New upstream release.

[samtools.git] / bam_import.c

diff --git a/bam_import.c b/bam_import.c
index 9d84328bdbdafb5f4e76a19e7edf176121aca5b4..5518a9cbba694b2ce3b24d6460938103e44fde0e 100644 (file)
--- a/bam_import.c
+++ b/bam_import.c
@@ -14,7 +14,7 @@
 #include "kseq.h"
 #include "khash.h"
 
-KSTREAM_INIT(gzFile, gzread, 8192)
+KSTREAM_INIT(gzFile, gzread, 16384)
 KHASH_MAP_INIT_STR(ref, uint64_t)
 
 void bam_init_header_hash(bam_header_t *header);
@@ -292,20 +292,22 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
                z += str->l + 1;
                if (str->s[0] != '*') {
                        for (s = str->s; *s; ++s) {
-                               if (isalpha(*s)) ++c->n_cigar;
+                               if ((isalpha(*s)) || (*s=='=')) ++c->n_cigar;
                                else if (!isdigit(*s)) parse_error(fp->n_lines, "invalid CIGAR character");
                        }
                        b->data = alloc_data(b, doff + c->n_cigar * 4);
                        for (i = 0, s = str->s; i != c->n_cigar; ++i) {
                                x = strtol(s, &t, 10);
                                op = toupper(*t);
-                               if (op == 'M' || op == '=' || op == 'X') op = BAM_CMATCH;
+                               if (op == 'M') op = BAM_CMATCH;
                                else if (op == 'I') op = BAM_CINS;
                                else if (op == 'D') op = BAM_CDEL;
                                else if (op == 'N') op = BAM_CREF_SKIP;
                                else if (op == 'S') op = BAM_CSOFT_CLIP;
                                else if (op == 'H') op = BAM_CHARD_CLIP;
                                else if (op == 'P') op = BAM_CPAD;
+                               else if (op == '=') op = BAM_CEQUAL;
+                               else if (op == 'X') op = BAM_CDIFF;
                                else parse_error(fp->n_lines, "invalid CIGAR operation");
                                s = t + 1;
                                bam1_cigar(b)[i] = x << BAM_CIGAR_SHIFT | op;
@@ -337,8 +339,11 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
                z += str->l + 1;
                if (strcmp(str->s, "*")) {
                        c->l_qseq = strlen(str->s);
-                       if (c->n_cigar && c->l_qseq != (int32_t)bam_cigar2qlen(c, bam1_cigar(b)))
-                               parse_error(fp->n_lines, "CIGAR and sequence length are inconsistent");
+                       if (c->n_cigar && c->l_qseq != (int32_t)bam_cigar2qlen(c, bam1_cigar(b))) {
+                         fprintf(stderr, "Line %ld, sequence length %i vs %i from CIGAR\n",
+                                 (long)fp->n_lines, c->l_qseq, (int32_t)bam_cigar2qlen(c, bam1_cigar(b)));
+                         parse_error(fp->n_lines, "CIGAR and sequence length are inconsistent");
+                       }
                        p = (uint8_t*)alloc_data(b, doff + c->l_qseq + (c->l_qseq+1)/2) + doff;
                        memset(p, 0, (c->l_qseq+1)/2);
                        for (i = 0; i < c->l_qseq; ++i)
@@ -427,6 +432,27 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
                                memcpy(s, str->s + 5, str->l - 5);
                                s[str->l - 5] = 0;
                                doff += size;
+                       } else if (type == 'B') {
+                               int32_t n = 0, Bsize, k = 0, size;
+                               char *p;
+                               if (str->l < 8) parse_error(fp->n_lines, "too few values in aux type B");
+                               Bsize = bam_aux_type2size(str->s[5]); // the size of each element
+                               for (p = (char*)str->s + 6; *p; ++p) // count the number of elements in the array
+                                       if (*p == ',') ++n;
+                               p = str->s + 7; // now p points to the first number in the array
+                               size = 6 + Bsize * n; // total number of bytes allocated to this tag
+                               s = alloc_data(b, doff + 6 * Bsize * n) + doff; // allocate memory
+                               *s++ = 'B'; *s++ = str->s[5];
+                               memcpy(s, &n, 4); s += 4; // write the number of elements
+                               if (str->s[5] == 'c')      while (p < str->s + str->l) ((int8_t*)s)[k++]   = (int8_t)strtol(p, &p, 0),   ++p;
+                               else if (str->s[5] == 'C') while (p < str->s + str->l) ((uint8_t*)s)[k++]  = (uint8_t)strtol(p, &p, 0),  ++p;
+                               else if (str->s[5] == 's') while (p < str->s + str->l) ((int16_t*)s)[k++]  = (int16_t)strtol(p, &p, 0),  ++p; // FIXME: avoid unaligned memory
+                               else if (str->s[5] == 'S') while (p < str->s + str->l) ((uint16_t*)s)[k++] = (uint16_t)strtol(p, &p, 0), ++p;
+                               else if (str->s[5] == 'i') while (p < str->s + str->l) ((int32_t*)s)[k++]  = (int32_t)strtol(p, &p, 0),  ++p;
+                               else if (str->s[5] == 'I') while (p < str->s + str->l) ((uint32_t*)s)[k++] = (uint32_t)strtol(p, &p, 0), ++p;
+                               else if (str->s[5] == 'f') while (p < str->s + str->l) ((float*)s)[k++]    = (float)strtod(p, &p),       ++p;
+                               else parse_error(fp->n_lines, "unrecognized array type");
+                               s += Bsize * n; doff += size;
                        } else parse_error(fp->n_lines, "unrecognized type");
                        if (dret == '\n' || dret == '\r') break;
                }