X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_aux.c;h=a63e2aeadccf35e95b786097cd33394cb31a7a06;hb=1a23a35867ee992dcffcf3d17df2b7d41732f33b;hp=98690487a517497976e0cfe0ac40e5c0dc2d932a;hpb=f08c0abe0850773c68bd72280f6063ef6d4505f1;p=samtools.git

diff --git a/bam_aux.c b/bam_aux.c
index 9869048..a63e2ae 100644
--- 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)
 {
@@ -17,13 +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_core(bam1_t *b, const char tag[2])
 {
 	return bam_aux_get(b, tag);
 }
-
-uint8_t *bam_aux_get(bam1_t *b, const char tag[2])
+*/
+uint8_t *bam_aux_get(const bam1_t *b, const char tag[2])
 {
 	uint8_t *s;
 	int y = tag[0]<<8 | tag[1];
@@ -158,104 +160,69 @@ char *bam_aux2Z(const uint8_t *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;
+/******************
+ * rg2lib related *
+ ******************/
 
-	cs = bam_aux2Z(c);
-	// adjust for strandedness and leading adaptor
-	if(bam1_strand(b)) i = strlen(cs) - 1 - i;
-	else i++;
-	return cs[i];
+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;
 }
 
-char bam_aux_getCQi(bam1_t *b, int i)
+const char *bam_strmap_get(const void *rg2lib, const char *rg)
 {
-	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];
+	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;
 }
 
-char bam_aux_nt2int(char a)
+void *bam_strmap_dup(const void *rg2lib)
 {
-	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;
+	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;
 }
 
-char bam_aux_ntnt2cs(char a, char b)
+void *bam_strmap_init()
 {
-	a = bam_aux_nt2int(a);
-	b = bam_aux_nt2int(b);
-	if(4 == a || 4 == b) return '4';
-	return "0123"[(int)(a ^ b)];
+	return (void*)kh_init(r2l);
 }
 
-char bam_aux_getCEi(bam1_t *b, int i)
+void bam_strmap_destroy(void *rg2lib)
 {
-	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;
+	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);
 }