+AUX samtools-0.1.20-buildsystem.patch 6737 SHA256 3ea8caadb8df363b5c4b21f0d6205cc5ade79bbab13070483fad5d5145323bea SHA512 ecb05971fbea4570ec161a165cb581b38ed727bb7e5b769862984bf035414cd564ab809882dc3272f8b192feeb86e29247d7327afa73ff668b01c03c58bb177d WHIRLPOOL 469588de06a4dc81c2d2b15d7502a2419af6b42561be5935792ec13d2938e141c7fb7f2fd0d8361975157db613964ebacca9f0129ca57204a51bd09e5a82f12e

+AUX samtools-1.5-buildsystem.patch 18442 SHA256 a7784c89cc06da00fa3f8470402a65a0298ef64edcb94d83694cde3cd04c16c4 SHA512 2405c9c5bd2892756dd70147d0bc57f11f869ac2b6bb12d4350e3f7145727a4c8a602489bca5dbcbe8131d52572d4573e8507a2b989ac0ac86aa8dfef92e58d4 WHIRLPOOL 54afdce038497f040e99ab6690142d9245ddb634bb11abf5f84b78d8297884d30be7073efdb09a2fc9d304a5f48ae3fe31518d171eaea16c668b7a5fce625ec8

+DIST samtools-0.1.20.tar.gz 566387 SHA256 500019b4d1886ad995513d5ce8b413b14b51f16f251ce76bc0b35a446b182a47 SHA512 15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5 WHIRLPOOL 3ea05df172ea6afe31bd3880f918e0b286f65839f78ed846a0d3aef84ec70df1e3741ff6dcad5f70d62a06687f07b35609829aabd33c6688fac0d59effd979e0

+DIST samtools-1.5.tar.bz2 4190142 SHA256 8542da26832ee08c1978713f5f6188ff750635b50d8ab126a0c7bb2ac1ae2df6 SHA512 ff3e39ba867ecbd88f3363b038508c1557e349ea4223483f8f4ecb17ff8864fb53cd193bc2059a147e30f07395bbf53c8518d0f70219e454375c8bffe56e3059 WHIRLPOOL 1a88c9617857f1f6d146df179aef5b5c6bb83de8c9d127c405e5756842ced84c194a3f09f69a4757a8adf6ca623c9fdc972f4bf609649d3e991dda8f616e3582

+EBUILD samtools-0.1.20-r3.ebuild 2363 SHA256 7aad766c195ec2ffce65fc9d85664125699cb632b0e6f45e77ad505bbdc25c4c SHA512 f79e0f723d86e7c2060163a3b79e6624ea58d21e7c8ddeb87be40a7972cd97e60df82dacaae23b8a89cec2a0517ffdae8804ac71044685b40d5c5769f8964557 WHIRLPOOL 3ad8461dfae0a9d094c9048d83f4911f9a319c6320e0d7e56c348a86b56f58be4cce5d750df75d989c2680e79d81882c5a32ddc3e987a3908b9397e857a06ada

+EBUILD samtools-1.5.ebuild 1107 SHA256 ceb19acb7c14de84d61421c03e1640122fb05d260e31a04466483b7c1b1cb048 SHA512 2f1701695fe3aa270bd75bedc3f847b3057ea1a6d9dca386a8f420df22ab78f51b12c8e1ca80d7d2fb1221d246047a78e914022c8e4c8bae5b0b053f3b130cfd WHIRLPOOL 5e21fcaf76e8f2402abb9196a6d263153c45d05bc81a8af89ea84e637c89b65c765537f0f5e43ae80d9d668edd38192617cdd8242e903986cb564321ab113b75

+MISC ChangeLog 5897 SHA256 5e04325ac9db41a8fa4ad4a91178e93f599c103ef650c0eda17d7ba879cbc328 SHA512 3bb0ec0ff92dae1e328168131e092b122dc95bae412852943788483b145e957254e9c13e85ef81966c1d6afe5db267ea85348d8aefd5c0f21cc13842cf9bdc2a WHIRLPOOL a82733920c2e050d36d2f42ebc6e54cd4782de68788e7d74ee360bfd25ca04dffda1bacfac6c50fb4205ca40707aa5a06f6370b654e48e714e689b61f1dfe432

+MISC ChangeLog-2015 4690 SHA256 d2354c1ec9f2e04bcf587f514dcf487bc93986e1dd5ff5b253a1c3dcd5b8308a SHA512 11d76e3d8992ad22f9425c9f6fc25353dd4ba5ac33785a5d51ec2b34fa427d89a28ccce0cbd252e4c6b6859709fbbd7594a77934e290cb0bb26da4a9e0285b26 WHIRLPOOL 3646b90ee112bbdc3f1cf07114196734447b5753add80a9c1f10d46d5eb42662fa5cabbb3b696d85aae6dc050eec054e4a2aab49d7114bc9e38fab8b68991a33

+MISC metadata.xml 408 SHA256 84d96be1669841f99c7cad425f22f88a835762fd5423ac0ea84929659cd7cda6 SHA512 8c8d240fd37400e43637e12f008f8f2b03fcca062883dd63ccc6956bbfc46d05709f032d146a95452db35b546ff828239b108b3a331f5295ec97872d6c9478fb WHIRLPOOL 1f8c3b08c0264503a911ce0f7e0495a441f73500bed6bb36fbf0507311d491b794e547537c8ad7917dcdd3f59a4f4af3b742caa4dbbc29eaed5ed180e05944de

+--- samtools-0.1.20/bcftools/Makefile

++++ samtools-0.1.20/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 @@

+ .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 @@

+ $(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

+--- samtools-0.1.20/Makefile

++++ samtools-0.1.20/Makefile

+@@ -4,10 +4,10 @@

+ # make git-stamp

+ VERSION=

+

+-CC= gcc

+-CFLAGS= -g -Wall $(VERSION) -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 $(VERSION) -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 \

+@@ -28,14 +28,14 @@

+ .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;

+@@ -48,22 +48,22 @@

+ .PHONY:all lib clean cleanlocal

+ .PHONY:all-recur lib-recur clean-recur cleanlocal-recur install-recur

+

+-lib:libbam.a

++lib:libbam-0.1-legacy.a

+

+-libbam.a:$(LOBJS)

++libbam-0.1-legacy.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) -L. -lbam-0.1-legacy -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

+@@ -90,17 +90,17 @@

+ faidx_main.o:faidx.h razf.h

+

+

+-libbam.1.dylib-local:$(LOBJS)

+- libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz

++libbam-0.1-legacy.1.dylib-local:$(LOBJS)

++ libtool -dynamic $(LOBJS) -o libbam-0.1-legacy.1.dylib -lc -lz

+

+-libbam.so.1-local:$(LOBJS)

+- $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz

++libbam-0.1-legacy.so.1-local:$(LOBJS)

++ $(CC) $(LDFLAGS) -shared -Wl,-soname,libbam-0.1-legacy.so -o libbam-0.1-legacy.so.1 $(LOBJS) -lc -lz -lm -lpthread

+

+ dylib:

+ @$(MAKE) cleanlocal; \

+ case `uname` in \

+- Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.so.1-local;; \

+- Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.1.dylib-local;; \

++ Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam-0.1-legacy.so.1-local;; \

++ Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam-0.1-legacy.1.dylib-local;; \

+ *) echo 'Unknown OS';; \

+ esac

+

+--- samtools-0.1.20/misc/Makefile

++++ samtools-0.1.20/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 @@

+ .SUFFIXES:.c .o

+

+ .c.o:

+- $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@

++ $(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@

+

+ all:$(PROG)

+

+@@ -20,7 +20,7 @@

+ 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:

+

+ bamcheck:bamcheck.o

+- $(CC) $(CFLAGS) -o $@ bamcheck.o -L.. -lm -lbam -lpthread -lz

++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ bamcheck.o -L.. -lm -lbam-0.1-legacy -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

+--- samtools-0.1.20/misc/varfilter.py

++++ samtools-0.1.20/misc/varfilter.py

+@@ -1,4 +1,4 @@

+-#!/software/bin/python

++#!/usr/bin/env python

+

+ # Author: lh3, converted to python and modified to add -C option by Aylwyn Scally

+ #

+--- a/config.mk.in

++++ b/config.mk.in

+@@ -28,27 +28,26 @@

+ # in the Makefile to reflect your configuration choices. If you don't run

+ # configure, the main Makefile contains suitable conservative defaults.

+

+-prefix = @prefix@

+-exec_prefix = @exec_prefix@

+-bindir = @bindir@

+-datarootdir = @datarootdir@

+-mandir = @mandir@

++prefix = @prefix@

++exec_prefix = @exec_prefix@

++bindir = @bindir@

++libdir = @libdir@

++datarootdir = @datarootdir@

++mandir = @mandir@

++man1dir = $(mandir)/man1

+

+ CC = @CC@

++AR = @AR@

+ CPPFLAGS = @CPPFLAGS@

+ CFLAGS = @CFLAGS@

+ LDFLAGS = @LDFLAGS@

+ LIBS = @LIBS@

+

+-@Hsource@HTSDIR = @HTSDIR@

+-@Hsource@include $(HTSDIR)/htslib.mk

+-@Hsource@include $(HTSDIR)/htslib_static.mk

+-@Hsource@HTSLIB = $(HTSDIR)/libhts.a

+-@Hsource@HTSLIB_LIB = $(HTSLIB) $(HTSLIB_static_LIBS)

+-@Hsource@HTSLIB_LDFLAGS = $(HTSLIB_static_LDFLAGS)

+-@Hsource@BGZIP = $(HTSDIR)/bgzip

+-HTSLIB_CPPFLAGS = @HTSLIB_CPPFLAGS@

+-@Hinstall@HTSLIB_LDFLAGS = @HTSLIB_LDFLAGS@

+-@Hinstall@HTSLIB_LIB = -lhts

++HTSLIB_CFLAGS = @HTSLIB_CFLAGS@

++HTSLIB_LIBS = @HTSLIB_LIBS@

+

+-CURSES_LIB = @CURSES_LIB@

++NCURSES_CFLAGS = @NCURSES_CFLAGS@

++NCURSES_LIBS = @NCURSES_LIBS@

++

++ZLIB_CFLAGS = @ZLIB_CFLAGS@

++ZLIB_LIBS = @ZLIB_LIBS@

+--- a/configure.ac

++++ b/configure.ac

+@@ -29,9 +29,6 @@

+ AC_CONFIG_SRCDIR([bamtk.c])

+ AC_CONFIG_HEADERS([config.h])

+

+-m4_include([m4/ax_with_curses.m4])

+-m4_include([m4/ax_with_htslib.m4])

+-

+ dnl Copyright notice to be copied into the generated configure script

+ AC_COPYRIGHT([Portions copyright (C) 2015 Genome Research Ltd.

+

+@@ -39,73 +36,27 @@

+ redistribute it. There is NO WARRANTY, to the extent permitted by law.])

+

+ AC_PROG_CC

++AM_PROG_AR

+

+ AC_SYS_LARGEFILE

+

+-AX_WITH_HTSLIB

+-if test "$ax_cv_htslib" != yes; then

+- AC_MSG_ERROR([HTSlib development files not found

+-

+-Samtools uses HTSlib to parse bioinformatics file formats etc. Building it

+-requires an unpacked HTSlib source tree (which will be built in conjunction

+-with samtools) or a previously-installed HTSlib. In either case you may

+-need to configure --with-htslib=DIR to locate the appropriate HTSlib.

+-

+-FAILED. You must supply an HTSlib in order to build samtools successfully.])

+-fi

+-

+-if test "$ax_cv_htslib_which" = source; then

+- Hsource=

+- Hinstall='#'

+-else

+- Hsource='#'

+- Hinstall=

+-fi

+-AC_SUBST([Hsource])

+-AC_SUBST([Hinstall])

++dnl htslib

++PKG_CHECK_MODULES([HTSLIB], [htslib])

+

++dnl ncurses

+ AC_ARG_WITH([curses],

+ [AS_HELP_STRING([--without-curses],

+ [omit curses support, so no curses library needed])])

+

+-if test "$with_curses" != no; then

+- AX_WITH_CURSES

+- if test "$ax_cv_curses" != yes; then

+- AC_MSG_ERROR([curses development files not found

+-

+-The 'samtools tview' command uses the curses text user interface library.

+-Building samtools with tview requires curses/ncurses/etc development files

+-to be installed on the build machine; you may need to ensure a package such

+-as libncurses5-dev (on Debian or Ubuntu Linux) or ncurses-devel (on RPM-based

+-Linux distributions) is installed.

+-

+-FAILED. Either configure --without-curses or resolve this error to build

+-samtools successfully.])

+- fi

+-else

+- CURSES_LIB=

+- CURSES_CPPFLAGS=

+- AC_SUBST([CURSES_LIB])

+- AC_SUBST([CURSES_CPPFLAGS])

+-fi

+-

+-save_LIBS=$LIBS

+-zlib_devel=ok

+-dnl Set a trivial non-empty INCLUDES to avoid excess default includes tests

+-AC_CHECK_HEADER([zlib.h], [], [zlib_devel=missing], [;])

+-AC_CHECK_LIB(z, inflate, [], [zlib_devel=missing])

+-LIBS=$save_LIBS

+-

+-if test $zlib_devel != ok; then

+- AC_MSG_ERROR([zlib development files not found

+-

+-Samtools uses compression routines from the zlib library <http://zlib.net>.

+-Building samtools requires zlib development files to be installed on the build

+-machine; you may need to ensure a package such as zlib1g-dev (on Debian or

+-Ubuntu Linux) or zlib-devel (on RPM-based Linux distributions) is installed.

++AS_IF([test "x$with_curses" != "xno"], [

++ PKG_CHECK_MODULES([NCURSES], [ncurses])

++

++ AC_DEFINE([HAVE_CURSES], [1])

++ AC_DEFINE([HAVE_NCURSES_H], [1])

++])

+

+-FAILED. This error must be resolved in order to build samtools successfully.])

+-fi

++dnl zlib

++PKG_CHECK_MODULES([ZLIB], [zlib])

+

+ AC_CONFIG_FILES([config.mk])

+ AC_OUTPUT

+--- a/Makefile

++++ b/Makefile

+@@ -21,14 +21,6 @@

+ # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER

+ # DEALINGS IN THE SOFTWARE.

+

+-CC = gcc

+-AR = ar

+-CPPFLAGS =

+-#CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600

+-CFLAGS = -g -Wall -O2

+-LDFLAGS =

+-LIBS =

+-

+ LOBJS= bam_aux.o bam.o bam_import.o sam.o \

+ sam_header.o bam_plbuf.o

+ AOBJS= bam_index.o bam_plcmd.o sam_view.o \

+@@ -40,13 +32,6 @@

+ bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o \

+ bam_quickcheck.o bam_addrprg.o

+

+-prefix = /usr/local

+-exec_prefix = $(prefix)

+-bindir = $(exec_prefix)/bin

+-datarootdir = $(prefix)/share

+-mandir = $(datarootdir)/man

+-man1dir = $(mandir)/man1

+-

+ # Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS)

+ misc_bindir = $(bindir)

+

+@@ -85,15 +70,14 @@

+

+ all: $(PROGRAMS) $(MISC_PROGRAMS) $(TEST_PROGRAMS)

+

+-ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS)

+-ALL_LDFLAGS = $(HTSLIB_LDFLAGS) $(LDFLAGS)

+-ALL_LIBS = -lz $(LIBS)

++ALL_CPPFLAGS = -I. $(HTSLIB_CFLAGS) $(CPPFLAGS)

++ALL_LIBS = $(ZLIB_LIBS) $(LIBS)

+

+ # Usually config.mk and config.h are generated by running configure

+ # or config.status, but if those aren't used create defaults here.

+

+ config.mk:

+- @sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.5#g;s/@HTSLIB_CPPFLAGS@/-I$$(HTSDIR)/g;s/@CURSES_LIB@/-lcurses/g' config.mk.in > $@

++ @sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.5#g;s/@HTSLIB_CFLAGS@/-I$$(HTSDIR)/g;s/@NCURSES_LIBS@/-lcurses/g' config.mk.in > $@

+

+ config.h:

+ echo '/* Basic config.h generated by Makefile */' > $@

+@@ -133,17 +117,22 @@

+ .c.o:

+ $(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ $<

+

++$(LOBJS):

++ $(CC) $(CFLAGS) $(ALL_CPPFLAGS) -fPIC -c -o $@ $<

++

+

+ LIBST_OBJS = sam_opts.o sam_utils.o

+

+

+-lib:libbam.a

++lib: libbam.so.1.0

+

+-libbam.a:$(LOBJS)

+- $(AR) -csru $@ $(LOBJS)

++libbam.so.1.0:$(LOBJS)

++ $(CC) $(CFLAGS) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB)

++ ln -sf $@ libbam.so.1

++ ln -sf $@ libbam.so

+

+-samtools: $(AOBJS) libbam.a libst.a $(HTSLIB)

+- $(CC) $(ALL_LDFLAGS) -o $@ $(AOBJS) libbam.a libst.a $(HTSLIB_LIB) $(CURSES_LIB) -lm $(ALL_LIBS) -lpthread

++samtools: $(AOBJS) libbam.so.1.0 libst.a

++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) libbam.so.1.0 libst.a $(HTSLIB_LIBS) $(NCURSES_LIBS) -lm $(ALL_LIBS) -lpthread

+

+ # For building samtools and its test suite only: NOT to be installed.

+ libst.a: $(LIBST_OBJS)

+@@ -151,58 +140,58 @@

+ $(AR) -rcs $@ $(LIBST_OBJS)

+

+

+-bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h)

+-bam2bcf_h = bam2bcf.h $(htslib_hts_h) $(htslib_vcf_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)

+-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)

+-

+-bam.o: bam.c config.h $(bam_h) $(htslib_kstring_h) sam_header.h

+-bam2bcf.o: bam2bcf.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_kstring_h) $(htslib_kfunc_h) $(bam2bcf_h)

+-bam2bcf_indel.o: bam2bcf_indel.c config.h $(htslib_hts_h) $(htslib_sam_h) $(bam2bcf_h) $(htslib_khash_h) $(htslib_ksort_h)

+-bam2depth.o: bam2depth.c config.h $(htslib_sam_h) samtools.h $(sam_opts_h)

+-bam_addrprg.o: bam_addrprg.c config.h $(htslib_sam_h) $(htslib_kstring_h) samtools.h $(sam_opts_h)

++bam_h = bam.h

++bam2bcf_h = bam2bcf.h

++bam_lpileup_h = bam_lpileup.h

++bam_plbuf_h = bam_plbuf.h

++bam_tview_h = bam_tview.h $(bam2bcf_h) $(bam_lpileup_h)

++sam_h = sam.h $(bam_h)

++sam_opts_h = sam_opts.h

++sample_h = sample.h

++

++bam.o: bam.c config.h $(bam_h) sam_header.h

++bam2bcf.o: bam2bcf.c config.h $(bam2bcf_h)

++bam2bcf_indel.o: bam2bcf_indel.c config.h $(bam2bcf_h)

++bam2depth.o: bam2depth.c config.h samtools.h $(sam_opts_h)

++bam_addrprg.o: bam_addrprg.c config.h samtools.h $(sam_opts_h)

+ bam_aux.o: bam_aux.c config.h $(bam_h)

+-bam_cat.o: bam_cat.c config.h $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_cram_h) $(htslib_khash_h) samtools.h

++bam_cat.o: bam_cat.c config.h samtools.h

+ bam_color.o: bam_color.c config.h $(bam_h)

+-bam_import.o: bam_import.c config.h $(htslib_kstring_h) $(bam_h) $(htslib_kseq_h)

+-bam_index.o: bam_index.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_h) samtools.h

+-bam_lpileup.o: bam_lpileup.c config.h $(bam_plbuf_h) $(bam_lpileup_h) $(htslib_ksort_h)

+-bam_mate.o: bam_mate.c config.h $(sam_opts_h) $(htslib_kstring_h) $(htslib_sam_h) samtools.h

+-bam_md.o: bam_md.c config.h $(htslib_faidx_h) $(htslib_sam_h) $(htslib_kstring_h) $(sam_opts_h) samtools.h

+-bam_plbuf.o: bam_plbuf.c config.h $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h)

+-bam_plcmd.o: bam_plcmd.c config.h $(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_quickcheck.o: bam_quickcheck.c config.h $(htslib_hts_h) $(htslib_sam_h)

+-bam_reheader.o: bam_reheader.c config.h $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_hfile_h) $(htslib_cram_h) samtools.h

+-bam_rmdup.o: bam_rmdup.c config.h $(htslib_sam_h) $(sam_opts_h) samtools.h $(bam_h) $(htslib_khash_h)

+-bam_rmdupse.o: bam_rmdupse.c config.h $(bam_h) $(htslib_sam_h) $(htslib_khash_h) $(htslib_klist_h) samtools.h

+-bam_sort.o: bam_sort.c config.h $(htslib_ksort_h) $(htslib_khash_h) $(htslib_klist_h) $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) samtools.h

+-bam_split.o: bam_split.c config.h $(htslib_sam_h) $(htslib_khash_h) $(htslib_kstring_h) $(htslib_cram_h) $(sam_opts_h) samtools.h

+-bam_stat.o: bam_stat.c config.h $(htslib_sam_h) samtools.h

+-bam_tview.o: bam_tview.c config.h $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h) samtools.h $(sam_opts_h)

++bam_import.o: bam_import.c config.h $(bam_h)

++bam_index.o: bam_index.c config.h samtools.h

++bam_lpileup.o: bam_lpileup.c config.h $(bam_plbuf_h) $(bam_lpileup_h)

++bam_mate.o: bam_mate.c config.h $(sam_opts_h) samtools.h

++bam_md.o: bam_md.c config.h $(sam_opts_h) samtools.h

++bam_plbuf.o: bam_plbuf.c config.h $(bam_plbuf_h)

++bam_plcmd.o: bam_plcmd.c config.h sam_header.h samtools.h $(sam_opts_h) $(bam2bcf_h) $(sample_h)

++bam_quickcheck.o: bam_quickcheck.c config.h

++bam_reheader.o: bam_reheader.c config.h samtools.h

++bam_rmdup.o: bam_rmdup.c config.h $(sam_opts_h) samtools.h $(bam_h)

++bam_rmdupse.o: bam_rmdupse.c config.h $(bam_h) samtools.h

++bam_sort.o: bam_sort.c config.h $(sam_opts_h) samtools.h

++bam_split.o: bam_split.c config.h $(sam_opts_h) samtools.h

++bam_stat.o: bam_stat.c config.h samtools.h

++bam_tview.o: bam_tview.c config.h $(bam_tview_h) samtools.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 config.h $(bam_tview_h)

+-bam_flags.o: bam_flags.c config.h $(htslib_sam_h)

+-bamshuf.o: bamshuf.c config.h $(htslib_sam_h) $(htslib_hts_h) $(htslib_ksort_h) samtools.h $(sam_opts_h)

+-bamtk.o: bamtk.c config.h $(htslib_hts_h) samtools.h version.h

+-bedcov.o: bedcov.c config.h $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) $(htslib_kseq_h)

+-bedidx.o: bedidx.c config.h $(htslib_ksort_h) $(htslib_kseq_h) $(htslib_khash_h)

+-cut_target.o: cut_target.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) samtools.h $(sam_opts_h)

+-dict.o: dict.c config.h $(htslib_kseq_h) $(htslib_hts_h)

+-faidx.o: faidx.c config.h $(htslib_faidx_h) samtools.h

+-padding.o: padding.c config.h $(htslib_kstring_h) $(htslib_sam_h) $(htslib_faidx_h) sam_header.h $(sam_opts_h) samtools.h

+-phase.o: phase.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_kstring_h) $(sam_opts_h) samtools.h $(htslib_kseq_h) $(htslib_khash_h) $(htslib_ksort_h)

+-sam.o: sam.c config.h $(htslib_faidx_h) $(sam_h)

+-sam_header.o: sam_header.c config.h sam_header.h $(htslib_khash_h)

++bam_flags.o: bam_flags.c config.h

++bamshuf.o: bamshuf.c config.h samtools.h $(sam_opts_h)

++bamtk.o: bamtk.c config.h samtools.h version.h

++bedcov.o: bedcov.c config.h $(sam_opts_h)

++bedidx.o: bedidx.c config.h

++cut_target.o: cut_target.c config.h samtools.h $(sam_opts_h)

++dict.o: dict.c config.h

++faidx.o: faidx.c config.h samtools.h

++padding.o: padding.c config.h sam_header.h $(sam_opts_h) samtools.h

++phase.o: phase.c config.h $(sam_opts_h) samtools.h

++sam.o: sam.c config.h $(sam_h)

++sam_header.o: sam_header.c config.h sam_header.h

+ sam_opts.o: sam_opts.c config.h $(sam_opts_h)

+ sam_utils.o: sam_utils.c config.h samtools.h

+-sam_view.o: sam_view.c config.h $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_h) samtools.h $(sam_opts_h)

+-sample.o: sample.c config.h $(sample_h) $(htslib_khash_h)

+-stats_isize.o: stats_isize.c config.h stats_isize.h $(htslib_khash_h)

+-stats.o: stats.c config.h $(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 config.h samtools.h $(sam_opts_h)

++sample.o: sample.c config.h $(sample_h)

++stats_isize.o: stats_isize.c config.h stats_isize.h

++stats.o: stats.c config.h sam_header.h samtools.h stats_isize.h $(sam_opts_h)

+

+

+ # test programs

+@@ -224,30 +213,30 @@

+

+

+ test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o libst.a $(HTSLIB)

+- $(CC) $(ALL_LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread

++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread

+

+ test/merge/test_rtrans_build: test/merge/test_rtrans_build.o libst.a $(HTSLIB)

+- $(CC) $(ALL_LDFLAGS) -o $@ test/merge/test_rtrans_build.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread

++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/merge/test_rtrans_build.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread

+

+ test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o libst.a $(HTSLIB)

+- $(CC) $(ALL_LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread

++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread

+

+ test/split/test_count_rg: test/split/test_count_rg.o test/test.o libst.a $(HTSLIB)

+- $(CC) $(ALL_LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread

++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread

+

+ test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o libst.a $(HTSLIB)

+- $(CC) $(ALL_LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread

++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread

+

+ test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o libst.a $(HTSLIB)

+- $(CC) $(ALL_LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread

++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread

+

+ test/split/test_parse_args: test/split/test_parse_args.o test/test.o libst.a $(HTSLIB)

+- $(CC) $(ALL_LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread

++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread

+

+ test/vcf-miniview: test/vcf-miniview.o $(HTSLIB)

+- $(CC) $(ALL_LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB_LIB) $(ALL_LIBS) -lpthread

++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread

+

+-test_test_h = test/test.h $(htslib_sam_h)

++test_test_h = test/test.h

+

+ test/merge/test_bam_translate.o: test/merge/test_bam_translate.c config.h bam_sort.o $(test_test_h)

+ test/merge/test_rtrans_build.o: test/merge/test_rtrans_build.c config.h bam_sort.o

+@@ -256,34 +245,34 @@

+ test/split/test_expand_format_string.o: test/split/test_expand_format_string.c config.h bam_split.o $(test_test_h)

+ test/split/test_filter_header_rg.o: test/split/test_filter_header_rg.c config.h bam_split.o $(test_test_h)

+ test/split/test_parse_args.o: test/split/test_parse_args.c config.h bam_split.o $(test_test_h)

+-test/test.o: test/test.c config.h $(htslib_sam_h) $(test_test_h)

+-test/vcf-miniview.o: test/vcf-miniview.c config.h $(htslib_vcf_h)

++test/test.o: test/test.c config.h $(test_test_h)

++test/vcf-miniview.o: test/vcf-miniview.c config.h

+

+

+ # misc programs

+

+ misc/ace2sam: misc/ace2sam.o

+- $(CC) $(LDFLAGS) -o $@ misc/ace2sam.o $(ALL_LIBS)

++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/ace2sam.o $(ALL_LIBS)

+

+ misc/maq2sam-short: misc/maq2sam-short.o

+- $(CC) $(LDFLAGS) -o $@ misc/maq2sam-short.o $(ALL_LIBS)

++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/maq2sam-short.o $(ALL_LIBS)

+

+ misc/maq2sam-long: misc/maq2sam-long.o

+- $(CC) $(LDFLAGS) -o $@ misc/maq2sam-long.o $(ALL_LIBS)

++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/maq2sam-long.o $(ALL_LIBS)

+

+ misc/md5fa: misc/md5fa.o $(HTSLIB)

+- $(CC) $(ALL_LDFLAGS) -o $@ misc/md5fa.o $(HTSLIB_LIB) $(ALL_LIBS)

++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/md5fa.o $(HTSLIB_LIBS) $(ALL_LIBS)

+

+ misc/md5sum-lite: misc/md5sum-lite.o $(HTSLIB)

+- $(CC) $(ALL_LDFLAGS) -o $@ misc/md5sum-lite.o $(HTSLIB_LIB) $(ALL_LIBS)

++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/md5sum-lite.o $(HTSLIB_LIBS) $(ALL_LIBS)

+

+ misc/wgsim: misc/wgsim.o

+- $(CC) $(LDFLAGS) -o $@ misc/wgsim.o -lm $(ALL_LIBS)

++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/wgsim.o -lm $(ALL_LIBS)

+

+-misc/ace2sam.o: misc/ace2sam.c config.h $(htslib_kstring_h) $(htslib_kseq_h)

+-misc/md5fa.o: misc/md5fa.c config.h $(htslib_kseq_h) $(htslib_hts_h)

+-misc/md5sum-lite.o: misc/md5sum-lite.c config.h $(htslib_hts_h)

+-misc/wgsim.o: misc/wgsim.c config.h $(htslib_kseq_h)

++misc/ace2sam.o: misc/ace2sam.c config.h

++misc/md5fa.o: misc/md5fa.c config.h

++misc/md5sum-lite.o: misc/md5sum-lite.c config.h

++misc/wgsim.o: misc/wgsim.c config.h

+

+ misc/maq2sam-short.o: misc/maq2sam.c config.h

+ $(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ misc/maq2sam.c

+<?xml version='1.0' encoding='UTF-8'?>

+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">

+<pkgmetadata>

+ <maintainer type="project">

+ <email>sci-biology@gentoo.org</email>

+ <name>Gentoo Biology Project</name>

+ </maintainer>

+ <upstream>

+ <remote-id type="sourceforge">samtools</remote-id>

+ <remote-id type="github">samtools/samtools</remote-id>

+ </upstream>

+</pkgmetadata>

+# Copyright 1999-2016 Gentoo Foundation

+# Distributed under the terms of the GNU General Public License v2

+

+EAPI=6

+

+PYTHON_COMPAT=( python2_7 )

+

+inherit python-single-r1 toolchain-funcs

+

+DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"

+HOMEPAGE="http://samtools.sourceforge.net/"

+SRC_URI="https://github.com/samtools/samtools/archive/${PV}.tar.gz -> ${P}.tar.gz"

+

+LICENSE="MIT"

+SLOT="0.1-legacy"

+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"

+IUSE="examples"

+REQUIRED_USE="${PYTHON_REQUIRED_USE}"

+

+RDEPEND="${PYTHON_DEPS}

+ sys-libs/ncurses:0=

+ dev-lang/perl"

+DEPEND="${RDEPEND}

+ virtual/pkgconfig"

+

+PATCHES=(

+ "${FILESDIR}/${P}-buildsystem.patch"

+)

+

+src_prepare() {

+ default

+ # required, otherwise python_fix_shebang errors out

+ sed -i 's~/software/bin/python~/usr/bin/env python~' 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() {

+ # install executables and hide them away from sight

+ dobin samtools bcftools/{bcftools,vcfutils.pl} misc/{*.py,*.pl,wgsim,ace2sam} \

+ misc/{md5sum-lite,maq2sam-short,bamcheck,maq2sam-long,md5fa,plot-bamcheck}

+ mv "${ED%/}"/usr/{bin,${PN}-${SLOT}} || die

+ mkdir "${ED%/}"/usr/bin || die

+ mv "${ED%/}"/usr/{${PN}-${SLOT},bin/} || die

+

+ # ... do the same with the python script, but also fix the shebang

+ mv "${ED%/}"/usr/bin/${PN}-${SLOT}/varfilter{,-${SLOT}}.py || die

+ python_fix_shebang "${ED%/}"/usr/bin/${PN}-${SLOT}/varfilter-${SLOT}.py

+

+ # fix perl shebangs

+ pushd "${ED%/}"/usr/bin/${PN}-${SLOT} >/dev/null || die

+ local i

+ for i in plot-bamcheck *.pl; do

+ sed -e '1s:.*:#!/usr/bin/env perl:' -i "${i}" || die

+ done

+ popd >/dev/null || die

+

+ dolib.so libbam-${SLOT}$(get_libname 1)

+ dosym libbam-${SLOT}$(get_libname 1) /usr/$(get_libdir)/libbam-${SLOT}$(get_libname)

+

+ insinto /usr/include/bam-${SLOT}

+ doins *.h

+

+ mv ${PN}{,-${SLOT}}.1 || die

+ doman ${PN}-${SLOT}.1

+ einstalldocs

+

+ if use examples; then

+ dodoc -r examples

+ docompress -x /usr/share/doc/${PF}/examples

+ fi

+}

+

+pkg_postinst() {

+ elog "This version of samtools should *not* be your first choice for working"

+ elog "with NGS data. It is installed solely for programs requiring it."

+ elog "It is recommended that you use >=sci-biology/samtools-1.2."

+}

+# 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="

+ dev-lang/perl

+ =sci-libs/htslib-${PV}*

+ sys-libs/ncurses:0=

+ sys-libs/zlib

+ ${PYTHON_DEPS}"

+DEPEND="${RDEPEND}

+ virtual/pkgconfig"

+

+PATCHES=( "${FILESDIR}/${PN}-1.5-buildsystem.patch" )

+

+src_prepare() {

+ default

+

+ python_setup

+ python_fix_shebang misc/varfilter.py

+

+ # remove bundled htslib

+ rm -r htslib-* || die

+

+ eautoreconf

+}

+

+src_test() {

+ local -x LD_LIBRARY_PATH="${S}"

+ default

+}

+

+src_install() {

+ default

+

+ # install libbam and headers

+ dolib.so libbam.so*

+

+ insinto /usr/include/bam

+ doins *.h

+

+ if use examples; then

+ dodoc -r examples

+ docompress -x /usr/share/doc/${PF}/examples

+ fi

+}