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View file @ 0e782133
2019-09-12 twu
* concordance.c, concordance.h, distant-dna.c, distant-dna.h,
extension-search.c, extension-search.h, gsnap.c, junction.c, junction.h,
kmer-search.c, kmer-search.h, list.c, list.h, src, stage1hr.c, stage1hr.h,
stage3hr.c, stage3hr.h, stage3hrdef.h, substring.c, substring.h: Merged
revisions 220290 through 220325 from
branches/2019-09-11-zero-length-introns to handle cases where ambiguous
ends are resolved and where distant DNA alignments yield a zero-length
intron
* index.html: Updated for latest version
2019-08-09 twu
* inbuffer.c, inbuffer.h: Removed references to interleavedp from GMAP
* gsnap.c: Added --interleaved feature
* bzip2.c: Saving a file handle and closing it
* Makefile.gsnaptoo.am: Including bzip2.c and bzip2.h to relevant programs
* atoiindex.c: Initializing filenames to be NULL
* cmetindex.c: Initializing filenames to be NULL
2019-07-15 twu
* inbuffer.c, inbuffer.h: Added interleavedp parameter
* shortread.h: Added interleavedp parameter
* shortread.c: Implemented interleaved format for gzip- and bzip2-compressed
files.
* getline.c, getline.h: Implemented Getline_gzip and Getline_bzip2
* shortread.c: Implemented Shortread_read_interleaved_text
2019-06-11 twu
* stage1hr.c: Added debugging statements
* concordance.c: Limiting number of overlaps to avoid combinatorial
explosion in some cases
2019-05-21 twu
* index.html: Updated for latest version
* ax_ext.m4: Improved structure for AVX2 and AVX512
2019-05-12 twu
 
* gmap.c: Adding support for avx512bw
......
INSTALL deleted 100644 → 0
View file @ 79330547
Installation Instructions
*************************
Copyright (C) 1994-1996, 1999-2002, 2004-2013 Free Software Foundation,
Inc.
Copying and distribution of this file, with or without modification,
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==================
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=====================
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====================================
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CXX="g++ -arch i386 -arch x86_64 -arch ppc -arch ppc64" \
CPP="gcc -E" CXXCPP="g++ -E"
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==================
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=================
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==================
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./configure CC="cc -Ae -D_XOPEN_SOURCE=500"
and if that doesn't work, install pre-built binaries of GCC for HP-UX.
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and if that doesn't work, try
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==========================
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platform different from the build platform, you should specify the
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eventually be run) with `--host=TYPE'.
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================
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`CONFIG_SITE' environment variable to the location of the site script.
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Defining Variables
==================
Variables not defined in a site shell script can be set in the
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causes the specified `gcc' to be used as the C compiler (unless it is
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Unfortunately, this technique does not work for `CONFIG_SHELL' due to
an Autoconf limitation. Until the limitation is lifted, you can use
this workaround:
CONFIG_SHELL=/bin/bash ./configure CONFIG_SHELL=/bin/bash
`configure' Invocation
======================
`configure' recognizes the following options to control how it
operates.
`--help'
`-h'
Print a summary of all of the options to `configure', and exit.
`--help=short'
`--help=recursive'
Print a summary of the options unique to this package's
`configure', and exit. The `short' variant lists options used
only in the top level, while the `recursive' variant lists options
also present in any nested packages.
`--version'
`-V'
Print the version of Autoconf used to generate the `configure'
script, and exit.
`--cache-file=FILE'
Enable the cache: use and save the results of the tests in FILE,
traditionally `config.cache'. FILE defaults to `/dev/null' to
disable caching.
`--config-cache'
`-C'
Alias for `--cache-file=config.cache'.
`--quiet'
`--silent'
`-q'
Do not print messages saying which checks are being made. To
suppress all normal output, redirect it to `/dev/null' (any error
messages will still be shown).
`--srcdir=DIR'
Look for the package's source code in directory DIR. Usually
`configure' can determine that directory automatically.
`--prefix=DIR'
Use DIR as the installation prefix. *note Installation Names::
for more details, including other options available for fine-tuning
the installation locations.
`--no-create'
`-n'
Run the configure checks, but stop before creating any output
files.
`configure' also accepts some other, not widely useful, options. Run
`configure --help' for more details.
Makefile.in deleted 100644 → 0
View file @ 79330547
This diff is collapsed.
VERSION
View file @ 0e782133
2019-05-12
\ No newline at end of file
2019-09-12
\ No newline at end of file
aclocal.m4 deleted 100644 → 0
View file @ 79330547
This diff is collapsed.
config/ax_ext.m4
View file @ 0e782133
......@@ -17,9 +17,13 @@
#
# AC_SUBST(SIMD_CFLAGS)
#
# And defines:
# And previously defined:
#
# HAVE_MMX / HAVE_SSE / HAVE_SSE2 / HAVE_SSE3 / HAVE_SSSE3 / HAVE_SSE4_1 / HAVE_SSE4_2 / HAVE_AVX
# HAVE_MMX / HAVE_SSE / HAVE_SSE2 / HAVE_SSE3 / HAVE_SSSE3 / HAVE_SSE4_1 / HAVE_SSE4_2
#
# But now defines:
#
# HAVE_MM_POPCNT / HAVE_POPCNT / HAVE_LZCNT / HAVE_TZCNT / HAVE_PEXT
#
#
# LICENSE
......@@ -65,6 +69,7 @@ AC_DEFUN([AX_EXT],
# AX_CHECK_COMPILE_FLAG tests CFLAGS EXTRA-FLAGS FLAG
if test x"$ax_cv_cpu_has_sse2_ext" = xyes; then
#AC_MSG_CHECKING(for sse2 compiler/linker support)
CFLAGS=
TEST_CFLAGS=-msse2
AX_CHECK_COMPILE_FLAG([$TEST_CFLAGS], [ax_cv_compile_sse2_ext=yes], [ax_cv_ext_compile_problem=yes])
......@@ -77,7 +82,6 @@ AC_DEFUN([AX_EXT],
[ax_cv_link_emmintrin_h=yes],
[ax_cv_ext_linker_problem=yes])
if test x"$ax_cv_link_emmintrin_h" != xyes; then
AC_MSG_RESULT([no])
AC_MSG_WARN([Your compiler supports SSE2 instructions but not your linker.])
else
AC_MSG_RESULT([yes])
......@@ -88,7 +92,9 @@ AC_DEFUN([AX_EXT],
fi
fi
if test x"$ax_cv_cpu_has_ssse3_ext" = xyes; then
#AC_MSG_CHECKING(for ssse3 compiler/linker support)
CFLAGS=
if test x"$ax_cv_c_compiler_vendor" = xintel; then
TEST_CFLAGS="-mssse3"
......@@ -105,7 +111,6 @@ AC_DEFUN([AX_EXT],
[ax_cv_link_tmmintrin_h=yes],
[ax_cv_ext_linker_problem=yes])
if test x"$ax_cv_link_tmmintrin_h" != xyes; then
AC_MSG_RESULT([no])
AC_MSG_WARN([Your compiler supports SSSE3 instructions but not your linker.])
else
AC_MSG_RESULT([yes])
......@@ -119,7 +124,9 @@ AC_DEFUN([AX_EXT],
fi
fi
if test x"$ax_cv_cpu_has_sse41_ext" = xyes; then
#AC_MSG_CHECKING(for sse41 compiler/linker support)
CFLAGS=
if test x"$ax_cv_c_compiler_vendor" = xintel; then
TEST_CFLAGS="-msse4.1"
......@@ -136,7 +143,6 @@ AC_DEFUN([AX_EXT],
[ax_cv_link_smmintrin_h=yes],
[ax_cv_ext_linker_problem=yes])
if test x"$ax_cv_link_smmintrin_h" != xyes; then
AC_MSG_RESULT([no])
AC_MSG_WARN([Your compiler supports SSE4.1 instructions but not your linker.])
else
AC_MSG_RESULT([yes])
......@@ -151,7 +157,9 @@ AC_DEFUN([AX_EXT],
fi
fi
if test x"$ax_cv_cpu_has_sse42_ext" = xyes; then
#AC_MSG_CHECKING(for sse42 compiler/linker support)
CFLAGS=
if test x"$ax_cv_c_compiler_vendor" = xintel; then
TEST_CFLAGS="-march=corei7"
......@@ -168,7 +176,6 @@ AC_DEFUN([AX_EXT],
[ax_cv_link_nmmintrin_h=yes],
[ax_cv_ext_linker_problem=yes])
if test x"$ax_cv_link_nmmintrin_h" != xyes; then
AC_MSG_RESULT([no])
AC_MSG_WARN([Your compiler supports SSE4.2 instructions but not your linker.])
else
AC_MSG_RESULT([yes])
......@@ -183,11 +190,13 @@ AC_DEFUN([AX_EXT],
fi
fi
# Extra options for SSE42
if test x"$ax_make_sse42" = xyes; then
AC_MSG_CHECKING(for mm_popcnt support)
if test x"$ax_cv_cpu_has_popcnt_ext" != xyes; then
AC_MSG_RESULT([no])
else
AC_MSG_CHECKING(for mm_popcnt run support)
AC_RUN_IFELSE(
[AC_LANG_PROGRAM([[#include <nmmintrin.h>]],
[[return (_mm_popcnt_u32(0xffffffffu) == 32) ? 0 : 9;]])],
......@@ -195,7 +204,6 @@ AC_DEFUN([AX_EXT],
AC_DEFINE(HAVE_MM_POPCNT,1,[Define to 1 if you support Intel intrinsic _mm_popcnt_u32/64 instructions])],
[AC_MSG_RESULT(no)])
fi
fi
if test x"$ax_cv_cpu_has_bmi1_ext" = xyes; then
......@@ -210,15 +218,18 @@ AC_DEFUN([AX_EXT],
AC_MSG_WARN([Your CPU supports BMI1 instructions but not your compiler. Can you try another compiler or update yours?])
else
CFLAGS=$TEST_CFLAGS
AC_MSG_CHECKING(for abm linker support)
AC_LINK_IFELSE([AC_LANG_PROGRAM([])],
[ax_cv_link_abm=yes],
[ax_cv_ext_linker_problem=yes])
if test x"$ax_cv_link_abm" != xyes; then
AC_MSG_WARN([Your compiler supports -mabm but not your linker])
else
AC_MSG_RESULT([yes])
SIMD_SSE4_2_CFLAGS=$CFLAGS
# Test for functionality with the -mabm compiler flag
AC_MSG_CHECKING(for _popcnt32 support)
AC_MSG_CHECKING(for _popcnt32 run support)
AC_RUN_IFELSE(
[AC_LANG_PROGRAM([[#include <immintrin.h>]],
[[return (_popcnt32(0xffffffffu) == 32) ? 0 : 9;]])],
......@@ -226,7 +237,7 @@ AC_DEFUN([AX_EXT],
AC_DEFINE(HAVE_POPCNT,1,[Define to 1 if you support Intel intrinsic _popcnt instruction])],
[AC_MSG_RESULT(no)])
AC_MSG_CHECKING(for _lzcnt support)
AC_MSG_CHECKING(for _lzcnt run support)
AC_RUN_IFELSE(
[AC_LANG_PROGRAM([[#include <immintrin.h>]],
[[return (_lzcnt_u32(0x0fffffffu) == 4) ? 0 : 9;]])],
......@@ -237,7 +248,9 @@ AC_DEFUN([AX_EXT],
fi
fi
if test x"$ax_cv_cpu_has_bmi1_ext" = xyes; then
#AC_MSG_CHECKING(for bmi compiler/linker support)
CFLAGS=
if test x"$ax_cv_c_compiler_vendor" = xintel; then
TEST_CFLAGS="$SIMD_SSE4_2_CFLAGS"
......@@ -249,15 +262,18 @@ AC_DEFUN([AX_EXT],
AC_MSG_WARN([Your CPU supports BMI1 instructions but not your compiler. Can you try another compiler or update yours?])
else
CFLAGS=$TEST_CFLAGS
AC_MSG_CHECKING(for bmi linker support)
AC_LINK_IFELSE([AC_LANG_PROGRAM([])],
[ax_cv_link_bmi=yes],
[ax_cv_ext_linker_problem=yes])
if test x"$ax_cv_link_bmi" != xyes; then
AC_MSG_WARN([Your compiler supports -mbmi but not your linker])
else
AC_MSG_RESULT([yes])
SIMD_SSE4_2_CFLAGS=$CFLAGS
# Test for functionality with the -mbmi compiler flag
AC_MSG_CHECKING(for _tzcnt support)
AC_MSG_CHECKING(for _tzcnt run support)
AC_RUN_IFELSE(
[AC_LANG_PROGRAM([[#include <immintrin.h>]],
[[return (_tzcnt_u32(0xfffffff0u) == 4) ? 0 : 9;]])],
......@@ -267,13 +283,17 @@ AC_DEFUN([AX_EXT],
fi
fi
fi
fi
if test x"$ax_cv_cpu_has_avx2_ext" = xyes; then
#AC_MSG_CHECKING(for avx2 compiler/linker support)
CFLAGS=
if test x"$ax_cv_c_compiler_vendor" = xintel; then
TEST_CFLAGS="-march=core-avx2"
else
TEST_CFLAGS="$SIMD_SSE4_2_CFLAGS -mavx2 -mbmi2"
TEST_CFLAGS="$SIMD_SSE4_2_CFLAGS -mavx2"
fi
AX_CHECK_COMPILE_FLAG([$TEST_CFLAGS], [ax_cv_compile_avx2_ext=yes], [ax_cv_ext_compile_problem=yes])
if test x"$ax_cv_compile_avx2_ext" != xyes; then
......@@ -285,7 +305,6 @@ AC_DEFUN([AX_EXT],
[ax_cv_link_immintrin_h=yes],
[ax_cv_ext_linker_problem=yes])
if test x"$ax_cv_link_immintrin_h" != xyes; then
AC_MSG_RESULT([no])
AC_MSG_WARN([Your compiler supports AVX2 instructions but not your linker.])
else
AC_MSG_RESULT([yes])
......@@ -302,6 +321,9 @@ AC_DEFUN([AX_EXT],
fi
fi
# Extra option for AVX2
if test x"$ax_make_avx2" = xyes; then
if test x"$ax_cv_cpu_has_bmi2_ext" = xyes; then
CFLAGS=
if test x"$ax_cv_c_compiler_vendor" = xintel; then
......@@ -314,12 +336,14 @@ AC_DEFUN([AX_EXT],
AC_MSG_WARN([Your CPU supports BMI2 instructions but not your compiler. Can you try another compiler or update yours?])
else
CFLAGS=$TEST_CFLAGS
AC_MSG_CHECKING(for bmi2 linker support)
AC_LINK_IFELSE([AC_LANG_PROGRAM([])],
[ax_cv_link_bmi2=yes],
[ax_cv_ext_linker_problem=yes])
if test x"$ax_cv_link_bmi2" != xyes; then
AC_MSG_WARN([Your compiler supports -mbmi2 but not your linker. Can you try another linker or update yours?])
else
AC_MSG_RESULT([yes])
SIMD_AVX2_CFLAGS=$CFLAGS
if test x"$ax_cv_c_compiler_vendor" != xintel; then
SIMD_SSE2_CFLAGS="$SIMD_SSE2_CFLAGS -mno-bmi2"
......@@ -327,7 +351,8 @@ AC_DEFUN([AX_EXT],
SIMD_SSE4_1_CFLAGS="$SIMD_SSE4_1_CFLAGS -mno-bmi2"
SIMD_SSE4_2_CFLAGS="$SIMD_SSE4_2_CFLAGS -mno-bmi2"
fi
AC_MSG_CHECKING(for _pext support)
AC_MSG_CHECKING(for _pext run support)
AC_RUN_IFELSE(
[AC_LANG_PROGRAM([[#include <immintrin.h>]],
[[return (_pext_u32(0x01234567u,0x0f33aa55) == 0x00001b0b) ? 0 : 9;]])],
......@@ -337,16 +362,16 @@ AC_DEFUN([AX_EXT],
fi
fi
fi
fi
if test x"$ax_cv_cpu_has_avx512_ext" = xyes; then
#AC_MSG_CHECKING(for avx512f and avx512cd support)
CFLAGS=
if test x"$ax_cv_c_compiler_vendor" = xintel; then
TEST_CFLAGS="-xCOMMON-AVX512"
elif test x"$ax_cv_cpu_has_avx512bw_ext" != xyes; then
TEST_CFLAGS="$SIMD_AVX2_CFLAGS -mavx512f -mavx512cd -mno-avx512bw -mno-avx512vl"
else
TEST_CFLAGS="$SIMD_AVX2_CFLAGS -mavx512f -mavx512cd -mavx512bw -mavx512vl"
TEST_CFLAGS="$SIMD_AVX2_CFLAGS -mavx512f -mavx512cd"
fi
AX_CHECK_COMPILE_FLAG([$TEST_CFLAGS], [ax_cv_compile_avx512_ext=yes], [ax_cv_ext_compile_problem=yes])
if test x"$ax_cv_compile_avx512_ext" != xyes; then
......@@ -358,8 +383,7 @@ AC_DEFUN([AX_EXT],
[ax_cv_link_nmmintrin_h=yes],
[ax_cv_ext_linker_problem=yes])
if test x"$ax_cv_link_nmmintrin_h" != xyes; then
AC_MSG_RESULT([no])
AC_MSG_WARN([Your compiler supports AVX512 instructions but not your linker.])
AC_MSG_WARN([Your compiler supports AVX512 instructions but not your linker. Can you try another linker or update yours?])
else
AC_MSG_RESULT([yes])
ax_make_avx512=yes
......@@ -372,6 +396,41 @@ AC_DEFUN([AX_EXT],
SIMD_AVX2_CFLAGS="$SIMD_AVX2_CFLAGS -mno-avx512f -mno-avx512cd"
fi
# AC_DEFINE(HAVE_AVX512,1,[Define to 1 if you support AVX512 (Advanced Vector Extensions 512) instructions]) -- Defines run-type
# AC_DEFINE(HAVE_AVX512BW,1,[Define to 1 if you support AVX512BW (Advanced Vector Extensions 512) BW instructions]) -- Defines run-type
fi
fi
fi
# Extra options for AVX512
if test x"$ax_make_avx512" = xyes; then
CFLAGS=
if test x"$ax_cv_c_compiler_vendor" = xintel; then
TEST_CFLAGS="$SIMD_AVX512_CFLAGS"
else
TEST_CFLAGS="$SIMD_AVX512_CFLAGS -mavx512vl -mavx512bw"
fi
AX_CHECK_COMPILE_FLAG([$TEST_CFLAGS], [ax_cv_compile_avx512bw_ext=yes], [ax_cv_ext_compile_problem=yes])
if test x"$ax_cv_compile_avx512bw_ext" != xyes; then
AC_MSG_WARN([Your CPU supports AVX512BW instructions but not your compiler. Can you try another compiler or update yours?])
else
CFLAGS=$TEST_CFLAGS
AC_MSG_CHECKING(for avx512vl and avx512bw linker support)
AC_LINK_IFELSE([AC_LANG_PROGRAM([])],
[ax_cv_link_avx512bw=yes],
[ax_cv_ext_linker_problem=yes])
if test x"$ax_cv_link_avx512bw" != xyes; then
AC_MSG_WARN([Your compiler supports AVX512BW instructions but not your linker.])
else
AC_MSG_RESULT([yes])
SIMD_AVX512_CFLAGS=$CFLAGS
if test x"$ax_cv_c_compiler_vendor" != xintel; then
SIMD_SSE2_CFLAGS="$SIMD_SSE2_CFLAGS -mno-avx512vl -mno-avx512bw"
SIMD_SSSE3_CFLAGS="$SIMD_SSSE3_CFLAGS -mno-avx512vl -mno-avx512bw"
SIMD_SSE4_1_CFLAGS="$SIMD_SSE4_1_CFLAGS -mno-avx512vl -mno-avx512bw"
SIMD_SSE4_2_CFLAGS="$SIMD_SSE4_2_CFLAGS -mno-avx512vl -mno-avx512bw"
SIMD_AVX2_CFLAGS="$SIMD_AVX2_CFLAGS -mno-avx512vl -mno-avx512bw"
fi
# AC_DEFINE(HAVE_AVX512,1,[Define to 1 if you support AVX512 (Advanced Vector Extensions 512) instructions]) -- Defines run-type
# AC_DEFINE(HAVE_AVX512BW,1,[Define to 1 if you support AVX512BW (Advanced Vector Extensions 512) BW instructions]) -- Defines run-type
fi
fi
......
config/compile deleted 100755 → 0
View file @ 79330547
#! /bin/sh
# Wrapper for compilers which do not understand '-c -o'.
scriptversion=2012-10-14.11; # UTC
# Copyright (C) 1999-2014 Free Software Foundation, Inc.
# Written by Tom Tromey <tromey@cygnus.com>.
#
# This program 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 2, or (at your option)
# any later version.
#
# This program 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.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
# As a special exception to the GNU General Public License, if you
# distribute this file as part of a program that contains a
# configuration script generated by Autoconf, you may include it under
# the same distribution terms that you use for the rest of that program.
# This file is maintained in Automake, please report
# bugs to <bug-automake@gnu.org> or send patches to
# <automake-patches@gnu.org>.
nl='
'
# We need space, tab and new line, in precisely that order. Quoting is
# there to prevent tools from complaining about whitespace usage.
IFS=" "" $nl"
file_conv=
# func_file_conv build_file lazy
# Convert a $build file to $host form and store it in $file
# Currently only supports Windows hosts. If the determined conversion
# type is listed in (the comma separated) LAZY, no conversion will
# take place.
func_file_conv ()
{
file=$1
case $file in
/ | /[!/]*) # absolute file, and not a UNC file
if test -z "$file_conv"; then
# lazily determine how to convert abs files
case `uname -s` in
MINGW*)
file_conv=mingw
;;
CYGWIN*)
file_conv=cygwin
;;
*)
file_conv=wine
;;
esac
fi
case $file_conv/,$2, in
*,$file_conv,*)
;;
mingw/*)
file=`cmd //C echo "$file " | sed -e 's/"\(.*\) " *$/\1/'`
;;
cygwin/*)
file=`cygpath -m "$file" || echo "$file"`
;;
wine/*)
file=`winepath -w "$file" || echo "$file"`
;;
esac
;;
esac
}
# func_cl_dashL linkdir
# Make cl look for libraries in LINKDIR
func_cl_dashL ()
{
func_file_conv "$1"
if test -z "$lib_path"; then
lib_path=$file
else
lib_path="$lib_path;$file"
fi
linker_opts="$linker_opts -LIBPATH:$file"
}
# func_cl_dashl library
# Do a library search-path lookup for cl
func_cl_dashl ()
{
lib=$1
found=no
save_IFS=$IFS
IFS=';'
for dir in $lib_path $LIB
do
IFS=$save_IFS
if $shared && test -f "$dir/$lib.dll.lib"; then
found=yes
lib=$dir/$lib.dll.lib
break
fi
if test -f "$dir/$lib.lib"; then
found=yes
lib=$dir/$lib.lib
break
fi
if test -f "$dir/lib$lib.a"; then
found=yes
lib=$dir/lib$lib.a
break
fi
done
IFS=$save_IFS
if test "$found" != yes; then
lib=$lib.lib
fi
}
# func_cl_wrapper cl arg...
# Adjust compile command to suit cl
func_cl_wrapper ()
{
# Assume a capable shell
lib_path=
shared=:
linker_opts=
for arg
do
if test -n "$eat"; then
eat=
else
case $1 in
-o)
# configure might choose to run compile as 'compile cc -o foo foo.c'.
eat=1
case $2 in
*.o | *.[oO][bB][jJ])
func_file_conv "$2"
set x "$@" -Fo"$file"
shift
;;
*)
func_file_conv "$2"
set x "$@" -Fe"$file"
shift
;;
esac
;;
-I)
eat=1
func_file_conv "$2" mingw
set x "$@" -I"$file"
shift
;;
-I*)
func_file_conv "${1#-I}" mingw
set x "$@" -I"$file"
shift
;;
-l)
eat=1
func_cl_dashl "$2"
set x "$@" "$lib"
shift
;;
-l*)
func_cl_dashl "${1#-l}"
set x "$@" "$lib"
shift
;;
-L)
eat=1
func_cl_dashL "$2"
;;
-L*)
func_cl_dashL "${1#-L}"
;;
-static)
shared=false
;;
-Wl,*)
arg=${1#-Wl,}
save_ifs="$IFS"; IFS=','
for flag in $arg; do
IFS="$save_ifs"
linker_opts="$linker_opts $flag"
done
IFS="$save_ifs"
;;
-Xlinker)
eat=1
linker_opts="$linker_opts $2"
;;
-*)
set x "$@" "$1"
shift
;;
*.cc | *.CC | *.cxx | *.CXX | *.[cC]++)
func_file_conv "$1"
set x "$@" -Tp"$file"
shift
;;
*.c | *.cpp | *.CPP | *.lib | *.LIB | *.Lib | *.OBJ | *.obj | *.[oO])
func_file_conv "$1" mingw
set x "$@" "$file"
shift
;;
*)
set x "$@" "$1"
shift
;;
esac
fi
shift
done
if test -n "$linker_opts"; then
linker_opts="-link$linker_opts"
fi
exec "$@" $linker_opts
exit 1
}
eat=
case $1 in
'')
echo "$0: No command. Try '$0 --help' for more information." 1>&2
exit 1;
;;
-h | --h*)
cat <<\EOF
Usage: compile [--help] [--version] PROGRAM [ARGS]
Wrapper for compilers which do not understand '-c -o'.
Remove '-o dest.o' from ARGS, run PROGRAM with the remaining
arguments, and rename the output as expected.
If you are trying to build a whole package this is not the
right script to run: please start by reading the file 'INSTALL'.
Report bugs to <bug-automake@gnu.org>.
EOF
exit $?
;;
-v | --v*)
echo "compile $scriptversion"
exit $?
;;
cl | *[/\\]cl | cl.exe | *[/\\]cl.exe )
func_cl_wrapper "$@" # Doesn't return...
;;
esac
ofile=
cfile=
for arg
do
if test -n "$eat"; then
eat=
else
case $1 in
-o)
# configure might choose to run compile as 'compile cc -o foo foo.c'.
# So we strip '-o arg' only if arg is an object.
eat=1
case $2 in
*.o | *.obj)
ofile=$2
;;
*)
set x "$@" -o "$2"
shift
;;
esac
;;
*.c)
cfile=$1
set x "$@" "$1"
shift
;;
*)
set x "$@" "$1"
shift
;;
esac
fi
shift
done
if test -z "$ofile" || test -z "$cfile"; then
# If no '-o' option was seen then we might have been invoked from a
# pattern rule where we don't need one. That is ok -- this is a
# normal compilation that the losing compiler can handle. If no
# '.c' file was seen then we are probably linking. That is also
# ok.
exec "$@"
fi
# Name of file we expect compiler to create.
cofile=`echo "$cfile" | sed 's|^.*[\\/]||; s|^[a-zA-Z]:||; s/\.c$/.o/'`
# Create the lock directory.
# Note: use '[/\\:.-]' here to ensure that we don't use the same name
# that we are using for the .o file. Also, base the name on the expected
# object file name, since that is what matters with a parallel build.
lockdir=`echo "$cofile" | sed -e 's|[/\\:.-]|_|g'`.d
while true; do
if mkdir "$lockdir" >/dev/null 2>&1; then
break
fi
sleep 1
done
# FIXME: race condition here if user kills between mkdir and trap.
trap "rmdir '$lockdir'; exit 1" 1 2 15
# Run the compile.
"$@"
ret=$?
if test -f "$cofile"; then
test "$cofile" = "$ofile" || mv "$cofile" "$ofile"
elif test -f "${cofile}bj"; then
test "${cofile}bj" = "$ofile" || mv "${cofile}bj" "$ofile"
fi
rmdir "$lockdir"
exit $ret
# Local Variables:
# mode: shell-script
# sh-indentation: 2
# eval: (add-hook 'write-file-hooks 'time-stamp)
# time-stamp-start: "scriptversion="
# time-stamp-format: "%:y-%02m-%02d.%02H"
# time-stamp-time-zone: "UTC"
# time-stamp-end: "; # UTC"
# End:
config/config.guess deleted 100755 → 0
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This diff is collapsed.
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View file @ 79330547
This diff is collapsed.
config/depcomp deleted 100755 → 0
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This diff is collapsed.
config/install-sh deleted 100755 → 0
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config/ltmain.sh deleted 100644 → 0
View file @ 79330547
This diff is collapsed.
config/missing deleted 100755 → 0
View file @ 79330547
#! /bin/sh
# Common wrapper for a few potentially missing GNU programs.
scriptversion=2013-10-28.13; # UTC
# Copyright (C) 1996-2014 Free Software Foundation, Inc.
# Originally written by Fran,cois Pinard <pinard@iro.umontreal.ca>, 1996.
# This program 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 2, or (at your option)
# any later version.
# This program 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.
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
# As a special exception to the GNU General Public License, if you
# distribute this file as part of a program that contains a
# configuration script generated by Autoconf, you may include it under
# the same distribution terms that you use for the rest of that program.
if test $# -eq 0; then
echo 1>&2 "Try '$0 --help' for more information"
exit 1
fi
case $1 in
--is-lightweight)
# Used by our autoconf macros to check whether the available missing
# script is modern enough.
exit 0
;;
--run)
# Back-compat with the calling convention used by older automake.
shift
;;
-h|--h|--he|--hel|--help)
echo "\
$0 [OPTION]... PROGRAM [ARGUMENT]...
Run 'PROGRAM [ARGUMENT]...', returning a proper advice when this fails due
to PROGRAM being missing or too old.
Options:
-h, --help display this help and exit
-v, --version output version information and exit
Supported PROGRAM values:
aclocal autoconf autoheader autom4te automake makeinfo
bison yacc flex lex help2man
Version suffixes to PROGRAM as well as the prefixes 'gnu-', 'gnu', and
'g' are ignored when checking the name.
Send bug reports to <bug-automake@gnu.org>."
exit $?
;;
-v|--v|--ve|--ver|--vers|--versi|--versio|--version)
echo "missing $scriptversion (GNU Automake)"
exit $?
;;
-*)
echo 1>&2 "$0: unknown '$1' option"
echo 1>&2 "Try '$0 --help' for more information"
exit 1
;;
esac
# Run the given program, remember its exit status.
"$@"; st=$?
# If it succeeded, we are done.
test $st -eq 0 && exit 0
# Also exit now if we it failed (or wasn't found), and '--version' was
# passed; such an option is passed most likely to detect whether the
# program is present and works.
case $2 in --version|--help) exit $st;; esac
# Exit code 63 means version mismatch. This often happens when the user
# tries to use an ancient version of a tool on a file that requires a
# minimum version.
if test $st -eq 63; then
msg="probably too old"
elif test $st -eq 127; then
# Program was missing.
msg="missing on your system"
else
# Program was found and executed, but failed. Give up.
exit $st
fi
perl_URL=http://www.perl.org/
flex_URL=http://flex.sourceforge.net/
gnu_software_URL=http://www.gnu.org/software
program_details ()
{
case $1 in
aclocal|automake)
echo "The '$1' program is part of the GNU Automake package:"
echo "<$gnu_software_URL/automake>"
echo "It also requires GNU Autoconf, GNU m4 and Perl in order to run:"
echo "<$gnu_software_URL/autoconf>"
echo "<$gnu_software_URL/m4/>"
echo "<$perl_URL>"
;;
autoconf|autom4te|autoheader)
echo "The '$1' program is part of the GNU Autoconf package:"
echo "<$gnu_software_URL/autoconf/>"
echo "It also requires GNU m4 and Perl in order to run:"
echo "<$gnu_software_URL/m4/>"
echo "<$perl_URL>"
;;
esac
}
give_advice ()
{
# Normalize program name to check for.
normalized_program=`echo "$1" | sed '
s/^gnu-//; t
s/^gnu//; t
s/^g//; t'`
printf '%s\n' "'$1' is $msg."
configure_deps="'configure.ac' or m4 files included by 'configure.ac'"
case $normalized_program in
autoconf*)
echo "You should only need it if you modified 'configure.ac',"
echo "or m4 files included by it."
program_details 'autoconf'
;;
autoheader*)
echo "You should only need it if you modified 'acconfig.h' or"
echo "$configure_deps."
program_details 'autoheader'
;;
automake*)
echo "You should only need it if you modified 'Makefile.am' or"
echo "$configure_deps."
program_details 'automake'
;;
aclocal*)
echo "You should only need it if you modified 'acinclude.m4' or"
echo "$configure_deps."
program_details 'aclocal'
;;
autom4te*)
echo "You might have modified some maintainer files that require"
echo "the 'autom4te' program to be rebuilt."
program_details 'autom4te'
;;
bison*|yacc*)
echo "You should only need it if you modified a '.y' file."
echo "You may want to install the GNU Bison package:"
echo "<$gnu_software_URL/bison/>"
;;
lex*|flex*)
echo "You should only need it if you modified a '.l' file."
echo "You may want to install the Fast Lexical Analyzer package:"
echo "<$flex_URL>"
;;
help2man*)
echo "You should only need it if you modified a dependency" \
"of a man page."
echo "You may want to install the GNU Help2man package:"
echo "<$gnu_software_URL/help2man/>"
;;
makeinfo*)
echo "You should only need it if you modified a '.texi' file, or"
echo "any other file indirectly affecting the aspect of the manual."
echo "You might want to install the Texinfo package:"
echo "<$gnu_software_URL/texinfo/>"
echo "The spurious makeinfo call might also be the consequence of"
echo "using a buggy 'make' (AIX, DU, IRIX), in which case you might"
echo "want to install GNU make:"
echo "<$gnu_software_URL/make/>"
;;
*)
echo "You might have modified some files without having the proper"
echo "tools for further handling them. Check the 'README' file, it"
echo "often tells you about the needed prerequisites for installing"
echo "this package. You may also peek at any GNU archive site, in"
echo "case some other package contains this missing '$1' program."
;;
esac
}
give_advice "$1" | sed -e '1s/^/WARNING: /' \
-e '2,$s/^/ /' >&2
# Propagate the correct exit status (expected to be 127 for a program
# not found, 63 for a program that failed due to version mismatch).
exit $st
# Local variables:
# eval: (add-hook 'write-file-hooks 'time-stamp)
# time-stamp-start: "scriptversion="
# time-stamp-format: "%:y-%02m-%02d.%02H"
# time-stamp-time-zone: "UTC"
# time-stamp-end: "; # UTC"
# End:
config/test-driver deleted 100755 → 0
View file @ 79330547
#! /bin/sh
# test-driver - basic testsuite driver script.
scriptversion=2013-07-13.22; # UTC
# Copyright (C) 2011-2014 Free Software Foundation, Inc.
#
# This program 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 2, or (at your option)
# any later version.
#
# This program 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.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
# As a special exception to the GNU General Public License, if you
# distribute this file as part of a program that contains a
# configuration script generated by Autoconf, you may include it under
# the same distribution terms that you use for the rest of that program.
# This file is maintained in Automake, please report
# bugs to <bug-automake@gnu.org> or send patches to
# <automake-patches@gnu.org>.
# Make unconditional expansion of undefined variables an error. This
# helps a lot in preventing typo-related bugs.
set -u
usage_error ()
{
echo "$0: $*" >&2
print_usage >&2
exit 2
}
print_usage ()
{
cat <<END
Usage:
test-driver --test-name=NAME --log-file=PATH --trs-file=PATH
[--expect-failure={yes|no}] [--color-tests={yes|no}]
[--enable-hard-errors={yes|no}] [--]
TEST-SCRIPT [TEST-SCRIPT-ARGUMENTS]
The '--test-name', '--log-file' and '--trs-file' options are mandatory.
END
}
test_name= # Used for reporting.
log_file= # Where to save the output of the test script.
trs_file= # Where to save the metadata of the test run.
expect_failure=no
color_tests=no
enable_hard_errors=yes
while test $# -gt 0; do
case $1 in
--help) print_usage; exit $?;;
--version) echo "test-driver $scriptversion"; exit $?;;
--test-name) test_name=$2; shift;;
--log-file) log_file=$2; shift;;
--trs-file) trs_file=$2; shift;;
--color-tests) color_tests=$2; shift;;
--expect-failure) expect_failure=$2; shift;;
--enable-hard-errors) enable_hard_errors=$2; shift;;
--) shift; break;;
-*) usage_error "invalid option: '$1'";;
*) break;;
esac
shift
done
missing_opts=
test x"$test_name" = x && missing_opts="$missing_opts --test-name"
test x"$log_file" = x && missing_opts="$missing_opts --log-file"
test x"$trs_file" = x && missing_opts="$missing_opts --trs-file"
if test x"$missing_opts" != x; then
usage_error "the following mandatory options are missing:$missing_opts"
fi
if test $# -eq 0; then
usage_error "missing argument"
fi
if test $color_tests = yes; then
# Keep this in sync with 'lib/am/check.am:$(am__tty_colors)'.
red='' # Red.
grn='' # Green.
lgn='' # Light green.
blu='' # Blue.
mgn='' # Magenta.
std='' # No color.
else
red= grn= lgn= blu= mgn= std=
fi
do_exit='rm -f $log_file $trs_file; (exit $st); exit $st'
trap "st=129; $do_exit" 1
trap "st=130; $do_exit" 2
trap "st=141; $do_exit" 13
trap "st=143; $do_exit" 15
# Test script is run here.
"$@" >$log_file 2>&1
estatus=$?
if test $enable_hard_errors = no && test $estatus -eq 99; then
tweaked_estatus=1
else
tweaked_estatus=$estatus
fi
case $tweaked_estatus:$expect_failure in
0:yes) col=$red res=XPASS recheck=yes gcopy=yes;;
0:*) col=$grn res=PASS recheck=no gcopy=no;;
77:*) col=$blu res=SKIP recheck=no gcopy=yes;;
99:*) col=$mgn res=ERROR recheck=yes gcopy=yes;;
*:yes) col=$lgn res=XFAIL recheck=no gcopy=yes;;
*:*) col=$red res=FAIL recheck=yes gcopy=yes;;
esac
# Report the test outcome and exit status in the logs, so that one can
# know whether the test passed or failed simply by looking at the '.log'
# file, without the need of also peaking into the corresponding '.trs'
# file (automake bug#11814).
echo "$res $test_name (exit status: $estatus)" >>$log_file
# Report outcome to console.
echo "${col}${res}${std}: $test_name"
# Register the test result, and other relevant metadata.
echo ":test-result: $res" > $trs_file
echo ":global-test-result: $res" >> $trs_file
echo ":recheck: $recheck" >> $trs_file
echo ":copy-in-global-log: $gcopy" >> $trs_file
# Local Variables:
# mode: shell-script
# sh-indentation: 2
# eval: (add-hook 'write-file-hooks 'time-stamp)
# time-stamp-start: "scriptversion="
# time-stamp-format: "%:y-%02m-%02d.%02H"
# time-stamp-time-zone: "UTC"
# time-stamp-end: "; # UTC"
# End:
configure deleted 100755 → 0
View file @ 79330547
This diff is collapsed.
src/Makefile.am
View file @ 0e782133
......@@ -778,7 +778,8 @@ TRINDEX_FILES = fopen.h bool.h types.h univcoord.h \
bitpack64-access.c bitpack64-access.h bitpack64-write.c bitpack64-write.h \
uintlist.c uintlist.h intlist.c intlist.h \
list.c list.h datadir.c datadir.h \
getline.c getline.h getopt.c getopt1.c getopt.h trindex.c
bzip2.c bzip2.h getline.c getline.h \
getopt.c getopt1.c getopt.h trindex.c
trindex_CC = $(PTHREAD_CC)
trindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
......@@ -821,13 +822,13 @@ IIT_STORE_FILES = fopen.h bool.h types.h univcoord.h \
doublelist.c doublelist.h \
iit-write-univ.c iit-write-univ.h iitdef.h iit-write.c iit-write.h \
tableint.c tableint.h table.c table.h chrom.c chrom.h \
getline.c getline.h \
bzip2.c bzip2.h getline.c getline.h \
getopt.c getopt1.c getopt.h iit_store.c
iit_store_CC = $(PTHREAD_CC)
iit_store_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DUTILITYP=1
iit_store_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
iit_store_LDADD = $(PTHREAD_LIBS)
iit_store_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_iit_store_SOURCES = $(IIT_STORE_FILES)
......@@ -841,13 +842,13 @@ IIT_GET_FILES = fopen.h bool.h types.h univcoord.h \
filestring.c filestring.h \
iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
complement.h parserange.c parserange.h \
getline.c getline.h \
bzip2.c bzip2.h getline.c getline.h \
getopt.c getopt1.c getopt.h iit_get.c
iit_get_CC = $(PTHREAD_CC)
iit_get_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DUTILITYP=1
iit_get_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
iit_get_LDADD = $(PTHREAD_LIBS)
iit_get_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_iit_get_SOURCES = $(IIT_GET_FILES)
IIT_DUMP_FILES = fopen.h bool.h types.h univcoord.h \
......@@ -895,13 +896,13 @@ SAM_SORT_FILES = bool.h types.h univcoord.h \
filestring.c filestring.h \
parserange.c parserange.h iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
samflags.h samheader.c samheader.h samread.c samread.h \
getline.c getline.h datadir.c datadir.h \
bzip2.c bzip2.h getline.c getline.h datadir.c datadir.h \
getopt.c getopt1.c getopt.h sam_sort.c
sam_sort_CC = $(PTHREAD_CC)
sam_sort_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
sam_sort_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
sam_sort_LDADD = $(PTHREAD_LIBS)
sam_sort_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_sam_sort_SOURCES = $(SAM_SORT_FILES)
......
src/Makefile.in deleted 100644 → 0
View file @ 79330547
This diff is collapsed.
src/atoiindex.c
View file @ 0e782133
static char rcsid[] = "$Id: atoiindex.c 218151 2019-01-17 05:36:54Z twu $";
static char rcsid[] = "$Id: atoiindex.c 219865 2019-08-09 19:56:50Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
......@@ -1469,8 +1469,8 @@ main (int argc, char *argv[]) {
char *sourcedir = NULL, *destdir = NULL, *filename, *fileroot;
Indexdb_filenames_T ifilenames;
Localdb_filenames_T lfilenames;
char *new_region_filename, *new_pointers_filename, *new_offsets_filename,
*new_positions_high_filename, *new_positions_filename;
char *new_region_filename = NULL, *new_pointers_filename = NULL, *new_offsets_filename = NULL,
*new_positions_high_filename = NULL, *new_positions_filename = NULL;
Univ_IIT_T chromosome_iit;
Univcoord_T genomelength;
......
src/bzip2.c
View file @ 0e782133
static char rcsid[] = "$Id: bzip2.c 83593 2013-01-16 22:59:40Z twu $";
static char rcsid[] = "$Id: bzip2.c 219867 2019-08-09 20:06:43Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
......@@ -19,6 +19,7 @@ static char rcsid[] = "$Id: bzip2.c 83593 2013-01-16 22:59:40Z twu $";
#define T Bzip2_T
struct T {
FILE *fp;
#ifdef HAVE_BZLIB
BZFILE *bzfile;
#endif
......@@ -46,6 +47,8 @@ Bzip2_new (char *filename) {
if (fp == NULL) {
fprintf(stderr,"Unable to open bzip2 file %s\n",filename);
exit(9);
} else {
new->fp = fp;
}
new->bzfile = BZ2_bzReadOpen(&error,fp,/*small*/0,/*verbosity*/0,/*unused*/NULL,/*nunused*/0);
......@@ -73,6 +76,7 @@ Bzip2_free (T *old) {
fprintf(stderr,"BZ2_bzReadClose gave error %d\n",error);
exit(9);
}
fclose((*old)->fp);
#endif
FREE((*old)->buffer);
......