.m = 0; r.s = q.s = 0;
 129         int read_ret;
 130         h = in->header;
 131         while ((read_ret = samread(in, b)) >= 0) { // read one alignment from `in'
 132                 uint32_t *cigar = bam1_cigar(b);
 133                 n2 = 0;
 134                 if (b->core.pos == 0 && b->core.tid >= 0 && strcmp(bam1_qname(b), h->target_name[b->core.tid]) == 0) {
 135                         // fprintf(stderr, "[depad] Found embedded reference %s\n", bam1_qname(b));
 136                         // TODO - Check this embedded reference matches the FASTA file (if given)
 137                         r_tid = b->core.tid;
 138                         unpad_seq(b, &r);
 139                         if (h->target_len[r_tid] != r.l) {
 140                                 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);
 141                                 return -1;
 142                         }
 143                         write_cigar(cigar2, n2, m2, bam_cigar_gen(b->core.l_qseq, BAM_CMATCH));
 144                         replace_cigar(b, n2, cigar2);
 145                         posmap = update_posmap(posmap, r);
 146                         /*
 147                         posmap = realloc(posmap, r.m * sizeof(int));
 148                         for (i = k = 0; i < r.l; ++i) {
 149                                 posmap[i] = k;
 150                                 if (r.s[i]) ++k;
 151                         }
 152                         */
 153                 } else if (b->core.n_cigar > 0) {
 154                         int i, k, op;
 155                         if (b->core.tid < 0) {
 156                                 fprintf(stderr, "[depad] ERROR: Read %s has CIGAR but no RNAME\n", bam1_qname(b));
 157                                 return -1;
 158                         } else if (b->core.tid == r_tid) {
 159                                 ; // good case, reference available
 160                         } else if (fai) {
 161                                 if (load_unpadded_ref(fai, h->target_name[b->core.tid], h->target_len[b->core.tid], &r)) return -1;
 162                                 posmap = update_posmap(posmap, r);
 163                                 r_tid = b->core.tid;
 164                                 // fprintf(stderr, "[depad] Loaded %s from FASTA file\n", h->target_name[b->core.tid]);
 165                         } else {
 166                                 fprintf(stderr, "[depad] ERROR: Missing %s embedded reference sequence (and no FASTA file)\n", h->target_name[b->core.tid]);
 167                                 return -1;
 168                         }
 169                         unpad_seq(b, &q);
 170                         if (bam_cigar_op(cigar[0]) == BAM_CSOFT_CLIP) {
 171                                 write_cigar(cigar2, n2, m2, cigar[0]);
 172                         } else if (bam_cigar_op(cigar[0]) == BAM_CHARD_CLIP) {
 173                                 write_cigar(cigar2, n2, m2, cigar[0]);
 174                                 if (b->core.n_cigar > 2 && bam_cigar_op(cigar[1]) == BAM_CSOFT_CLIP) {
 175                                         write_cigar(cigar2, n2, m2, cigar[1]);
 176                                 }
 177                         }
 178                         /* Determine CIGAR operator for each base in the aligned read */
 179                         for (i = 0, k = b->core.pos; i < q.l; ++i, ++k)
 180                                 q.s[i] = q.s[i]? (r.s[k]? BAM_CMATCH : BAM_CINS) : (r.s[k]? BAM_CDEL : BAM_CPAD);
 181                         /* Include any pads if starts with an insert */
 182                         if (q.s[0] == BAM_CINS) {
 183                                 for (k = 0; k+1 < b->core.pos && !r.s[b->core.pos - k - 1]; ++k);
 184                                 if (k) write_cigar(cigar2, n2, m2, bam_cigar_gen(k, BAM_CPAD));
 185                         }
 186                         /* Count consecutive CIGAR operators to turn into a CIGAR string */
 187                         for (i = k = 1, op = q.s[0]; i < q.l; ++i) {
 188                                 if (op != q.s[i]) {
 189                                         write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op));
 190                                         op = q.s[i]; k = 1;
 191                                 } else ++k;
 192                         }
 193                         write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op));
 194                         if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CSOFT_CLIP) {
 195                                 write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
 196                         } else if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CHARD_CLIP) {
 197                                 if (b->core.n_cigar > 2 && bam_cigar_op(cigar[b->core.n_cigar-2]) == BAM_CSOFT_CLIP) {
 198                                         write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-2]);
 199                                 }
 200                                 write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
 201                         }
 202                         /* Remove redundant P operators between M/X/=/D operators, e.g. 5M2P10M -> 15M */
 203                         int pre_op, post_op;
 204                         for (i = 2; i < n2; ++i)
 205                                 if (bam_cigar_op(cigar2[i-1]) == BAM_CPAD) {
 206                                         pre_op = bam_cigar_op(cigar2[i-2]);
 207                                         post_op = bam_cigar_op(cigar2[i]);
 208                                         /* Note don't need to check for X/= as code above will use M only */
 209                                         if ((pre_op == BAM_CMATCH || pre_op == BAM_CDEL) && (post_op == BAM_CMATCH || post_op == BAM_CDEL)) {
 210                                                 /* This is a redundant P operator */
 211                                                 cigar2[i-1] = 0; // i.e. 0M
 212                                                 /* If had same operator either side, combine them in post_op */
 213                                                 if (pre_op == post_op) {
 214                                                         /* If CIGAR M, could treat as simple integers since BAM_CMATCH is zero*/
 215                                                         cigar2[i] = bam_cigar_gen(bam_cigar_oplen(cigar2[i-2]) + bam_cigar_oplen(cigar2[i]), post_op);
 216                                                         cigar2[i-2] = 0; // i.e. 0M
 217                                                 }
 218                                         }
 219                                 }
 220                         /* Remove the zero'd operators (0M) */
 221                         for (i = k = 0; i < n2; ++i)
 222                                 if (cigar2[i]) cigar2[k++] = cigar2[i];
 223                         n2 = k;
 224                         replace_cigar(b, n2, cigar2);
 225                         b->core.pos = posmap[b->core.pos];
 226                 }
 227                 samwrite(out, b);
 228         }
 229         if (read_ret < -1) {
 230                 fprintf(stderr, "[depad] truncated file.\n");
 231                 ret = 1;
 232         }
 233         free(r.s); free(q.s); free(posmap);
 234         bam_destroy1(b);
 235         return ret;
 236 }
 237
 238 static int usage(int is_long_help);
 239
 240 int main_pad2unpad(int argc, char *argv[])
 241 {
 242         samfile_t *in = 0, *out = 0;
 243         faidx_t *fai = 0;
 244         int c, is_bamin = 1, compress_level = -1, is_bamout = 1, is_long_help = 0;
 245         char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0, *fn_ref = 0;
 246         int ret=0;
 247
 248         /* parse command-line options */
 249         strcpy(in_mode, "r"); strcpy(out_mode, "w");
 250         while ((c = getopt(argc, argv, "Sso:u1T:?")) >= 0) {
 251                 switch (c) {
 252                 case 'S': is_bamin = 0; break;
 253                 case 's': assert(compress_level == -1); is_bamout = 0; break;
 254                 case 'o': fn_out = strdup(optarg); break;
 255                 case 'u': assert(is_bamout == 1); compress_level = 0; break;
 256                 case '1': assert(is_bamout == 1); compress_level = 1; break;
 257                 case 'T': fn_ref = strdup(optarg); is_bamin = 0; break;
 258                 case '?': is_long_help = 1; break;
 259                 default: return usage(is_long_help);
 260                 }
 261         }
 262         if (argc == optind) return usage(is_long_help);
 263
 264         if (is_bamin) strcat(in_mode, "b");
 265         if (is_bamout) strcat(out_mode, "b");
 266         strcat(out_mode, "h");
 267         if (compress_level >= 0) {
 268                 char tmp[2];
 269                 tmp[0] = compress_level + '0'; tmp[1] = '\0';
 270                 strcat(out_mode, tmp);
 271         }
 272
 273         // Load FASTA reference (also needed for SAM -> BAM if missing header)
 274         if (fn_ref) {
 275                 fn_list = samfaipath(fn_ref);
 276                 fai = fai_load(fn_ref);
 277         }
 278         // open file handlers
 279         if ((in = samopen(argv[optind], in_mode, fn_list)) == 0) {
 280                 fprintf(stderr, "[depad] fail to open \"%s\" for reading.\n", argv[optind]);
 281                 ret = 1;
 282                 goto depad_end;
 283         }
 284         if (in->header == 0) {
 285                 fprintf(stderr, "[depad] fail to read the header from \"%s\".\n", argv[optind]);
 286                 ret = 1;
 287                 goto depad_end;
 288         }
 289         /* TODO - The reference sequence lengths in the BAM + SAM headers should be updated */
 290         if ((out = samopen(fn_out? fn_out : "-", out_mode, in->header)) == 0) {
 291                 fprintf(stderr, "[depad] fail to open \"%s\" for writing.\n", fn_out? fn_out : "standard output");
 292                 ret = 1;
 293                 goto depad_end;
 294         }
 295
 296         // Do the depad
 297         ret = bam_pad2unpad(in, out, fai);
 298
 299 depad_end:
 300         // close files, free and return
 301         free(fn_list); free(fn_out);
 302         samclose(in);
 303         samclose(out);
 304         fai_destroy(fai);
 305         return ret;
 306 }
 307
 308 static int usage(int is_long_help)
 309 {
 310         fprintf(stderr, "\n");
 311         fprintf(stderr, "Usage:   samtools depad <in.bam>\n\n");
 312         fprintf(stderr, "Options: -s       output is SAM (default is BAM)\n");
 313         fprintf(stderr, "         -S       input is SAM (default is BAM)\n");
 314         fprintf(stderr, "         -u       uncompressed BAM output (can't use with -s)\n");
 315         fprintf(stderr, "         -1       fast compression BAM output (can't use with -s)\n");
 316         fprintf(stderr, "         -T FILE  reference sequence file [null]\n");
 317         fprintf(stderr, "         -o FILE  output file name [stdout]\n");
 318         fprintf(stderr, "         -?       longer help\n");
 319         fprintf(stderr, "\n");
 320         if (is_long_help)
 321                 fprintf(stderr, "Notes:\n\
 322 \n\
 323   1. Requires embedded reference sequences (before the reads for that reference),\n\
 324      with the future aim to also support a FASTA padded reference sequence file.\n\
 325 \n\
 326   2. The input padded alignment read's CIGAR strings must not use P or I operators.\n\
 327 \n");
 328         return 1;
 329 }