Index: head/biology/samtools/Makefile
===================================================================
--- head/biology/samtools/Makefile	(revision 544097)
+++ head/biology/samtools/Makefile	(revision 544098)
@@ -1,31 +1,28 @@
 # Created by: Reed A. Cartwright <cartwright@asu.edu>
 # $FreeBSD$
 
 PORTNAME=	samtools
-DISTVERSION=	1.9
-PORTREVISION=	1
+DISTVERSION=	1.10
 CATEGORIES=	biology
 
-MAINTAINER=	cartwright@asu.edu
+MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Tools for manipulating next-generation sequencing data
 
 LICENSE=	MIT
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
-BUILD_DEPENDS=	htslib>=1.6:biology/htslib
-LIB_DEPENDS=	libhts.so:biology/htslib
+LIB_DEPENDS=	libhts.so.3:biology/htslib
 TEST_DEPENDS=	bash:shells/bash
 
-USES=		autoreconf gmake localbase ncurses \
-		perl5 python:env shebangfix
+USES=		autoreconf gmake localbase ncurses perl5 python:env shebangfix
 
 USE_GITHUB=	yes
 
 USE_PERL5=	test
 GNU_CONFIGURE=	yes
 SUB_FILES=	pkg-message
-SHEBANG_FILES=	misc/*.pl misc/*.py misc/plot-bamstats test/test.pl
+SHEBANG_FILES=	misc/*.pl misc/plot-bamstats test/test.pl
 
 TEST_TARGET=	test
 
 .include <bsd.port.mk>
Index: head/biology/samtools/distinfo
===================================================================
--- head/biology/samtools/distinfo	(revision 544097)
+++ head/biology/samtools/distinfo	(revision 544098)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1532906637
-SHA256 (samtools-samtools-1.9_GH0.tar.gz) = 211600bd180d01030b3fe25baa7ae1c105106bed6c3f8d993f41dd278d44c637
-SIZE (samtools-samtools-1.9_GH0.tar.gz) = 4098992
+TIMESTAMP = 1595117115
+SHA256 (samtools-samtools-1.10_GH0.tar.gz) = 382843e85fdb55868cebaaf2585c43776762d099581341b5803677de5ed117a9
+SIZE (samtools-samtools-1.10_GH0.tar.gz) = 4457760

Property changes on: head/biology/samtools/distinfo
___________________________________________________________________
Modified: fbsd:nokeywords
## -1 +1 ##
-on
\ No newline at end of property
+yes
\ No newline at end of property
Index: head/biology/samtools/files/patch-Makefile
===================================================================
--- head/biology/samtools/files/patch-Makefile	(revision 544097)
+++ head/biology/samtools/files/patch-Makefile	(revision 544098)
@@ -1,34 +1,54 @@
---- Makefile.orig	2017-09-28 11:12:01 UTC
+--- Makefile.orig	2019-12-06 16:40:42 UTC
 +++ Makefile
-@@ -40,23 +40,22 @@ AOBJS=      bam_index.o bam_plcmd.o sam_
-             bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o \
-             bam_quickcheck.o bam_addrprg.o bam_markdup.o
+@@ -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
+ LZ4OBJS  =  $(LZ4DIR)/lz4.o
+ 
 -prefix      = /usr/local
-+prefix      = ${PREFIX}
++PREFIX      ?= /usr/local
++prefix      = $(PREFIX)
  exec_prefix = $(prefix)
  bindir      = $(exec_prefix)/bin
  datarootdir = $(prefix)/share
 -mandir      = $(datarootdir)/man
 +mandir      = $(prefix)/man
  man1dir     = $(mandir)/man1
  
  # Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS)
 -misc_bindir = $(bindir)
 +misc_bindir = $(bindir)/samtools_misc
  
++# Use BSD_INSTALL_PROGRAM to strip when WITH_DEBUG not set
  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

Property changes on: head/biology/samtools/files/patch-Makefile
___________________________________________________________________
Modified: fbsd:nokeywords
## -1 +1 ##
-on
\ No newline at end of property
+yes
\ No newline at end of property
Index: head/biology/samtools/files/patch-test_test.pl
===================================================================
--- head/biology/samtools/files/patch-test_test.pl	(revision 544097)
+++ head/biology/samtools/files/patch-test_test.pl	(revision 544098)
@@ -1,20 +1,20 @@
---- test/test.pl.orig	2017-10-18 06:08:39 UTC
+--- test/test.pl.orig	2020-07-21 20:48:50 UTC
 +++ test/test.pl
-@@ -636,7 +636,7 @@ sub test_usage
+@@ -907,7 +907,7 @@ sub test_usage
      my $command = $args{cmd};
      my $commandpath = $$opts{bin}."/".$command;
      my ($ret,$out,$err) = _cmd("$commandpath $args{redirection}");
 -    if ( $err =~ m/\/bin\/bash.*no.*such/i ) { failed($opts,msg=>$test,reason=>"could not run $commandpath: $out"); return; }
-+    if ( $err =~ m/\/usr\/local\/bin\/bash.*no.*such/i ) { failed($opts,msg=>$test,reason=>"could not run $commandpath: $out"); return; }
++    if ( $err =~ m/bash.*no.*such/i ) { failed($opts,msg=>$test,reason=>"could not run $commandpath: $out"); return; }
  
      my @sections = ($err =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)|\z)/msg);
  
-@@ -694,7 +694,7 @@ sub test_usage_subcommand
+@@ -965,7 +965,7 @@ sub test_usage_subcommand
      my $commandpath = $$opts{bin}."/".$command;
      my ($ret,$out,$err) = _cmd("$commandpath $subcommand $args{redirection}");
  
 -    if ( $err =~ m/\/bin\/bash.*no.*such/i ) { failed($opts,msg=>$test,reason=>"could not run $commandpath $subcommand: $out"); return; }
-+    if ( $err =~ m/\/usr\/local\/bin\/bash.*no.*such/i ) { failed($opts,msg=>$test,reason=>"could not run $commandpath $subcommand: $out"); return; }
++    if ( $err =~ m/bash.*no.*such/i ) { failed($opts,msg=>$test,reason=>"could not run $commandpath $subcommand: $out"); return; }
  
      if ( $err =~ m/not.*implemented/is ) { failed($opts,msg=>$test,reason=>"subcommand indicates it is not implemented",expect_fail=>1); return; }
  
Index: head/biology/samtools/pkg-plist
===================================================================
--- head/biology/samtools/pkg-plist	(revision 544097)
+++ head/biology/samtools/pkg-plist	(revision 544098)
@@ -1,23 +1,52 @@
 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/varfilter.py
 bin/samtools_misc/wgsim
 bin/samtools_misc/wgsim_eval.pl
 bin/samtools_misc/zoom2sam.pl
+man/man1/samtools-addreplacerg.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-depad.1.gz
+man/man1/samtools-depth.1.gz
+man/man1/samtools-dict.1.gz
+man/man1/samtools-faidx.1.gz
+man/man1/samtools-fasta.1.gz
+man/man1/samtools-fastq.1.gz
+man/man1/samtools-fixmate.1.gz
+man/man1/samtools-flags.1.gz
+man/man1/samtools-flagstat.1.gz
+man/man1/samtools-fqidx.1.gz
+man/man1/samtools-idxstats.1.gz
+man/man1/samtools-index.1.gz
+man/man1/samtools-markdup.1.gz
+man/man1/samtools-merge.1.gz
+man/man1/samtools-mpileup.1.gz
+man/man1/samtools-phase.1.gz
+man/man1/samtools-quickcheck.1.gz
+man/man1/samtools-reheader.1.gz
+man/man1/samtools-rmdup.1.gz
+man/man1/samtools-sort.1.gz
+man/man1/samtools-split.1.gz
+man/man1/samtools-stats.1.gz
+man/man1/samtools-targetcut.1.gz
+man/man1/samtools-tview.1.gz
+man/man1/samtools-view.1.gz
 man/man1/samtools.1.gz
 man/man1/wgsim.1.gz

Property changes on: head/biology/samtools/pkg-plist
___________________________________________________________________
Modified: fbsd:nokeywords
## -1 +1 ##
-on
\ No newline at end of property
+yes
\ No newline at end of property