Verified Commit 36c81322 authored by Michael R. Crusoe's avatar Michael R. Crusoe 🏳️‍🌈
Browse files

Enable for all architectures using simde

parent fb7a59ff

debian/changelog

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Original line number Diff line number Diff line 
bwa (0.7.17-4) unstable; urgency=medium



  * debian/control: update my email address

  * debian/patches/spelling: fix a few typos

  * Enable for all architectures using simde



 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Sat, 14 Dec 2019 11:38:00 +0100



bwa (0.7.17-3) unstable; urgency=medium



  * Team upload.

debian/control

+7 −7
Original line number Diff line number Diff line
@@ -4,20 +4,21 @@ Uploaders: Charles Plessy <plessy@debian.org>, 
           Andreas Tille <tille@debian.org>,

           Carlos Borroto <carlos.borroto@gmail.com>,

           Ognyan Kulev <ogi@debian.org>,

           Michael R. Crusoe <crusoe@ucdavis.edu>

           Michael R. Crusoe <michael.crusoe@gmail.com>

Section: science

Priority: optional

Build-Depends: debhelper (>= 11~),

               zlib1g-dev

Standards-Version: 4.2.1

Standards-Version: 4.4.1

Vcs-Browser: https://salsa.debian.org/med-team/bwa

Vcs-Git: https://salsa.debian.org/med-team/bwa.git

Homepage: http://bio-bwa.sourceforge.net/



Package: bwa

Architecture: amd64 kfreebsd-amd64

Architecture: any

Depends: ${shlibs:Depends},

         ${misc:Depends}

         ${misc:Depends},

         ${perl:Depends}

Suggests: samtools

Description: Burrows-Wheeler Aligner

 BWA is a software package for mapping low-divergent sequences against
@@ -32,10 +33,9 @@ Description: Burrows-Wheeler Aligner 
 reads.



Package: libbwa-dev

Architecture: amd64 kfreebsd-amd64

Architecture: any

Section: libdevel

Depends: ${shlibs:Depends},

         ${misc:Depends}

Depends: ${misc:Depends}

Suggests: samtools

Description: Burrows-Wheeler Aligner source files

 BWA is a software package for mapping low-divergent sequences against

debian/copyright

+24 −19
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@@ -12,25 +12,6 @@ Copyright: © 2008 Genome Research Ltd (GRL) 
           © 2008 Yuta Mori

           © 2011 by Attractive Chaos <attractor@live.co.uk>

License: MIT

 Permission is hereby granted, free of charge, to any person obtaining

 a copy of this software and associated documentation files (the

 "Software"), to deal in the Software without restriction, including

 without limitation the rights to use, copy, modify, merge, publish,

 distribute, sublicense, and/or sell copies of the Software, and to

 permit persons to whom the Software is furnished to do so, subject to

 the following conditions:

 . 

 The above copyright notice and this permission notice shall be

 included in all copies or substantial portions of the Software.

 .

 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,

 EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF

 MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND

 NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS

 BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN

 ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN

 CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE

 SOFTWARE.



Files: kbtree.h

Copyright: © 1997-1999, 2001, John-Mark Gurney.
@@ -86,3 +67,27 @@ License: other 
 the code must be clearly marked. No warranty is given regarding the quality

 of this software.



Files: debian/include/simde/*

Copyright: 2013-2019, Evan Nemerson <evan@nemerson.com>

License: MIT



License: MIT

 Permission is hereby granted, free of charge, to any person obtaining

 a copy of this software and associated documentation files (the

 "Software"), to deal in the Software without restriction, including

 without limitation the rights to use, copy, modify, merge, publish,

 distribute, sublicense, and/or sell copies of the Software, and to

 permit persons to whom the Software is furnished to do so, subject to

 the following conditions:

 .

 The above copyright notice and this permission notice shall be

 included in all copies or substantial portions of the Software.

 .

 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,

 EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF

 MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND

 NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS

 BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN

 ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN

 CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE

 SOFTWARE.

debian/include/simde/check.h

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/* Check (assertions)

 * Portable Snippets - https://gitub.com/nemequ/portable-snippets

 * Created by Evan Nemerson <evan@nemerson.com>

 *

 *   To the extent possible under law, the authors have waived all

 *   copyright and related or neighboring rights to this code.  For

 *   details, see the Creative Commons Zero 1.0 Universal license at

 *   https://creativecommons.org/publicdomain/zero/1.0/

 */



#if !defined(SIMDE_CHECK_H)

#define SIMDE_CHECK_H



#if !defined(SIMDE_NDEBUG) && !defined(SIMDE_DEBUG)

#  define SIMDE_NDEBUG 1

#endif



#include <stdint.h>



#if !defined(_WIN32)

#  define SIMDE_SIZE_MODIFIER "z"

#  define SIMDE_CHAR_MODIFIER "hh"

#  define SIMDE_SHORT_MODIFIER "h"

#else

#  if defined(_M_X64) || defined(__amd64__)

#    define SIMDE_SIZE_MODIFIER "I64"

#  else

#    define SIMDE_SIZE_MODIFIER ""

#  endif

#  define SIMDE_CHAR_MODIFIER ""

#  define SIMDE_SHORT_MODIFIER ""

#endif



#if defined(_MSC_VER) &&  (_MSC_VER >= 1500)

#  define SIMDE__PUSH_DISABLE_MSVC_C4127 __pragma(warning(push)) __pragma(warning(disable:4127))

#  define SIMDE__POP_DISABLE_MSVC_C4127 __pragma(warning(pop))

#else

#  define SIMDE__PUSH_DISABLE_MSVC_C4127

#  define SIMDE__POP_DISABLE_MSVC_C4127

#endif



#if !defined(simde_errorf)

#  include <stdio.h>

#  include <stdlib.h>

#  define simde_errorf(format, ...) (fprintf(stderr, format, __VA_ARGS__), abort())

#endif



#define simde_error(msg) simde_errorf("%s", msg)



#if defined(SIMDE_NDEBUG)

#  if defined(SIMDE_CHECK_FAIL_DEFINED)

#    define simde_assert(expr)

#  else

#    if defined(HEDLEY_ASSUME)

#      define simde_assert(expr) HEDLEY_ASSUME(expr)

#    elif HEDLEY_GCC_VERSION_CHECK(4,5,0)

#      define simde_assert(expr) ((void) (!!(expr) ? 1 : (__builtin_unreachable(), 1)))

#    elif HEDLEY_MSVC_VERSION_CHECK(13,10,0)

#      define simde_assert(expr) __assume(expr)

#    else

#      define simde_assert(expr)

#    endif

#  endif

#  define simde_assert_true(expr) simde_assert(expr)

#  define simde_assert_false(expr) simde_assert(!(expr))

#  define simde_assert_type_full(prefix, suffix, T, fmt, a, op, b) simde_assert(((a) op (b)))

#  define simde_assert_double_equal(a, b, precision)

#  define simde_assert_string_equal(a, b)

#  define simde_assert_string_not_equal(a, b)

#  define simde_assert_memory_equal(size, a, b)

#  define simde_assert_memory_not_equal(size, a, b)

#else

#  define simde_assert(expr) \

    do { \

      if (!HEDLEY_LIKELY(expr)) { \

        simde_error("assertion failed: " #expr "\n"); \

      } \

      SIMDE__PUSH_DISABLE_MSVC_C4127 \

    } while (0) \

    SIMDE__POP_DISABLE_MSVC_C4127



#  define simde_assert_true(expr) \

    do { \

      if (!HEDLEY_LIKELY(expr)) { \

        simde_error("assertion failed: " #expr " is not true\n"); \

      } \

      SIMDE__PUSH_DISABLE_MSVC_C4127 \

    } while (0) \

    SIMDE__POP_DISABLE_MSVC_C4127



#  define simde_assert_false(expr) \

    do { \

      if (!HEDLEY_LIKELY(!(expr))) { \

        simde_error("assertion failed: " #expr " is not false\n"); \

      } \

      SIMDE__PUSH_DISABLE_MSVC_C4127 \

    } while (0) \

    SIMDE__POP_DISABLE_MSVC_C4127



#  define simde_assert_type_full(prefix, suffix, T, fmt, a, op, b)   \

    do { \

      T simde_tmp_a_ = (a); \

      T simde_tmp_b_ = (b); \

      if (!(simde_tmp_a_ op simde_tmp_b_)) { \

        simde_errorf("assertion failed: %s %s %s (" prefix "%" fmt suffix " %s " prefix "%" fmt suffix ")\n", \

                     #a, #op, #b, simde_tmp_a_, #op, simde_tmp_b_); \

      } \

      SIMDE__PUSH_DISABLE_MSVC_C4127 \

    } while (0) \

    SIMDE__POP_DISABLE_MSVC_C4127



#  define simde_assert_double_equal(a, b, precision) \

    do { \

      const double simde_tmp_a_ = (a); \

      const double simde_tmp_b_ = (b); \

      const double simde_tmp_diff_ = ((simde_tmp_a_ - simde_tmp_b_) < 0) ? \

        -(simde_tmp_a_ - simde_tmp_b_) : \

        (simde_tmp_a_ - simde_tmp_b_); \

      if (HEDLEY_UNLIKELY(simde_tmp_diff_ > 1e-##precision)) { \

        simde_errorf("assertion failed: %s == %s (%0." #precision "g == %0." #precision "g)\n", \

                     #a, #b, simde_tmp_a_, simde_tmp_b_); \

      } \

      SIMDE__PUSH_DISABLE_MSVC_C4127 \

    } while (0) \

    SIMDE__POP_DISABLE_MSVC_C4127



#  include <string.h>

#  define simde_assert_string_equal(a, b) \

    do { \

      const char* simde_tmp_a_ = a; \

      const char* simde_tmp_b_ = b; \

      if (HEDLEY_UNLIKELY(strcmp(simde_tmp_a_, simde_tmp_b_) != 0)) { \

        simde_errorf("assertion failed: string %s == %s (\"%s\" == \"%s\")\n", \

                     #a, #b, simde_tmp_a_, simde_tmp_b_); \

      } \

      SIMDE__PUSH_DISABLE_MSVC_C4127 \

    } while (0) \

    SIMDE__POP_DISABLE_MSVC_C4127



#  define simde_assert_string_not_equal(a, b) \

    do { \

      const char* simde_tmp_a_ = a; \

      const char* simde_tmp_b_ = b; \

      if (HEDLEY_UNLIKELY(strcmp(simde_tmp_a_, simde_tmp_b_) == 0)) { \

        simde_errorf("assertion failed: string %s != %s (\"%s\" == \"%s\")\n", \

                     #a, #b, simde_tmp_a_, simde_tmp_b_); \

      } \

      SIMDE__PUSH_DISABLE_MSVC_C4127 \

    } while (0) \

    SIMDE__POP_DISABLE_MSVC_C4127



#  define simde_assert_memory_equal(size, a, b) \

    do { \

      const unsigned char* simde_tmp_a_ = (const unsigned char*) (a); \

      const unsigned char* simde_tmp_b_ = (const unsigned char*) (b); \

      const size_t simde_tmp_size_ = (size); \

      if (HEDLEY_UNLIKELY(memcmp(simde_tmp_a_, simde_tmp_b_, simde_tmp_size_)) != 0) { \

        size_t simde_tmp_pos_; \

        for (simde_tmp_pos_ = 0 ; simde_tmp_pos_ < simde_tmp_size_ ; simde_tmp_pos_++) { \

          if (simde_tmp_a_[simde_tmp_pos_] != simde_tmp_b_[simde_tmp_pos_]) { \

            simde_errorf("assertion failed: memory %s == %s, at offset %" SIMDE_SIZE_MODIFIER "u\n", \

                         #a, #b, simde_tmp_pos_); \

            break; \

          } \

        } \

      } \

      SIMDE__PUSH_DISABLE_MSVC_C4127 \

    } while (0) \

    SIMDE__POP_DISABLE_MSVC_C4127



#  define simde_assert_memory_not_equal(size, a, b) \

    do { \

      const unsigned char* simde_tmp_a_ = (const unsigned char*) (a); \

      const unsigned char* simde_tmp_b_ = (const unsigned char*) (b); \

      const size_t simde_tmp_size_ = (size); \

      if (HEDLEY_UNLIKELY(memcmp(simde_tmp_a_, simde_tmp_b_, simde_tmp_size_)) == 0) { \

        simde_errorf("assertion failed: memory %s != %s (%" SIMDE_SIZE_MODIFIER "u bytes)\n", \

                     #a, #b, simde_tmp_size_); \

      } \

      SIMDE__PUSH_DISABLE_MSVC_C4127 \

    } while (0) \

    SIMDE__POP_DISABLE_MSVC_C4127

#endif



#define simde_assert_type(T, fmt, a, op, b) \

  simde_assert_type_full("", "", T, fmt, a, op, b)



#define simde_assert_char(a, op, b) \

  simde_assert_type_full("'\\x", "'", char, "02" SIMDE_CHAR_MODIFIER "x", a, op, b)

#define simde_assert_uchar(a, op, b) \

  simde_assert_type_full("'\\x", "'", unsigned char, "02" SIMDE_CHAR_MODIFIER "x", a, op, b)

#define simde_assert_short(a, op, b) \

  simde_assert_type(short, SIMDE_SHORT_MODIFIER "d", a, op, b)

#define simde_assert_ushort(a, op, b) \

  simde_assert_type(unsigned short, SIMDE_SHORT_MODIFIER "u", a, op, b)

#define simde_assert_int(a, op, b) \

  simde_assert_type(int, "d", a, op, b)

#define simde_assert_uint(a, op, b) \

  simde_assert_type(unsigned int, "u", a, op, b)

#define simde_assert_long(a, op, b) \

  simde_assert_type(long int, "ld", a, op, b)

#define simde_assert_ulong(a, op, b) \

  simde_assert_type(unsigned long int, "lu", a, op, b)

#define simde_assert_llong(a, op, b) \

  simde_assert_type(long long int, "lld", a, op, b)

#define simde_assert_ullong(a, op, b) \

  simde_assert_type(unsigned long long int, "llu", a, op, b)



#define simde_assert_size(a, op, b) \

  simde_assert_type(size_t, SIMDE_SIZE_MODIFIER "u", a, op, b)



#define simde_assert_float(a, op, b) \

  simde_assert_type(float, "f", a, op, b)

#define simde_assert_double(a, op, b) \

  simde_assert_type(double, "g", a, op, b)

#define simde_assert_ptr(a, op, b) \

  simde_assert_type(const void*, "p", a, op, b)



#define simde_assert_int8(a, op, b) \

  simde_assert_type(int8_t, PRIi8, a, op, b)

#define simde_assert_uint8(a, op, b) \

  simde_assert_type(uint8_t, PRIu8, a, op, b)

#define simde_assert_int16(a, op, b) \

  simde_assert_type(int16_t, PRIi16, a, op, b)

#define simde_assert_uint16(a, op, b) \

  simde_assert_type(uint16_t, PRIu16, a, op, b)

#define simde_assert_int32(a, op, b) \

  simde_assert_type(int32_t, PRIi32, a, op, b)

#define simde_assert_uint32(a, op, b) \

  simde_assert_type(uint32_t, PRIu32, a, op, b)

#define simde_assert_int64(a, op, b) \

  simde_assert_type(int64_t, PRIi64, a, op, b)

#define simde_assert_uint64(a, op, b) \

  simde_assert_type(uint64_t, PRIu64, a, op, b)



#define simde_assert_ptr_equal(a, b) \

  simde_assert_ptr(a, ==, b)

#define simde_assert_ptr_not_equal(a, b) \

  simde_assert_ptr(a, !=, b)

#define simde_assert_null(ptr) \

  simde_assert_ptr(ptr, ==, NULL)

#define simde_assert_not_null(ptr) \

  simde_assert_ptr(ptr, !=, NULL)

#define simde_assert_ptr_null(ptr) \

  simde_assert_ptr(ptr, ==, NULL)

#define simde_assert_ptr_not_null(ptr) \

  simde_assert_ptr(ptr, !=, NULL)



#endif /* !defined(SIMDE_CHECK_H) */

debian/include/simde/hedley.h

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File added.

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