biology/samtools: Upgrade to 1.10

Numerous performance and feature improvements and several bug fixes since 1.9

4 files changed, 119 insertions, 20 deletions

diff --git a/biology/samtools/Makefile b/biology/samtools/Makefile
index 5ea403b6591..0188dcfa275 100644
--- a/biology/samtools/Makefile
+++ b/biology/samtools/Makefile
@@ -1,29 +1,42 @@
-# $NetBSD: Makefile,v 1.7 2020/01/26 17:30:46 rillig Exp $
+# $NetBSD: Makefile,v 1.8 2020/07/26 23:30:29 bacon Exp $
 
-DISTNAME=	samtools-1.9
-PKGREVISION=	2
+DISTNAME=	samtools-1.10
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=samtools/}
-EXTRACT_SUFX=	.tar.bz2
-GITHUB_RELEASE=	${PKGVERSION_NOREV}
 
 MAINTAINER=	bacon@NetBSD.org
 HOMEPAGE=	https://www.htslib.org/
-COMMENT=	Tools for manipulating next-generation sequencing data
+COMMENT=	Tools for manipulating sequence alignment maps
 LICENSE=	mit
 
-USE_TOOLS+=		gmake perl:run
-GNU_CONFIGURE=		yes
+USE_TOOLS+=	autoconf automake autoreconf bash gmake perl
+GNU_CONFIGURE=	yes
+
+SUBST_CLASSES+=		version
+SUBST_STAGE.version=	pre-configure
+SUBST_SED.version+=	-e "s|m4_esyscmd_s(\[./version.sh 2>/dev/null\])|[${PKGVERSION_NOREV}]|"
+SUBST_FILES.version+=	configure.ac
+
+SUBST_CLASSES+=		bash
+SUBST_STAGE.bash=	pre-configure
+SUBST_SED.bash+=	-e "s|'bash'|'${TOOLS_PATH.bash}'|"
+SUBST_SED.bash+=	-e 's|\\/bin\\/bash|${TOOLS_PATH.bash:S,/,\\\/,g}|'
+SUBST_FILES.bash+=	test/test.pl
+
+REPLACE_PERL+=		misc/*.pl
+REPLACE_PERL+=		test/*.pl
+REPLACE_PERL+=		misc/plot-bamstats
+REPLACE_LUA+=		misc/*.lua
+
 CONFIGURE_ARGS+=	--with-htslib=system
 TEST_TARGET=		test
 
-REPLACE_PERL=		misc/*.pl
-REPLACE_PERL+=		misc/plot-bamstats
-REPLACE_PERL+=		test/test.pl
-REPLACE_PYTHON=		misc/*.py
+pre-configure:
+	cd ${WRKSRC} && autoreconf -if
 
-.include "../../devel/zlib/buildlink3.mk"
+BUILDLINK_API_DEPENDS.htslib+=	htslib>=1.10.2
 .include "../../biology/htslib/buildlink3.mk"
+.include "../../devel/zlib/buildlink3.mk"
 .include "../../lang/python/application.mk"
 .include "../../mk/curses.buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/biology/samtools/PLIST b/biology/samtools/PLIST
index 7b812362b52..01cac0afb68 100644
--- a/biology/samtools/PLIST
+++ b/biology/samtools/PLIST
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.1 2018/05/07 18:37:31 bacon Exp $
+@comment $NetBSD: PLIST,v 1.2 2020/07/26 23:30:29 bacon Exp $
 bin/ace2sam
 bin/blast2sam.pl
 bin/bowtie2sam.pl
@@ -16,9 +16,38 @@ bin/samtools
 bin/samtools.pl
 bin/seq_cache_populate.pl
 bin/soap2sam.pl
-bin/varfilter.py
 bin/wgsim
 bin/wgsim_eval.pl
 bin/zoom2sam.pl
+man/man1/samtools-addreplacerg.1
+man/man1/samtools-bedcov.1
+man/man1/samtools-calmd.1
+man/man1/samtools-cat.1
+man/man1/samtools-collate.1
+man/man1/samtools-depad.1
+man/man1/samtools-depth.1
+man/man1/samtools-dict.1
+man/man1/samtools-faidx.1
+man/man1/samtools-fasta.1
+man/man1/samtools-fastq.1
+man/man1/samtools-fixmate.1
+man/man1/samtools-flags.1
+man/man1/samtools-flagstat.1
+man/man1/samtools-fqidx.1
+man/man1/samtools-idxstats.1
+man/man1/samtools-index.1
+man/man1/samtools-markdup.1
+man/man1/samtools-merge.1
+man/man1/samtools-mpileup.1
+man/man1/samtools-phase.1
+man/man1/samtools-quickcheck.1
+man/man1/samtools-reheader.1
+man/man1/samtools-rmdup.1
+man/man1/samtools-sort.1
+man/man1/samtools-split.1
+man/man1/samtools-stats.1
+man/man1/samtools-targetcut.1
+man/man1/samtools-tview.1
+man/man1/samtools-view.1
 man/man1/samtools.1
 man/man1/wgsim.1
diff --git a/biology/samtools/distinfo b/biology/samtools/distinfo
index 5100c09cb1f..07f9aabbe1b 100644
--- a/biology/samtools/distinfo
+++ b/biology/samtools/distinfo
@@ -1,6 +1,7 @@
-$NetBSD: distinfo,v 1.2 2018/11/06 10:49:41 adam Exp $
+$NetBSD: distinfo,v 1.3 2020/07/26 23:30:29 bacon Exp $
 
-SHA1 (samtools-1.9.tar.bz2) = 267191dc2f5d24eb0b22c0094138270ed5384241
-RMD160 (samtools-1.9.tar.bz2) = b7f49e1bdd569f63ec53330f43df7e5566ba8a16
-SHA512 (samtools-1.9.tar.bz2) = 6c8207754615ae8dad84b278f93e7d57eb40b818efb80f6aff6aba22fde5772247724e86596e765791e3175ffbb683393dd3ddfe7681c73eef4eb4f2342bf68f
-Size (samtools-1.9.tar.bz2) = 4440405 bytes
+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
diff --git a/biology/samtools/patches/patch-Makefile b/biology/samtools/patches/patch-Makefile
new file mode 100644
index 00000000000..59adadc7690
--- /dev/null
+++ b/biology/samtools/patches/patch-Makefile
@@ -0,0 +1,56 @@
+$NetBSD: patch-Makefile,v 1.1 2020/07/26 23:30:30 bacon Exp $
+
+# Respect pkgsrc env
+
+--- Makefile.orig	2020-07-21 20:20:56.996788479 +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)
+ 
+ MKDIR_P = mkdir -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