biology/htslib biology/bcftools biology/samtools: Update to 1.6

PR:		223094
Submitted by:	mzaki@niid.go.jp
Approved by:	cartwright@asu.edu (maintainer)
Approved by:	olivier (mentor)
Differential Revision:	https://reviews.freebsd.org/D12768

10 files changed, 29 insertions, 777 deletions

diff --git a/biology/samtools/Makefile b/biology/samtools/Makefile
index 632d0a9c001e..da12548a1714 100644
--- a/biology/samtools/Makefile
+++ b/biology/samtools/Makefile
@@ -2,7 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	samtools
-PORTVERSION=	1.3.1
+PORTVERSION=	1.6
 CATEGORIES=	biology
 
 MAINTAINER=	cartwright@asu.edu
@@ -11,34 +11,22 @@ COMMENT=	Tools for manipulating next-generation sequencing data
 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>
diff --git a/biology/samtools/distinfo b/biology/samtools/distinfo
index 439a947c14cb..a0736b452989 100644
--- a/biology/samtools/distinfo
+++ b/biology/samtools/distinfo
@@ -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
diff --git a/biology/samtools/files/ax_with_curses.m4 b/biology/samtools/files/ax_with_curses.m4
deleted file mode 100644
index e4cbd31bae42..000000000000
--- a/biology/samtools/files/ax_with_curses.m4
+++ /dev/null
@@ -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
diff --git a/biology/samtools/files/ax_with_htslib.m4 b/biology/samtools/files/ax_with_htslib.m4
deleted file mode 100644
index f39e4eb1427b..000000000000
--- a/biology/samtools/files/ax_with_htslib.m4
+++ /dev/null
@@ -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])])
diff --git a/biology/samtools/files/patch-Makefile b/biology/samtools/files/patch-Makefile
index eaa977f79e05..afdbfd1ed1ab 100644
--- a/biology/samtools/files/patch-Makefile
+++ b/biology/samtools/files/patch-Makefile
@@ -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)
- 
- 
diff --git a/biology/samtools/files/patch-configure.ac b/biology/samtools/files/patch-configure.ac
deleted file mode 100644
index 94264e9994f1..000000000000
--- a/biology/samtools/files/patch-configure.ac
+++ /dev/null
@@ -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.
- 
diff --git a/biology/samtools/files/patch-dict.c b/biology/samtools/files/patch-dict.c
deleted file mode 100644
index 5f00387a43c0..000000000000
--- a/biology/samtools/files/patch-dict.c
+++ /dev/null
@@ -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"
- 
diff --git a/biology/samtools/files/patch-errmod.c b/biology/samtools/files/patch-errmod.c
deleted file mode 100644
index 4473c96af530..000000000000
--- a/biology/samtools/files/patch-errmod.c
+++ /dev/null
@@ -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)
diff --git a/biology/samtools/files/patch-test_test.pl b/biology/samtools/files/patch-test_test.pl
index 918afb8be324..c8450c500568 100644
--- a/biology/samtools/files/patch-test_test.pl
+++ b/biology/samtools/files/patch-test_test.pl
@@ -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}");
  
diff --git a/biology/samtools/files/pkg-message.in b/biology/samtools/files/pkg-message.in
index e996d1340a7e..388a94893ec9 100644
--- a/biology/samtools/files/pkg-message.in
+++ b/biology/samtools/files/pkg-message.in
@@ -3,5 +3,5 @@ The miscellaneous tools included with Samtools have been installed to
 
 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.