commit: 47592cb35c03ac6c245cf22a5883dd7e5ba7b69e
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Sep 2 12:45:48 2017 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Sep 2 12:45:48 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=47592cb3
sci-biology/samtools: Remove old
.../samtools/files/samtools-1.0-buildsystem.patch | 59 -------
.../samtools/files/samtools-1.0-rmdup.patch | 47 -----
.../samtools/files/samtools-1.1-buildsystem.patch | 153 ----------------
.../samtools/files/samtools-1.1-rmdup.patch | 47 -----
.../samtools/files/samtools-1.2-buildsystem.patch | 193 ---------------------
.../samtools/files/samtools-1.2-rmdup.patch | 47 -----
.../files/samtools-1.3.1-buildsystem.patch | 75 --------
sci-biology/samtools/metadata.xml | 11 --
sci-biology/samtools/samtools-1.0-r2.ebuild | 73 --------
sci-biology/samtools/samtools-1.1-r1.ebuild | 83 ---------
sci-biology/samtools/samtools-1.2-r1.ebuild | 83 ---------
sci-biology/samtools/samtools-1.3.1.ebuild | 83 ---------
sci-biology/samtools/samtools-1.5.ebuild | 82 ---------
13 files changed, 1036 deletions(-)
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 53a8b66f9..000000000
--- 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-1.0-rmdup.patch
b/sci-biology/samtools/files/samtools-1.0-rmdup.patch
deleted file mode 100644
index 023b5d73d..000000000
--- a/sci-biology/samtools/files/samtools-1.0-rmdup.patch
+++ /dev/null
@@ -1,47 +0,0 @@
-From 05fb5c2e17576b1d0ea5a0b8203b9eba236f2455 Mon Sep 17 00:00:00 2001
-From: kirkmcclure <kirkmccl...@users.noreply.github.com>
-Date: Mon, 23 Mar 2015 05:35:00 -0800
-Subject: [PATCH] Update bam.c
-
- For issue #138 - Samtools view -l no longer works.
-Implement bam_get_library()
----
- bam.c | 23 ++++++++++++-----------
- 1 file changed, 12 insertions(+), 11 deletions(-)
-
-diff --git a/bam.c b/bam.c
-index f909b7e..864d3f0 100644
---- a/bam.c
-+++ b/bam.c
-@@ -61,19 +61,20 @@ int bam_validate1(const bam_header_t *header, const bam1_t
*b)
- return 1;
- }
-
--// FIXME: we should also check the LB tag associated with each alignment
- const char *bam_get_library(bam_header_t *h, const bam1_t *b)
- {
--#if 0
-- const uint8_t *rg;
-- if (h->dict == 0) h->dict = sam_header_parse2(h->text);
-- if (h->rg2lib == 0) h->rg2lib = sam_header2tbl(h->dict, "RG", "ID", "LB");
-- rg = bam_aux_get(b, "RG");
-- return (rg == 0)? 0 : sam_tbl_get(h->rg2lib, (const char*)(rg + 1));
--#else
-- fprintf(stderr, "Samtools-htslib-API: bam_get_library() not yet
implemented\n");
-- abort();
--#endif
-+ const uint8_t *rg = 0;
-+ const uint8_t *pLibName, *pDict;
-+ if ( b != 0 && h != 0 ) {
-+ if ( (rg = bam_aux_get(b, "RG") ) != 0
-+ && (pDict = sam_header_parse2(h->text)) != 0 ) {
-+ pLibName = sam_header2tbl(pDict, "RG", "ID", "LB");
-+ if ( pLibName && strlen( (char*)pLibName ) > 0 ) {
-+ return sam_tbl_get((void*)pLibName, (const char*)(rg + 1));
-+ }
-+ }
-+ }
-+ return 0;
- }
-
- int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end,
void *data, bam_fetch_f func)
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 b9ae77de6..000000000
--- 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-1.1-rmdup.patch
b/sci-biology/samtools/files/samtools-1.1-rmdup.patch
deleted file mode 100644
index 023b5d73d..000000000
--- a/sci-biology/samtools/files/samtools-1.1-rmdup.patch
+++ /dev/null
@@ -1,47 +0,0 @@
-From 05fb5c2e17576b1d0ea5a0b8203b9eba236f2455 Mon Sep 17 00:00:00 2001
-From: kirkmcclure <kirkmccl...@users.noreply.github.com>
-Date: Mon, 23 Mar 2015 05:35:00 -0800
-Subject: [PATCH] Update bam.c
-
- For issue #138 - Samtools view -l no longer works.
-Implement bam_get_library()
----
- bam.c | 23 ++++++++++++-----------
- 1 file changed, 12 insertions(+), 11 deletions(-)
-
-diff --git a/bam.c b/bam.c
-index f909b7e..864d3f0 100644
---- a/bam.c
-+++ b/bam.c
-@@ -61,19 +61,20 @@ int bam_validate1(const bam_header_t *header, const bam1_t
*b)
- return 1;
- }
-
--// FIXME: we should also check the LB tag associated with each alignment
- const char *bam_get_library(bam_header_t *h, const bam1_t *b)
- {
--#if 0
-- const uint8_t *rg;
-- if (h->dict == 0) h->dict = sam_header_parse2(h->text);
-- if (h->rg2lib == 0) h->rg2lib = sam_header2tbl(h->dict, "RG", "ID", "LB");
-- rg = bam_aux_get(b, "RG");
-- return (rg == 0)? 0 : sam_tbl_get(h->rg2lib, (const char*)(rg + 1));
--#else
-- fprintf(stderr, "Samtools-htslib-API: bam_get_library() not yet
implemented\n");
-- abort();
--#endif
-+ const uint8_t *rg = 0;
-+ const uint8_t *pLibName, *pDict;
-+ if ( b != 0 && h != 0 ) {
-+ if ( (rg = bam_aux_get(b, "RG") ) != 0
-+ && (pDict = sam_header_parse2(h->text)) != 0 ) {
-+ pLibName = sam_header2tbl(pDict, "RG", "ID", "LB");
-+ if ( pLibName && strlen( (char*)pLibName ) > 0 ) {
-+ return sam_tbl_get((void*)pLibName, (const char*)(rg + 1));
-+ }
-+ }
-+ }
-+ return 0;
- }
-
- int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end,
void *data, bam_fetch_f func)
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 2343b2245..000000000
--- 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-1.2-rmdup.patch
b/sci-biology/samtools/files/samtools-1.2-rmdup.patch
deleted file mode 100644
index 023b5d73d..000000000
--- a/sci-biology/samtools/files/samtools-1.2-rmdup.patch
+++ /dev/null
@@ -1,47 +0,0 @@
-From 05fb5c2e17576b1d0ea5a0b8203b9eba236f2455 Mon Sep 17 00:00:00 2001
-From: kirkmcclure <kirkmccl...@users.noreply.github.com>
-Date: Mon, 23 Mar 2015 05:35:00 -0800
-Subject: [PATCH] Update bam.c
-
- For issue #138 - Samtools view -l no longer works.
-Implement bam_get_library()
----
- bam.c | 23 ++++++++++++-----------
- 1 file changed, 12 insertions(+), 11 deletions(-)
-
-diff --git a/bam.c b/bam.c
-index f909b7e..864d3f0 100644
---- a/bam.c
-+++ b/bam.c
-@@ -61,19 +61,20 @@ int bam_validate1(const bam_header_t *header, const bam1_t
*b)
- return 1;
- }
-
--// FIXME: we should also check the LB tag associated with each alignment
- const char *bam_get_library(bam_header_t *h, const bam1_t *b)
- {
--#if 0
-- const uint8_t *rg;
-- if (h->dict == 0) h->dict = sam_header_parse2(h->text);
-- if (h->rg2lib == 0) h->rg2lib = sam_header2tbl(h->dict, "RG", "ID", "LB");
-- rg = bam_aux_get(b, "RG");
-- return (rg == 0)? 0 : sam_tbl_get(h->rg2lib, (const char*)(rg + 1));
--#else
-- fprintf(stderr, "Samtools-htslib-API: bam_get_library() not yet
implemented\n");
-- abort();
--#endif
-+ const uint8_t *rg = 0;
-+ const uint8_t *pLibName, *pDict;
-+ if ( b != 0 && h != 0 ) {
-+ if ( (rg = bam_aux_get(b, "RG") ) != 0
-+ && (pDict = sam_header_parse2(h->text)) != 0 ) {
-+ pLibName = sam_header2tbl(pDict, "RG", "ID", "LB");
-+ if ( pLibName && strlen( (char*)pLibName ) > 0 ) {
-+ return sam_tbl_get((void*)pLibName, (const char*)(rg + 1));
-+ }
-+ }
-+ }
-+ return 0;
- }
-
- int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end,
void *data, bam_fetch_f func)
diff --git a/sci-biology/samtools/files/samtools-1.3.1-buildsystem.patch
b/sci-biology/samtools/files/samtools-1.3.1-buildsystem.patch
deleted file mode 100644
index bd0f20c7c..000000000
--- a/sci-biology/samtools/files/samtools-1.3.1-buildsystem.patch
+++ /dev/null
@@ -1,75 +0,0 @@
---- samtools-1.3.1/Makefile.ori 2016-04-22 11:51:16.000000000 +0200
-+++ samtools-1.3.1/Makefile 2017-02-16 23:41:19.819951687 +0100
-@@ -21,9 +21,9 @@
- # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
- # DEALINGS IN THE SOFTWARE.
-
--CC = gcc
-+CC ?= gcc
- CPPFLAGS =
--CFLAGS = -g -Wall -O2
-+CFLAGS ?= -g -Wall -O2
- LDFLAGS =
- LIBS =
-
-@@ -197,8 +203,8 @@
- # 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 +216,28 @@
- 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
sam_opts.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 sam_opts.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 sam_opts.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 sam_opts.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 sam_opts.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 sam_opts.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
sam_opts.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)
-@@ -258,10 +264,10 @@
- misc/maq2sam-long: misc/maq2sam-long.o
- $(CC) $(LDFLAGS) -o $@ misc/maq2sam-long.o $(ALL_LIBS)
-
--misc/md5fa: misc/md5fa.o $(HTSLIB)
-+misc/md5fa: misc/md5fa.o
- $(CC) $(ALL_LDFLAGS) -o $@ misc/md5fa.o $(HTSLIB_LIB) $(ALL_LIBS)
-
--misc/md5sum-lite: misc/md5sum-lite.o $(HTSLIB)
-+misc/md5sum-lite: misc/md5sum-lite.o
- $(CC) $(ALL_LDFLAGS) -o $@ misc/md5sum-lite.o $(HTSLIB_LIB) $(ALL_LIBS)
-
- misc/wgsim: misc/wgsim.o
diff --git a/sci-biology/samtools/metadata.xml
b/sci-biology/samtools/metadata.xml
deleted file mode 100644
index 5b953af48..000000000
--- a/sci-biology/samtools/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";>
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-biol...@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="sourceforge">samtools</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/samtools/samtools-1.0-r2.ebuild
b/sci-biology/samtools/samtools-1.0-r2.ebuild
deleted file mode 100644
index 6be28b674..000000000
--- a/sci-biology/samtools/samtools-1.0-r2.ebuild
+++ /dev/null
@@ -1,73 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils multilib python-r1 toolchain-funcs
-
-DESCRIPTION="Utilities for SAM (Sequence Alignment/Map)"
-HOMEPAGE="http://www.htslib.org/";
-SRC_URI="mirror://sourceforge/${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:0="
-
-RDEPEND="${CDEPEND}
- dev-lang/lua
- dev-lang/perl"
-DEPEND="${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}"/${P}-buildsystem.patch \
- "${FILESDIR}"/${P}-rmdup.patch
-
- tc-export CC AR
-
- sed \
- -e '/htslib.mk/d' \
- -i Makefile || die
-}
-
-src_compile() {
- local mymakeargs=(
- LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)"
- HTSDIR="${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-1.1-r1.ebuild
b/sci-biology/samtools/samtools-1.1-r1.ebuild
deleted file mode 100644
index 19cada025..000000000
--- a/sci-biology/samtools/samtools-1.1-r1.ebuild
+++ /dev/null
@@ -1,83 +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 SAM (Sequence Alignment/Map)"
-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}:0="
-
-RDEPEND="${CDEPEND}
- dev-lang/lua
- dev-lang/perl"
-DEPEND="${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}"/${P}-buildsystem.patch \
- "${FILESDIR}"/${P}-rmdup.patch
-
- tc-export CC AR
-
- sed \
- -e '/htslib.mk/d' \
- -i Makefile || die
-}
-
-src_compile() {
- local mymakeargs=(
- LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)"
- HTSDIR="${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-r1.ebuild
b/sci-biology/samtools/samtools-1.2-r1.ebuild
deleted file mode 100644
index 702d9bcb9..000000000
--- a/sci-biology/samtools/samtools-1.2-r1.ebuild
+++ /dev/null
@@ -1,83 +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 SAM (Sequence Alignment/Map)"
-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}:0="
-
-RDEPEND="${CDEPEND}
- dev-lang/lua
- dev-lang/perl"
-DEPEND="${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}"/${P}-buildsystem.patch \
- "${FILESDIR}"/${P}-rmdup.patch
-
- tc-export CC AR
-
- sed \
- -e '/htslib.mk/d' \
- -i Makefile || die
-}
-
-src_compile() {
- local mymakeargs=(
- LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)"
- HTSDIR="${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-1.3.1.ebuild
b/sci-biology/samtools/samtools-1.3.1.ebuild
deleted file mode 100644
index 98649e6ec..000000000
--- a/sci-biology/samtools/samtools-1.3.1.ebuild
+++ /dev/null
@@ -1,83 +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 SAM (Sequence Alignment/Map)"
-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}:0="
-
-RDEPEND="${CDEPEND}
- dev-lang/lua
- dev-lang/perl"
-DEPEND="${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*
- dolib libbam.a
-
- 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-1.5.ebuild
b/sci-biology/samtools/samtools-1.5.ebuild
deleted file mode 100644
index 2a2d80423..000000000
--- a/sci-biology/samtools/samtools-1.5.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 SAM (Sequence Alignment/Map) and BAM files"
-HOMEPAGE="http://www.htslib.org/";
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS=""
-# 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}:2="
-
-RDEPEND="${CDEPEND}
- dev-lang/lua
- dev-lang/perl"
-DEPEND="${CDEPEND}
- virtual/pkgconfig"
-
-src_prepare() {
- find htslib-* -delete || die
-
- sed -i 's~/software/bin/python~/usr/bin/env python~'
"${S}"/misc/varfilter.py || die
-
- tc-export CC AR
-
- sed \
- -e '/htslib.mk/d' \
- -i Makefile || die
-}
-
-src_compile() {
- local mymakeargs=(
- LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)"
- HTSDIR="${EPREFIX}/usr/include"
- HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib)
- BAMLIB="libbam.so"
- CC=$(tc-getCC) CFLAGS="${CFLAGS}"
- )
- 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*
- dolib libbam.a
-
- 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
-}
