* samtools-0.1.3-7 (r246)

[samtools.git] / bam_aux.c

diff --git a/bam_aux.c b/bam_aux.c
index f9be398f0e820d9b48b2002073039af1ebeb95d5..2fa9ac2e83a7a00e2e83a523fe687448e3c4255e 100644 (file)
--- a/bam_aux.c
+++ b/bam_aux.c
@@ -3,6 +3,21 @@
 #include "khash.h"
 KHASH_MAP_INIT_STR(s, int)
 
+void bam_aux_append(bam1_t *b, const char tag[2], char type, int len, uint8_t *data)
+{
+       int ori_len = b->data_len;
+       b->data_len += 3 + len;
+       b->l_aux += 3 + len;
+       if (b->m_data < b->data_len) {
+               b->m_data = b->data_len;
+               kroundup32(b->m_data);
+               b->data = (uint8_t*)realloc(b->data, b->m_data);
+       }
+       b->data[ori_len] = tag[0]; b->data[ori_len + 1] = tag[1];
+       b->data[ori_len + 2] = type;
+       memcpy(b->data + ori_len + 3, data, len);
+}
+
 uint8_t *bam_aux_get(bam1_t *b, const char tag[2])
 {
        uint8_t *s;
@@ -59,7 +74,7 @@ void bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *b
 
        bam_init_header_hash(header);
        h = (khash_t(s)*)header->hash;
-       
+
        l = strlen(str);
        p = s = (char*)malloc(l+1);
        /* squeeze out "," */
@@ -137,3 +152,105 @@ char *bam_aux2Z(const uint8_t *s)
        if (type == 'Z' || type == 'H') return (char*)s;
        else return 0;
 }
+
+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;
+       }
+}