diff --git a/cram/cram_encode.c b/cram/cram_encode.c
index 94c2cebec..5a154f3cc 100644
--- a/cram/cram_encode.c
+++ b/cram/cram_encode.c
@@ -1858,6 +1858,12 @@ static char *cram_encode_aux_1_0(cram_fd *fd, bam_seq_t *b, cram_container *c,
     return rg;
 }
 
+static inline int is_big_endian(){
+    int x = 0x01;
+    char *c = (char*)&x;
+    return (c[0] != 0x01);
+}
+
 /*
  * Encodes auxiliary data. Largely duplicated from above, but done so to
  * keep it simple and avoid a myriad of version ifs.
@@ -1949,10 +1955,21 @@ static char *cram_encode_aux(cram_fd *fd, bam_seq_t *b, cram_container *c,
 
 	case 'B': {
 	    int type = aux[3], blen;
-	    uint32_t count = (uint32_t)((((unsigned char *)aux)[4]<< 0) +
-					(((unsigned char *)aux)[5]<< 8) +
-					(((unsigned char *)aux)[6]<<16) +
-					(((unsigned char *)aux)[7]<<24));
+	    uint32_t count;
+	    if(is_big_endian())
+	    {
+	        count = (uint32_t)((((unsigned char *)aux)[7]<< 0) +
+				(((unsigned char *)aux)[6]<< 8) +
+				(((unsigned char *)aux)[5]<<16) +
+				(((unsigned char *)aux)[4]<<24));
+	    }
+	    else
+	    {
+	        count = (uint32_t)((((unsigned char *)aux)[4]<< 0) +
+				(((unsigned char *)aux)[5]<< 8) +
+				(((unsigned char *)aux)[6]<<16) +
+				(((unsigned char *)aux)[7]<<24));
+	    }
 	    // skip TN field
 	    aux+=3;
 
diff --git a/cram/os.h b/cram/os.h
index b2affe0b2..1dd253a59 100644
--- a/cram/os.h
+++ b/cram/os.h
@@ -88,8 +88,15 @@ extern "C" {
  * processor type too.
  */
 
-/* Set by autoconf */
-#define SP_LITTLE_ENDIAN
+#if !defined(SP_BIG_ENDIAN) && !defined(SP_LITTLE_ENDIAN)
+
+# if __BYTE_ORDER == __BIG_ENDIAN
+#   define SP_BIG_ENDIAN
+#elif __BYTE_ORDER == __LITTLE_ENDIAN
+#   define SP_LITTLE_ENDIAN
+#endif
+
+#endif
 
 /* Mac FAT binaries or unknown. Auto detect based on CPU type */
 #if !defined(SP_BIG_ENDIAN) && !defined(SP_LITTLE_ENDIAN)
diff --git a/htslib/hts.h b/htslib/hts.h
index dad085740..28303c118 100644
--- a/htslib/hts.h
+++ b/htslib/hts.h
@@ -4,6 +4,8 @@
 #include <stddef.h>
 #include <stdint.h>
 
+#include "cram/os.h"
+
 #ifndef HTS_BGZF_TYPEDEF
 typedef struct BGZF BGZF;
 #define HTS_BGZF_TYPEDEF
@@ -280,7 +282,17 @@ static inline uint16_t ed_swap_2(uint16_t v)
 }
 static inline void *ed_swap_2p(void *x)
 {
+#ifdef ALLOW_UAC
 	*(uint16_t*)x = ed_swap_2(*(uint16_t*)x);
+#else
+	uint8_t tmpData[2];
+	uint16_t *ptmpData = (uint16_t*)&tmpData;
+	uint8_t *px = (uint8_t*)x;
+	int j;
+	for(j=0;j<2;j++) tmpData[j] = px[j];
+        *ptmpData = ed_swap_2(*ptmpData);
+	for(j=0;j<2;j++) px[j] = tmpData[j];
+#endif
 	return x;
 }
 static inline uint32_t ed_swap_4(uint32_t v)
@@ -290,7 +302,17 @@ static inline uint32_t ed_swap_4(uint32_t v)
 }
 static inline void *ed_swap_4p(void *x)
 {
+#ifdef ALLOW_UAC
 	*(uint32_t*)x = ed_swap_4(*(uint32_t*)x);
+#else
+	uint8_t tmpData[4];
+	uint32_t *ptmpData = (uint32_t*)&tmpData;
+	uint8_t *px = (uint8_t*)x;
+	int j;
+	for(j=0;j<4;j++) tmpData[j] = px[j];
+	*ptmpData = ed_swap_4(*ptmpData);
+	for(j=0;j<4;j++) px[j] = tmpData[j];
+#endif
 	return x;
 }
 static inline uint64_t ed_swap_8(uint64_t v)
@@ -301,7 +323,17 @@ static inline uint64_t ed_swap_8(uint64_t v)
 }
 static inline void *ed_swap_8p(void *x)
 {
+#ifdef ALLOW_UAC
 	*(uint64_t*)x = ed_swap_8(*(uint64_t*)x);
+#else
+	uint8_t tmpData[8];
+	uint64_t *ptmpData = (uint64_t*)&tmpData;
+	uint8_t *px = (uint8_t*)x;
+	int j;
+	for(j=0;j<8;j++) tmpData[j] = px[j];
+	*ptmpData = ed_swap_8(*ptmpData);
+	for(j=0;j<8;j++) px[j] = tmpData[j];
+#endif
 	return x;
 }
 
diff --git a/sam.c b/sam.c
index 5a64255ac..50042815c 100644
--- a/sam.c
+++ b/sam.c
@@ -7,6 +7,7 @@
 #include "htslib/sam.h"
 #include "htslib/bgzf.h"
 #include "cram/cram.h"
+#include "cram/os.h"
 #include "htslib/hfile.h"
 
 #include "htslib/khash.h"
@@ -259,9 +260,14 @@ static inline int aux_type2size(uint8_t type)
 	}
 }
 
-static void swap_data(const bam1_core_t *c, int l_data, uint8_t *data)
+typedef enum swap_data_rw {
+	SWAP_DATA_READ,
+	SWAP_DATA_WRITE
+}swap_data_rw_t;
+
+static void swap_data(const bam1_core_t *c, int l_data, uint8_t *data, swap_data_rw_t rw_mode)
 {
-	uint8_t *s;
+	uint8_t *s, *s_tmp;
 	uint32_t *cigar = (uint32_t*)(data + c->l_qname);
 	uint32_t i, n;
 	s = data + c->n_cigar*4 + c->l_qname + c->l_qseq + (c->l_qseq + 1)/2;
@@ -282,13 +288,22 @@ static void swap_data(const bam1_core_t *c, int l_data, uint8_t *data)
 			break;
 		case 'B':
 			size = aux_type2size(*s); ++s;
-			ed_swap_4p(s); memcpy(&n, s, 4); s += 4;
+			if(SWAP_DATA_READ == rw_mode)
+			{
+				ed_swap_4p(s);
+			}
+			s_tmp = s;
+			memcpy(&n, s, 4); s += 4;
 			switch (size) {
 			case 1: s += n; break;
 			case 2: for (i = 0; i < n; ++i, s += 2) ed_swap_2p(s); break;
 			case 4: for (i = 0; i < n; ++i, s += 4) ed_swap_4p(s); break;
 			case 8: for (i = 0; i < n; ++i, s += 8) ed_swap_8p(s); break;
 			}
+			if(SWAP_DATA_WRITE == rw_mode)
+			{
+				ed_swap_4p(s_tmp);
+			}
 			break;
 		}
 	}
@@ -326,7 +341,7 @@ int bam_read1(BGZF *fp, bam1_t *b)
 	}
 	if (bgzf_read(fp, b->data, b->l_data) != b->l_data) return -4;
 	//b->l_aux = b->l_data - c->n_cigar * 4 - c->l_qname - c->l_qseq - (c->l_qseq+1)/2;
-	if (fp->is_be) swap_data(c, b->l_data, b->data);
+	if (fp->is_be) swap_data(c, b->l_data, b->data, SWAP_DATA_READ);
 	return 4 + block_len;
 }
 
@@ -348,13 +363,13 @@ int bam_write1(BGZF *fp, const bam1_t *b)
 		for (i = 0; i < 8; ++i) ed_swap_4p(x + i);
 		y = block_len;
 		if (ok) ok = (bgzf_write(fp, ed_swap_4p(&y), 4) >= 0);
-		swap_data(c, b->l_data, b->data);
+		swap_data(c, b->l_data, b->data, SWAP_DATA_WRITE);
 	} else {
 		if (ok) ok = (bgzf_write(fp, &block_len, 4) >= 0);
 	}
 	if (ok) ok = (bgzf_write(fp, x, 32) >= 0);
 	if (ok) ok = (bgzf_write(fp, b->data, b->l_data) >= 0);
-	if (fp->is_be) swap_data(c, b->l_data, b->data);
+	if (fp->is_be) swap_data(c, b->l_data, b->data, SWAP_DATA_WRITE);
 	return ok? 4 + block_len : -1;
 }
 
@@ -909,6 +924,10 @@ int sam_format1(const bam_hdr_t *h, const bam1_t *b, kstring_t *str)
 	s = bam_get_aux(b); // aux
 	while (s+4 <= b->data + b->l_data) {
 		uint8_t type, key[2];
+#ifndef ALLOW_UAC
+		uint8_t tmpData[8];
+		int j;
+#endif
 		key[0] = s[0]; key[1] = s[1];
 		s += 2; type = *s++;
 		kputc('\t', str); kputsn((char*)key, 2, str); kputc(':', str);
@@ -924,6 +943,7 @@ int sam_format1(const bam_hdr_t *h, const bam1_t *b, kstring_t *str)
 			kputsn("i:", 2, str);
 			kputw(*(int8_t*)s, str);
 			++s;
+#ifdef ALLOW_UAC
 		} else if (type == 'S') {
 			if (s+2 <= b->data + b->l_data) {
 				kputsn("i:", 2, str);
@@ -959,6 +979,54 @@ int sam_format1(const bam_hdr_t *h, const bam1_t *b, kstring_t *str)
 				ksprintf(str, "d:%g", *(double*)s);
 				s += 8;
 			} else return -1;
+#else
+		} else if (type == 'S') {
+			if (s+2 <= b->data + b->l_data) {
+				uint16_t *ptmpData = (uint16_t*)tmpData;
+				for(j=0;j<2;j++) tmpData[j]=s[j];
+				kputsn("i:", 2, str);
+				kputw(*ptmpData, str);
+				s += 2;
+			} else return -1;
+		} else if (type == 's') {
+			if (s+2 <= b->data + b->l_data) {
+				int16_t *ptmpData = (int16_t*)tmpData;
+				for(j=0;j<2;j++) tmpData[j]=s[j];
+				kputsn("i:", 2, str);
+				kputw(*ptmpData, str);
+				s += 2;
+			} else return -1;
+		} else if (type == 'I') {
+			if (s+4 <= b->data + b->l_data) {
+				uint32_t *ptmpData = (uint32_t*)tmpData;
+				for(j=0;j<4;j++) tmpData[j]=s[j];
+				kputsn("i:", 2, str);
+				kputuw(*ptmpData, str);
+				s += 4;
+			} else return -1;
+		} else if (type == 'i') {
+			if (s+4 <= b->data + b->l_data) {
+				int32_t *ptmpData = (int32_t*)tmpData;
+				for(j=0;j<4;j++) tmpData[j]=s[j];
+				kputsn("i:", 2, str);
+				kputw(*ptmpData, str);
+				s += 4;
+			} else return -1;
+		} else if (type == 'f') {
+			if (s+4 <= b->data + b->l_data) {
+				float *ptmpData = (float*)tmpData;
+				for(j=0;j<4;j++) tmpData[j]=s[j];
+				ksprintf(str, "f:%g", *ptmpData);
+				s += 4;
+			} else return -1;
+		} else if (type == 'd') {
+			if (s+8 <= b->data + b->l_data) {
+				double *ptmpData = (double*)tmpData;
+				for(j=0;j<8;j++) tmpData[j]=s[j];
+				ksprintf(str, "d:%g", *ptmpData);
+				s += 8;
+			} else return -1;
+#endif
 		} else if (type == 'Z' || type == 'H') {
 			kputc(type, str); kputc(':', str);
 			while (s < b->data + b->l_data && *s) kputc(*s++, str);
@@ -977,11 +1045,49 @@ int sam_format1(const bam_hdr_t *h, const bam1_t *b, kstring_t *str)
 				kputc(',', str);
 				if ('c' == sub_type)	  { kputw(*(int8_t*)s, str); ++s; }
 				else if ('C' == sub_type) { kputw(*(uint8_t*)s, str); ++s; }
+#ifdef ALLOW_UAC
 				else if ('s' == sub_type) { kputw(*(int16_t*)s, str); s += 2; }
 				else if ('S' == sub_type) { kputw(*(uint16_t*)s, str); s += 2; }
 				else if ('i' == sub_type) { kputw(*(int32_t*)s, str); s += 4; }
 				else if ('I' == sub_type) { kputuw(*(uint32_t*)s, str); s += 4; }
 				else if ('f' == sub_type) { ksprintf(str, "%g", *(float*)s); s += 4; }
+#else
+				else if ('s' == sub_type) 
+				{
+					int16_t *ptmpData = (int16_t*)tmpData;
+					for(j=0;j<2;j++)tmpData[j]=s[j];
+					kputw(*ptmpData, str);
+					s += 2;
+				}
+				else if ('S' == sub_type)
+				{
+					uint16_t *ptmpData = (uint16_t*)tmpData;
+					for(j=0;j<2;j++)tmpData[j]=s[j];
+					kputw(*ptmpData, str);
+					s += 2;
+				}
+				else if ('i' == sub_type)
+				{
+					int32_t *ptmpData = (int32_t*)tmpData;
+					for(j=0;j<4;j++)tmpData[j]=s[j];
+					kputw(*ptmpData, str);
+					s += 4;
+				}
+				else if ('I' == sub_type)
+				{
+					uint32_t *ptmpData = (uint32_t*)tmpData;
+					for(j=0;j<4;j++)tmpData[j]=s[j];
+					kputuw(*ptmpData, str);
+					s += 4;
+				}
+				else if ('f' == sub_type)
+				{
+					float *ptmpData = (float*)tmpData;
+					for(j=0;j<4;j++)tmpData[j]=s[j];
+					ksprintf(str, "%g", *ptmpData);
+					s += 4;
+				}
+#endif
 			}
 		}
 	}
@@ -1071,11 +1177,22 @@ int32_t bam_aux2i(const uint8_t *s)
 {
 	int type;
 	type = *s++;
+#ifdef ALLOW_UAC
 	if (type == 'c') return (int32_t)*(int8_t*)s;
 	else if (type == 'C') return (int32_t)*(uint8_t*)s;
 	else if (type == 's') return (int32_t)*(int16_t*)s;
 	else if (type == 'S') return (int32_t)*(uint16_t*)s;
 	else if (type == 'i' || type == 'I') return *(int32_t*)s;
+#else
+	uint8_t tmpData[4];
+	int j;
+	if (type == 'c') return (int32_t)*(int8_t*)s;
+	else if (type == 'C') return (int32_t)*(uint8_t*)s;
+	else if (type == 's'){ int16_t *ptmpData = (int16_t*)tmpData; for(j=0;j<2;j++)tmpData[j]=s[j]; return (int32_t)(*ptmpData);}
+	else if (type == 'S'){ uint16_t *ptmpData = (uint16_t*)tmpData; for(j=0;j<2;j++)tmpData[j]=s[j]; return (int32_t)(*ptmpData);}
+	else if (type == 'i'){ int32_t *ptmpData = (int32_t*)tmpData; for(j=0;j<4;j++)tmpData[j]=s[j]; return *ptmpData;}
+	else if (type == 'I'){ uint32_t *ptmpData = (uint32_t*)tmpData; for(j=0;j<4;j++)tmpData[j]=s[j]; return *ptmpData;}
+#endif
 	else return 0;
 }
 
@@ -1083,8 +1200,15 @@ double bam_aux2f(const uint8_t *s)
 {
 	int type;
 	type = *s++;
+#ifdef ALLOW_UAC
 	if (type == 'd') return *(double*)s;
 	else if (type == 'f') return *(float*)s;
+#else
+	uint8_t tmpData[8];
+	int j;
+	if (type == 'd'){ double *ptmpData = (double*)tmpData; for(j=0;j<sizeof(double);j++)tmpData[j]=s[j]; return *ptmpData;}
+	else if (type == 'f'){ float *ptmpData = (float*)tmpData; for(j=0;j<sizeof(float);j++)tmpData[j]=s[j]; return *ptmpData;}
+#endif
 	else return 0.0;
 }
 
diff --git a/test/sam.c b/test/sam.c
index 160b6662d..48d1c0440 100644
--- a/test/sam.c
+++ b/test/sam.c
@@ -30,6 +30,7 @@ DEALINGS IN THE SOFTWARE.  */
 
 #include "htslib/sam.h"
 #include "htslib/kstring.h"
+#include "cram/os.h"
 
 int status;
 
@@ -102,7 +103,11 @@ static int aux_fields1(void)
             fail("XH field is \"%s\", expected \"%s\"", bam_aux2Z(p), BEEF);
 
         // TODO Invent and use bam_aux2B()
+#ifdef SP_LITTLE_ENDIAN
         if ((p = check_bam_aux_get(aln, "XB", 'B')) && memcmp(p, "Bc\3\0\0\0\xfe\x00\x02", 9) != 0)
+#elif defined SP_BIG_ENDIAN
+        if ((p = check_bam_aux_get(aln, "XB", 'B')) && memcmp(p, "Bc\0\0\0\3\xfe\x00\x02", 9) != 0)
+#endif
             fail("XB field is %c,..., expected c,-2,0,+2", p[1]);
 
         if ((p = check_bam_aux_get(aln, "ZZ", 'I')) && bam_aux2i(p) != 1000000)
diff --git a/vcf.c b/vcf.c
index cc2c3976e..6a2c11971 100644
--- a/vcf.c
+++ b/vcf.c
@@ -10,6 +10,7 @@
 #include "htslib/vcf.h"
 #include "htslib/tbx.h"
 #include "htslib/hfile.h"
+#include "cram/os.h"
 
 #include "htslib/khash.h"
 KHASH_MAP_INIT_STR(vdict, bcf_idinfo_t)
@@ -1765,6 +1766,10 @@ static inline uint8_t *bcf_unpack_fmt_core1(uint8_t *ptr, int n_sample, bcf_fmt_
 static inline uint8_t *bcf_unpack_info_core1(uint8_t *ptr, bcf_info_t *info)
 {
     uint8_t *ptr_start = ptr;
+#ifndef ALLOW_UAC
+    uint8_t tmpData[4];
+    int j;
+#endif
     info->key = bcf_dec_typed_int1(ptr, &ptr);
     info->len = bcf_dec_size(ptr, &ptr, &info->type);
     info->vptr = ptr;
@@ -1773,9 +1778,15 @@ static inline uint8_t *bcf_unpack_info_core1(uint8_t *ptr, bcf_info_t *info)
     info->v1.i = 0;
     if (info->len == 1) {
         if (info->type == BCF_BT_INT8 || info->type == BCF_BT_CHAR) info->v1.i = *(int8_t*)ptr;
+#ifdef ALLOW_UAC
         else if (info->type == BCF_BT_INT32) info->v1.i = *(int32_t*)ptr;
         else if (info->type == BCF_BT_FLOAT) info->v1.f = *(float*)ptr;
         else if (info->type == BCF_BT_INT16) info->v1.i = *(int16_t*)ptr;
+#else
+        else if (info->type == BCF_BT_INT32) { int32_t *ptmpData = (int32_t*)&tmpData; for(j=0;j<4;j++) tmpData[j]=ptr[j]; info->v1.i = *ptmpData;}
+        else if (info->type == BCF_BT_FLOAT) { float *ptmpData = (float*)&tmpData; for(j=0;j<4;j++) tmpData[j]=ptr[j]; info->v1.f = *ptmpData;}
+        else if (info->type == BCF_BT_INT16) { int16_t *ptmpData = (int16_t*)&tmpData; for(j=0;j<2;j++) tmpData[j]=ptr[j]; info->v1.i = *ptmpData;}
+#endif
     }
     ptr += info->len << bcf_type_shift[info->type];
     info->vptr_len = ptr - info->vptr;