[pkgsrc/trunk]: pkgsrc/biology/samtools biology/samtools: Upgrade to 1.10

[bacon <bacon%pkgsrc.org@localhost>]

details:   https://anonhg.NetBSD.org/pkgsrc/rev/e7357444d7a4
branches:  trunk
changeset: 436074:e7357444d7a4
user:      bacon <bacon%pkgsrc.org@localhost>
date:      Sun Jul 26 23:30:29 2020 +0000

description:
biology/samtools: Upgrade to 1.10

Numerous performance and feature improvements and several bug fixes since 1.9

diffstat:

 biology/samtools/Makefile               |  39 +++++++++++++++-------
 biology/samtools/PLIST                  |  33 ++++++++++++++++++-
 biology/samtools/distinfo               |  11 +++--
 biology/samtools/patches/patch-Makefile |  56 +++++++++++++++++++++++++++++++++
 4 files changed, 119 insertions(+), 20 deletions(-)

diffs (184 lines):

diff -r 503c40b05ee3 -r e7357444d7a4 biology/samtools/Makefile
--- a/biology/samtools/Makefile Sun Jul 26 23:10:44 2020 +0000
+++ b/biology/samtools/Makefile Sun Jul 26 23:30:29 2020 +0000
@@ -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@localhost
 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
 
+BUILDLINK_API_DEPENDS.htslib+= htslib>=1.10.2
+.include "../../biology/htslib/buildlink3.mk"
 .include "../../devel/zlib/buildlink3.mk"
-.include "../../biology/htslib/buildlink3.mk"
 .include "../../lang/python/application.mk"
 .include "../../mk/curses.buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff -r 503c40b05ee3 -r e7357444d7a4 biology/samtools/PLIST
--- a/biology/samtools/PLIST    Sun Jul 26 23:10:44 2020 +0000
+++ b/biology/samtools/PLIST    Sun Jul 26 23:30:29 2020 +0000
@@ -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.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 -r 503c40b05ee3 -r e7357444d7a4 biology/samtools/distinfo
--- a/biology/samtools/distinfo Sun Jul 26 23:10:44 2020 +0000
+++ b/biology/samtools/distinfo Sun Jul 26 23:30:29 2020 +0000
@@ -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 -r 503c40b05ee3 -r e7357444d7a4 biology/samtools/patches/patch-Makefile
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/samtools/patches/patch-Makefile   Sun Jul 26 23:30:29 2020 +0000
@@ -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