* samtools-0.1.4-10 (r341)

[samtools.git] / bam_aux.c

diff --git a/bam_aux.c b/bam_aux.c
index d6f18ea281712a7d89007d7d87291cbf13718c1b..a63e2aeadccf35e95b786097cd33394cb31a7a06 100644 (file)
--- a/bam_aux.c
+++ b/bam_aux.c
@@ -1,7 +1,9 @@
 #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)
 
 void bam_aux_append(bam1_t *b, const char tag[2], char type, int len, uint8_t *data)
 {
@@ -17,8 +19,13 @@ 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(bam1_t *b, const char tag[2])
+/*
+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];
@@ -74,7 +81,7 @@ 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 "," */
@@ -152,3 +159,70 @@ char *bam_aux2Z(const uint8_t *s)
        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;
+       if (h == 0) return 1;
+       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;
+       if (h == 0) return 0;
+       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;
+       khint_t k, l;
+       int ret;
+       if (h == 0) return 0;
+       g = kh_init(r2l);
+       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);
+}