I just look at the patch provided by Aleksandar. I believe unaligned access is still possible after applying it.
The reason is that an auto array of uint8_t is still only guaranteed to be 1-byte aligned. These discussions confirm this: http://stackoverflow.com/questions/4009463/alignment-of-char-arrays http://bytes.com/topic/c/answers/811633-alignment-stack-arrays So I updated the patch to fix this issue. Plamen
diff -urN htslib-0.2.0~rc3/htslib/hts.h htslib-0.2.0~rc3.mine/htslib/hts.h
--- htslib-0.2.0~rc3/htslib/hts.h 2014-06-26 14:09:17.000000000 +0000
+++ htslib-0.2.0~rc3.mine/htslib/hts.h 2014-06-26 14:22:45.794658401 +0000
@@ -238,7 +238,18 @@
}
static inline void *ed_swap_2p(void *x)
{
+#ifdef ALLOW_UAC
*(uint16_t*)x = ed_swap_2(*(uint16_t*)x);
+#else
+ uint16_t tmpDataBuffer;
+ uint8_t *tmpData = (uint8_t *)&tmpDataBuffer;
+ 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)
@@ -248,7 +259,18 @@
}
static inline void *ed_swap_4p(void *x)
{
+#ifdef ALLOW_UAC
*(uint32_t*)x = ed_swap_4(*(uint32_t*)x);
+#else
+ uint32_t tmpDataBuffer;
+ uint8_t *tmpData = (uint8_t *)&tmpDataBuffer;
+ 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)
@@ -259,7 +281,18 @@
}
static inline void *ed_swap_8p(void *x)
{
+#ifdef ALLOW_UAC
*(uint64_t*)x = ed_swap_8(*(uint64_t*)x);
+#else
+ uint64_t tmpDataBuffer;
+ uint8_t *tmpData = (uint8_t *)&tmpDataBuffer;
+ 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 -urN htslib-0.2.0~rc3/sam.c htslib-0.2.0~rc3.mine/sam.c
--- htslib-0.2.0~rc3/sam.c 2014-06-26 14:09:17.000000000 +0000
+++ htslib-0.2.0~rc3.mine/sam.c 2014-06-26 14:23:27.282606547 +0000
@@ -7,6 +7,7 @@
#include "htslib/sam.h"
#include "htslib/bgzf.h"
#include "cram/cram.h"
+#include "cram/os.h"
#include "hfile.h"
#include "htslib/khash.h"
@@ -713,18 +714,70 @@
s = bam_get_aux(b); // aux
while (s < b->data + b->l_data) {
uint8_t type, key[2];
+ uint64_t tmpDataBuffer;
+ uint8_t *tmpData = (uint8_t *)&tmpDataBuffer;
+ int j;
key[0] = s[0]; key[1] = s[1];
s += 2; type = *s++;
kputc('\t', str); kputsn((char*)key, 2, str); kputc(':', str);
if (type == 'A') { kputsn("A:", 2, str); kputc(*s, str); ++s; }
else if (type == 'C') { kputsn("i:", 2, str); kputw(*s, str); ++s; }
else if (type == 'c') { kputsn("i:", 2, str); kputw(*(int8_t*)s, str); ++s; }
+#ifdef ALLOW_UAC
else if (type == 'S') { kputsn("i:", 2, str); kputw(*(uint16_t*)s, str); s += 2; }
else if (type == 's') { kputsn("i:", 2, str); kputw(*(int16_t*)s, str); s += 2; }
else if (type == 'I') { kputsn("i:", 2, str); kputuw(*(uint32_t*)s, str); s += 4; }
else if (type == 'i') { kputsn("i:", 2, str); kputw(*(int32_t*)s, str); s += 4; }
else if (type == 'f') { ksprintf(str, "f:%g", *(float*)s); s += 4; }
else if (type == 'd') { ksprintf(str, "d:%g", *(double*)s); s += 8; }
+#else
+ else if (type == 'S')
+ {
+ 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 if (type == 's')
+ {
+ 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 if (type == 'I')
+ {
+ 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 if (type == 'i')
+ {
+ 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 if (type == 'f')
+ {
+ float *ptmpData = (float*)&tmpData;
+ for(j=0;j<4;j++) tmpData[j]=s[j];
+ ksprintf(str, "f:%g", *ptmpData);
+ s += 4;
+ }
+ else if (type == 'd')
+ {
+ float *ptmpData = (float*)&tmpData;
+ for(j=0;j<8;j++) tmpData[j]=s[j];
+ ksprintf(str, "d:%g", *ptmpData);
+ s += 8;
+ }
+#endif
else if (type == 'Z' || type == 'H') { kputc(type, str); kputc(':', str); while (*s) kputc(*s++, str); ++s; }
else if (type == 'B') {
uint8_t sub_type = *(s++);
@@ -736,11 +789,49 @@
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
}
}
}
@@ -825,11 +916,22 @@
{
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
+ uint32_t tmpDataBuffer;
+ uint8_t *tmpData = (uint8_t *)&tmpDataBuffer;
+ 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' || type == 'I'){ int32_t *ptmpData = (int32_t*)&tmpData; for(j=0;j<4;j++)tmpData[j]=s[j]; return *ptmpData;}
+#endif
else return 0;
}
@@ -837,8 +939,26 @@
{
int type;
type = *s++;
+#ifdef ALLOW_UAC
if (type == 'd') return *(double*)s;
else if (type == 'f') return *(float*)s;
+#else
+ uint64_t tmpDataBuffer;
+ uint8_t *tmpData = (uint8_t *)&tmpDataBuffer;
+ 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 -urN htslib-0.2.0~rc3/vcf.c htslib-0.2.0~rc3.mine/vcf.c
--- htslib-0.2.0~rc3/vcf.c 2013-10-28 13:03:29.000000000 +0000
+++ htslib-0.2.0~rc3.mine/vcf.c 2014-06-26 14:20:54.834797082 +0000
@@ -10,6 +10,7 @@
#include "htslib/vcf.h"
#include "htslib/tbx.h"
#include "hfile.h"
+#include "cram/os.h"
#include "htslib/khash.h"
KHASH_MAP_INIT_STR(vdict, bcf_idinfo_t)
@@ -1435,6 +1436,11 @@
static inline uint8_t *bcf_unpack_info_core1(uint8_t *ptr, bcf_info_t *info)
{
uint8_t *ptr_start = ptr;
+#ifndef ALLOW_UAC
+ uint32_t tmpDataBuffer;
+ uint8_t *tmpData = (uint8_t *)&tmpDataBuffer;
+ int j;
+#endif
info->key = bcf_dec_typed_int1(ptr, &ptr);
info->len = bcf_dec_size(ptr, &ptr, &info->type);
info->vptr = ptr;
@@ -1443,9 +1449,30 @@
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;
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