samtools: Begin work on 1.11

[Jason Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Sat Feb 6 12:45:01 2021 -0600
Changeset:	135f4f26818bd5cbab8ec7131083a7708b98cf84

Modified Files:
	samtools/Makefile
	samtools/distinfo
	samtools/patches/patch-Makefile

Log Message:
samtools: Begin work on 1.11

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=135f4f26818bd5cbab8ec7131083a7708b98cf84

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

diffstat:
 samtools/Makefile               |  2 +-
 samtools/distinfo               | 10 +++++-----
 samtools/patches/patch-Makefile | 26 ++++++++++++++------------
 3 files changed, 20 insertions(+), 18 deletions(-)

diffs:
diff --git a/samtools/Makefile b/samtools/Makefile
index 8a10b33247..014e952fea 100644
--- a/samtools/Makefile
+++ b/samtools/Makefile
@@ -1,6 +1,6 @@
 # $NetBSD: Makefile,v 1.7 2020/01/26 17:30:46 rillig Exp $
 
-DISTNAME=	samtools-1.10
+DISTNAME=	samtools-1.11
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=samtools/}
 
diff --git a/samtools/distinfo b/samtools/distinfo
index 9376bd1e4d..6402f53bd2 100644
--- a/samtools/distinfo
+++ b/samtools/distinfo
@@ -1,7 +1,7 @@
 $NetBSD$
 
-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-1.11.tar.gz) = c3e697ea05ab65c5d6f2c447f842e45b41240d60
+RMD160 (samtools-1.11.tar.gz) = e325f48492b830773d240b8af01536fb13b68b19
+SHA512 (samtools-1.11.tar.gz) = 27037a750227d1ad0558875e6ce2ee98f55a58b20295699a14b58654807db260a21f45d30920e28bc5bbdf300bd55a0cafc1c7c447bce307d42b81499ba51339
+Size (samtools-1.11.tar.gz) = 4516328 bytes
+SHA1 (patch-Makefile) = 12dd394dcf9d29f612f5ebac5731f3369109397e
diff --git a/samtools/patches/patch-Makefile b/samtools/patches/patch-Makefile
index 700da6f837..608c84c00d 100644
--- a/samtools/patches/patch-Makefile
+++ b/samtools/patches/patch-Makefile
@@ -1,34 +1,36 @@
 $NetBSD$
 
-# Respect pkgsrc env
+# Use pkgsrc install commands
 
---- Makefile.orig	2020-07-21 20:20:56.996788479 +0000
+--- Makefile.orig	2020-09-22 12:15:55.000000000 +0000
 +++ Makefile
-@@ -21,12 +21,12 @@
+@@ -21,13 +21,13 @@
  # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
  # DEALINGS IN THE SOFTWARE.
  
 -CC       = gcc
 -AR       = ar
+-AWK      = awk
 -CPPFLAGS =
 +CC       ?= gcc
 +AR       ?= ar
-+# CPPFLAGS =
++AWK      ?= awk
++CPPFLAGS ?=
  #CFLAGS   = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600
 -CFLAGS   = -g -Wall -O2
 -LDFLAGS  =
 +CFLAGS   ?= -g -Wall -O2
-+#LDFLAGS  =
++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
+@@ -49,10 +49,10 @@ AOBJS=      bam_index.o bam_plcmd.o sam_
+ 	    bam_ampliconclip.o amplicon_stats.o
  LZ4OBJS  =  $(LZ4DIR)/lz4.o
  
 -prefix      = /usr/local
 -exec_prefix = $(prefix)
-+PREFIX      ?= /usr/local
++PREFIX      = /usr/local
 +exec_prefix = $(PREFIX)
  bindir      = $(exec_prefix)/bin
 -datarootdir = $(prefix)/share
@@ -36,21 +38,21 @@ $NetBSD$
  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
+