biology/samtools: Upgrade to 1.11

Numerous new features, bug fixes and performance enhancements
https://github.com/samtools/samtools/releases/tag/1.11

Reported by:    portscout

5 files changed, 38 insertions, 67 deletions

diff --git a/biology/samtools/Makefile b/biology/samtools/Makefile
index 4534b1f3e448..74b6236a030a 100644
--- a/biology/samtools/Makefile
+++ b/biology/samtools/Makefile
@@ -2,7 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	samtools
-DISTVERSION=	1.10
+DISTVERSION=	1.11
 CATEGORIES=	biology
 
 MAINTAINER=	jwb@FreeBSD.org
@@ -20,7 +20,6 @@ USE_GITHUB=	yes
 
 USE_PERL5=	test
 GNU_CONFIGURE=	yes
-SUB_FILES=	pkg-message
 SHEBANG_FILES=	misc/*.pl misc/plot-bamstats test/test.pl
 
 TEST_TARGET=	test
diff --git a/biology/samtools/distinfo b/biology/samtools/distinfo
index 5f5077ceedf4..d0c046e7d011 100644
--- a/biology/samtools/distinfo
+++ b/biology/samtools/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1595117115
-SHA256 (samtools-samtools-1.10_GH0.tar.gz) = 382843e85fdb55868cebaaf2585c43776762d099581341b5803677de5ed117a9
-SIZE (samtools-samtools-1.10_GH0.tar.gz) = 4457760
+TIMESTAMP = 1602982679
+SHA256 (samtools-samtools-1.11_GH0.tar.gz) = 80a54e93c5d111c15c005ee96a578bcd7e1bde34dba2242d981c539ff32f1738
+SIZE (samtools-samtools-1.11_GH0.tar.gz) = 4516328
diff --git a/biology/samtools/files/patch-Makefile b/biology/samtools/files/patch-Makefile
index a958a9919ad7..3a175dd2115b 100644
--- a/biology/samtools/files/patch-Makefile
+++ b/biology/samtools/files/patch-Makefile
@@ -1,25 +1,7 @@
---- Makefile.orig	2019-12-06 16:40:42 UTC
+--- Makefile.orig	2020-10-18 00:55:50 UTC
 +++ 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
-@@ -47,23 +47,24 @@ AOBJS=      bam_index.o bam_plcmd.o sam_view.o bam_fas
-             bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o
+@@ -49,7 +49,8 @@ AOBJS=      bam_index.o bam_plcmd.o sam_view.o bam_fas
+ 	    bam_ampliconclip.o amplicon_stats.o
  LZ4OBJS  =  $(LZ4DIR)/lz4.o
  
 -prefix      = /usr/local
@@ -28,27 +10,26 @@
  exec_prefix = $(prefix)
  bindir      = $(exec_prefix)/bin
  datarootdir = $(prefix)/share
--mandir      = $(datarootdir)/man
-+mandir      = $(prefix)/man
- man1dir     = $(mandir)/man1
- 
+@@ -59,14 +60,14 @@ man1dir     = $(mandir)/man1
  # Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS)
--misc_bindir = $(bindir)
-+misc_bindir = $(bindir)/samtools_misc
+ misc_bindir = $(bindir)
  
-+# Use BSD_INSTALL_PROGRAM to strip when WITH_DEBUG not set
- MKDIR_P = mkdir -p
+-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)
+-
++# Use BSD_INSTALL_PROGRAM to strip when WITH_DEBUG not set
++MKDIR_P 	= mkdir -p
++INSTALL 	= install -p
 +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
+ 
diff --git a/biology/samtools/files/pkg-message.in b/biology/samtools/files/pkg-message.in
deleted file mode 100644
index 3e6d67a8199e..000000000000
--- a/biology/samtools/files/pkg-message.in
+++ /dev/null
@@ -1,13 +0,0 @@
-[
-{ type: install
-  message: <<EOM
-The miscellaneous tools included with Samtools have been installed to
-%%PREFIX%%/bin/samtools_misc
-
-Add that directory to your path if you want to use these tools.
-
-Some of these tools depend on Perl5/Python, and it will need to be installed to
-use them.
-EOM
-}
-]
diff --git a/biology/samtools/pkg-plist b/biology/samtools/pkg-plist
index 2280f471b674..4c35d4bb0e69 100644
--- a/biology/samtools/pkg-plist
+++ b/biology/samtools/pkg-plist
@@ -1,28 +1,32 @@
+bin/ace2sam
+bin/blast2sam.pl
+bin/bowtie2sam.pl
+bin/export2sam.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
 bin/samtools
-bin/samtools_misc/ace2sam
-bin/samtools_misc/blast2sam.pl
-bin/samtools_misc/bowtie2sam.pl
-bin/samtools_misc/export2sam.pl
-bin/samtools_misc/interpolate_sam.pl
-bin/samtools_misc/maq2sam-long
-bin/samtools_misc/maq2sam-short
-bin/samtools_misc/md5fa
-bin/samtools_misc/md5sum-lite
-bin/samtools_misc/novo2sam.pl
-bin/samtools_misc/plot-bamstats
-bin/samtools_misc/psl2sam.pl
-bin/samtools_misc/sam2vcf.pl
-bin/samtools_misc/samtools.pl
-bin/samtools_misc/seq_cache_populate.pl
-bin/samtools_misc/soap2sam.pl
-bin/samtools_misc/wgsim
-bin/samtools_misc/wgsim_eval.pl
-bin/samtools_misc/zoom2sam.pl
+bin/samtools.pl
+bin/seq_cache_populate.pl
+bin/soap2sam.pl
+bin/wgsim
+bin/wgsim_eval.pl
+bin/zoom2sam.pl
 man/man1/samtools-addreplacerg.1.gz
+man/man1/samtools-ampliconclip.1.gz
+man/man1/samtools-ampliconstats.1.gz
 man/man1/samtools-bedcov.1.gz
 man/man1/samtools-calmd.1.gz
 man/man1/samtools-cat.1.gz
 man/man1/samtools-collate.1.gz
+man/man1/samtools-coverage.1.gz
 man/man1/samtools-depad.1.gz
 man/man1/samtools-depth.1.gz
 man/man1/samtools-dict.1.gz