#include <ctype.h>
#include "bam.h"
#include "khash.h"
+typedef char *str_p;
KHASH_MAP_INIT_STR(s, int)
+KHASH_MAP_INIT_STR(r2l, str_p)
-uint8_t *bam_aux_get(bam1_t *b, const char tag[2])
+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_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;
int y = tag[0]<<8 | tag[1];
bam_init_header_hash(header);
h = (khash_t(s)*)header->hash;
-
+
l = strlen(str);
p = s = (char*)malloc(l+1);
/* squeeze out "," */
if (type == 'Z' || type == 'H') return (char*)s;
else return 0;
}
+
+/******************
+ * rg2lib related *
+ ******************/
+
+int bam_strmap_put(void *rg2lib, const char *rg, const char *lib)
+{
+ int ret;
+ khint_t k;
+ khash_t(r2l) *h = (khash_t(r2l)*)rg2lib;
+ char *key = strdup(rg);
+ k = kh_put(r2l, h, key, &ret);
+ if (ret) kh_val(h, k) = strdup(lib);
+ else {
+ fprintf(stderr, "[bam_rg2lib_put] duplicated @RG ID: %s\n", rg);
+ free(key);
+ }
+ return 0;
+}
+
+const char *bam_strmap_get(const void *rg2lib, const char *rg)
+{
+ const khash_t(r2l) *h = (const khash_t(r2l)*)rg2lib;
+ khint_t k;
+ k = kh_get(r2l, h, rg);
+ if (k != kh_end(h)) return (const char*)kh_val(h, k);
+ else return 0;
+}
+
+void *bam_strmap_dup(const void *rg2lib)
+{
+ const khash_t(r2l) *h = (const khash_t(r2l)*)rg2lib;
+ khash_t(r2l) *g = kh_init(r2l);
+ khint_t k, l;
+ int ret;
+ for (k = kh_begin(h); k < kh_end(h); ++k) {
+ if (kh_exist(h, k)) {
+ char *key = strdup(kh_key(h, k));
+ l = kh_put(r2l, g, key, &ret);
+ kh_val(g, l) = strdup(kh_val(h, k));
+ }
+ }
+ return g;
+}
+
+void *bam_strmap_init()
+{
+ return (void*)kh_init(r2l);
+}
+
+void bam_strmap_destroy(void *rg2lib)
+{
+ khash_t(r2l) *h = (khash_t(r2l)*)rg2lib;
+ khint_t k;
+ if (h == 0) return;
+ for (k = kh_begin(h); k < kh_end(h); ++k) {
+ if (kh_exist(h, k)) {
+ free((char*)kh_key(h, k)); free(kh_val(h, k));
+ }
+ }
+ 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;
+ }
+}
projects / samtools.git / blobdiff