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 14:09:17.0 +
+++ htslib-0.2.0~rc3.mine/htslib/hts.h 2014-06-26 14:22:45.794658401 +
@@ -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 14:09:17.0 +
+++ htslib-0.2.0~rc3.mine/sam.c 2014-06-26 14:23:27.282606547 +
@@ -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')
+{
+f
