sci-biology/samtools: version bump to 1.3, to match htslib

* EAPI=6
* Added modern AX_WITH_CURSES that works with pkg-config
* Fixed incorrect symlinks for libbam.so

Package-Manager: portage-2.2.28

4 files changed, 998 insertions, 0 deletions

diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index fd88ba4947d3..d25774fee86c 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -4,3 +4,4 @@ DIST samtools-0.1.20.tar.gz 566387 SHA256 500019b4d1886ad995513d5ce8b413b14b51f1
 DIST samtools-1.0.tar.bz2 4459669 SHA256 7340b843663c3f54a902a06f2f73c68198f3a62d29a2ed20671139957f7fd7c0 SHA512 5b80995c522d08b06a4c559f60a5e200d9085be7f44c3c9618db91e3de85e36c1473e42715eae8175520d7da3df8245bafa82e625d2fc08e0197adb395851693 WHIRLPOOL 2aa0f8639da9b0b828ca7296969e5c600b0e5452ad3231b914e4a7be418700906a4d695c928eaf837b643255567ec82cfadf0b53007e0f1e3a956856f6c4c832
 DIST samtools-1.1.tar.bz2 4495373 SHA256 c24d26c303153d72b5bf3cc11f72c6c375a4ca1140cc485648c8c5473414b7f8 SHA512 a5552a6c8c4b0808b725b39ddb2fafa36c4f6623bfc7f84faadae7690223e4eec8d722af09c77145796ad9b3f01e04115dd0207207ccfafbb52ffc22d5fc09f0 WHIRLPOOL ed3131b2a8d8b4dab40b53d35a9b00b657670a949dc1597c91fbcd00392c1c1715a85a1d1e49bf0c73ae082738ccfb13d2c6809dbbeba17ff3028f6023ebc449
 DIST samtools-1.2.tar.bz2 4547126 SHA256 420e7a4a107fe37619b9d300b6379452eb8eb04a4a9b65c3ec69de82ccc26daa SHA512 4849c3274e732267516b63799f5430c5415d575d46eddf6b704dac51053281094b03b90dd9f5367bcd14c22fb0fb1bd6a412f7d4225f7be5f5385437c5d2101d WHIRLPOOL 273185764a807365a20c381769f987ef02d14ae8e20a3a7fd5af4344769c5fab68d7155523e8c0c8c3cc86092898c2c8454cce8f1560d415bc2b41549cdf04f4
+DIST samtools-1.3.tar.bz2 3978333 SHA256 beea4003c795a0a25224656815b4036f6864b8753053ed30c590bb052b70b60e SHA512 72920d4f0f10aa7b54ef448e03e6e769e1e07abd07388a2307d0e52548fa2909c03ca2c7eec5c63cf5b67724b2356833accb0079ce1486bb2ac66a45963a24ea WHIRLPOOL 3f798078100b4ed164f6c89d18cc8f62159437e2cfb2a228ac00f8d08313f7c39ef546214c0796c25a419c0a1065dc21d14b966fed769726b9b1975ec07e3b3e
diff --git a/sci-biology/samtools/files/samtools-1.3-buildsystem.patch b/sci-biology/samtools/files/samtools-1.3-buildsystem.patch
new file mode 100644
index 000000000000..61f6b03bd8ef
--- /dev/null
+++ b/sci-biology/samtools/files/samtools-1.3-buildsystem.patch
@@ -0,0 +1,174 @@
+--- samtools-1.3/Makefile
++++ samtools-1.3/Makefile
+@@ -21,11 +21,12 @@
+ # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ # DEALINGS IN THE SOFTWARE.
+ 
+-CC       = gcc
+-CPPFLAGS =
+-CFLAGS   = -g -Wall -O2
+-LDFLAGS  =
+-LIBS     =
++CC       ?= gcc
++CPPFLAGS +=
++CFLAGS   ?= -g -Wall -O2
++LDFLAGS  +=
++LIBS     +=
++BAMLIB   ?= libbam.a
+ 
+ DFLAGS=     -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE
+ LOBJS=      bam_aux.o bam.o bam_import.o sam.o \
+@@ -42,6 +43,7 @@
+ prefix      = /usr/local
+ exec_prefix = $(prefix)
+ bindir      = $(exec_prefix)/bin
++libdir     ?= $(exec_prefix)/lib
+ datarootdir = $(prefix)/share
+ mandir      = $(datarootdir)/man
+ man1dir     = $(mandir)/man1
+@@ -129,67 +131,74 @@
+ .c.o:
+ 	$(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ $<
+ 
++$(LOBJS):
++	$(CC) $(CFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $<
+ 
+-lib:libbam.a
++lib:libbam.a libbam.so.1.0
+ 
+ libbam.a:$(LOBJS)
+ 	$(AR) -csru $@ $(LOBJS)
+ 
+-samtools: $(AOBJS) libbam.a $(HTSLIB)
+-	$(CC) -pthread $(ALL_LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB_LIB) $(CURSES_LIB) -lm $(ALL_LIBS)
++libbam.so.1.0:$(LOBJS)
++	$(CC) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB) -lz
++	ln -sf $@ libbam.so.1
++	ln -sf $@ libbam.so
++
++samtools: $(AOBJS) lib
++	$(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) $(BAMLIB) $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz
+ 
+ bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h)
+ bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.h
+ bam_lpileup_h = bam_lpileup.h $(htslib_sam_h)
+ bam_plbuf_h = bam_plbuf.h $(htslib_sam_h)
+-bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(htslib_khash_h) $(bam_lpileup_h)
++bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(bam_lpileup_h)
+ sam_h = sam.h $(htslib_sam_h) $(bam_h)
+ sam_opts_h = sam_opts.h $(htslib_hts_h)
+-sample_h = sample.h $(htslib_kstring_h)
++sample_h = sample.h
+ 
+ bam.o: bam.c $(bam_h) $(htslib_kstring_h) sam_header.h
+-bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(htslib_kstring_h) $(htslib_kfunc_h) $(bam2bcf_h) errmod.h
++bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(bam2bcf_h) errmod.h
+ bam2bcf_indel.o: bam2bcf_indel.c $(htslib_sam_h) $(bam2bcf_h) kprobaln.h $(htslib_khash_h) $(htslib_ksort_h)
+ bam2depth.o: bam2depth.c $(htslib_sam_h) samtools.h $(sam_opts_h)
+ bam_addrprg.o: bam_addrprg.c $(htslib_sam_h) $(htslib_kstring_h) samtools.h $(sam_opts_h)
+ bam_aux.o: bam_aux.c $(bam_h)
+ bam_cat.o: bam_cat.c $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_cram_h) $(htslib_khash_h)
+ bam_color.o: bam_color.c $(bam_h)
+-bam_import.o: bam_import.c $(htslib_kstring_h) $(bam_h) $(htslib_kseq_h)
+-bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_h) samtools.h
+-bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) $(htslib_ksort_h)
++bam_import.o: bam_import.c $(bam_h)
++bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h)
++bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h)
+ bam_mate.o: bam_mate.c $(sam_opts_h) $(htslib_kstring_h) $(htslib_sam_h)
+ bam_md.o: bam_md.c $(htslib_faidx_h) $(htslib_sam_h) $(htslib_kstring_h) kprobaln.h $(sam_opts_h)
+ bam_plbuf.o: bam_plbuf.c $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h)
+-bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) sam_header.h samtools.h $(sam_opts_h) $(bam2bcf_h) $(sample_h)
++bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) sam_header.h samtools.h $(bam2bcf_h) $(sample_h)
+ bam_quickcheck.o: bam_quickcheck.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_bgzf_h)
+ bam_reheader.o: bam_reheader.c $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_hfile_h) $(htslib_cram_h) samtools.h
+-bam_rmdup.o: bam_rmdup.c $(htslib_sam_h) $(sam_opts_h) $(bam_h) $(htslib_khash_h)
+-bam_rmdupse.o: bam_rmdupse.c $(bam_h) $(htslib_sam_h) $(htslib_khash_h) $(htslib_klist_h)
+-bam_sort.o: bam_sort.c $(htslib_ksort_h) $(htslib_khash_h) $(htslib_klist_h) $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h)
++bam_rmdup.o: bam_rmdup.c $(sam_h)
++bam_rmdupse.o: bam_rmdupse.c $(sam_h)
++bam_sort.o: bam_sort.c  $(htslib_sam_h)
+ bam_split.o: bam_split.c $(htslib_sam_h) $(htslib_khash_h) $(htslib_kstring_h) $(sam_opts_h)
+ bam_stat.o: bam_stat.c $(htslib_sam_h) samtools.h
+ bam_tview.o: bam_tview.c $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h) $(sam_opts_h)
+ bam_tview_curses.o: bam_tview_curses.c config.h $(bam_tview_h)
+ bam_tview_html.o: bam_tview_html.c $(bam_tview_h)
+ bam_flags.o: bam_flags.c $(htslib_sam_h)
+-bamshuf.o: bamshuf.c $(htslib_sam_h) $(htslib_hts_h) $(htslib_ksort_h) samtools.h $(sam_opts_h)
++bamshuf.o: bamshuf.c $(htslib_sam_h) samtools.h
+ bamtk.o: bamtk.c $(htslib_hts_h) samtools.h version.h
+-bedcov.o: bedcov.c $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) $(htslib_kseq_h)
+-bedidx.o: bedidx.c $(htslib_ksort_h) $(htslib_kseq_h) $(htslib_khash_h)
++bedcov.o: bedcov.c $(htslib_sam_h)
++bedidx.o: bedidx.c
+ cut_target.o: cut_target.c $(htslib_sam_h) errmod.h $(htslib_faidx_h) $(sam_opts_h)
+ dict.o: dict.c $(htslib_kseq_h) $(htslib_hts_h)
+-errmod.o: errmod.c errmod.h $(htslib_ksort_h)
++errmod.o: errmod.c errmod.h
+ kprobaln.o: kprobaln.c kprobaln.h
+ padding.o: padding.c $(htslib_kstring_h) $(htslib_sam_h) $(htslib_faidx_h) sam_header.h $(sam_opts_h)
+-phase.o: phase.c $(htslib_sam_h) errmod.h $(sam_opts_h) $(htslib_kseq_h) $(htslib_khash_h) $(htslib_ksort_h)
++phase.o: phase.c $(htslib_sam_h) errmod.h
+ sam.o: sam.c $(htslib_faidx_h) $(sam_h)
+-sam_header.o: sam_header.c sam_header.h $(htslib_khash_h)
++sam_header.o: sam_header.c sam_header.h
+ sam_opts.o: sam_opts.c $(sam_opts_h)
+-sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_h) samtools.h $(sam_opts_h)
+-sample.o: sample.c $(sample_h) $(htslib_khash_h)
+-stats_isize.o: stats_isize.c stats_isize.h $(htslib_khash_h)
+-stats.o: stats.c $(htslib_faidx_h) $(htslib_sam_h) $(htslib_hts_h) sam_header.h $(htslib_khash_str2int_h) samtools.h $(htslib_khash_h) $(htslib_kstring_h) stats_isize.h $(sam_opts_h)
++sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) samtools.h
++sample.o: sample.c $(sample_h)
++stats_isize.o: stats_isize.c stats_isize.h
++stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(htslib_faidx_h)
+ 
+ 
+ # test programs
+@@ -197,8 +206,8 @@
+ # For tests that might use it, set $REF_PATH explicitly to use only reference
+ # areas within the test suite (or set it to ':' to use no reference areas).
+ # (regression.sh sets $REF_PATH to a subdirectory itself.)
+-check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS)
+-	REF_PATH=: test/test.pl --exec bgzip=$(BGZIP)
++check test: samtools $(BUILT_TEST_PROGRAMS)
++	REF_PATH=: test/test.pl --exec bgzip=bgzip
+ 	test/merge/test_bam_translate test/merge/test_bam_translate.tmp
+ 	test/merge/test_rtrans_build
+ 	test/merge/test_trans_tbl_init
+@@ -210,28 +219,28 @@
+ 	test/split/test_parse_args
+ 
+ 
+-test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o sam_opts.o $(HTSLIB)
++test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o
+ 	$(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS)
+ 
+-test/merge/test_rtrans_build: test/merge/test_rtrans_build.o sam_opts.o $(HTSLIB)
++test/merge/test_rtrans_build: test/merge/test_rtrans_build.o
+ 	$(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_rtrans_build.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS)
+ 
+-test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o sam_opts.o $(HTSLIB)
++test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o
+ 	$(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS)
+ 
+-test/split/test_count_rg: test/split/test_count_rg.o test/test.o sam_opts.o $(HTSLIB)
++test/split/test_count_rg: test/split/test_count_rg.o test/test.o
+ 	$(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS)
+ 
+-test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o sam_opts.o $(HTSLIB)
++test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o
+ 	$(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS)
+ 
+-test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o sam_opts.o $(HTSLIB)
++test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o
+ 	$(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS)
+ 
+-test/split/test_parse_args: test/split/test_parse_args.o test/test.o sam_opts.o $(HTSLIB)
++test/split/test_parse_args: test/split/test_parse_args.o test/test.o
+ 	$(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS)
+ 
+-test/vcf-miniview: test/vcf-miniview.o $(HTSLIB)
++test/vcf-miniview: test/vcf-miniview.o
+ 	$(CC) -pthread $(ALL_LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB_LIB) $(ALL_LIBS)
+ 
+ test_test_h = test/test.h $(htslib_sam_h)
diff --git a/sci-biology/samtools/files/samtools-1.3-ncurses.patch b/sci-biology/samtools/files/samtools-1.3-ncurses.patch
new file mode 100644
index 000000000000..baeb6701cd2f
--- /dev/null
+++ b/sci-biology/samtools/files/samtools-1.3-ncurses.patch
@@ -0,0 +1,737 @@
+* Add modern AX_WITH_CURSES that prefers using pkg-config for detecting ncurses
+* Change macro structure by moving AX_WITH_HTSLIB into its own file
+
+--- samtools-1.3/configure.ac
++++ samtools-1.3/configure.ac
+@@ -28,6 +28,7 @@
+ AC_PREREQ([2.63])  dnl This version introduced 4-argument AC_CHECK_HEADER
+ AC_CONFIG_SRCDIR([bamtk.c])
+ AC_CONFIG_HEADERS([config.h])
++AC_CONFIG_MACRO_DIR([m4])
+ 
+ dnl Copyright notice to be copied into the generated configure script
+ AC_COPYRIGHT([Portions copyright (C) 2015 Genome Research Ltd.
+--- samtools-1.3/m4/ax_with_curses.m4
++++ samtools-1.3/m4/ax_with_curses.m4
+@@ -0,0 +1,578 @@
++# ===========================================================================
++#      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. Finding libraries will first be attempted by using
++#   pkg-config, and should the pkg-config files not be available, will
++#   fallback to combinations of known flags itself.
++#
++#   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 variables are defined by this macro; they are
++#   precious and may be overridden on the ./configure command line:
++#
++#     CURSES_LIB  - library to add to xxx_LDADD
++#     CURSES_CPPFLAGS  - include paths to add to xxx_CPPFLAGS
++#
++#   Neither the library listed in CURSES_LIB, nor the flags in
++#   CURSES_CPPFLAGS are added to LIBS, respectively CPPFLAGS, by default.
++#   You need to add both to the appropriate xxx_LDADD/xxx_CPPFLAGS line in
++#   your Makefile.am. For example:
++#
++#     prog_LDADD = @CURSES_LIB@
++#     prog_CPPFLAGS = @CURSES_CPPFLAGS@
++#
++#   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>. 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 16
++
++# internal function to factorize common code that is used by both ncurses
++# and ncursesw
++AC_DEFUN([_FIND_CURSES_FLAGS], [
++    AC_MSG_CHECKING([for $1 via pkg-config])
++
++    _PKG_CONFIG([_ax_cv_$1_lib], [libs], [$1])
++    _PKG_CONFIG([_ax_cv_$1_cppflags], [cflags], [$1])
++
++    AS_IF([test "x$pkg_failed" = "xyes" || test "x$pkg_failed" = "xuntried"],[
++        AC_MSG_RESULT([no])
++        # No suitable .pc file found, have to find flags via fallback
++        AC_CACHE_CHECK([for $1 via fallback], [ax_cv_$1], [
++            AS_ECHO()
++            pkg_cv__ax_cv_$1_lib="-l$1"
++            pkg_cv__ax_cv_$1_cppflags="$CURSES_CPPFLAGS"
++            LIBS="$ax_saved_LIBS $pkg_cv__ax_cv_$1_lib"
++            CPPFLAGS="$ax_saved_CPPFLAGS $pkg_cv__ax_cv_$1_cppflags"
++
++            AC_MSG_CHECKING([for initscr() with $pkg_cv__ax_cv_$1_lib])
++            AC_LINK_IFELSE([AC_LANG_CALL([], [initscr])],
++                [
++                    AC_MSG_RESULT([yes])
++                    AC_MSG_CHECKING([for nodelay() with $pkg_cv__ax_cv_$1_lib])
++                    AC_LINK_IFELSE([AC_LANG_CALL([], [nodelay])],[
++                        ax_cv_$1=yes
++                        ],[
++                        AC_MSG_RESULT([no])
++                        m4_if(
++                            [$1],[ncursesw],[pkg_cv__ax_cv_$1_lib="$pkg_cv__ax_cv_$1_lib -ltinfow"],
++                            [$1],[ncurses],[pkg_cv__ax_cv_$1_lib="$pkg_cv__ax_cv_$1_lib -ltinfo"]
++                        )
++                        LIBS="$ax_saved_LIBS $pkg_cv__ax_cv_$1_lib"
++
++                        AC_MSG_CHECKING([for nodelay() with $pkg_cv__ax_cv_$1_lib])
++                        AC_LINK_IFELSE([AC_LANG_CALL([], [nodelay])],[
++                            ax_cv_$1=yes
++                            ],[
++                            ax_cv_$1=no
++                        ])
++                    ])
++                ],[
++                    ax_cv_$1=no
++            ])
++        ])
++        ],[
++        AC_MSG_RESULT([yes])
++        # Found .pc file, using its information
++        LIBS="$ax_saved_LIBS $pkg_cv__ax_cv_$1_lib"
++        CPPFLAGS="$ax_saved_CPPFLAGS $pkg_cv__ax_cv_$1_cppflags"
++        ax_cv_$1=yes
++    ])
++])
++
++AU_ALIAS([MP_WITH_CURSES], [AX_WITH_CURSES])
++AC_DEFUN([AX_WITH_CURSES], [
++    AC_ARG_VAR([CURSES_LIB], [linker library for Curses, e.g. -lcurses])
++    AC_ARG_VAR([CURSES_CPPFLAGS], [preprocessor flags for Curses, e.g. -I/usr/include/ncursesw])
++    AC_ARG_WITH([ncurses], [AS_HELP_STRING([--with-ncurses],
++        [force the use of Ncurses or NcursesW])],
++        [], [with_ncurses=check])
++    AC_ARG_WITH([ncursesw], [AS_HELP_STRING([--without-ncursesw],
++        [do not use NcursesW (wide character support)])],
++        [], [with_ncursesw=check])
++    AC_REQUIRE([PKG_PROG_PKG_CONFIG])
++
++    ax_saved_LIBS=$LIBS
++    ax_saved_CPPFLAGS=$CPPFLAGS
++
++    AS_IF([test "x$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$with_ncursesw" != xno], [
++        _FIND_CURSES_FLAGS([ncursesw])
++
++        AS_IF([test "x$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="$pkg_cv__ax_cv_ncursesw_lib"
++            CURSES_CPPFLAGS="$pkg_cv__ax_cv_ncursesw_cppflags"
++            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])
++            ])
++        ])
++    ])
++    unset pkg_cv__ax_cv_ncursesw_lib
++    unset pkg_cv__ax_cv_ncursesw_cppflags
++
++    # Test for Ncurses
++    AS_IF([test "x$CURSES_LIB" = x && test "x$with_ncurses" != xno && test "x$ax_cv_curses_which" = xno], [
++        _FIND_CURSES_FLAGS([ncurses])
++
++        AS_IF([test "x$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="$pkg_cv__ax_cv_ncurses_lib"
++            CURSES_CPPFLAGS="$pkg_cv__ax_cv_ncurses_cppflags"
++            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])
++            ])
++        ])
++    ])
++    unset pkg_cv__ax_cv_ncurses_lib
++    unset pkg_cv__ax_cv_ncurses_cppflags
++
++    # 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
++    CPPFLAGS=$ax_saved_CPPFLAGS
++
++    unset ax_saved_LIBS
++    unset ax_saved_CPPFLAGS
++])dnl
+--- samtools-1.3/m4/ax_with_htslib.m4
++++ samtools-1.3/m4/ax_with_htslib.m4
+@@ -0,0 +1,140 @@
++# ===========================================================================
++#      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/sci-biology/samtools/samtools-1.3.ebuild b/sci-biology/samtools/samtools-1.3.ebuild
new file mode 100644
index 000000000000..ec510ec82664
--- /dev/null
+++ b/sci-biology/samtools/samtools-1.3.ebuild
@@ -0,0 +1,86 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit autotools python-r1 toolchain-funcs
+
+DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
+HOMEPAGE="http://www.htslib.org/"
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+IUSE="examples"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="sys-libs/ncurses:0=
+	>=sci-libs/htslib-${PV}
+	dev-lang/lua:0
+	dev-lang/perl"
+DEPEND="${RDEPEND}
+	virtual/pkgconfig"
+
+PATCHES=(
+	"${FILESDIR}/${P}-buildsystem.patch"
+	"${FILESDIR}/${P}-ncurses.patch"
+)
+
+src_prepare() {
+	default
+
+	# unbundle libs
+	find htslib-* -delete || die
+
+	sed -i -e 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die
+	sed -i -e '/htslib.mk/d' -i Makefile || die
+
+	tc-export CC AR
+
+	rm -f aclocal.m4 || die
+	eautoreconf
+}
+
+src_compile() {
+	local mymakeargs=(
+		LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)"
+		HTSDIR="${EPREFIX}/usr/include"
+		HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib)
+		BAMLIB="libbam.so"
+		libdir=/usr/$(get_libdir)
+		)
+	emake "${mymakeargs[@]}"
+}
+
+src_test() {
+	local mymakeargs=(
+		LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)"
+		HTSDIR="${EPREFIX}/usr/include"
+		HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib)
+		BAMLIB="libbam.so"
+		)
+	LD_LIBRARY_PATH="${S}" emake "${mymakeargs[@]}" test
+}
+
+src_install() {
+	dobin samtools $(find misc -type f -executable)
+
+	python_replicate_script "${ED}"/usr/bin/varfilter.py
+	dolib.so libbam.so*
+
+	insinto /usr/include/bam
+	doins *.h
+
+	doman ${PN}.1
+	dodoc AUTHORS NEWS README
+
+	if use examples; then
+		insinto /usr/share/${PN}
+		doins -r examples
+	fi
+}