CVS commit: pkgsrc/biology

To: pkgsrc-changes%NetBSD.org@localhost
Subject: CVS commit: pkgsrc/biology
From: "Jason Bacon" <bacon%netbsd.org@localhost>
Date: Sat, 20 Mar 2021 18:17:08 +0000

Module Name:    pkgsrc
Committed By:   bacon
Date:           Sat Mar 20 18:17:08 UTC 2021

Modified Files:
        pkgsrc/biology/bcftools: Makefile PLIST distinfo
        pkgsrc/biology/bcftools/patches: patch-Makefile
        pkgsrc/biology/htslib: Makefile PLIST buildlink3.mk distinfo
        pkgsrc/biology/samtools: Makefile PLIST distinfo
        pkgsrc/biology/samtools/patches: patch-Makefile
Removed Files:
        pkgsrc/biology/bcftools/patches: patch-misc_run-roh.pl
        pkgsrc/biology/htslib/patches: patch-Makefile
            patch-cram_open__trace__file.c patch-hfile__libcurl.c

Log Message:
biology/htslib: Update to 1.12
biology/bcftools: Update to 1.12
biology/samtools: Update to 1.12

Numerous enhancements, performance improvements, and bug fixes since 1.10
Minimized pkgsrc patches in all three packages
Moved htslib to custom tarball since Github-generated distfiles are incomplete


To generate a diff of this commit:
cvs rdiff -u -r1.9 -r1.10 pkgsrc/biology/bcftools/Makefile
cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/bcftools/PLIST \
    pkgsrc/biology/bcftools/distinfo
cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/bcftools/patches/patch-Makefile
cvs rdiff -u -r1.1 -r0 pkgsrc/biology/bcftools/patches/patch-misc_run-roh.pl
cvs rdiff -u -r1.18 -r1.19 pkgsrc/biology/htslib/Makefile
cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/htslib/PLIST
cvs rdiff -u -r1.4 -r1.5 pkgsrc/biology/htslib/buildlink3.mk
cvs rdiff -u -r1.3 -r1.4 pkgsrc/biology/htslib/distinfo
cvs rdiff -u -r1.1 -r0 pkgsrc/biology/htslib/patches/patch-Makefile \
    pkgsrc/biology/htslib/patches/patch-cram_open__trace__file.c \
    pkgsrc/biology/htslib/patches/patch-hfile__libcurl.c
cvs rdiff -u -r1.10 -r1.11 pkgsrc/biology/samtools/Makefile
cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/samtools/PLIST
cvs rdiff -u -r1.3 -r1.4 pkgsrc/biology/samtools/distinfo
cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/samtools/patches/patch-Makefile

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/biology/bcftools/Makefile
diff -u pkgsrc/biology/bcftools/Makefile:1.9 pkgsrc/biology/bcftools/Makefile:1.10
--- pkgsrc/biology/bcftools/Makefile:1.9        Fri Dec  4 20:45:00 2020
+++ pkgsrc/biology/bcftools/Makefile    Sat Mar 20 18:17:07 2021
@@ -1,7 +1,6 @@
-# $NetBSD: Makefile,v 1.9 2020/12/04 20:45:00 nia Exp $
+# $NetBSD: Makefile,v 1.10 2021/03/20 18:17:07 bacon Exp $
 
-DISTNAME=      bcftools-1.10.2
-PKGREVISION=   2
+DISTNAME=      bcftools-1.12
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=samtools/}
 

Index: pkgsrc/biology/bcftools/PLIST
diff -u pkgsrc/biology/bcftools/PLIST:1.2 pkgsrc/biology/bcftools/PLIST:1.3
--- pkgsrc/biology/bcftools/PLIST:1.2   Mon Jul 27 00:29:04 2020
+++ pkgsrc/biology/bcftools/PLIST       Sat Mar 20 18:17:07 2021
@@ -1,6 +1,7 @@
-@comment $NetBSD: PLIST,v 1.2 2020/07/27 00:29:04 bacon Exp $
+@comment $NetBSD: PLIST,v 1.3 2021/03/20 18:17:07 bacon Exp $
 bin/bcftools
 bin/color-chrs
+bin/gff2gff.py
 bin/guess-ploidy
 bin/plot-roh
 bin/plot-vcfstats
@@ -34,12 +35,13 @@ libexec/bcftools/missing2ref.so
 libexec/bcftools/parental-origin.so
 libexec/bcftools/prune.so
 libexec/bcftools/remove-overlaps.so
+libexec/bcftools/scatter.so
 libexec/bcftools/setGT.so
 libexec/bcftools/smpl-stats.so
 libexec/bcftools/split-vep.so
 libexec/bcftools/split.so
 libexec/bcftools/tag2tag.so
-libexec/bcftools/trio-dnm.so
+libexec/bcftools/trio-dnm2.so
 libexec/bcftools/trio-stats.so
 libexec/bcftools/trio-switch-rate.so
 libexec/bcftools/variantkey-hex.so
Index: pkgsrc/biology/bcftools/distinfo
diff -u pkgsrc/biology/bcftools/distinfo:1.2 pkgsrc/biology/bcftools/distinfo:1.3
--- pkgsrc/biology/bcftools/distinfo:1.2        Mon Jul 27 00:29:04 2020
+++ pkgsrc/biology/bcftools/distinfo    Sat Mar 20 18:17:07 2021
@@ -1,8 +1,7 @@
-$NetBSD: distinfo,v 1.2 2020/07/27 00:29:04 bacon Exp $
+$NetBSD: distinfo,v 1.3 2021/03/20 18:17:07 bacon Exp $
 
-SHA1 (bcftools-1.10.2.tar.gz) = b19c9ba06b1c8e8f135c1e0ab0e4ff713a291bf4
-RMD160 (bcftools-1.10.2.tar.gz) = 7713e8c5bd4195eb610544adb26158c16525fdac
-SHA512 (bcftools-1.10.2.tar.gz) = 12c004603db557ac69098e83ad3aaa5762b02b4718b79f3dc259fbcc5c74b8dad3726b5f61efb57f0b8e3d0349577f7934240f36c82bd98849885a5593791995
-Size (bcftools-1.10.2.tar.gz) = 2880994 bytes
-SHA1 (patch-Makefile) = 1f1397e9b0389a7b4fccc9eae87981e7ce1d7980
-SHA1 (patch-misc_run-roh.pl) = 8a29ee7b1001af6670955f174ce4dbab31f05659
+SHA1 (bcftools-1.12.tar.gz) = 17ded5a60da7a42d18fef5a846791ed295f69622
+RMD160 (bcftools-1.12.tar.gz) = 9d3a16c8266bcdd8f2a10f099aec3fc19da82a98
+SHA512 (bcftools-1.12.tar.gz) = f43074989a01cf4ef32a968935f5e5f3eacf2c04b9aa558d739166e3d96d3a498965d27db6482b2992b5d60fed3d2945ef3fd61fcc79b5dbe062994d49df4ad2
+Size (bcftools-1.12.tar.gz) = 3048508 bytes
+SHA1 (patch-Makefile) = 9dfe7b5dcf77deac6d248d7612440780ec8a3731

Index: pkgsrc/biology/bcftools/patches/patch-Makefile
diff -u pkgsrc/biology/bcftools/patches/patch-Makefile:1.1 pkgsrc/biology/bcftools/patches/patch-Makefile:1.2
--- pkgsrc/biology/bcftools/patches/patch-Makefile:1.1  Mon Jul 27 00:29:04 2020
+++ pkgsrc/biology/bcftools/patches/patch-Makefile      Sat Mar 20 18:17:07 2021
@@ -1,49 +1,13 @@
-$NetBSD: patch-Makefile,v 1.1 2020/07/27 00:29:04 bacon Exp $
+$NetBSD: patch-Makefile,v 1.2 2021/03/20 18:17:07 bacon Exp $
 
 # Respect pkgsrc env
 
---- Makefile.orig      2019-12-19 09:57:32.000000000 +0000
+--- Makefile.orig      2021-03-19 17:42:33.842623449 +0000
 +++ Makefile
-@@ -22,12 +22,12 @@
- # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
- # DEALINGS IN THE SOFTWARE.
- 
--CC       = gcc
--AR       = ar
--RANLIB   = ranlib
--CPPFLAGS =
--CFLAGS   = -g -Wall -O2
--LDFLAGS  =
-+CC       ?= gcc
-+AR       ?= ar
-+RANLIB   ?= ranlib
-+# CPPFLAGS =
-+CFLAGS   ?= -g -Wall -O2
-+# LDFLAGS  =
- LIBS     =
- 
- DYNAMIC_FLAGS = -rdynamic
-@@ -45,12 +45,12 @@ OBJS     = main.o vcfindex.o tabix.o \
-            ccall.o em.o prob1.o kmin.o # the original samtools calling
- PLUGIN_OBJS = vcfplugin.o
- 
--prefix      = /usr/local
--exec_prefix = $(prefix)
-+PREFIX      ?= /usr/local
-+exec_prefix = $(PREFIX)
- bindir      = $(exec_prefix)/bin
- libdir      = $(exec_prefix)/lib
- libexecdir  = $(exec_prefix)/libexec
--mandir      = $(prefix)/share/man
-+mandir      = $(PREFIX)/share/man
- man1dir     = $(mandir)/man1
- # Installation location for $(PLUGINS)
- plugindir   = $(libexecdir)/bcftools
-@@ -59,12 +59,11 @@ pluginpath  = $(plugindir)
- misc_bindir = $(bindir)
+@@ -60,11 +60,11 @@ misc_bindir = $(bindir)
  
  MKDIR_P = mkdir -p
--INSTALL = install -p
+ INSTALL = install -p
 -INSTALL_DATA    = $(INSTALL) -m 644
 -INSTALL_DIR     = $(MKDIR_P) -m 755
 -INSTALL_MAN     = $(INSTALL_DATA)
@@ -57,12 +21,3 @@ $NetBSD: patch-Makefile,v 1.1 2020/07/27
  
  PROGRAMS = bcftools
  MISC_SCRIPTS = \
-@@ -78,7 +77,7 @@ TEST_PROGRAMS = test/test-rbuf test/test
- 
- ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS)
- ALL_LDFLAGS  = $(HTSLIB_LDFLAGS) $(LDFLAGS)
--ALL_LIBS     = -lz $(DL_LIBS) $(LIBS)
-+ALL_LIBS     = -lz $(LIBS)
- 
- all: $(PROGRAMS) $(TEST_PROGRAMS) plugins
- 

Index: pkgsrc/biology/htslib/Makefile
diff -u pkgsrc/biology/htslib/Makefile:1.18 pkgsrc/biology/htslib/Makefile:1.19
--- pkgsrc/biology/htslib/Makefile:1.18 Mon Aug 31 18:06:39 2020
+++ pkgsrc/biology/htslib/Makefile      Sat Mar 20 18:17:07 2021
@@ -1,9 +1,10 @@
-# $NetBSD: Makefile,v 1.18 2020/08/31 18:06:39 wiz Exp $
+# $NetBSD: Makefile,v 1.19 2021/03/20 18:17:07 bacon Exp $
 
-DISTNAME=      htslib-1.10.2
-PKGREVISION=   2
+DISTNAME=      htslib-1.12
 CATEGORIES=    biology
-MASTER_SITES=  ${MASTER_SITE_GITHUB:=samtools/}
+# Github-generated distfiles are incomplete, use custom tarballs instead
+MASTER_SITES=  https://github.com/samtools/htslib/releases/download/${PKGVERSION_NOREV}/
+EXTRACT_SUFX=  .tar.bz2
 
 MAINTAINER=    bacon%NetBSD.org@localhost
 HOMEPAGE=      https://www.htslib.org/
@@ -23,6 +24,7 @@ REPLACE_PERL+=                test/*.pl
 CONFIGURE_ARGS+=       --enable-libcurl
 PKGCONFIG_OVERRIDE=    htslib.pc.in
 TEST_TARGET=           test
+MAKE_ENV+=             BUILT_TEST_PROGRAMS=''
 
 pre-configure:
        cd ${WRKSRC} && autoreconf -if

Index: pkgsrc/biology/htslib/PLIST
diff -u pkgsrc/biology/htslib/PLIST:1.2 pkgsrc/biology/htslib/PLIST:1.3
--- pkgsrc/biology/htslib/PLIST:1.2     Wed Jul 22 14:50:14 2020
+++ pkgsrc/biology/htslib/PLIST Sat Mar 20 18:17:07 2021
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.2 2020/07/22 14:50:14 bacon Exp $
+@comment $NetBSD: PLIST,v 1.3 2021/03/20 18:17:07 bacon Exp $
 bin/bgzip
 bin/htsfile
 bin/tabix
@@ -9,6 +9,7 @@ include/htslib/hfile.h
 include/htslib/hts.h
 include/htslib/hts_defs.h
 include/htslib/hts_endian.h
+include/htslib/hts_expr.h
 include/htslib/hts_log.h
 include/htslib/hts_os.h
 include/htslib/kbitset.h
@@ -17,6 +18,7 @@ include/htslib/khash.h
 include/htslib/khash_str2int.h
 include/htslib/klist.h
 include/htslib/knetfile.h
+include/htslib/kroundup.h
 include/htslib/kseq.h
 include/htslib/ksort.h
 include/htslib/kstring.h

Index: pkgsrc/biology/htslib/buildlink3.mk
diff -u pkgsrc/biology/htslib/buildlink3.mk:1.4 pkgsrc/biology/htslib/buildlink3.mk:1.5
--- pkgsrc/biology/htslib/buildlink3.mk:1.4     Wed Jul 22 15:36:55 2020
+++ pkgsrc/biology/htslib/buildlink3.mk Sat Mar 20 18:17:07 2021
@@ -1,11 +1,11 @@
-# $NetBSD: buildlink3.mk,v 1.4 2020/07/22 15:36:55 bacon Exp $
+# $NetBSD: buildlink3.mk,v 1.5 2021/03/20 18:17:07 bacon Exp $
 
 BUILDLINK_TREE+=       htslib
 
 .if !defined(HTSLIB_BUILDLINK3_MK)
 HTSLIB_BUILDLINK3_MK:=
 
-BUILDLINK_API_DEPENDS.htslib+= htslib>=1.8
+BUILDLINK_API_DEPENDS.htslib+= htslib>=1.10.2
 BUILDLINK_ABI_DEPENDS.htslib+= htslib>=1.10.2
 BUILDLINK_PKGSRCDIR.htslib?=   ../../biology/htslib
 

Index: pkgsrc/biology/htslib/distinfo
diff -u pkgsrc/biology/htslib/distinfo:1.3 pkgsrc/biology/htslib/distinfo:1.4
--- pkgsrc/biology/htslib/distinfo:1.3  Wed Jul 22 14:50:14 2020
+++ pkgsrc/biology/htslib/distinfo      Sat Mar 20 18:17:07 2021
@@ -1,9 +1,6 @@
-$NetBSD: distinfo,v 1.3 2020/07/22 14:50:14 bacon Exp $
+$NetBSD: distinfo,v 1.4 2021/03/20 18:17:07 bacon Exp $
 
-SHA1 (htslib-1.10.2.tar.gz) = 0ac4b86e49556d7dcaa89d4cce2661c9ca706631
-RMD160 (htslib-1.10.2.tar.gz) = 6d8b6a362297345420dc9acc544029276ce4b1b6
-SHA512 (htslib-1.10.2.tar.gz) = 7a91c15ca1de35653d068dc57ae511ad791ae0bd8504867d4e60c46e813e58b441409541197cde3b2a37840e60331336aebc627ecbf5c64fca1af63dd05f8f9e
-Size (htslib-1.10.2.tar.gz) = 1452177 bytes
-SHA1 (patch-Makefile) = e13333dd97ecd6c6753d14c1b738d6e5934a2911
-SHA1 (patch-cram_open__trace__file.c) = 49b47e13786317e652a8ec810cc91f10d21bb8ea
-SHA1 (patch-hfile__libcurl.c) = 2a143818f1099ef01c57a3c904060a76abb63f14
+SHA1 (htslib-1.12.tar.bz2) = 8cab518f97bbdf43165320c3a4bdef1e9a42893a
+RMD160 (htslib-1.12.tar.bz2) = 3d93d91db8c382f42b8ad0843609cabd3b502b46
+SHA512 (htslib-1.12.tar.bz2) = a810c646561f5c8b3a19b73ac22ec5f25b04d4e88e1314988881a8120c54106591d1d65aa708bbe2608f0065ca8abe92bdd70ef59a0dd0cdf63ff45c10957092
+Size (htslib-1.12.tar.bz2) = 4094458 bytes

Index: pkgsrc/biology/samtools/Makefile
diff -u pkgsrc/biology/samtools/Makefile:1.10 pkgsrc/biology/samtools/Makefile:1.11
--- pkgsrc/biology/samtools/Makefile:1.10       Fri Dec  4 20:45:00 2020
+++ pkgsrc/biology/samtools/Makefile    Sat Mar 20 18:17:07 2021
@@ -1,7 +1,6 @@
-# $NetBSD: Makefile,v 1.10 2020/12/04 20:45:00 nia Exp $
+# $NetBSD: Makefile,v 1.11 2021/03/20 18:17:07 bacon Exp $
 
-DISTNAME=      samtools-1.10
-PKGREVISION=   2
+DISTNAME=      samtools-1.12
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=samtools/}
 
@@ -26,7 +25,7 @@ SUBST_FILES.bash+=    test/test.pl
 
 REPLACE_PERL+=         misc/*.pl
 REPLACE_PERL+=         test/*.pl
-REPLACE_PERL+=         misc/plot-bamstats
+REPLACE_PERL+=         misc/plot-bamstats misc/plot-ampliconstats
 REPLACE_LUA+=          misc/*.lua
 
 CONFIGURE_ARGS+=       --with-htslib=system

Index: pkgsrc/biology/samtools/PLIST
diff -u pkgsrc/biology/samtools/PLIST:1.2 pkgsrc/biology/samtools/PLIST:1.3
--- pkgsrc/biology/samtools/PLIST:1.2   Sun Jul 26 23:30:29 2020
+++ pkgsrc/biology/samtools/PLIST       Sat Mar 20 18:17:07 2021
@@ -1,14 +1,16 @@
-@comment $NetBSD: PLIST,v 1.2 2020/07/26 23:30:29 bacon Exp $
+@comment $NetBSD: PLIST,v 1.3 2021/03/20 18:17:07 bacon Exp $
 bin/ace2sam
 bin/blast2sam.pl
 bin/bowtie2sam.pl
 bin/export2sam.pl
+bin/fasta-sanitize.pl
 bin/interpolate_sam.pl
 bin/maq2sam-long
 bin/maq2sam-short
 bin/md5fa
 bin/md5sum-lite
 bin/novo2sam.pl
+bin/plot-ampliconstats
 bin/plot-bamstats
 bin/psl2sam.pl
 bin/sam2vcf.pl
@@ -20,10 +22,13 @@ bin/wgsim
 bin/wgsim_eval.pl
 bin/zoom2sam.pl
 man/man1/samtools-addreplacerg.1
+man/man1/samtools-ampliconclip.1
+man/man1/samtools-ampliconstats.1
 man/man1/samtools-bedcov.1
 man/man1/samtools-calmd.1
 man/man1/samtools-cat.1
 man/man1/samtools-collate.1
+man/man1/samtools-coverage.1
 man/man1/samtools-depad.1
 man/man1/samtools-depth.1
 man/man1/samtools-dict.1

Index: pkgsrc/biology/samtools/distinfo
diff -u pkgsrc/biology/samtools/distinfo:1.3 pkgsrc/biology/samtools/distinfo:1.4
--- pkgsrc/biology/samtools/distinfo:1.3        Sun Jul 26 23:30:29 2020
+++ pkgsrc/biology/samtools/distinfo    Sat Mar 20 18:17:07 2021
@@ -1,7 +1,7 @@
-$NetBSD: distinfo,v 1.3 2020/07/26 23:30:29 bacon Exp $
+$NetBSD: distinfo,v 1.4 2021/03/20 18:17:07 bacon Exp $
 
-SHA1 (samtools-1.10.tar.gz) = 98b24393629d63f2203f59c108b840b1e046f209
-RMD160 (samtools-1.10.tar.gz) = e8d91dfc0970a0faa85d45962f76f831af331007
-SHA512 (samtools-1.10.tar.gz) = 7760a1e8a89780ac80053b136930a8ed0cc130b72c9f66cdc9c211e93b6bcc8923140e7caae9824c81caa4a2bfab3a14280e3e7d7245abeaa6f91f0f96123fda
-Size (samtools-1.10.tar.gz) = 4457760 bytes
-SHA1 (patch-Makefile) = 409ef37ff0730257d82989d866c8cba705e3ef8a
+SHA1 (samtools-1.12.tar.gz) = f46eb3a18885fb352d8746d51a206f7f34916232
+RMD160 (samtools-1.12.tar.gz) = 511ba541e9f3dbbab333d4a24a83f63c628b5b18
+SHA512 (samtools-1.12.tar.gz) = 7f468a4740610c2fdc42d8f020d3082e5b2b2e73b0c2dfc19b212ca259d703f34f7df0922e409a94500ccc0357d4d46306035be29c23a523ef6e959022f9d1db
+Size (samtools-1.12.tar.gz) = 4528460 bytes
+SHA1 (patch-Makefile) = 3fc1f1d67167c8ca8eff1ed17f7a084ec3d4579d

Index: pkgsrc/biology/samtools/patches/patch-Makefile
diff -u pkgsrc/biology/samtools/patches/patch-Makefile:1.1 pkgsrc/biology/samtools/patches/patch-Makefile:1.2
--- pkgsrc/biology/samtools/patches/patch-Makefile:1.1  Sun Jul 26 23:30:30 2020
+++ pkgsrc/biology/samtools/patches/patch-Makefile      Sat Mar 20 18:17:07 2021
@@ -1,56 +1,24 @@
-$NetBSD: patch-Makefile,v 1.1 2020/07/26 23:30:30 bacon Exp $
+$NetBSD: patch-Makefile,v 1.2 2021/03/20 18:17:07 bacon Exp $
 
 # Respect pkgsrc env
 
---- Makefile.orig      2020-07-21 20:20:56.996788479 +0000
+--- Makefile.orig      2021-03-19 17:48:34.572594186 +0000
 +++ Makefile
-@@ -21,12 +21,12 @@
- # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
- # DEALINGS IN THE SOFTWARE.
- 
--CC       = gcc
--AR       = ar
--CPPFLAGS =
-+CC       ?= gcc
-+AR       ?= ar
-+# CPPFLAGS =
- #CFLAGS   = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600
--CFLAGS   = -g -Wall -O2
--LDFLAGS  =
-+CFLAGS   ?= -g -Wall -O2
-+#LDFLAGS  =
- LIBS     =
- 
- LZ4DIR   = ./lz4
-@@ -47,10 +47,10 @@ AOBJS=      bam_index.o bam_plcmd.o sam_
-             bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o
- LZ4OBJS  =  $(LZ4DIR)/lz4.o
- 
--prefix      = /usr/local
--exec_prefix = $(prefix)
-+PREFIX      ?= /usr/local
-+exec_prefix = $(PREFIX)
- bindir      = $(exec_prefix)/bin
--datarootdir = $(prefix)/share
-+datarootdir = $(PREFIX)/share
- mandir      = $(datarootdir)/man
- man1dir     = $(mandir)/man1
- 
-@@ -58,12 +58,11 @@ man1dir     = $(mandir)/man1
- misc_bindir = $(bindir)
+@@ -61,12 +61,11 @@ misc_bindir = $(bindir)
  
  MKDIR_P = mkdir -p
--INSTALL = install -p
+ INSTALL = install -p
 -INSTALL_DATA    = $(INSTALL) -m 644
 -INSTALL_DIR     = $(MKDIR_P) -m 755
 -INSTALL_MAN     = $(INSTALL_DATA)
 -INSTALL_PROGRAM = $(INSTALL)
 -INSTALL_SCRIPT  = $(INSTALL_PROGRAM)
+-
 +INSTALL_DATA    = ${BSD_INSTALL_DATA}
 +INSTALL_DIR     = $(MKDIR_P)
 +INSTALL_MAN     = ${BSD_INSTALL_MAN}
 +INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM}
 +INSTALL_SCRIPT  = ${BSD_INSTALL_SCRIPT}
  
- 
  PROGRAMS = samtools
+

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