release 1.0.1

doc/website/rhsidebar.ssi

@@ -15,10 +15,10 @@
       <table width="100%">
         <tr>
           <td>
-            <a href="https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.0.0">Bowtie 1.0.0</a>
+            <a href="https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.0.1">Bowtie 1.0.1</a>
           </td>
           <td align="right">
-            4/9/13
+            3/14/14
           </td>
         </tr>
         <tr>

third_party/macos/cpuid.h

@@ -1,187 +0,0 @@
-/*
- * Copyright (C) 2007, 2008, 2009 Free Software Foundation, Inc.
- *
- * This file is free software; you can redistribute it and/or modify it
- * under the terms of the GNU General Public License as published by the
- * Free Software Foundation; either version 3, or (at your option) any
- * later version.
- * 
- * This file is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- * General Public License for more details.
- * 
- * Under Section 7 of GPL version 3, you are granted additional
- * permissions described in the GCC Runtime Library Exception, version
- * 3.1, as published by the Free Software Foundation.
- * 
- * You should have received a copy of the GNU General Public License and
- * a copy of the GCC Runtime Library Exception along with this program;
- * see the files COPYING3 and COPYING.RUNTIME respectively.  If not, see
- * <http://www.gnu.org/licenses/>.
- */
-
-/* %ecx */
-#define bit_SSE3	(1 << 0)
-#define bit_PCLMUL	(1 << 1)
-#define bit_SSSE3	(1 << 9)
-#define bit_FMA		(1 << 12)
-#define bit_CMPXCHG16B	(1 << 13)
-#define bit_SSE4_1	(1 << 19)
-#define bit_SSE4_2	(1 << 20)
-#define bit_MOVBE	(1 << 22)
-#define bit_POPCNT	(1 << 23)
-#define bit_AES		(1 << 25)
-#define bit_XSAVE	(1 << 26)
-#define bit_OSXSAVE	(1 << 27)
-#define bit_AVX		(1 << 28)
-#define bit_F16C	(1 << 29)
-#define bit_RDRND	(1 << 30)
-
-/* %edx */
-#define bit_CMPXCHG8B	(1 << 8)
-#define bit_CMOV	(1 << 15)
-#define bit_MMX		(1 << 23)
-#define bit_FXSAVE	(1 << 24)
-#define bit_SSE		(1 << 25)
-#define bit_SSE2	(1 << 26)
-
-/* Extended Features */
-/* %ecx */
-#define bit_LAHF_LM	(1 << 0)
-#define bit_ABM		(1 << 5)
-#define bit_SSE4a	(1 << 6)
-#define bit_XOP         (1 << 11)
-#define bit_LWP 	(1 << 15)
-#define bit_FMA4        (1 << 16)
-#define bit_TBM         (1 << 21)
-
-/* %edx */
-#define bit_LM		(1 << 29)
-#define bit_3DNOWP	(1 << 30)
-#define bit_3DNOW	(1 << 31)
-
-/* Extended Features (%eax == 7) */
-#define bit_FSGSBASE	(1 << 0)
-#define bit_BMI		(1 << 3)
-
-#if defined(__i386__) && defined(__PIC__)
-/* %ebx may be the PIC register.  */
-#if __GNUC__ >= 3
-#define __cpuid(level, a, b, c, d)			\
-  __asm__ ("xchg{l}\t{%%}ebx, %1\n\t"			\
-	   "cpuid\n\t"					\
-	   "xchg{l}\t{%%}ebx, %1\n\t"			\
-	   : "=a" (a), "=r" (b), "=c" (c), "=d" (d)	\
-	   : "0" (level))
-
-#define __cpuid_count(level, count, a, b, c, d)		\
-  __asm__ ("xchg{l}\t{%%}ebx, %1\n\t"			\
-	   "cpuid\n\t"					\
-	   "xchg{l}\t{%%}ebx, %1\n\t"			\
-	   : "=a" (a), "=r" (b), "=c" (c), "=d" (d)	\
-	   : "0" (level), "2" (count))
-#else
-/* Host GCCs older than 3.0 weren't supporting Intel asm syntax
-   nor alternatives in i386 code.  */
-#define __cpuid(level, a, b, c, d)			\
-  __asm__ ("xchgl\t%%ebx, %1\n\t"			\
-	   "cpuid\n\t"					\
-	   "xchgl\t%%ebx, %1\n\t"			\
-	   : "=a" (a), "=r" (b), "=c" (c), "=d" (d)	\
-	   : "0" (level))
-
-#define __cpuid_count(level, count, a, b, c, d)		\
-  __asm__ ("xchgl\t%%ebx, %1\n\t"			\
-	   "cpuid\n\t"					\
-	   "xchgl\t%%ebx, %1\n\t"			\
-	   : "=a" (a), "=r" (b), "=c" (c), "=d" (d)	\
-	   : "0" (level), "2" (count))
-#endif
-#else
-#define __cpuid(level, a, b, c, d)			\
-  __asm__ ("cpuid\n\t"					\
-	   : "=a" (a), "=b" (b), "=c" (c), "=d" (d)	\
-	   : "0" (level))
-
-#define __cpuid_count(level, count, a, b, c, d)		\
-  __asm__ ("cpuid\n\t"					\
-	   : "=a" (a), "=b" (b), "=c" (c), "=d" (d)	\
-	   : "0" (level), "2" (count))
-#endif
-
-/* Return highest supported input value for cpuid instruction.  ext can
-   be either 0x0 or 0x8000000 to return highest supported value for
-   basic or extended cpuid information.  Function returns 0 if cpuid
-   is not supported or whatever cpuid returns in eax register.  If sig
-   pointer is non-null, then first four bytes of the signature
-   (as found in ebx register) are returned in location pointed by sig.  */
-
-static __inline unsigned int
-__get_cpuid_max (unsigned int __ext, unsigned int *__sig)
-{
-  unsigned int __eax, __ebx, __ecx, __edx;
-
-#ifndef __x86_64__
-#if __GNUC__ >= 3
-  /* See if we can use cpuid.  On AMD64 we always can.  */
-  __asm__ ("pushf{l|d}\n\t"
-	   "pushf{l|d}\n\t"
-	   "pop{l}\t%0\n\t"
-	   "mov{l}\t{%0, %1|%1, %0}\n\t"
-	   "xor{l}\t{%2, %0|%0, %2}\n\t"
-	   "push{l}\t%0\n\t"
-	   "popf{l|d}\n\t"
-	   "pushf{l|d}\n\t"
-	   "pop{l}\t%0\n\t"
-	   "popf{l|d}\n\t"
-	   : "=&r" (__eax), "=&r" (__ebx)
-	   : "i" (0x00200000));
-#else
-/* Host GCCs older than 3.0 weren't supporting Intel asm syntax
-   nor alternatives in i386 code.  */
-  __asm__ ("pushfl\n\t"
-	   "pushfl\n\t"
-	   "popl\t%0\n\t"
-	   "movl\t%0, %1\n\t"
-	   "xorl\t%2, %0\n\t"
-	   "pushl\t%0\n\t"
-	   "popfl\n\t"
-	   "pushfl\n\t"
-	   "popl\t%0\n\t"
-	   "popfl\n\t"
-	   : "=&r" (__eax), "=&r" (__ebx)
-	   : "i" (0x00200000));
-#endif
-
-  if (!((__eax ^ __ebx) & 0x00200000))
-    return 0;
-#endif
-
-  /* Host supports cpuid.  Return highest supported cpuid input value.  */
-  __cpuid (__ext, __eax, __ebx, __ecx, __edx);
-
-  if (__sig)
-    *__sig = __ebx;
-
-  return __eax;
-}
-
-/* Return cpuid data for requested cpuid level, as found in returned
-   eax, ebx, ecx and edx registers.  The function checks if cpuid is
-   supported and returns 1 for valid cpuid information or 0 for
-   unsupported cpuid level.  All pointers are required to be non-null.  */
-
-static __inline int
-__get_cpuid (unsigned int __level,
-	     unsigned int *__eax, unsigned int *__ebx,
-	     unsigned int *__ecx, unsigned int *__edx)
-{
-  unsigned int __ext = __level & 0x80000000;
-
-  if (__get_cpuid_max (__ext, 0) < __level)
-    return 0;
-
-  __cpuid (__level, *__eax, *__ebx, *__ecx, *__edx);
-  return 1;
-}