X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=blobdiff_plain;f=padding.c;h=27bbd4b6cd982864262dc909cb068df8f9355f3c;hp=8d0df07a838b849cfb2ad8d09672f856dfdb81b9;hb=09ad722ca25bd51716d24531bd199ca24269786d;hpb=181c7c1165d171e0de9858d76aff23617a83044f diff --git a/padding.c b/padding.c index 8d0df07..27bbd4b 100644 --- a/padding.c +++ b/padding.c @@ -1,7 +1,11 @@ #include #include +#include #include "kstring.h" +#include "sam_header.h" +#include "sam.h" #include "bam.h" +#include "faidx.h" static void replace_cigar(bam1_t *b, int n, uint32_t *cigar) { @@ -30,71 +34,163 @@ static void replace_cigar(bam1_t *b, int n, uint32_t *cigar) static void unpad_seq(bam1_t *b, kstring_t *s) { int k, j, i; + int length; uint32_t *cigar = bam1_cigar(b); uint8_t *seq = bam1_seq(b); - ks_resize(s, b->core.l_qseq); + // b->core.l_qseq gives length of the SEQ entry (including soft clips, S) + // We need the padded length after alignment from the CIGAR (excluding + // soft clips S, but including pads from CIGAR D operations) + length = 0; + for (k = 0; k < b->core.n_cigar; ++k) { + int op, ol; + op= bam_cigar_op(cigar[k]); + ol = bam_cigar_oplen(cigar[k]); + if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF || op == BAM_CDEL) + length += ol; + } + ks_resize(s, length); for (k = 0, s->l = 0, j = 0; k < b->core.n_cigar; ++k) { int op, ol; op = bam_cigar_op(cigar[k]); ol = bam_cigar_oplen(cigar[k]); if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) { - for (i = 0; i < ol; ++i) s->s[s->l++] = bam1_seqi(seq, j); - ++j; + for (i = 0; i < ol; ++i, ++j) s->s[s->l++] = bam1_seqi(seq, j); } else if (op == BAM_CSOFT_CLIP) { j += ol; - } else if (op == BAM_CDEL || op == BAM_CPAD) { + } else if (op == BAM_CHARD_CLIP) { + /* do nothing */ + } else if (op == BAM_CDEL) { for (i = 0; i < ol; ++i) s->s[s->l++] = 0; } else { - fprintf(stderr, "[depad] ERROR: Didn't expect CIGAR op %c in embedded reference %s\n", BAM_CIGAR_STR[op], bam1_qname(b)); + fprintf(stderr, "[depad] ERROR: Didn't expect CIGAR op %c in read %s\n", BAM_CIGAR_STR[op], bam1_qname(b)); assert(-1); } } + assert(length == s->l); } -int bam_pad2unpad(bamFile in, bamFile out) +int load_unpadded_ref(faidx_t *fai, char *ref_name, int ref_len, kstring_t *seq) +{ + char base; + char *fai_ref = 0; + int fai_ref_len = 0, k; + + fai_ref = fai_fetch(fai, ref_name, &fai_ref_len); + if (fai_ref_len != ref_len) { + fprintf(stderr, "[depad] ERROR: FASTA sequence %s length %i, expected %i\n", ref_name, fai_ref_len, ref_len); + free(fai_ref); + return -1; + } + ks_resize(seq, ref_len); + seq->l = 0; + for (k = 0; k < ref_len; ++k) { + base = fai_ref[k]; + if (base == '-' || base == '*') { + // Map gaps to null to match unpad_seq function + seq->s[seq->l++] = 0; + } else { + int i = bam_nt16_table[(int)base]; + if (i == 0 || i==16) { // Equals maps to 0, anything unexpected to 16 + fprintf(stderr, "[depad] ERROR: Invalid character %c (ASCII %i) in FASTA sequence %s\n", base, (int)base, ref_name); + free(fai_ref); + return -1; + } + seq->s[seq->l++] = i; + } + } + assert(ref_len == seq->l); + free(fai_ref); + return 0; +} + +inline int * update_posmap(int *posmap, kstring_t ref) +{ + int i, k; + posmap = realloc(posmap, ref.m * sizeof(int)); + for (i = k = 0; i < ref.l; ++i) { + posmap[i] = k; + if (ref.s[i]) ++k; + } + return posmap; +} + +int bam_pad2unpad(samfile_t *in, samfile_t *out, faidx_t *fai) { bam_header_t *h; bam1_t *b; kstring_t r, q; - int r_tid = -1; + int r_tid = -1; uint32_t *cigar2 = 0; - int n2 = 0, m2 = 0, *posmap = 0; + int ret = 0, n2 = 0, m2 = 0, *posmap = 0; - h = bam_header_read(in); - /* TODO - The reference sequence lengths in the BAM + SAM headers should be updated */ - bam_header_write(out, h); b = bam_init1(); r.l = r.m = q.l = q.m = 0; r.s = q.s = 0; - while (bam_read1(in, b) >= 0) { + int read_ret; + h = in->header; + while ((read_ret = samread(in, b)) >= 0) { // read one alignment from `in' uint32_t *cigar = bam1_cigar(b); n2 = 0; if (b->core.pos == 0 && b->core.tid >= 0 && strcmp(bam1_qname(b), h->target_name[b->core.tid]) == 0) { - int i, k; - /* - fprintf(stderr, "[depad] Found embedded reference %s\n", bam1_qname(b)); - */ + // fprintf(stderr, "[depad] Found embedded reference %s\n", bam1_qname(b)); r_tid = b->core.tid; unpad_seq(b, &r); + if (h->target_len[r_tid] != r.l) { + 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); + return -1; + } + if (fai) { + // Check the embedded reference matches the FASTA file + if (load_unpadded_ref(fai, h->target_name[b->core.tid], h->target_len[b->core.tid], &q)) return -1; + assert(r.l == q.l); + int i; + for (i = 0; i < r.l; ++i) { + if (r.s[i] != q.s[i]) { + // Show gaps as ASCII 45 + fprintf(stderr, "[depad] ERROR: Embedded sequence and reference FASTA don't match for %s base %i, '%c' vs '%c'\n", + h->target_name[b->core.tid], i+1, + r.s[i] ? bam_nt16_rev_table[r.s[i]] : 45, + q.s[i] ? bam_nt16_rev_table[q.s[i]] : 45); + return -1; + } + } + } write_cigar(cigar2, n2, m2, bam_cigar_gen(b->core.l_qseq, BAM_CMATCH)); replace_cigar(b, n2, cigar2); - posmap = realloc(posmap, r.m * sizeof(int)); - for (i = k = 0; i < r.l; ++i) { - posmap[i] = k; // note that a read should NOT start at a padding - if (r.s[i]) ++k; - } + posmap = update_posmap(posmap, r); } else if (b->core.n_cigar > 0) { int i, k, op; if (b->core.tid < 0) { fprintf(stderr, "[depad] ERROR: Read %s has CIGAR but no RNAME\n", bam1_qname(b)); return -1; - } else if (b->core.tid != r_tid) { - fprintf(stderr, "[depad] ERROR: Missing %s embedded reference sequence\n", h->target_name[b->core.tid]); + } else if (b->core.tid == r_tid) { + ; // good case, reference available + } else if (fai) { + if (load_unpadded_ref(fai, h->target_name[b->core.tid], h->target_len[b->core.tid], &r)) return -1; + posmap = update_posmap(posmap, r); + r_tid = b->core.tid; + // fprintf(stderr, "[depad] Loaded %s from FASTA file\n", h->target_name[b->core.tid]); + } else { + fprintf(stderr, "[depad] ERROR: Missing %s embedded reference sequence (and no FASTA file)\n", h->target_name[b->core.tid]); return -1; } unpad_seq(b, &q); - if (bam_cigar_op(cigar[0]) == BAM_CSOFT_CLIP) write_cigar(cigar2, n2, m2, cigar[0]); + if (bam_cigar_op(cigar[0]) == BAM_CSOFT_CLIP) { + write_cigar(cigar2, n2, m2, cigar[0]); + } else if (bam_cigar_op(cigar[0]) == BAM_CHARD_CLIP) { + write_cigar(cigar2, n2, m2, cigar[0]); + if (b->core.n_cigar > 2 && bam_cigar_op(cigar[1]) == BAM_CSOFT_CLIP) { + write_cigar(cigar2, n2, m2, cigar[1]); + } + } + /* Determine CIGAR operator for each base in the aligned read */ for (i = 0, k = b->core.pos; i < q.l; ++i, ++k) q.s[i] = q.s[i]? (r.s[k]? BAM_CMATCH : BAM_CINS) : (r.s[k]? BAM_CDEL : BAM_CPAD); + /* Include any pads if starts with an insert */ + if (q.s[0] == BAM_CINS) { + for (k = 0; k+1 < b->core.pos && !r.s[b->core.pos - k - 1]; ++k); + if (k) write_cigar(cigar2, n2, m2, bam_cigar_gen(k, BAM_CPAD)); + } + /* Count consecutive CIGAR operators to turn into a CIGAR string */ for (i = k = 1, op = q.s[0]; i < q.l; ++i) { if (op != q.s[i]) { write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op)); @@ -102,35 +198,139 @@ int bam_pad2unpad(bamFile in, bamFile out) } else ++k; } write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op)); - if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CSOFT_CLIP) write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]); + if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CSOFT_CLIP) { + write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]); + } else if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CHARD_CLIP) { + if (b->core.n_cigar > 2 && bam_cigar_op(cigar[b->core.n_cigar-2]) == BAM_CSOFT_CLIP) { + write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-2]); + } + write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]); + } + /* Remove redundant P operators between M/X/=/D operators, e.g. 5M2P10M -> 15M */ + int pre_op, post_op; for (i = 2; i < n2; ++i) - if (bam_cigar_op(cigar2[i]) == BAM_CMATCH && bam_cigar_op(cigar2[i-1]) == BAM_CPAD && bam_cigar_op(cigar2[i-2]) == BAM_CMATCH) - cigar2[i] += cigar2[i-2], cigar2[i-2] = cigar2[i-1] = 0; + if (bam_cigar_op(cigar2[i-1]) == BAM_CPAD) { + pre_op = bam_cigar_op(cigar2[i-2]); + post_op = bam_cigar_op(cigar2[i]); + /* Note don't need to check for X/= as code above will use M only */ + if ((pre_op == BAM_CMATCH || pre_op == BAM_CDEL) && (post_op == BAM_CMATCH || post_op == BAM_CDEL)) { + /* This is a redundant P operator */ + cigar2[i-1] = 0; // i.e. 0M + /* If had same operator either side, combine them in post_op */ + if (pre_op == post_op) { + /* If CIGAR M, could treat as simple integers since BAM_CMATCH is zero*/ + cigar2[i] = bam_cigar_gen(bam_cigar_oplen(cigar2[i-2]) + bam_cigar_oplen(cigar2[i]), post_op); + cigar2[i-2] = 0; // i.e. 0M + } + } + } + /* Remove the zero'd operators (0M) */ for (i = k = 0; i < n2; ++i) if (cigar2[i]) cigar2[k++] = cigar2[i]; n2 = k; replace_cigar(b, n2, cigar2); b->core.pos = posmap[b->core.pos]; } - bam_write1(out, b); + samwrite(out, b); + } + if (read_ret < -1) { + fprintf(stderr, "[depad] truncated file.\n"); + ret = 1; } free(r.s); free(q.s); free(posmap); bam_destroy1(b); - bam_header_destroy(h); - return 0; + return ret; } +static int usage(int is_long_help); + int main_pad2unpad(int argc, char *argv[]) { - bamFile in, out; - int result=0; - if (argc == 1) { - fprintf(stderr, "Usage: samtools depad \n"); - return 1; + samfile_t *in = 0, *out = 0; + faidx_t *fai = 0; + int c, is_bamin = 1, compress_level = -1, is_bamout = 1, is_long_help = 0; + char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0, *fn_ref = 0; + int ret=0; + + /* parse command-line options */ + strcpy(in_mode, "r"); strcpy(out_mode, "w"); + while ((c = getopt(argc, argv, "Sso:u1T:?")) >= 0) { + switch (c) { + case 'S': is_bamin = 0; break; + case 's': assert(compress_level == -1); is_bamout = 0; break; + case 'o': fn_out = strdup(optarg); break; + case 'u': assert(is_bamout == 1); compress_level = 0; break; + case '1': assert(is_bamout == 1); compress_level = 1; break; + case 'T': fn_ref = strdup(optarg); break; + case '?': is_long_help = 1; break; + default: return usage(is_long_help); + } + } + if (argc == optind) return usage(is_long_help); + + if (is_bamin) strcat(in_mode, "b"); + if (is_bamout) strcat(out_mode, "b"); + strcat(out_mode, "h"); + if (compress_level >= 0) { + char tmp[2]; + tmp[0] = compress_level + '0'; tmp[1] = '\0'; + strcat(out_mode, tmp); } - in = strcmp(argv[1], "-")? bam_open(argv[1], "r") : bam_dopen(fileno(stdin), "r"); - out = bam_dopen(fileno(stdout), "w"); - result = bam_pad2unpad(in, out); - bam_close(in); bam_close(out); - return result; + + // Load FASTA reference (also needed for SAM -> BAM if missing header) + if (fn_ref) { + fn_list = samfaipath(fn_ref); + fai = fai_load(fn_ref); + } + // open file handlers + if ((in = samopen(argv[optind], in_mode, fn_list)) == 0) { + fprintf(stderr, "[depad] failed to open \"%s\" for reading.\n", argv[optind]); + ret = 1; + goto depad_end; + } + if (in->header == 0) { + fprintf(stderr, "[depad] failed to read the header from \"%s\".\n", argv[optind]); + ret = 1; + goto depad_end; + } + /* TODO - The reference sequence lengths in the BAM + SAM headers should be updated */ + if ((out = samopen(fn_out? fn_out : "-", out_mode, in->header)) == 0) { + fprintf(stderr, "[depad] failed to open \"%s\" for writing.\n", fn_out? fn_out : "standard output"); + ret = 1; + goto depad_end; + } + + // Do the depad + ret = bam_pad2unpad(in, out, fai); + +depad_end: + // close files, free and return + free(fn_list); free(fn_out); + samclose(in); + samclose(out); + fai_destroy(fai); + return ret; +} + +static int usage(int is_long_help) +{ + fprintf(stderr, "\n"); + fprintf(stderr, "Usage: samtools depad \n\n"); + fprintf(stderr, "Options: -s output is SAM (default is BAM)\n"); + fprintf(stderr, " -S input is SAM (default is BAM)\n"); + fprintf(stderr, " -u uncompressed BAM output (can't use with -s)\n"); + fprintf(stderr, " -1 fast compression BAM output (can't use with -s)\n"); + fprintf(stderr, " -T FILE reference sequence file [null]\n"); + fprintf(stderr, " -o FILE output file name [stdout]\n"); + fprintf(stderr, " -? longer help\n"); + fprintf(stderr, "\n"); + if (is_long_help) + fprintf(stderr, "Notes:\n\ +\n\ + 1. Requires embedded reference sequences (before the reads for that reference),\n\ + with the future aim to also support a FASTA padded reference sequence file.\n\ +\n\ + 2. The input padded alignment read's CIGAR strings must not use P or I operators.\n\ +\n"); + return 1; }