sci-biology/samtools: Version BUmp

Package-Manager: portage-2.2.15/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

4 files changed, 262 insertions, 17 deletions

diff --git a/sci-biology/samtools/ChangeLog b/sci-biology/samtools/ChangeLog
index 41e7af409c0d..1813f4f41444 100644
--- a/sci-biology/samtools/ChangeLog
+++ b/sci-biology/samtools/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/samtools
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/ChangeLog,v 1.20 2014/09/25 15:20:53 jlec Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/ChangeLog,v 1.21 2015/01/06 12:57:48 jlec Exp $
+
+*samtools-1.1 (06 Jan 2015)
+
+  06 Jan 2015; Justin Lecher <jlec@gentoo.org> +samtools-1.1.ebuild,
+  +files/samtools-1.1-buildsystem.patch:
+  Version BUmp
 
 *samtools-1.0-r1 (25 Sep 2014)
 
diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index c8da084205e3..b4bc3f5d31a8 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -3,31 +3,34 @@ Hash: SHA512
 
 AUX samtools-0.1.19-buildsystem.patch 6227 SHA256 44c6e4df3ceb36e539716350ef10e0f4e348d524c5dfdb96ad7c9ccbed9570d0 SHA512 dd41a0ab20ad216273f38b42e6abafd70378bcf966403379e73d08c93e92f04ee79dae07baf7f626b30d57deea29d56a729928c18c5d012d950cfe10912adf3d WHIRLPOOL 9ba69f11b8071fe1c9a3269a482e1de0c6563a0a94b96bcef97a1442a6e4d594aea55b4e1c75381b6ed792e7e3e3809da80c9b8a22ec74af63c14315a51e9771
 AUX samtools-1.0-buildsystem.patch 1672 SHA256 fe82984a2475ce4666bd386bb6f1ab9aff4e6402dc02e671171f41ad082345c1 SHA512 b75a9c6a57fa5f4c4dc9eda529eb500f1828c6e0910922ac34869c0972661a4fa51a65b83a153905a090b4f67e0bb7a9316ecc33b04a09a46c74d2bd67c84cf6 WHIRLPOOL eb72243b5e2376df4c417e0b171eb3f71c11ca842014fc72f75463a4bebde11771484049a12650e9169f1c4ba390699af99ebf63d6459b4cc673195b273bedcc
+AUX samtools-1.1-buildsystem.patch 7030 SHA256 a4751ad60699c18c081ced0fa4f5bd494ad072bcc73147d16cf90b35aa9b0bca SHA512 cb0190cfb0d31a9feef068df285734d218b05dcc3b4fae95cb31007ed513986a571d4e0533e918b503c9e3d1fbef18af5c7371294218a5fd0e8837eda56c854a WHIRLPOOL b450a1d971f9e443b14c4a555d6cf43b3e6fc20c4a24ecba32faef47fbb4fbac49260feb92f056d54824721db787295bec3b5a682cec2c7dd6d5c0d1d0157b0b
 DIST samtools-0.1.12a.tar.bz2 355633 SHA256 377ed5cd2a4bb2b1ad572ca6fcafdd8ed644b67f01ab00fa020618fac11e59ac
 DIST samtools-0.1.19.tar.bz2 514507 SHA256 d080c9d356e5f0ad334007e4461cbcee3c4ca97b8a7a5a48c44883cf9dee63d4 SHA512 d145f1d65eefefbdfb781945684b8b591419fb109ac7401a62cae65b9ca1e1271f001496e1038334ff9ab1c0e5bf9bcc059f70aaa273551193fbd68101fd188d WHIRLPOOL 7811388ae8b24c5d7a328d2da252b8d3afaefdab508bd97684d556d2d4ee60d9c8846ffa562beaa9d0c6a5e6bfac24fcd9d211dfee20383cf452609badc8ecd5
 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
 EBUILD samtools-0.1.12.ebuild 827 SHA256 7f8dec32073313ec5a0a7801bcaf7675d74f4eefb2478b19615b22f1bd7e3708 SHA512 b67feeb1909327b6ab19fdb3167e602ab01bd075685bded200109b5def4ad80353f39c77dd8c8e1de1b6a43482acc0b85626951503f42f6dbf416bdbbf740851 WHIRLPOOL 58c4f8c129b41cf068fc08a225ebdd6fc6724efb0ba50eeb44ee0ec586d0634fd3a1fb24c89ee484bfc7cf5affad35c217192bf8eea4d548b220f8789329533d
 EBUILD samtools-0.1.19-r2.ebuild 1474 SHA256 97a44dcd4e7236838f4263146a3a87d39f057e8177e4161b48434b85aa69ed16 SHA512 550b629adfc54dacbd3d381d216e000730ac58dc2e7e3f72ae02f5adf61e3a3f06ec8d3a1159a559c71b05015e179f8c69b752e370ec1845bc783f7a0875f6c9 WHIRLPOOL bc13a6883ae5a1abdfff8f06d04987f9b3f825f6b500a1ab7689089dbc99bb3b3c24f3db4f50f6f3fe30a9719a3d159cc910407ca70b1b07de32c32037bde94b
 EBUILD samtools-1.0-r1.ebuild 1554 SHA256 f63e30721951a432240284ce6d451fd1d497ea9350f3137321e4e0d7c0a433ba SHA512 240ae645a9e7591b3f32efb31d96810eef7f507a080e9cb1296494c7309416029c63f3e239238e3621f69f42a904de281f446cdd7d368683df790f6535025219 WHIRLPOOL 18b6b4073d4b5232dd0e1991b26026800f681c5aa4f5d374a1a288506555b5c756a48f58874bb14ba88b48996d413f24622c455edb344c7c6fa4dc928307af0e
 EBUILD samtools-1.0.ebuild 1488 SHA256 f1b8623d24fc3ce95b39ba1f66a334d9a0df1dd8880227fbb50a32cf96c800d5 SHA512 84b937c3b5143a84a8d9c2062e4e3b91b8a4fe5a50be379ce0dfecba19fc1735a90b1f7690762c7a33aede06229ff229e84a3c31a704ae56cb2241be33a88002 WHIRLPOOL ccc11832e93be31003f41fcd6789537f4c1cf16e0972f0d6cfcd6ef0dc4ee18e4d34907c8f5c32a84137f9bcc5bde2f5d7ea3e61d39e837b4bf0f2319930bb11
-MISC ChangeLog 3931 SHA256 20f76948927192c6d06843b709a3a22be2b17ff580b5cabad5c9540a0901ed29 SHA512 c028a7c6409305a80c359372d3cff855eb4776f34f5b4f2381375a986ceb9ce1e066597af93cfd38a2772be5483baeed139b571fe2d22cdc76898c3a50e8498b WHIRLPOOL ea4608633e47883f2e4c60f4330827e17fb3da3d7f6aba65ee5d0f44ded74e13a7188e402e56505f7ca7afb0dec4d8e122ae20cda6a53a8876ae49a08b7169ec
+EBUILD samtools-1.1.ebuild 1780 SHA256 7939d37f2dfea1a0f190a57bc02374a8787d4e6a21325677b6c175bc42e19561 SHA512 14be9b8002b38f2fe6f7f0c01629ada05539cba20476436f2de691cb8a73f8751e66045e81dc5aa01cb1fe7d2971cb660e6cc66c9191eba71bc3d87741b3a7b5 WHIRLPOOL 63e66aa4a04932f3cb5269d45d2d746ad712a9302dd1efb0c4a39cdaaf44e6c93a088429ad1b86533928897ed5f12a81a72a1d011123baacf29049850e109de1
+MISC ChangeLog 4086 SHA256 f9f922e269f14e7df866c5fc9e8442afc4ecfba842e83bf95547451983e205f3 SHA512 58ad9c137fe29afaef3932f5f72d6077a37d442f0012b68e07a03ff0d1246dda42e361db1e9601c553aacddae2aa4d728812fab58232f9364295e4aa06faa4f0 WHIRLPOOL 9fc1b53d7a1d6b37d9b6a2c5bf417fe873dfbb31bf89860df5acc500d4bf3c36920764ac17c54106e6485d091e8252cd1bd140e3ec11008eb66dc2e3fec379a2
 MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
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diff --git a/sci-biology/samtools/files/samtools-1.1-buildsystem.patch b/sci-biology/samtools/files/samtools-1.1-buildsystem.patch
new file mode 100644
index 000000000000..b9ae77de67d2
--- /dev/null
+++ b/sci-biology/samtools/files/samtools-1.1-buildsystem.patch
@@ -0,0 +1,153 @@
+ 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/samtools-1.1.ebuild b/sci-biology/samtools/samtools-1.1.ebuild
new file mode 100644
index 000000000000..7f596efe1100
--- /dev/null
+++ b/sci-biology/samtools/samtools-1.1.ebuild
@@ -0,0 +1,83 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-1.1.ebuild,v 1.1 2015/01/06 12:57:48 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit eutils multilib python-r1 toolchain-funcs
+
+DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments"
+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="${PYTHON_REQUIRED_USE}"
+
+CDEPEND="
+	sys-libs/ncurses
+	~sci-libs/htslib-${PV}"
+
+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"
+		)
+	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
+}