X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_aux.c;h=89e99f281adb652e144eea0a77074a1c6cec023a;hb=d0e30eec1158752010659982342a611fc91ae8e3;hp=41be81910d89478dc160fada8fe2b4c38f8052c5;hpb=11b0656ab8ca22edb2fb7fb54fe761ea4c9e05e3;p=samtools.git

diff --git a/bam_aux.c b/bam_aux.c
index 41be819..89e99f2 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)
 {
@@ -17,30 +19,47 @@ 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])
+
+#define __skip_tag(s) do { \
+		int type = toupper(*(s));										\
+		++(s);															\
+		if (type == 'C' || type == 'A') ++(s);							\
+		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)) ++(s); ++(s); } \
+	} while (0)
+
+uint8_t *bam_aux_get(const bam1_t *b, const char tag[2])
 {
 	uint8_t *s;
 	int y = tag[0]<<8 | tag[1];
 	s = bam1_aux(b);
 	while (s < b->data + b->data_len) {
-		int type, x = (int)s[0]<<8 | s[1];
+		int x = (int)s[0]<<8 | s[1];
 		s += 2;
 		if (x == y) return s;
-		type = toupper(*s); ++s;
-		if (type == 'C') ++s;
-		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; }
+		__skip_tag(s);
 	}
 	return 0;
 }
+// s MUST BE returned by bam_aux_get()
+int bam_aux_del(bam1_t *b, uint8_t *s)
+{
+	uint8_t *p, *aux;
+	aux = bam1_aux(b);
+	p = s - 2;
+	__skip_tag(s);
+	memmove(p, s, b->l_aux - (s - aux));
+	b->data_len -= s - p;
+	b->l_aux -= s - p;
+	return 0;
+}
 
 void bam_init_header_hash(bam_header_t *header)
 {
@@ -70,7 +89,7 @@ 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;
@@ -91,12 +110,12 @@ 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);
@@ -105,8 +124,12 @@ 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)
@@ -157,105 +180,3 @@ 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;
-	}
-}