Release samtools-0.1.5a (for compatibility with Bio::DB::Sam)

[samtools.git] / bam_aux.c

diff --git a/bam_aux.c b/bam_aux.c
index f36bc2351ee0c74ad87f877f7a3797e3281461d8..7482500ef08a53f3471858793112d9c72263e33a 100644 (file)
--- a/bam_aux.c
+++ b/bam_aux.c
@@ -19,12 +19,12 @@ void bam_aux_append(bam1_t *b, const char tag[2], char type, int len, uint8_t *d
        b->data[ori_len + 2] = type;
        memcpy(b->data + ori_len + 3, data, len);
 }
-/*
+
 uint8_t *bam_aux_get_core(bam1_t *b, const char tag[2])
 {
        return bam_aux_get(b, tag);
 }
-*/
+
 uint8_t *bam_aux_get(const bam1_t *b, const char tag[2])
 {
        uint8_t *s;
@@ -39,7 +39,7 @@ uint8_t *bam_aux_get(const bam1_t *b, const char tag[2])
                else if (type == 'S') s += 2;
                else if (type == 'I' || type == 'F') s += 4;
                else if (type == 'D') s += 8;
-               else if (type == 'Z' || type == 'H') { while (*s) putchar(*s++); ++s; }
+               else if (type == 'Z' || type == 'H') { while (*s) ++s; ++s; }
        }
        return 0;
 }
@@ -72,7 +72,7 @@ int32_t bam_get_tid(const bam_header_t *header, const char *seq_name)
        return k == kh_end(h)? -1 : kh_value(h, k);
 }
 
-void bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *begin, int *end)
+int bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *begin, int *end)
 {
        char *s, *p;
        int i, l, k;
@@ -93,12 +93,12 @@ void bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *b
        iter = kh_get(s, h, s); /* get the ref_id */
        if (iter == kh_end(h)) { // name not found
                *ref_id = -1; free(s);
-               return;
+               return -1;
        }
        *ref_id = kh_value(h, iter);
        if (i == k) { /* dump the whole sequence */
                *begin = 0; *end = 1<<29; free(s);
-               return;
+               return -1;
        }
        for (p = s + i + 1; i != k; ++i) if (s[i] == '-') break;
        *begin = atoi(p);
@@ -107,8 +107,12 @@ void bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *b
                *end = atoi(p);
        } else *end = 1<<29;
        if (*begin > 0) --*begin;
-       assert(*begin <= *end);
        free(s);
+       if (*begin > *end) {
+               fprintf(stderr, "[bam_parse_region] invalid region.\n");
+               return -1;
+       }
+       return 0;
 }
 
 int32_t bam_aux2i(const uint8_t *s)
@@ -226,107 +230,3 @@ void bam_strmap_destroy(void *rg2lib)
        }
        kh_destroy(r2l, h);
 }
-
-/*** The following routines were implemented by Nils Homer for color-space support in tview ***/
-
-char bam_aux_getCSi(bam1_t *b, int i)
-{
-       uint8_t *c = bam_aux_get(b, "CS");
-       char *cs = NULL;
-
-       // return the base if the tag was not found
-       if(0 == c) return 0;
-
-       cs = bam_aux2Z(c);
-       // adjust for strandedness and leading adaptor
-       if(bam1_strand(b)) i = strlen(cs) - 1 - i;
-       else i++;
-       return cs[i];
-}
-
-char bam_aux_getCQi(bam1_t *b, int i)
-{
-       uint8_t *c = bam_aux_get(b, "CQ");
-       char *cq = NULL;
-       
-       // return the base if the tag was not found
-       if(0 == c) return 0;
-
-       cq = bam_aux2Z(c);
-       // adjust for strandedness
-       if(bam1_strand(b)) i = strlen(cq) - 1 - i;
-       return cq[i];
-}
-
-char bam_aux_nt2int(char a)
-{
-       switch(toupper(a)) {
-               case 'A':
-                       return 0;
-                       break;
-               case 'C':
-                       return 1;
-                       break;
-               case 'G':
-                       return 2;
-                       break;
-               case 'T':
-                       return 3;
-                       break;
-               default:
-                       return 4;
-                       break;
-       }
-}
-
-char bam_aux_ntnt2cs(char a, char b)
-{
-       a = bam_aux_nt2int(a);
-       b = bam_aux_nt2int(b);
-       if(4 == a || 4 == b) return '4';
-       return "0123"[(int)(a ^ b)];
-}
-
-char bam_aux_getCEi(bam1_t *b, int i)
-{
-       int cs_i;
-       uint8_t *c = bam_aux_get(b, "CS");
-       char *cs = NULL;
-       char prev_b, cur_b;
-       char cur_color, cor_color;
-
-       // return the base if the tag was not found
-       if(0 == c) return 0;
-       
-       cs = bam_aux2Z(c);
-
-       // adjust for strandedness and leading adaptor
-       if(bam1_strand(b)) { //reverse strand
-               cs_i = strlen(cs) - 1 - i;
-               // get current color
-               cur_color = cs[cs_i];
-               // get previous base
-               prev_b = (0 == cs_i) ? cs[0] : bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i+1)];
-               // get current base
-               cur_b = bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i)]; 
-       }
-       else {
-               cs_i=i+1;
-               // get current color
-               cur_color = cs[cs_i];
-               // get previous base
-               prev_b = (0 == i) ? cs[0] : bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i-1)];
-               // get current base
-               cur_b = bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i)];
-       }
-
-       // corrected color
-       cor_color = bam_aux_ntnt2cs(prev_b, cur_b);
-
-       if(cur_color == cor_color) { 
-               return '-';
-       }
-       else {
-               return cur_color;
-       }
-}