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authorDavid Seifert <soap@gentoo.org>2017-09-02 13:07:41 +0200
committerDavid Seifert <soap@gentoo.org>2017-09-02 14:37:02 +0200
commit70386b8c804f2bf2fb7aca4be74d511d765ad1e4 (patch)
tree77520e148716d1a086b35521e9664f48f1c3790e /sci-biology
parentsci-biology/pysam: Remove old (diff)
downloadgentoo-70386b8c804f2bf2fb7aca4be74d511d765ad1e4.tar.gz
gentoo-70386b8c804f2bf2fb7aca4be74d511d765ad1e4.tar.bz2
gentoo-70386b8c804f2bf2fb7aca4be74d511d765ad1e4.zip
sci-biology/samtools: Remove old
Bug: https://bugs.gentoo.org/show_bug.cgi?id=548170 Bug: https://bugs.gentoo.org/show_bug.cgi?id=620618 Bug: https://bugs.gentoo.org/show_bug.cgi?id=625504 Package-Manager: Portage-2.3.8, Repoman-2.3.3 Closes: https://github.com/gentoo/gentoo/pull/5593
Diffstat (limited to 'sci-biology')
-rw-r--r--sci-biology/samtools/Manifest6
-rw-r--r--sci-biology/samtools/files/samtools-0.1.19-buildsystem.patch183
-rw-r--r--sci-biology/samtools/files/samtools-1.0-buildsystem.patch59
-rw-r--r--sci-biology/samtools/files/samtools-1.1-buildsystem.patch153
-rw-r--r--sci-biology/samtools/files/samtools-1.2-buildsystem.patch193
-rw-r--r--sci-biology/samtools/files/samtools-1.3-buildsystem.patch174
-rw-r--r--sci-biology/samtools/files/samtools-1.3-ncurses.patch737
-rw-r--r--sci-biology/samtools/samtools-0.1.12.ebuild30
-rw-r--r--sci-biology/samtools/samtools-0.1.19-r2.ebuild60
-rw-r--r--sci-biology/samtools/samtools-1.0-r1.ebuild72
-rw-r--r--sci-biology/samtools/samtools-1.0.ebuild68
-rw-r--r--sci-biology/samtools/samtools-1.1.ebuild82
-rw-r--r--sci-biology/samtools/samtools-1.2.ebuild82
-rw-r--r--sci-biology/samtools/samtools-1.3-r1.ebuild96
14 files changed, 0 insertions, 1995 deletions
diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index 791e2050ee7f..a1c0aa6b4270 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,8 +1,2 @@
-DIST samtools-0.1.12a.tar.bz2 355633 SHA256 377ed5cd2a4bb2b1ad572ca6fcafdd8ed644b67f01ab00fa020618fac11e59ac SHA512 8a3273c174fb478772f31a9c73183b5f7c6841ba4e20586aafc2cd3e966830d3a4ca8c7485ce5981fe85d7cd820170e2ac2e124d8cf077e35218a7381f305012 WHIRLPOOL da61692666dffbb32e172f87e77287e145a0c0f6d62d47e5d04d153ce478db5df1d4694bd93d654af11643f9b656551232b5cc085b619bb8d8536720de36984c
-DIST samtools-0.1.19.tar.bz2 514507 SHA256 d080c9d356e5f0ad334007e4461cbcee3c4ca97b8a7a5a48c44883cf9dee63d4 SHA512 d145f1d65eefefbdfb781945684b8b591419fb109ac7401a62cae65b9ca1e1271f001496e1038334ff9ab1c0e5bf9bcc059f70aaa273551193fbd68101fd188d WHIRLPOOL 7811388ae8b24c5d7a328d2da252b8d3afaefdab508bd97684d556d2d4ee60d9c8846ffa562beaa9d0c6a5e6bfac24fcd9d211dfee20383cf452609badc8ecd5
DIST samtools-0.1.20.tar.gz 566387 SHA256 500019b4d1886ad995513d5ce8b413b14b51f16f251ce76bc0b35a446b182a47 SHA512 15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5 WHIRLPOOL 3ea05df172ea6afe31bd3880f918e0b286f65839f78ed846a0d3aef84ec70df1e3741ff6dcad5f70d62a06687f07b35609829aabd33c6688fac0d59effd979e0
-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
DIST samtools-1.5.tar.bz2 4190142 SHA256 8542da26832ee08c1978713f5f6188ff750635b50d8ab126a0c7bb2ac1ae2df6 SHA512 ff3e39ba867ecbd88f3363b038508c1557e349ea4223483f8f4ecb17ff8864fb53cd193bc2059a147e30f07395bbf53c8518d0f70219e454375c8bffe56e3059 WHIRLPOOL 1a88c9617857f1f6d146df179aef5b5c6bb83de8c9d127c405e5756842ced84c194a3f09f69a4757a8adf6ca623c9fdc972f4bf609649d3e991dda8f616e3582
diff --git a/sci-biology/samtools/files/samtools-0.1.19-buildsystem.patch b/sci-biology/samtools/files/samtools-0.1.19-buildsystem.patch
deleted file mode 100644
index d5ff3bd45da5..000000000000
--- a/sci-biology/samtools/files/samtools-0.1.19-buildsystem.patch
+++ /dev/null
@@ -1,183 +0,0 @@
- Makefile | 22 +++++++++++-----------
- bcftools/Makefile | 12 ++++++------
- misc/Makefile | 28 ++++++++++++++--------------
- 3 files changed, 31 insertions(+), 31 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index 2f51bfc..4dda5a4 100644
---- a/Makefile
-+++ b/Makefile
-@@ -1,7 +1,7 @@
--CC= gcc
--CFLAGS= -g -Wall -O2
--#LDFLAGS= -Wl,-rpath,\$$ORIGIN/../lib
--DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1
-+CC?= gcc
-+CFLAGS?= -g -Wall -O2
-+#LDFLAGS+= -Wl,-rpath,\$$ORIGIN/../lib
-+CPPFLAGS+= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1
- KNETFILE_O= knetfile.o
- LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \
- bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o \
-@@ -21,14 +21,14 @@ LIBCURSES= -lcurses # -lXCurses
- .PHONY: all lib
-
- .c.o:
-- $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
-+ $(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@
-
- all-recur lib-recur clean-recur cleanlocal-recur install-recur:
- @target=`echo $@ | sed s/-recur//`; \
- wdir=`pwd`; \
- list='$(SUBDIRS)'; for subdir in $$list; do \
- cd $$subdir; \
-- $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
-+ $(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \
- INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
- cd $$wdir; \
- done;
-@@ -44,16 +44,16 @@ libbam.a:$(LOBJS)
- $(AR) -csru $@ $(LOBJS)
-
- samtools:lib-recur $(AOBJS)
-- $(CC) $(CFLAGS) -o $@ $(AOBJS) $(LDFLAGS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread
-
- razip:razip.o razf.o $(KNETFILE_O)
-- $(CC) $(CFLAGS) -o $@ $^ -lz
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ -lz
-
- bgzip:bgzip.o bgzf.o $(KNETFILE_O)
-- $(CC) $(CFLAGS) -o $@ $^ -lz -lpthread
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ -lz -lpthread
-
- bgzf.o:bgzf.c bgzf.h
-- $(CC) -c $(CFLAGS) $(DFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@
-+ $(CC) -c $(CFLAGS) $(CPPFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@
-
- razip.o:razf.h
- bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h
-@@ -84,7 +84,7 @@ libbam.1.dylib-local:$(LOBJS)
- libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz
-
- libbam.so.1-local:$(LOBJS)
-- $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz
-+ $(CC) $(LDFLAGS) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz -lm -lpthread
-
- dylib:
- @$(MAKE) cleanlocal; \
-diff --git a/bcftools/Makefile b/bcftools/Makefile
-index be831de..7ef796c 100644
---- a/bcftools/Makefile
-+++ b/bcftools/Makefile
-@@ -1,6 +1,6 @@
--CC= gcc
--CFLAGS= -g -Wall -O2 #-m64 #-arch ppc
--DFLAGS= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE
-+CC?= gcc
-+CFLAGS?= -g -Wall -O2 #-m64 #-arch ppc
-+CPPFLAGS+= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE
- LOBJS= bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
- OMISC= ..
- AOBJS= call1.o main.o $(OMISC)/kstring.o $(OMISC)/bgzf.o $(OMISC)/knetfile.o $(OMISC)/bedidx.o
-@@ -11,14 +11,14 @@ SUBDIRS= .
- .SUFFIXES:.c .o
-
- .c.o:
-- $(CC) -c $(CFLAGS) $(DFLAGS) -I.. $(INCLUDES) $< -o $@
-+ $(CC) -c $(CFLAGS) $(CPPFLAGS) -I.. $(INCLUDES) $< -o $@
-
- all-recur lib-recur clean-recur cleanlocal-recur install-recur:
- @target=`echo $@ | sed s/-recur//`; \
- wdir=`pwd`; \
- list='$(SUBDIRS)'; for subdir in $$list; do \
- cd $$subdir; \
-- $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
-+ $(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \
- INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
- cd $$wdir; \
- done;
-@@ -31,7 +31,7 @@ libbcf.a:$(LOBJS)
- $(AR) -csru $@ $(LOBJS)
-
- bcftools:lib $(AOBJS)
-- $(CC) $(CFLAGS) -o $@ $(AOBJS) -L. $(LIBPATH) -lbcf -lm -lz -lpthread
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) -L. $(LIBPATH) -lbcf -lm -lz -lpthread
-
- bcf.o:bcf.h
- vcf.o:bcf.h
-diff --git a/misc/Makefile b/misc/Makefile
-index d36e7ac..7ae1dc3 100644
---- a/misc/Makefile
-+++ b/misc/Makefile
-@@ -1,8 +1,8 @@
--CC= gcc
--CXX= g++
--CFLAGS= -g -Wall -O2 #-m64 #-arch ppc
--CXXFLAGS= $(CFLAGS)
--DFLAGS= -D_FILE_OFFSET_BITS=64
-+CC?= gcc
-+CXX?= g++
-+CFLAGS?= -g -Wall -O2 #-m64 #-arch ppc
-+CXXFLAGS?= $(CFLAGS)
-+CPPFLAGS+= -D_FILE_OFFSET_BITS=64
- OBJS=
- PROG= md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck
- INCLUDES= -I..
-@@ -11,7 +11,7 @@ SUBDIRS= .
- .SUFFIXES:.c .o
-
- .c.o:
-- $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
-+ $(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@
-
- all:$(PROG)
-
-@@ -20,7 +20,7 @@ lib-recur all-recur clean-recur cleanlocal-recur install-recur:
- wdir=`pwd`; \
- list='$(SUBDIRS)'; for subdir in $$list; do \
- cd $$subdir; \
-- $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
-+ $(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \
- INCLUDES="$(INCLUDES)" $$target || exit 1; \
- cd $$wdir; \
- done;
-@@ -28,31 +28,31 @@ lib-recur all-recur clean-recur cleanlocal-recur install-recur:
- lib:
-
- bamcheck:bamcheck.o
-- $(CC) $(CFLAGS) -o $@ bamcheck.o -L.. -lm -lbam -lpthread -lz
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ bamcheck.o -L.. -lm -lbam -lpthread -lz
-
- bamcheck.o:bamcheck.c ../faidx.h ../khash.h ../sam.h ../razf.h
- $(CC) $(CFLAGS) -c -I.. -o $@ bamcheck.c
-
- ace2sam:ace2sam.o
-- $(CC) $(CFLAGS) -o $@ ace2sam.o -lz
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ ace2sam.o -lz
-
- wgsim:wgsim.o
-- $(CC) $(CFLAGS) -o $@ wgsim.o -lm -lz
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ wgsim.o -lm -lz
-
- md5fa:md5.o md5fa.o md5.h ../kseq.h
-- $(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ md5.o md5fa.o -lz
-
- md5sum-lite:md5sum-lite.o
-- $(CC) $(CFLAGS) -o $@ md5sum-lite.o
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ md5sum-lite.o
-
- md5sum-lite.o:md5.c md5.h
- $(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c
-
- maq2sam-short:maq2sam.c
-- $(CC) $(CFLAGS) -o $@ maq2sam.c -lz
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ maq2sam.c -lz
-
- maq2sam-long:maq2sam.c
-- $(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -lz
-+ $(CC) $(CFLAGS) -DMAQ_LONGREADS $(LDFLAGS) -o $@ maq2sam.c -lz
-
- md5fa.o:md5.h md5fa.c
- $(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c
diff --git a/sci-biology/samtools/files/samtools-1.0-buildsystem.patch b/sci-biology/samtools/files/samtools-1.0-buildsystem.patch
deleted file mode 100644
index 53a8b66f918f..000000000000
--- a/sci-biology/samtools/files/samtools-1.0-buildsystem.patch
+++ /dev/null
@@ -1,59 +0,0 @@
- Makefile | 26 ++++++++++++++++++--------
- 1 file changed, 18 insertions(+), 8 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index ae59abf..0d2788c 100644
---- a/Makefile
-+++ b/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 = $(DFLAGS) $(INCLUDES)
--CFLAGS = -g -Wall -O2
--LDFLAGS =
--LDLIBS =
-+CC ?= gcc
-+CPPFLAGS += $(DFLAGS) $(INCLUDES)
-+CFLAGS ?= -g -Wall -O2
-+LDFLAGS +=
-+LDLIBS +=
-+BAMLIB ?= libbam.a
- DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1
- LOBJS= bam_aux.o bam.o bam_import.o sam.o \
- sam_header.o bam_plbuf.o
-@@ -42,6 +43,7 @@ LIBCURSES= -lcurses # -lXCurses
- prefix = /usr/local
- exec_prefix = $(prefix)
- bindir = $(exec_prefix)/bin
-+bindir = $(exec_prefix)/lib
- mandir = $(prefix)/share/man
- man1dir = $(mandir)/man1
-
-@@ -115,14 +117,22 @@ version.h:
- .c.o:
- $(CC) $(CFLAGS) $(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 $(LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz
-+libbam.so.1.0:$(LOBJS)
-+ $(CC) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB) -lz
-+ ln -sf $@ libbam.so.0
-+ ln -sf $@ libbam.so
-+
-+samtools: $(AOBJS) $(HTSLIB) 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
diff --git a/sci-biology/samtools/files/samtools-1.1-buildsystem.patch b/sci-biology/samtools/files/samtools-1.1-buildsystem.patch
deleted file mode 100644
index b9ae77de67d2..000000000000
--- a/sci-biology/samtools/files/samtools-1.1-buildsystem.patch
+++ /dev/null
@@ -1,153 +0,0 @@
- Makefile | 76 ++++++++++++++++++++++++++++++++++++----------------------------
- 1 file changed, 43 insertions(+), 33 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index 43cefc3..743dd07 100644
---- a/Makefile
-+++ b/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 = $(DFLAGS) $(INCLUDES)
--CFLAGS = -g -Wall -O2
--LDFLAGS =
--LDLIBS =
-+CC ?= gcc
-+CPPFLAGS += $(DFLAGS) $(INCLUDES)
-+CFLAGS ?= -g -Wall -O2
-+LDFLAGS +=
-+LDLIBS +=
-+BAMLIB ?= libbam.a
- DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1
- LOBJS= bam_aux.o bam.o bam_import.o sam.o \
- sam_header.o bam_plbuf.o
-@@ -42,6 +43,7 @@ LIBCURSES= -lcurses # -lXCurses
- prefix = /usr/local
- exec_prefix = $(prefix)
- bindir = $(exec_prefix)/bin
-+libdir = $(exec_prefix)/lib
- mandir = $(prefix)/share/man
- man1dir = $(mandir)/man1
-
-@@ -115,63 +117,71 @@ version.h:
- .c.o:
- $(CC) $(CFLAGS) $(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 $(LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz
-+libbam.so.1.0:$(LOBJS)
-+ $(CC) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB) -lz
-+ ln -sf $@ libbam.so.0
-+ 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) $(HTSDIR)/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)
--sample_h = sample.h $(HTSDIR)/htslib/kstring.h
-+sample_h = sample.h
-
- bam.o: bam.c $(bam_h) sam_header.h
--bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kfunc.h $(bam2bcf_h) errmod.h
-+bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(bam2bcf_h) errmod.h
- bam2bcf_indel.o: bam2bcf_indel.c bam2bcf.h
- bam2depth.o: bam2depth.c $(htslib_sam_h) samtools.h
- bam_aux.o: bam_aux.c
- bam_cat.o: bam_cat.c $(htslib_bgzf_h) $(bam_h)
- bam_color.o: bam_color.c $(bam_h)
--bam_import.o: bam_import.c $(HTSDIR)/htslib/kstring.h $(bam_h) $(HTSDIR)/htslib/kseq.h
--bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) $(HTSDIR)/htslib/khash.h
--bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) $(HTSDIR)/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 $(bam_h)
- bam_md.o: bam_md.c $(htslib_faidx_h) $(sam_h) kaln.h kprobaln.h
- bam_pileup.o: bam_pileup.c $(sam_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) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/khash_str2int.h sam_header.h samtools.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_reheader.o: bam_reheader.c $(htslib_bgzf_h) $(bam_h)
--bam_rmdup.o: bam_rmdup.c $(sam_h) $(HTSDIR)/htslib/khash.h
--bam_rmdupse.o: bam_rmdupse.c $(sam_h) $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/klist.h
--bam_sort.o: bam_sort.c $(HTSDIR)/htslib/ksort.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/klist.h $(HTSDIR)/htslib/kstring.h $(htslib_sam_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_stat.o: bam_stat.c $(bam_h) samtools.h
- bam_tview.o: bam_tview.c $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h)
- bam_tview_curses.o: bam_tview_curses.c $(bam_tview_h)
- bam_tview_html.o: bam_tview_html.c $(bam_tview_h)
- bam_flags.o: bam_flags.c $(sam_h)
--bamshuf.o: bamshuf.c $(htslib_sam_h) $(HTSDIR)/htslib/ksort.h samtools.h
-+bamshuf.o: bamshuf.c $(htslib_sam_h) samtools.h
- bamtk.o: bamtk.c $(bam_h) version.h samtools.h
--bedcov.o: bedcov.c $(HTSDIR)/htslib/kstring.h $(htslib_sam_h) $(HTSDIR)/htslib/kseq.h
--bedidx.o: bedidx.c $(HTSDIR)/htslib/ksort.h $(HTSDIR)/htslib/kseq.h $(HTSDIR)/htslib/khash.h
-+bedcov.o: bedcov.c $(htslib_sam_h)
-+bedidx.o: bedidx.c
- cut_target.o: cut_target.c $(bam_h) errmod.h $(htslib_faidx_h)
--errmod.o: errmod.c errmod.h $(HTSDIR)/htslib/ksort.h
-+errmod.o: errmod.c errmod.h
- kaln.o: kaln.c kaln.h
- kprobaln.o: kprobaln.c kprobaln.h
- padding.o: padding.c sam_header.h $(sam_h) $(bam_h) $(htslib_faidx_h)
--phase.o: phase.c $(htslib_sam_h) errmod.h $(HTSDIR)/htslib/kseq.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/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 $(HTSDIR)/htslib/khash.h
--sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/khash.h samtools.h
--sample.o: sample.c $(sample_h) $(HTSDIR)/htslib/khash.h
--stats_isize.o: stats_isize.c stats_isize.h $(HTSDIR)/htslib/khash.h
--stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/khash_str2int.h $(htslib_faidx_h)
-+sam_header.o: sam_header.c sam_header.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
-@@ -179,8 +189,8 @@ stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(HTSDIR)/htslib
- # 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_pretty_header
- test/merge/test_rtrans_build
-@@ -253,10 +263,10 @@ misc/md5sum-lite: misc/md5sum-lite.o
- misc/wgsim: misc/wgsim.o
- $(CC) $(LDFLAGS) -o $@ misc/wgsim.o $(LDLIBS) -lm -lz
-
--misc/ace2sam.o: misc/ace2sam.c $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kseq.h
-+misc/ace2sam.o: misc/ace2sam.c
- misc/md5.o: misc/md5.c misc/md5.h
--misc/md5fa.o: misc/md5fa.c misc/md5.h $(HTSDIR)/htslib/kseq.h
--misc/wgsim.o: misc/wgsim.c $(HTSDIR)/htslib/kseq.h
-+misc/md5fa.o: misc/md5fa.c misc/md5.h
-+misc/wgsim.o: misc/wgsim.c
-
- misc/maq2sam-short.o: misc/maq2sam.c
- $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ misc/maq2sam.c
diff --git a/sci-biology/samtools/files/samtools-1.2-buildsystem.patch b/sci-biology/samtools/files/samtools-1.2-buildsystem.patch
deleted file mode 100644
index 2343b2245a29..000000000000
--- a/sci-biology/samtools/files/samtools-1.2-buildsystem.patch
+++ /dev/null
@@ -1,193 +0,0 @@
- Makefile | 94 +++++++++++++++++++++++++++++++++++-----------------------------
- 1 file changed, 52 insertions(+), 42 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index e368cee..9054526 100644
---- a/Makefile
-+++ b/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 = $(DFLAGS) $(INCLUDES)
--CFLAGS = -g -Wall -O2
--LDFLAGS =
--LDLIBS =
-+CC ?= gcc
-+CPPFLAGS += $(DFLAGS) $(INCLUDES)
-+CFLAGS ?= -g -Wall -O2
-+LDFLAGS +=
-+LDLIBS +=
-+BAMLIB ?= libbam.a
- DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1
- LOBJS= bam_aux.o bam.o bam_import.o sam.o \
- sam_header.o bam_plbuf.o
-@@ -42,6 +43,7 @@ LIBCURSES= -lcurses # -lXCurses
- prefix = /usr/local
- exec_prefix = $(prefix)
- bindir = $(exec_prefix)/bin
-+libdir = $(exec_prefix)/lib
- mandir = $(prefix)/share/man
- man1dir = $(mandir)/man1
-
-@@ -115,62 +117,70 @@ version.h:
- .c.o:
- $(CC) $(CFLAGS) $(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 $(LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz
-+libbam.so.1.0:$(LOBJS)
-+ $(CC) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB) -lz
-+ ln -sf $@ libbam.so.0
-+ 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) $(HTSDIR)/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)
--sample_h = sample.h $(HTSDIR)/htslib/kstring.h
-+sample_h = sample.h
-
- bam.o: bam.c $(bam_h) sam_header.h
--bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/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 $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/ksort.h
- bam2depth.o: bam2depth.c $(htslib_sam_h) samtools.h
- bam_aux.o: bam_aux.c
- bam_cat.o: bam_cat.c $(htslib_bgzf_h) $(bam_h)
- bam_color.o: bam_color.c $(bam_h)
--bam_import.o: bam_import.c $(HTSDIR)/htslib/kstring.h $(bam_h) $(HTSDIR)/htslib/kseq.h
--bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) $(HTSDIR)/htslib/khash.h
--bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) $(HTSDIR)/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 $(bam_h)
- bam_md.o: bam_md.c $(htslib_faidx_h) $(sam_h) kprobaln.h
- bam_pileup.o: bam_pileup.c $(sam_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) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/khash_str2int.h sam_header.h samtools.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_reheader.o: bam_reheader.c $(htslib_bgzf_h) $(bam_h)
--bam_rmdup.o: bam_rmdup.c $(sam_h) $(HTSDIR)/htslib/khash.h
--bam_rmdupse.o: bam_rmdupse.c $(sam_h) $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/klist.h
--bam_sort.o: bam_sort.c $(HTSDIR)/htslib/ksort.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/klist.h $(HTSDIR)/htslib/kstring.h $(htslib_sam_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_stat.o: bam_stat.c $(bam_h) samtools.h
- bam_tview.o: bam_tview.c $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h)
- bam_tview_curses.o: bam_tview_curses.c $(bam_tview_h)
- bam_tview_html.o: bam_tview_html.c $(bam_tview_h)
- bam_flags.o: bam_flags.c $(sam_h)
--bamshuf.o: bamshuf.c $(htslib_sam_h) $(HTSDIR)/htslib/ksort.h samtools.h
-+bamshuf.o: bamshuf.c $(htslib_sam_h) samtools.h
- bamtk.o: bamtk.c $(htslib_hts_h) version.h samtools.h
--bedcov.o: bedcov.c $(HTSDIR)/htslib/kstring.h $(htslib_sam_h) $(HTSDIR)/htslib/kseq.h
--bedidx.o: bedidx.c $(HTSDIR)/htslib/ksort.h $(HTSDIR)/htslib/kseq.h $(HTSDIR)/htslib/khash.h
-+bedcov.o: bedcov.c $(htslib_sam_h)
-+bedidx.o: bedidx.c
- cut_target.o: cut_target.c $(bam_h) errmod.h $(htslib_faidx_h)
--errmod.o: errmod.c errmod.h $(HTSDIR)/htslib/ksort.h
-+errmod.o: errmod.c errmod.h
- kprobaln.o: kprobaln.c kprobaln.h
- padding.o: padding.c sam_header.h $(sam_h) $(bam_h) $(htslib_faidx_h)
--phase.o: phase.c $(htslib_sam_h) errmod.h $(HTSDIR)/htslib/kseq.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/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 $(HTSDIR)/htslib/khash.h
--sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/khash.h samtools.h
--sample.o: sample.c $(sample_h) $(HTSDIR)/htslib/khash.h
--stats_isize.o: stats_isize.c stats_isize.h $(HTSDIR)/htslib/khash.h
--stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/khash_str2int.h $(htslib_faidx_h)
-+sam_header.o: sam_header.c sam_header.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
-@@ -178,8 +188,8 @@ stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(HTSDIR)/htslib
- # 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_pretty_header
- test/merge/test_rtrans_build
-@@ -191,31 +201,31 @@ check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS)
- test/split/test_parse_args
-
-
--test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o $(HTSLIB)
-+test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o
- $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o $(HTSLIB) $(LDLIBS) -lz
-
--test/merge/test_pretty_header: test/merge/test_pretty_header.o $(HTSLIB)
-+test/merge/test_pretty_header: test/merge/test_pretty_header.o
- $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_pretty_header.o $(HTSLIB) $(LDLIBS) -lz
-
--test/merge/test_rtrans_build: test/merge/test_rtrans_build.o $(HTSLIB)
-+test/merge/test_rtrans_build: test/merge/test_rtrans_build.o
- $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_rtrans_build.o $(HTSLIB) $(LDLIBS) -lz
-
--test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o $(HTSLIB)
-+test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o
- $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o $(HTSLIB) $(LDLIBS) -lz
-
--test/split/test_count_rg: test/split/test_count_rg.o test/test.o $(HTSLIB)
-+test/split/test_count_rg: test/split/test_count_rg.o test/test.o
- $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o $(HTSLIB) $(LDLIBS) -lz
-
--test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o $(HTSLIB)
-+test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o
- $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o $(HTSLIB) $(LDLIBS) -lz
-
--test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o $(HTSLIB)
-+test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o
- $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o $(HTSLIB) $(LDLIBS) -lz
-
--test/split/test_parse_args: test/split/test_parse_args.o test/test.o $(HTSLIB)
-+test/split/test_parse_args: test/split/test_parse_args.o test/test.o
- $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o $(HTSLIB) $(LDLIBS) -lz
-
--test/vcf-miniview: test/vcf-miniview.o $(HTSLIB)
-+test/vcf-miniview: test/vcf-miniview.o
- $(CC) -pthread $(LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB) $(LDLIBS) -lz
-
- test_test_h = test/test.h $(htslib_sam_h)
-@@ -252,10 +262,10 @@ misc/md5sum-lite: misc/md5sum-lite.o
- misc/wgsim: misc/wgsim.o
- $(CC) $(LDFLAGS) -o $@ misc/wgsim.o $(LDLIBS) -lm -lz
-
--misc/ace2sam.o: misc/ace2sam.c $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kseq.h
-+misc/ace2sam.o: misc/ace2sam.c
- misc/md5.o: misc/md5.c misc/md5.h
--misc/md5fa.o: misc/md5fa.c misc/md5.h $(HTSDIR)/htslib/kseq.h
--misc/wgsim.o: misc/wgsim.c $(HTSDIR)/htslib/kseq.h
-+misc/md5fa.o: misc/md5fa.c misc/md5.h
-+misc/wgsim.o: misc/wgsim.c
-
- misc/maq2sam-short.o: misc/maq2sam.c
- $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ misc/maq2sam.c
diff --git a/sci-biology/samtools/files/samtools-1.3-buildsystem.patch b/sci-biology/samtools/files/samtools-1.3-buildsystem.patch
deleted file mode 100644
index 61f6b03bd8ef..000000000000
--- a/sci-biology/samtools/files/samtools-1.3-buildsystem.patch
+++ /dev/null
@@ -1,174 +0,0 @@
---- 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
deleted file mode 100644
index baeb6701cd2f..000000000000
--- a/sci-biology/samtools/files/samtools-1.3-ncurses.patch
+++ /dev/null
@@ -1,737 +0,0 @@
-* 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=$ax_saved_LDFLAGS
-+ ;;
-+none)
-+ ax_cv_htslib=no
-+ ;;
-+esac
-+
-+AC_SUBST([HTSDIR])
-+AC_SUBST([HTSLIB_CPPFLAGS])
-+AC_SUBST([HTSLIB_LDFLAGS])])
diff --git a/sci-biology/samtools/samtools-0.1.12.ebuild b/sci-biology/samtools/samtools-0.1.12.ebuild
deleted file mode 100644
index d32746ae2ba9..000000000000
--- a/sci-biology/samtools/samtools-0.1.12.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=2
-
-MY_P="${P}a"
-
-DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
-HOMEPAGE="http://samtools.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.bz2"
-
-LICENSE="MIT"
-SLOT="0"
-IUSE=""
-KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
-
-S="${WORKDIR}/${MY_P}"
-
-src_prepare() {
- sed -i 's/^CFLAGS=/CFLAGS+=/' "${S}"/{Makefile,misc/Makefile}
-}
-
-src_install() {
- dobin samtools || die
- dobin $(find misc -type f -executable) || die
- insinto /usr/share/${PN}
- doins -r examples || die
- doman ${PN}.1 || die
- dodoc AUTHORS ChangeLog NEWS
-}
diff --git a/sci-biology/samtools/samtools-0.1.19-r2.ebuild b/sci-biology/samtools/samtools-0.1.19-r2.ebuild
deleted file mode 100644
index a401e5f9df83..000000000000
--- a/sci-biology/samtools/samtools-0.1.19-r2.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils multilib python-r1 toolchain-funcs
-
-DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
-HOMEPAGE="http://samtools.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
-IUSE="examples"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-CDEPEND="sys-libs/ncurses:0="
-RDEPEND="${CDEPEND}
- dev-lang/lua
- dev-lang/perl
- ${PYTHON_DEPS}"
-DEPEND="${CDEPEND}
- virtual/pkgconfig"
-
-src_prepare() {
- epatch "${FILESDIR}"/${P}-buildsystem.patch
-
- sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die
-
- tc-export CC AR
-}
-
-src_compile() {
- local _ncurses="$($(tc-getPKG_CONFIG) --libs ncurses)"
- emake dylib LIBCURSES="${_ncurses}"
- emake LIBCURSES="${_ncurses}"
-}
-
-src_install() {
- dobin samtools $(find bcftools misc -type f -executable)
-
- python_replicate_script "${ED}"/usr/bin/varfilter.py
-
- dolib.so libbam$(get_libname 1)
- dosym libbam$(get_libname 1) /usr/$(get_libdir)/libbam$(get_libname)
-
- insinto /usr/include/bam
- doins *.h
-
- doman ${PN}.1
- dodoc AUTHORS NEWS
-
- if use examples; then
- insinto /usr/share/${PN}
- doins -r examples
- fi
-}
diff --git a/sci-biology/samtools/samtools-1.0-r1.ebuild b/sci-biology/samtools/samtools-1.0-r1.ebuild
deleted file mode 100644
index b6e1aeb5831a..000000000000
--- a/sci-biology/samtools/samtools-1.0-r1.ebuild
+++ /dev/null
@@ -1,72 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils multilib 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="${PYTHON_REQUIRED_USE}"
-
-CDEPEND="
- sys-libs/ncurses:0=
- sci-libs/htslib"
-
-RDEPEND="${CDEPEND}
- dev-lang/lua
- dev-lang/perl
- ${PYTHON_DEPS}"
-DEPEND="${CDEPEND}
- virtual/pkgconfig"
-
-src_prepare() {
- find htslib-1.0 -delete || die
-
- sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die
-
- epatch "${FILESDIR}"/${P}-buildsystem.patch
-
- tc-export CC AR
-
- sed \
- -e '/htslib.mk/d' \
- -i Makefile || die
-
-}
-
-src_compile() {
- local mymakeargs=(
- LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)"
- HTSDIR="${EPREFIX}/usr/include"
- HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib)
- BAMLIB="libbam.so"
- )
- emake "${mymakeargs[@]}"
-}
-
-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
-}
diff --git a/sci-biology/samtools/samtools-1.0.ebuild b/sci-biology/samtools/samtools-1.0.ebuild
deleted file mode 100644
index 0fb9d04344bb..000000000000
--- a/sci-biology/samtools/samtools-1.0.ebuild
+++ /dev/null
@@ -1,68 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils multilib 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="${PYTHON_REQUIRED_USE}"
-
-CDEPEND="
- sys-libs/ncurses:0=
- sci-libs/htslib"
-
-RDEPEND="${CDEPEND}
- dev-lang/lua
- dev-lang/perl
- ${PYTHON_DEPS}"
-DEPEND="${CDEPEND}
- virtual/pkgconfig"
-
-src_prepare() {
- find htslib-1.0 -delete || die
-
- sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die
-
- tc-export CC AR
-
- sed \
- -e '/htslib.mk/d' \
- -i Makefile || die
-
-}
-
-src_compile() {
- local mymakeargs=(
- LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)"
- CC="$(tc-getCC)"
- LDFLAGS="${LDFLAGS}"
- CFLAGS="${CFLAGS}"
- HTSDIR="${EPREFIX}/usr/include"
- HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib)
- )
- emake "${mymakeargs[@]}"
-}
-
-src_install() {
- dobin samtools $(find misc -type f -executable)
-
- python_replicate_script "${ED}"/usr/bin/varfilter.py
-
- doman ${PN}.1
- dodoc AUTHORS NEWS README
-
- if use examples; then
- insinto /usr/share/${PN}
- doins -r examples
- fi
-}
diff --git a/sci-biology/samtools/samtools-1.1.ebuild b/sci-biology/samtools/samtools-1.1.ebuild
deleted file mode 100644
index ca3e4b46c22f..000000000000
--- a/sci-biology/samtools/samtools-1.1.ebuild
+++ /dev/null
@@ -1,82 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils multilib 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="${PYTHON_REQUIRED_USE}"
-
-CDEPEND="
- sys-libs/ncurses:0=
- ~sci-libs/htslib-${PV}"
-
-RDEPEND="${CDEPEND}
- dev-lang/lua
- dev-lang/perl
- ${PYTHON_DEPS}"
-DEPEND="${CDEPEND}
- virtual/pkgconfig"
-
-src_prepare() {
- find htslib-* -delete || die
-
- sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die
-
- epatch "${FILESDIR}"/${P}-buildsystem.patch
-
- tc-export CC AR
-
- sed \
- -e '/htslib.mk/d' \
- -i Makefile || die
-
-}
-
-src_compile() {
- local mymakeargs=(
- LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)"
- HTSDIR="${EPREFIX}/usr/include"
- HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib)
- BAMLIB="libbam.so"
- )
- 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"
- )
- 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
-}
diff --git a/sci-biology/samtools/samtools-1.2.ebuild b/sci-biology/samtools/samtools-1.2.ebuild
deleted file mode 100644
index 75dfbfae1f27..000000000000
--- a/sci-biology/samtools/samtools-1.2.ebuild
+++ /dev/null
@@ -1,82 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils multilib 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="${PYTHON_REQUIRED_USE}"
-
-CDEPEND="
- sys-libs/ncurses:0=
- >=sci-libs/htslib-${PV}"
-
-RDEPEND="${CDEPEND}
- dev-lang/lua
- dev-lang/perl
- ${PYTHON_DEPS}"
-DEPEND="${CDEPEND}
- virtual/pkgconfig"
-
-src_prepare() {
- find htslib-* -delete || die
-
- sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die
-
- epatch "${FILESDIR}"/${P}-buildsystem.patch
-
- tc-export CC AR
-
- sed \
- -e '/htslib.mk/d' \
- -i Makefile || die
-
-}
-
-src_compile() {
- local mymakeargs=(
- LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)"
- HTSDIR="${EPREFIX}/usr/include"
- HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib)
- BAMLIB="libbam.so"
- )
- 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
-}
diff --git a/sci-biology/samtools/samtools-1.3-r1.ebuild b/sci-biology/samtools/samtools-1.3-r1.ebuild
deleted file mode 100644
index 8d25bf84ad3c..000000000000
--- a/sci-biology/samtools/samtools-1.3-r1.ebuild
+++ /dev/null
@@ -1,96 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-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/perl
- ${PYTHON_DEPS}"
-DEPEND="${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
-
- # fix perl shebangs
- pushd "${ED}"usr/bin/ >> /dev/null
- local i
- for i in plot-bamstats *.pl; do
- sed -e '1s:.*:#!/usr/bin/env perl:' -i "${i}" || die
- done
-
- # remove lua scripts
- rm -f r2plot.lua vcfutils.lua || die
- popd >> /dev/null
-
- 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
-}