FreeBSD Bugzilla – Attachment 187280 Details for
Bug 223094
biology/htslib biology/samtools biology/bcftools: update to 1.6
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[patch]
svn diff for biology/samtools
samtools-1.6.diff (text/plain), 38.20 KB, created by
Motomichi Matsuzaki
on 2017-10-18 14:04:52 UTC
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Description:
svn diff for biology/samtools
Filename:
MIME Type:
Creator:
Motomichi Matsuzaki
Created:
2017-10-18 14:04:52 UTC
Size:
38.20 KB
patch
obsolete
>Index: Makefile >=================================================================== >--- Makefile (revision 452329) >+++ Makefile (working copy) >@@ -2,7 +2,7 @@ > # $FreeBSD$ > > PORTNAME= samtools >-PORTVERSION= 1.3.1 >+PORTVERSION= 1.6 > CATEGORIES= biology > > MAINTAINER= cartwright@asu.edu >@@ -11,34 +11,22 @@ > LICENSE= MIT > LICENSE_FILE= ${WRKSRC}/LICENSE > >-BUILD_DEPENDS= htslib>=1.3:biology/htslib >+BUILD_DEPENDS= htslib>=1.6:biology/htslib > LIB_DEPENDS= libhts.so:biology/htslib > TEST_DEPENDS= bash:shells/bash > > USE_GITHUB= yes > >-USES= autoreconf gmake ncurses perl5 shebangfix >+USES= autoreconf gmake ncurses perl5 python shebangfix > USE_PERL5= test >+PYTHON_NO_DEPENDS= yes > GNU_CONFIGURE= yes > SUB_FILES= pkg-message >-SHEBANG_FILES= misc/*.pl misc/plot-bamstats test/test.pl >+SHEBANG_FILES= misc/*.pl misc/*.py misc/plot-bamstats test/test.pl > > CPPFLAGS+= -I${LOCALBASE}/include > LDFLAGS+= -L${LOCALBASE}/lib > >-MAKE_ENV= INSTALL_LIB="${INSTALL_LIB}" \ >- INSTALL_DATA="${INSTALL_DATA}" \ >- INSTALL_PROGRAM="${INSTALL_PROGRAM}" \ >- INSTALL_SCRIPT="${INSTALL_SCRIPT}" \ >- INSTALL_DIR="${MKDIR}" >- >-PLIST_SUB= PORTVERSION="${PORTVERSION}" >- > TEST_TARGET= test > >-post-patch: >- @${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' ${WRKSRC}/configure.ac >- ${CP} ${FILESDIR}/ax_with_htslib.m4 ${WRKSRC}/ >- ${CP} ${FILESDIR}/ax_with_curses.m4 ${WRKSRC}/ >- > .include <bsd.port.mk> >Index: distinfo >=================================================================== >--- distinfo (revision 452329) >+++ distinfo (working copy) >@@ -1,3 +1,3 @@ >-TIMESTAMP = 1463691050 >-SHA256 (samtools-samtools-1.3.1_GH0.tar.gz) = 30752c7b92cd9e146f4017983b2a41beb58c8966e93572cea76a14719f95a768 >-SIZE (samtools-samtools-1.3.1_GH0.tar.gz) = 3757176 >+TIMESTAMP = 1508304738 >+SHA256 (samtools-samtools-1.6_GH0.tar.gz) = c0d1ffefe441297ee0eec0e032ac3131519f82fd1a11d38fbcec19e2d5822b28 >+SIZE (samtools-samtools-1.6_GH0.tar.gz) = 4014195 >Index: files/ax_with_curses.m4 >=================================================================== >--- files/ax_with_curses.m4 (revision 452329) >+++ files/ax_with_curses.m4 (working copy) >@@ -1,518 +0,0 @@ >-# =========================================================================== >-# http://www.gnu.org/software/autoconf-archive/ax_with_curses.html >-# =========================================================================== >-# >-# SYNOPSIS >-# >-# AX_WITH_CURSES >-# >-# DESCRIPTION >-# >-# This macro checks whether a SysV or X/Open-compatible Curses library is >-# present, along with the associated header file. The NcursesW >-# (wide-character) library is searched for first, followed by Ncurses, >-# then the system-default plain Curses. The first library found is the >-# one returned. >-# >-# The following options are understood: --with-ncursesw, --with-ncurses, >-# --without-ncursesw, --without-ncurses. The "--with" options force the >-# macro to use that particular library, terminating with an error if not >-# found. The "--without" options simply skip the check for that library. >-# The effect on the search pattern is: >-# >-# (no options) - NcursesW, Ncurses, Curses >-# --with-ncurses --with-ncursesw - NcursesW only [*] >-# --without-ncurses --with-ncursesw - NcursesW only [*] >-# --with-ncursesw - NcursesW only [*] >-# --with-ncurses --without-ncursesw - Ncurses only [*] >-# --with-ncurses - NcursesW, Ncurses [**] >-# --without-ncurses --without-ncursesw - Curses only >-# --without-ncursesw - Ncurses, Curses >-# --without-ncurses - NcursesW, Curses >-# >-# [*] If the library is not found, abort the configure script. >-# >-# [**] If the second library (Ncurses) is not found, abort configure. >-# >-# The following preprocessor symbols may be defined by this macro if the >-# appropriate conditions are met: >-# >-# HAVE_CURSES - if any SysV or X/Open Curses library found >-# HAVE_CURSES_ENHANCED - if library supports X/Open Enhanced functions >-# HAVE_CURSES_COLOR - if library supports color (enhanced functions) >-# HAVE_CURSES_OBSOLETE - if library supports certain obsolete features >-# HAVE_NCURSESW - if NcursesW (wide char) library is to be used >-# HAVE_NCURSES - if the Ncurses library is to be used >-# >-# HAVE_CURSES_H - if <curses.h> is present and should be used >-# HAVE_NCURSESW_H - if <ncursesw.h> should be used >-# HAVE_NCURSES_H - if <ncurses.h> should be used >-# HAVE_NCURSESW_CURSES_H - if <ncursesw/curses.h> should be used >-# HAVE_NCURSES_CURSES_H - if <ncurses/curses.h> should be used >-# >-# (These preprocessor symbols are discussed later in this document.) >-# >-# The following output variable is defined by this macro; it is precious >-# and may be overridden on the ./configure command line: >-# >-# CURSES_LIB - library to add to xxx_LDADD >-# >-# The library listed in CURSES_LIB is NOT added to LIBS by default. You >-# need to add CURSES_LIB to the appropriate xxx_LDADD line in your >-# Makefile.am. For example: >-# >-# prog_LDADD = @CURSES_LIB@ >-# >-# If CURSES_LIB is set on the configure command line (such as by running >-# "./configure CURSES_LIB=-lmycurses"), then the only header searched for >-# is <curses.h>. The user may use the CPPFLAGS precious variable to >-# override the standard #include search path. If the user needs to >-# specify an alternative path for a library (such as for a non-standard >-# NcurseW), the user should use the LDFLAGS variable. >-# >-# The following shell variables may be defined by this macro: >-# >-# ax_cv_curses - set to "yes" if any Curses library found >-# ax_cv_curses_enhanced - set to "yes" if Enhanced functions present >-# ax_cv_curses_color - set to "yes" if color functions present >-# ax_cv_curses_obsolete - set to "yes" if obsolete features present >-# >-# ax_cv_ncursesw - set to "yes" if NcursesW library found >-# ax_cv_ncurses - set to "yes" if Ncurses library found >-# ax_cv_plaincurses - set to "yes" if plain Curses library found >-# ax_cv_curses_which - set to "ncursesw", "ncurses", "plaincurses" or "no" >-# >-# These variables can be used in your configure.ac to determine the level >-# of support you need from the Curses library. For example, if you must >-# have either Ncurses or NcursesW, you could include: >-# >-# AX_WITH_CURSES >-# if test "x$ax_cv_ncursesw" != xyes && test "x$ax_cv_ncurses" != xyes; then >-# AC_MSG_ERROR([requires either NcursesW or Ncurses library]) >-# fi >-# >-# If any Curses library will do (but one must be present and must support >-# color), you could use: >-# >-# AX_WITH_CURSES >-# if test "x$ax_cv_curses" != xyes || test "x$ax_cv_curses_color" != xyes; then >-# AC_MSG_ERROR([requires an X/Open-compatible Curses library with color]) >-# fi >-# >-# Certain preprocessor symbols and shell variables defined by this macro >-# can be used to determine various features of the Curses library. In >-# particular, HAVE_CURSES and ax_cv_curses are defined if the Curses >-# library found conforms to the traditional SysV and/or X/Open Base Curses >-# definition. Any working Curses library conforms to this level. >-# >-# HAVE_CURSES_ENHANCED and ax_cv_curses_enhanced are defined if the >-# library supports the X/Open Enhanced Curses definition. In particular, >-# the wide-character types attr_t, cchar_t and wint_t, the functions >-# wattr_set() and wget_wch() and the macros WA_NORMAL and _XOPEN_CURSES >-# are checked. The Ncurses library does NOT conform to this definition, >-# although NcursesW does. >-# >-# HAVE_CURSES_COLOR and ax_cv_curses_color are defined if the library >-# supports color functions and macros such as COLOR_PAIR, A_COLOR, >-# COLOR_WHITE, COLOR_RED and init_pair(). These are NOT part of the >-# X/Open Base Curses definition, but are part of the Enhanced set of >-# functions. The Ncurses library DOES support these functions, as does >-# NcursesW. >-# >-# HAVE_CURSES_OBSOLETE and ax_cv_curses_obsolete are defined if the >-# library supports certain features present in SysV and BSD Curses but not >-# defined in the X/Open definition. In particular, the functions >-# getattrs(), getcurx() and getmaxx() are checked. >-# >-# To use the HAVE_xxx_H preprocessor symbols, insert the following into >-# your system.h (or equivalent) header file: >-# >-# #if defined HAVE_NCURSESW_CURSES_H >-# # include <ncursesw/curses.h> >-# #elif defined HAVE_NCURSESW_H >-# # include <ncursesw.h> >-# #elif defined HAVE_NCURSES_CURSES_H >-# # include <ncurses/curses.h> >-# #elif defined HAVE_NCURSES_H >-# # include <ncurses.h> >-# #elif defined HAVE_CURSES_H >-# # include <curses.h> >-# #else >-# # error "SysV or X/Open-compatible Curses header file required" >-# #endif >-# >-# For previous users of this macro: you should not need to change anything >-# in your configure.ac or Makefile.am, as the previous (serial 10) >-# semantics are still valid. However, you should update your system.h (or >-# equivalent) header file to the fragment shown above. You are encouraged >-# also to make use of the extended functionality provided by this version >-# of AX_WITH_CURSES, as well as in the additional macros >-# AX_WITH_CURSES_PANEL, AX_WITH_CURSES_MENU and AX_WITH_CURSES_FORM. >-# >-# LICENSE >-# >-# Copyright (c) 2009 Mark Pulford <mark@kyne.com.au> >-# Copyright (c) 2009 Damian Pietras <daper@daper.net> >-# Copyright (c) 2012 Reuben Thomas <rrt@sc3d.org> >-# Copyright (c) 2011 John Zaitseff <J.Zaitseff@zap.org.au> >-# >-# 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 3 of the License, 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, the respective Autoconf Macro's copyright owner >-# gives unlimited permission to copy, distribute and modify the configure >-# scripts that are the output of Autoconf when processing the Macro. You >-# need not follow the terms of the GNU General Public License when using >-# or distributing such scripts, even though portions of the text of the >-# Macro appear in them. The GNU General Public License (GPL) does govern >-# all other use of the material that constitutes the Autoconf Macro. >-# >-# This special exception to the GPL applies to versions of the Autoconf >-# Macro released by the Autoconf Archive. When you make and distribute a >-# modified version of the Autoconf Macro, you may extend this special >-# exception to the GPL to apply to your modified version as well. >- >-#serial 15 >- >-AU_ALIAS([MP_WITH_CURSES], [AX_WITH_CURSES]) >-AC_DEFUN([AX_WITH_CURSES], [ >- AC_ARG_VAR([CURSES_LIB], [linker library for Curses, e.g. -lcurses]) >- AC_ARG_WITH([ncurses], [AS_HELP_STRING([--with-ncurses], >- [force the use of Ncurses or NcursesW])], >- [], [with_ncurses=check]) >- AC_ARG_WITH([ncursesw], [AS_HELP_STRING([--without-ncursesw], >- [do not use NcursesW (wide character support)])], >- [], [with_ncursesw=check]) >- >- ax_saved_LIBS=$LIBS >- AS_IF([test "x$with_ncurses" = xyes || test "x$with_ncursesw" = xyes], >- [ax_with_plaincurses=no], [ax_with_plaincurses=check]) >- >- ax_cv_curses_which=no >- >- # Test for NcursesW >- >- AS_IF([test "x$CURSES_LIB" = x && test "x$with_ncursesw" != xno], [ >- LIBS="$ax_saved_LIBS -lncursesw" >- >- AC_CACHE_CHECK([for NcursesW wide-character library], [ax_cv_ncursesw], [ >- AC_LINK_IFELSE([AC_LANG_CALL([], [initscr])], >- [ax_cv_ncursesw=yes], [ax_cv_ncursesw=no]) >- ]) >- AS_IF([test "x$ax_cv_ncursesw" = xno && test "x$with_ncursesw" = xyes], [ >- AC_MSG_ERROR([--with-ncursesw specified but could not find NcursesW library]) >- ]) >- >- AS_IF([test "x$ax_cv_ncursesw" = xyes], [ >- ax_cv_curses=yes >- ax_cv_curses_which=ncursesw >- CURSES_LIB="-lncursesw" >- AC_DEFINE([HAVE_NCURSESW], [1], [Define to 1 if the NcursesW library is present]) >- AC_DEFINE([HAVE_CURSES], [1], [Define to 1 if a SysV or X/Open compatible Curses library is present]) >- >- AC_CACHE_CHECK([for working ncursesw/curses.h], [ax_cv_header_ncursesw_curses_h], [ >- AC_LINK_IFELSE([AC_LANG_PROGRAM([[ >- @%:@define _XOPEN_SOURCE_EXTENDED 1 >- @%:@include <ncursesw/curses.h> >- ]], [[ >- chtype a = A_BOLD; >- int b = KEY_LEFT; >- chtype c = COLOR_PAIR(1) & A_COLOR; >- attr_t d = WA_NORMAL; >- cchar_t e; >- wint_t f; >- int g = getattrs(stdscr); >- int h = getcurx(stdscr) + getmaxx(stdscr); >- initscr(); >- init_pair(1, COLOR_WHITE, COLOR_RED); >- wattr_set(stdscr, d, 0, NULL); >- wget_wch(stdscr, &f); >- ]])], >- [ax_cv_header_ncursesw_curses_h=yes], >- [ax_cv_header_ncursesw_curses_h=no]) >- ]) >- AS_IF([test "x$ax_cv_header_ncursesw_curses_h" = xyes], [ >- ax_cv_curses_enhanced=yes >- ax_cv_curses_color=yes >- ax_cv_curses_obsolete=yes >- AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions]) >- AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) >- AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features]) >- AC_DEFINE([HAVE_NCURSESW_CURSES_H], [1], [Define to 1 if <ncursesw/curses.h> is present]) >- ]) >- >- AC_CACHE_CHECK([for working ncursesw.h], [ax_cv_header_ncursesw_h], [ >- AC_LINK_IFELSE([AC_LANG_PROGRAM([[ >- @%:@define _XOPEN_SOURCE_EXTENDED 1 >- @%:@include <ncursesw.h> >- ]], [[ >- chtype a = A_BOLD; >- int b = KEY_LEFT; >- chtype c = COLOR_PAIR(1) & A_COLOR; >- attr_t d = WA_NORMAL; >- cchar_t e; >- wint_t f; >- int g = getattrs(stdscr); >- int h = getcurx(stdscr) + getmaxx(stdscr); >- initscr(); >- init_pair(1, COLOR_WHITE, COLOR_RED); >- wattr_set(stdscr, d, 0, NULL); >- wget_wch(stdscr, &f); >- ]])], >- [ax_cv_header_ncursesw_h=yes], >- [ax_cv_header_ncursesw_h=no]) >- ]) >- AS_IF([test "x$ax_cv_header_ncursesw_h" = xyes], [ >- ax_cv_curses_enhanced=yes >- ax_cv_curses_color=yes >- ax_cv_curses_obsolete=yes >- AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions]) >- AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) >- AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features]) >- AC_DEFINE([HAVE_NCURSESW_H], [1], [Define to 1 if <ncursesw.h> is present]) >- ]) >- >- AC_CACHE_CHECK([for working ncurses.h], [ax_cv_header_ncurses_h_with_ncursesw], [ >- AC_LINK_IFELSE([AC_LANG_PROGRAM([[ >- @%:@define _XOPEN_SOURCE_EXTENDED 1 >- @%:@include <ncurses.h> >- ]], [[ >- chtype a = A_BOLD; >- int b = KEY_LEFT; >- chtype c = COLOR_PAIR(1) & A_COLOR; >- attr_t d = WA_NORMAL; >- cchar_t e; >- wint_t f; >- int g = getattrs(stdscr); >- int h = getcurx(stdscr) + getmaxx(stdscr); >- initscr(); >- init_pair(1, COLOR_WHITE, COLOR_RED); >- wattr_set(stdscr, d, 0, NULL); >- wget_wch(stdscr, &f); >- ]])], >- [ax_cv_header_ncurses_h_with_ncursesw=yes], >- [ax_cv_header_ncurses_h_with_ncursesw=no]) >- ]) >- AS_IF([test "x$ax_cv_header_ncurses_h_with_ncursesw" = xyes], [ >- ax_cv_curses_enhanced=yes >- ax_cv_curses_color=yes >- ax_cv_curses_obsolete=yes >- AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions]) >- AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) >- AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features]) >- AC_DEFINE([HAVE_NCURSES_H], [1], [Define to 1 if <ncurses.h> is present]) >- ]) >- >- AS_IF([test "x$ax_cv_header_ncursesw_curses_h" = xno && test "x$ax_cv_header_ncursesw_h" = xno && test "x$ax_cv_header_ncurses_h_with_ncursesw" = xno], [ >- AC_MSG_WARN([could not find a working ncursesw/curses.h, ncursesw.h or ncurses.h]) >- ]) >- ]) >- ]) >- >- # Test for Ncurses >- >- AS_IF([test "x$CURSES_LIB" = x && test "x$with_ncurses" != xno && test "x$ax_cv_curses_which" = xno], [ >- LIBS="$ax_saved_LIBS -lncurses" >- >- AC_CACHE_CHECK([for Ncurses library], [ax_cv_ncurses], [ >- AC_LINK_IFELSE([AC_LANG_CALL([], [initscr])], >- [ax_cv_ncurses=yes], [ax_cv_ncurses=no]) >- ]) >- AS_IF([test "x$ax_cv_ncurses" = xno && test "x$with_ncurses" = xyes], [ >- AC_MSG_ERROR([--with-ncurses specified but could not find Ncurses library]) >- ]) >- >- AS_IF([test "x$ax_cv_ncurses" = xyes], [ >- ax_cv_curses=yes >- ax_cv_curses_which=ncurses >- CURSES_LIB="-lncurses" >- AC_DEFINE([HAVE_NCURSES], [1], [Define to 1 if the Ncurses library is present]) >- AC_DEFINE([HAVE_CURSES], [1], [Define to 1 if a SysV or X/Open compatible Curses library is present]) >- >- AC_CACHE_CHECK([for working ncurses/curses.h], [ax_cv_header_ncurses_curses_h], [ >- AC_LINK_IFELSE([AC_LANG_PROGRAM([[ >- @%:@include <ncurses/curses.h> >- ]], [[ >- chtype a = A_BOLD; >- int b = KEY_LEFT; >- chtype c = COLOR_PAIR(1) & A_COLOR; >- int g = getattrs(stdscr); >- int h = getcurx(stdscr) + getmaxx(stdscr); >- initscr(); >- init_pair(1, COLOR_WHITE, COLOR_RED); >- ]])], >- [ax_cv_header_ncurses_curses_h=yes], >- [ax_cv_header_ncurses_curses_h=no]) >- ]) >- AS_IF([test "x$ax_cv_header_ncurses_curses_h" = xyes], [ >- ax_cv_curses_color=yes >- ax_cv_curses_obsolete=yes >- AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) >- AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features]) >- AC_DEFINE([HAVE_NCURSES_CURSES_H], [1], [Define to 1 if <ncurses/curses.h> is present]) >- ]) >- >- AC_CACHE_CHECK([for working ncurses.h], [ax_cv_header_ncurses_h], [ >- AC_LINK_IFELSE([AC_LANG_PROGRAM([[ >- @%:@include <ncurses.h> >- ]], [[ >- chtype a = A_BOLD; >- int b = KEY_LEFT; >- chtype c = COLOR_PAIR(1) & A_COLOR; >- int g = getattrs(stdscr); >- int h = getcurx(stdscr) + getmaxx(stdscr); >- initscr(); >- init_pair(1, COLOR_WHITE, COLOR_RED); >- ]])], >- [ax_cv_header_ncurses_h=yes], >- [ax_cv_header_ncurses_h=no]) >- ]) >- AS_IF([test "x$ax_cv_header_ncurses_h" = xyes], [ >- ax_cv_curses_color=yes >- ax_cv_curses_obsolete=yes >- AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) >- AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features]) >- AC_DEFINE([HAVE_NCURSES_H], [1], [Define to 1 if <ncurses.h> is present]) >- ]) >- >- AS_IF([test "x$ax_cv_header_ncurses_curses_h" = xno && test "x$ax_cv_header_ncurses_h" = xno], [ >- AC_MSG_WARN([could not find a working ncurses/curses.h or ncurses.h]) >- ]) >- ]) >- ]) >- >- # Test for plain Curses (or if CURSES_LIB was set by user) >- >- AS_IF([test "x$with_plaincurses" != xno && test "x$ax_cv_curses_which" = xno], [ >- AS_IF([test "x$CURSES_LIB" != x], [ >- LIBS="$ax_saved_LIBS $CURSES_LIB" >- ], [ >- LIBS="$ax_saved_LIBS -lcurses" >- ]) >- >- AC_CACHE_CHECK([for Curses library], [ax_cv_plaincurses], [ >- AC_LINK_IFELSE([AC_LANG_CALL([], [initscr])], >- [ax_cv_plaincurses=yes], [ax_cv_plaincurses=no]) >- ]) >- >- AS_IF([test "x$ax_cv_plaincurses" = xyes], [ >- ax_cv_curses=yes >- ax_cv_curses_which=plaincurses >- AS_IF([test "x$CURSES_LIB" = x], [ >- CURSES_LIB="-lcurses" >- ]) >- AC_DEFINE([HAVE_CURSES], [1], [Define to 1 if a SysV or X/Open compatible Curses library is present]) >- >- # Check for base conformance (and header file) >- >- AC_CACHE_CHECK([for working curses.h], [ax_cv_header_curses_h], [ >- AC_LINK_IFELSE([AC_LANG_PROGRAM([[ >- @%:@include <curses.h> >- ]], [[ >- chtype a = A_BOLD; >- int b = KEY_LEFT; >- initscr(); >- ]])], >- [ax_cv_header_curses_h=yes], >- [ax_cv_header_curses_h=no]) >- ]) >- AS_IF([test "x$ax_cv_header_curses_h" = xyes], [ >- AC_DEFINE([HAVE_CURSES_H], [1], [Define to 1 if <curses.h> is present]) >- >- # Check for X/Open Enhanced conformance >- >- AC_CACHE_CHECK([for X/Open Enhanced Curses conformance], [ax_cv_plaincurses_enhanced], [ >- AC_LINK_IFELSE([AC_LANG_PROGRAM([[ >- @%:@define _XOPEN_SOURCE_EXTENDED 1 >- @%:@include <curses.h> >- @%:@ifndef _XOPEN_CURSES >- @%:@error "this Curses library is not enhanced" >- "this Curses library is not enhanced" >- @%:@endif >- ]], [[ >- chtype a = A_BOLD; >- int b = KEY_LEFT; >- chtype c = COLOR_PAIR(1) & A_COLOR; >- attr_t d = WA_NORMAL; >- cchar_t e; >- wint_t f; >- initscr(); >- init_pair(1, COLOR_WHITE, COLOR_RED); >- wattr_set(stdscr, d, 0, NULL); >- wget_wch(stdscr, &f); >- ]])], >- [ax_cv_plaincurses_enhanced=yes], >- [ax_cv_plaincurses_enhanced=no]) >- ]) >- AS_IF([test "x$ax_cv_plaincurses_enhanced" = xyes], [ >- ax_cv_curses_enhanced=yes >- ax_cv_curses_color=yes >- AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions]) >- AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) >- ]) >- >- # Check for color functions >- >- AC_CACHE_CHECK([for Curses color functions], [ax_cv_plaincurses_color], [ >- AC_LINK_IFELSE([AC_LANG_PROGRAM([[ >- @%:@define _XOPEN_SOURCE_EXTENDED 1 >- @%:@include <curses.h> >- ]], [[ >- chtype a = A_BOLD; >- int b = KEY_LEFT; >- chtype c = COLOR_PAIR(1) & A_COLOR; >- initscr(); >- init_pair(1, COLOR_WHITE, COLOR_RED); >- ]])], >- [ax_cv_plaincurses_color=yes], >- [ax_cv_plaincurses_color=no]) >- ]) >- AS_IF([test "x$ax_cv_plaincurses_color" = xyes], [ >- ax_cv_curses_color=yes >- AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) >- ]) >- >- # Check for obsolete functions >- >- AC_CACHE_CHECK([for obsolete Curses functions], [ax_cv_plaincurses_obsolete], [ >- AC_LINK_IFELSE([AC_LANG_PROGRAM([[ >- @%:@include <curses.h> >- ]], [[ >- chtype a = A_BOLD; >- int b = KEY_LEFT; >- int g = getattrs(stdscr); >- int h = getcurx(stdscr) + getmaxx(stdscr); >- initscr(); >- ]])], >- [ax_cv_plaincurses_obsolete=yes], >- [ax_cv_plaincurses_obsolete=no]) >- ]) >- AS_IF([test "x$ax_cv_plaincurses_obsolete" = xyes], [ >- ax_cv_curses_obsolete=yes >- AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features]) >- ]) >- ]) >- >- AS_IF([test "x$ax_cv_header_curses_h" = xno], [ >- AC_MSG_WARN([could not find a working curses.h]) >- ]) >- ]) >- ]) >- >- AS_IF([test "x$ax_cv_curses" != xyes], [ax_cv_curses=no]) >- AS_IF([test "x$ax_cv_curses_enhanced" != xyes], [ax_cv_curses_enhanced=no]) >- AS_IF([test "x$ax_cv_curses_color" != xyes], [ax_cv_curses_color=no]) >- AS_IF([test "x$ax_cv_curses_obsolete" != xyes], [ax_cv_curses_obsolete=no]) >- >- LIBS=$ax_saved_LIBS >-])dnl >Index: files/ax_with_htslib.m4 >=================================================================== >--- files/ax_with_htslib.m4 (revision 452329) >+++ files/ax_with_htslib.m4 (working copy) >@@ -1,140 +0,0 @@ >-# =========================================================================== >-# http://www.gnu.org/software/autoconf-archive/ax_with_htslib.html >-# =========================================================================== >-# >-# SYNOPSIS >-# >-# AX_WITH_HTSLIB >-# >-# DESCRIPTION >-# >-# This macro checks whether HTSlib <http://www.htslib.org/> is installed >-# or nearby, and adds a --with-htslib=DIR option to the configure script >-# for specifying the location. It locates either an installation prefix >-# (with 'include' and 'lib' subdirectories) or an HTSlib source tree, as >-# HTSlib is fast-moving and users may wish to use an in-development tree. >-# >-# Different checks occur depending on the --with-htslib argument given: >-# >-# With --with-htslib=DIR, checks whether DIR is a source tree or contains >-# a working installation. >-# By default, searches for a source tree (with a name matching htslib*) >-# within or alongside $srcdir. Produces AC_MSG_ERROR if there are >-# several equally-likely candidates. If there are none, checks for >-# a working default installation. >-# With --with-htslib=system, checks for a working default installation. >-# >-# If a source tree is found or specified, it is added to AC_CONFIG_SUBDIRS >-# (which unfortunately may cause a "you should use literals" warning when >-# autoconf is run). >-# >-# The following output variables are set by this macro: >-# >-# HTSDIR Directory containing HTSlib source tree >-# HTSLIB_CPPFLAGS Preprocessor flags for compiling with HTSlib >-# HTSLIB_LDFLAGS Linker flags for linking with HTSlib >-# >-# The following shell variables may be defined: >-# >-# ax_cv_htslib Set to "yes" if HTSlib was found >-# ax_cv_htslib_which Set to "source", "install", or "none" >-# >-# LICENSE >-# >-# Copyright (C) 2015 Genome Research Ltd >-# >-# Copying and distribution of this file, with or without modification, are >-# permitted in any medium without royalty provided the copyright notice >-# and this notice are preserved. This file is offered as-is, without any >-# warranty. >- >-#serial 1 >- >-AC_DEFUN([AX_WITH_HTSLIB], >-[AC_ARG_WITH([htslib], >- [AS_HELP_STRING([--with-htslib=DIR], >- [use the HTSlib source tree or installation in DIR]) >-dnl Not indented, to avoid extra whitespace outwith AS_HELP_STRING() >-AS_HELP_STRING([--with-htslib=system], >- [use only a system HTSlib installation])], >- [], [with_htslib=search]) >- >-case $with_htslib in >-yes|search) >- AC_MSG_CHECKING([location of HTSlib source tree]) >- case $srcdir in >- .) srcp= ;; >- *) srcp=$srcdir/ ;; >- esac >- found= >- for dir in ${srcp}htslib* -- ${srcp}../htslib -- ${srcp}../htslib* >- do >- if test "$dir" = "--"; then >- test -n "$found" && break >- elif test -f "$dir/hts.c" && test -f "$dir/htslib/hts.h"; then >- found="${found}1" >- HTSDIR=$dir >- fi >- done >- if test -z "$found"; then >- AC_MSG_RESULT([none found]) >- ax_cv_htslib_which=system >- elif test "$found" = 1; then >- AC_MSG_RESULT([$HTSDIR]) >- ax_cv_htslib_which=source >- else >- AC_MSG_RESULT([several directories found]) >- AC_MSG_ERROR([use --with-htslib=DIR to select which HTSlib to use]) >- fi >- ;; >-no) ax_cv_htslib_which=none ;; >-system) ax_cv_htslib_which=system ;; >-*) >- HTSDIR=$with_htslib >- if test -f "$HTSDIR/hts.c" && test -f "$HTSDIR/htslib/hts.h"; then >- ax_cv_htslib_which=source >- else >- ax_cv_htslib_which=install >- fi >- ;; >-esac >- >-case $ax_cv_htslib_which in >-#source) >-# ax_cv_htslib=yes >-# HTSLIB_CPPFLAGS="-I$HTSDIR" >-# HTSLIB_LDFLAGS="-L$HTSDIR" >-# # We can't use a literal, because $HTSDIR is user-provided and variable >-# AC_CONFIG_SUBDIRS($HTSDIR) >-# ;; >-system) >- AC_CHECK_HEADER([htslib/sam.h], >- [AC_CHECK_LIB(hts, hts_version, [ax_cv_htslib=yes], [ax_cv_htslib=no])], >- [ax_cv_htslib=no], [;]) >- ax_cv_htslib_which=install >- HTSDIR= >- HTSLIB_CPPFLAGS= >- HTSLIB_LDFLAGS= >- ;; >-install) >- ax_saved_CPPFLAGS=$CPPFLAGS >- ax_saved_LDFLAGS=$LDFLAGS >- HTSLIB_CPPFLAGS="-I$HTSDIR/include" >- HTSLIB_LDFLAGS="-L$HTSDIR/lib" >- CPPFLAGS="$CPPFLAGS $HTSLIB_CPPFLAGS" >- LDFLAGS="$LDFLAGS $HTSLIB_LDFLAGS" >- AC_CHECK_HEADER([htslib/sam.h], >- [AC_CHECK_LIB(hts, hts_version, [ax_cv_htslib=yes], [ax_cv_htslib=no])], >- [ax_cv_htslib=no], [;]) >- HTSDIR= >- CPPFLAGS=$ax_saved_CPPFLAGS >- LDFLAGS=$ax_saved_LDFLAGS >- ;; >-none) >- ax_cv_htslib=no >- ;; >-esac >- >-AC_SUBST([HTSDIR]) >-AC_SUBST([HTSLIB_CPPFLAGS]) >-AC_SUBST([HTSLIB_LDFLAGS])]) >Index: files/patch-Makefile >=================================================================== >--- files/patch-Makefile (revision 452329) >+++ files/patch-Makefile (working copy) >@@ -1,11 +1,11 @@ >---- Makefile.orig 2016-04-22 09:22:44 UTC >+--- Makefile.orig 2017-09-28 11:12:01 UTC > +++ Makefile >-@@ -38,18 +38,18 @@ AOBJS= bam_index.o bam_plcmd.o sam_ >+@@ -40,23 +40,22 @@ AOBJS= bam_index.o bam_plcmd.o sam_ > bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o \ >- bam_quickcheck.o bam_addrprg.o >+ bam_quickcheck.o bam_addrprg.o bam_markdup.o > > -prefix = /usr/local >-+prefix = ${STAGEDIR}${PREFIX} >++prefix = ${PREFIX} > exec_prefix = $(prefix) > bindir = $(exec_prefix)/bin > datarootdir = $(prefix)/share >@@ -13,46 +13,22 @@ > +mandir = $(prefix)/man > man1dir = $(mandir)/man1 > >--MKDIR_P = mkdir -p >+ # Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS) >+-misc_bindir = $(bindir) >++misc_bindir = $(bindir)/samtools_misc >+ >+ MKDIR_P = mkdir -p > -INSTALL = install -p >--INSTALL_PROGRAM = $(INSTALL) > -INSTALL_DATA = $(INSTALL) -m 644 > -INSTALL_DIR = $(MKDIR_P) -m 755 >-+#MKDIR_P = mkdir -p >-+#INSTALL = install -p >-+#INSTALL_PROGRAM = $(INSTALL) >-+#INSTALL_DATA = $(INSTALL) -m 644 >-+#INSTALL_DIR = $(MKDIR_P) -m 755 >+-INSTALL_MAN = $(INSTALL_DATA) >+-INSTALL_PROGRAM = $(INSTALL) >+-INSTALL_SCRIPT = $(INSTALL_PROGRAM) >++INSTALL_DATA = ${BSD_INSTALL_DATA} >++INSTALL_DIR = $(MKDIR_P) >++INSTALL_MAN = ${BSD_INSTALL_MAN} >++INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM} >++INSTALL_SCRIPT = ${BSD_INSTALL_SCRIPT} > > > PROGRAMS = samtools >-@@ -59,7 +59,6 @@ BUILT_MISC_PROGRAMS = \ >- misc/md5fa misc/md5sum-lite misc/wgsim >- >- MISC_PROGRAMS = \ >-- $(BUILT_MISC_PROGRAMS) \ >- misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl \ >- misc/interpolate_sam.pl misc/novo2sam.pl \ >- misc/plot-bamstats misc/psl2sam.pl \ >-@@ -82,7 +81,7 @@ all: $(PROGRAMS) $(BUILT_MISC_PROGRAMS) >- # TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally >- ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) >- ALL_LDFLAGS = -rdynamic $(HTSLIB_LDFLAGS) $(LDFLAGS) >--ALL_LIBS = -lz -ldl $(LIBS) >-+ALL_LIBS = -lz $(LIBS) >- >- # Usually config.mk and config.h are generated by running configure >- # or config.status, but if those aren't used create defaults here. >-@@ -280,8 +279,10 @@ misc/maq2sam-long.o: misc/maq2sam.c conf >- >- >- install: $(PROGRAMS) $(BUILT_MISC_PROGRAMS) >-- $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir) >-- $(INSTALL_PROGRAM) $(PROGRAMS) $(MISC_PROGRAMS) $(DESTDIR)$(bindir) >-+ $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(bindir)/samtools_misc $(DESTDIR)$(man1dir) >-+ $(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir) >-+ $(INSTALL_PROGRAM) $(BUILT_MISC_PROGRAMS) $(DESTDIR)$(bindir)/samtools_misc >-+ $(INSTALL_SCRIPT) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)/samtools_misc >- $(INSTALL_DATA) samtools.1 misc/wgsim.1 $(DESTDIR)$(man1dir) >- >- >Index: files/patch-configure.ac >=================================================================== >--- files/patch-configure.ac (revision 452329) >+++ files/patch-configure.ac (working copy) >@@ -1,19 +0,0 @@ >---- configure.ac.orig 2015-12-15 21:26:20 UTC >-+++ configure.ac >-@@ -23,12 +23,15 @@ >- # DEALINGS IN THE SOFTWARE. >- >- dnl Process this file with autoconf to produce a configure script >--AC_INIT([Samtools], m4_esyscmd_s([make print-version]), >-+AC_INIT([Samtools], [1.3], >- [samtools-help@lists.sourceforge.net], [], [http://www.htslib.org/]) >- AC_PREREQ([2.63]) dnl This version introduced 4-argument AC_CHECK_HEADER >- AC_CONFIG_SRCDIR([bamtk.c]) >- AC_CONFIG_HEADERS([config.h]) >- >-+m4_include([ax_with_htslib.m4]) >-+m4_include([ax_with_curses.m4]) >-+ >- dnl Copyright notice to be copied into the generated configure script >- AC_COPYRIGHT([Portions copyright (C) 2015 Genome Research Ltd. >- >Index: files/patch-dict.c >=================================================================== >--- files/patch-dict.c (revision 452329) >+++ files/patch-dict.c (working copy) >@@ -1,10 +0,0 @@ >---- dict.c.orig 2015-12-15 21:26:20 UTC >-+++ dict.c >-@@ -25,6 +25,7 @@ DEALINGS IN THE SOFTWARE. */ >- #include <stdio.h> >- #include <zlib.h> >- #include <getopt.h> >-+#include <unistd.h> >- #include "htslib/kseq.h" >- #include "htslib/hts.h" >- >Index: files/patch-errmod.c >=================================================================== >--- files/patch-errmod.c (revision 452329) >+++ files/patch-errmod.c (working copy) >@@ -1,16 +0,0 @@ >---- errmod.c.orig 2015-12-15 21:26:20 UTC >-+++ errmod.c >-@@ -24,6 +24,13 @@ FROM, OUT OF OR IN CONNECTION WITH THE S >- DEALINGS IN THE SOFTWARE. */ >- >- #include <math.h> >-+ >-+#include <sys/param.h> >-+#if defined(__FreeBSD__) && (__FreeBSD_version < 1000034) >-+# define logl(x) log(x) >-+# define expl(x) exp(x) >-+#endif >-+ >- #include "errmod.h" >- #include "htslib/ksort.h" >- KSORT_INIT_GENERIC(uint16_t) >Index: files/patch-test_test.pl >=================================================================== >--- files/patch-test_test.pl (revision 452329) >+++ files/patch-test_test.pl (working copy) >@@ -1,15 +1,6 @@ >---- test/test.pl.orig 2015-12-22 22:43:15 UTC >+--- test/test.pl.orig 2017-10-18 06:08:39 UTC > +++ test/test.pl >-@@ -136,7 +136,7 @@ sub _cmd >- else >- { >- # child >-- exec('/bin/bash', '-o','pipefail','-c', "($cmd) 2> $err_filename") or error("Cannot execute the command [/bin/sh -o pipefail -c $cmd]: $!"); >-+ exec('/usr/local/bin/bash', '-o','pipefail','-c', "($cmd) 2> $err_filename") or error("Cannot execute the command [/usr/local/bin/bash -o pipefail -c $cmd]: $!"); >- } >- } >- sub cmd >-@@ -560,7 +560,7 @@ sub test_usage >+@@ -636,7 +636,7 @@ sub test_usage > my $command = $args{cmd}; > my $commandpath = $$opts{bin}."/".$command; > my ($ret,$out,$err) = _cmd("$commandpath $args{redirection}"); >@@ -18,7 +9,7 @@ > > my @sections = ($err =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)|\z)/msg); > >-@@ -615,7 +615,7 @@ sub test_usage_subcommand >+@@ -694,7 +694,7 @@ sub test_usage_subcommand > my $commandpath = $$opts{bin}."/".$command; > my ($ret,$out,$err) = _cmd("$commandpath $subcommand $args{redirection}"); > >Index: files/pkg-message.in >=================================================================== >--- files/pkg-message.in (revision 452329) >+++ files/pkg-message.in (working copy) >@@ -3,5 +3,5 @@ > > Add that directory to your path if you want to use these tools. > >-Some of these tools depend on Perl5, and it will need to be installed to >+Some of these tools depend on Perl5/Python, and it will need to be installed to > use them.
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