From 34dc72f5dfd57ce1d42b3aa7cbe0b40769e59f4b Mon Sep 17 00:00:00 2001
From: bacon <bacon@pkgsrc.org>
Date: Sat, 20 Mar 2021 18:17:07 +0000
Subject: biology/htslib: Update to 1.12 biology/bcftools: Update to 1.12
 biology/samtools: Update to 1.12

Numerous enhancements, performance improvements, and bug fixes since 1.10
Minimized pkgsrc patches in all three packages
Moved htslib to custom tarball since Github-generated distfiles are incomplete
---
 biology/bcftools/Makefile                          |  5 +-
 biology/bcftools/PLIST                             |  6 +-
 biology/bcftools/distinfo                          | 13 ++--
 biology/bcftools/patches/patch-Makefile            | 53 ++-------------
 biology/bcftools/patches/patch-misc_run-roh.pl     | 24 -------
 biology/htslib/Makefile                            | 10 +--
 biology/htslib/PLIST                               |  4 +-
 biology/htslib/buildlink3.mk                       |  4 +-
 biology/htslib/distinfo                            | 13 ++--
 biology/htslib/patches/patch-Makefile              | 76 ---------------------
 .../htslib/patches/patch-cram_open__trace__file.c  | 18 -----
 biology/htslib/patches/patch-hfile__libcurl.c      | 78 ----------------------
 biology/samtools/Makefile                          |  7 +-
 biology/samtools/PLIST                             |  7 +-
 biology/samtools/distinfo                          | 12 ++--
 biology/samtools/patches/patch-Makefile            | 44 ++----------
 16 files changed, 53 insertions(+), 321 deletions(-)
 delete mode 100644 biology/bcftools/patches/patch-misc_run-roh.pl
 delete mode 100644 biology/htslib/patches/patch-Makefile
 delete mode 100644 biology/htslib/patches/patch-cram_open__trace__file.c
 delete mode 100644 biology/htslib/patches/patch-hfile__libcurl.c

(limited to 'biology')

diff --git a/biology/bcftools/Makefile b/biology/bcftools/Makefile
index abb3f4402db..781a545d22f 100644
--- a/biology/bcftools/Makefile
+++ b/biology/bcftools/Makefile
@@ -1,7 +1,6 @@
-# $NetBSD: Makefile,v 1.9 2020/12/04 20:45:00 nia Exp $
+# $NetBSD: Makefile,v 1.10 2021/03/20 18:17:07 bacon Exp $
 
-DISTNAME=	bcftools-1.10.2
-PKGREVISION=	2
+DISTNAME=	bcftools-1.12
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=samtools/}
 
diff --git a/biology/bcftools/PLIST b/biology/bcftools/PLIST
index 2bc54f0f6f1..9e7b8ca2840 100644
--- a/biology/bcftools/PLIST
+++ b/biology/bcftools/PLIST
@@ -1,6 +1,7 @@
-@comment $NetBSD: PLIST,v 1.2 2020/07/27 00:29:04 bacon Exp $
+@comment $NetBSD: PLIST,v 1.3 2021/03/20 18:17:07 bacon Exp $
 bin/bcftools
 bin/color-chrs
+bin/gff2gff.py
 bin/guess-ploidy
 bin/plot-roh
 bin/plot-vcfstats
@@ -34,12 +35,13 @@ libexec/bcftools/missing2ref.so
 libexec/bcftools/parental-origin.so
 libexec/bcftools/prune.so
 libexec/bcftools/remove-overlaps.so
+libexec/bcftools/scatter.so
 libexec/bcftools/setGT.so
 libexec/bcftools/smpl-stats.so
 libexec/bcftools/split-vep.so
 libexec/bcftools/split.so
 libexec/bcftools/tag2tag.so
-libexec/bcftools/trio-dnm.so
+libexec/bcftools/trio-dnm2.so
 libexec/bcftools/trio-stats.so
 libexec/bcftools/trio-switch-rate.so
 libexec/bcftools/variantkey-hex.so
diff --git a/biology/bcftools/distinfo b/biology/bcftools/distinfo
index 658a1ae5df6..b0a3a104aac 100644
--- a/biology/bcftools/distinfo
+++ b/biology/bcftools/distinfo
@@ -1,8 +1,7 @@
-$NetBSD: distinfo,v 1.2 2020/07/27 00:29:04 bacon Exp $
+$NetBSD: distinfo,v 1.3 2021/03/20 18:17:07 bacon Exp $
 
-SHA1 (bcftools-1.10.2.tar.gz) = b19c9ba06b1c8e8f135c1e0ab0e4ff713a291bf4
-RMD160 (bcftools-1.10.2.tar.gz) = 7713e8c5bd4195eb610544adb26158c16525fdac
-SHA512 (bcftools-1.10.2.tar.gz) = 12c004603db557ac69098e83ad3aaa5762b02b4718b79f3dc259fbcc5c74b8dad3726b5f61efb57f0b8e3d0349577f7934240f36c82bd98849885a5593791995
-Size (bcftools-1.10.2.tar.gz) = 2880994 bytes
-SHA1 (patch-Makefile) = 1f1397e9b0389a7b4fccc9eae87981e7ce1d7980
-SHA1 (patch-misc_run-roh.pl) = 8a29ee7b1001af6670955f174ce4dbab31f05659
+SHA1 (bcftools-1.12.tar.gz) = 17ded5a60da7a42d18fef5a846791ed295f69622
+RMD160 (bcftools-1.12.tar.gz) = 9d3a16c8266bcdd8f2a10f099aec3fc19da82a98
+SHA512 (bcftools-1.12.tar.gz) = f43074989a01cf4ef32a968935f5e5f3eacf2c04b9aa558d739166e3d96d3a498965d27db6482b2992b5d60fed3d2945ef3fd61fcc79b5dbe062994d49df4ad2
+Size (bcftools-1.12.tar.gz) = 3048508 bytes
+SHA1 (patch-Makefile) = 9dfe7b5dcf77deac6d248d7612440780ec8a3731
diff --git a/biology/bcftools/patches/patch-Makefile b/biology/bcftools/patches/patch-Makefile
index a0069e971ba..8cb83b52df7 100644
--- a/biology/bcftools/patches/patch-Makefile
+++ b/biology/bcftools/patches/patch-Makefile
@@ -1,49 +1,13 @@
-$NetBSD: patch-Makefile,v 1.1 2020/07/27 00:29:04 bacon Exp $
+$NetBSD: patch-Makefile,v 1.2 2021/03/20 18:17:07 bacon Exp $
 
 # Respect pkgsrc env
 
---- Makefile.orig	2019-12-19 09:57:32.000000000 +0000
+--- Makefile.orig	2021-03-19 17:42:33.842623449 +0000
 +++ Makefile
-@@ -22,12 +22,12 @@
- # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
- # DEALINGS IN THE SOFTWARE.
- 
--CC       = gcc
--AR       = ar
--RANLIB   = ranlib
--CPPFLAGS =
--CFLAGS   = -g -Wall -O2
--LDFLAGS  =
-+CC       ?= gcc
-+AR       ?= ar
-+RANLIB   ?= ranlib
-+# CPPFLAGS =
-+CFLAGS   ?= -g -Wall -O2
-+# LDFLAGS  =
- LIBS     =
- 
- DYNAMIC_FLAGS = -rdynamic
-@@ -45,12 +45,12 @@ OBJS     = main.o vcfindex.o tabix.o \
-            ccall.o em.o prob1.o kmin.o # the original samtools calling
- PLUGIN_OBJS = vcfplugin.o
- 
--prefix      = /usr/local
--exec_prefix = $(prefix)
-+PREFIX      ?= /usr/local
-+exec_prefix = $(PREFIX)
- bindir      = $(exec_prefix)/bin
- libdir      = $(exec_prefix)/lib
- libexecdir  = $(exec_prefix)/libexec
--mandir      = $(prefix)/share/man
-+mandir      = $(PREFIX)/share/man
- man1dir     = $(mandir)/man1
- # Installation location for $(PLUGINS)
- plugindir   = $(libexecdir)/bcftools
-@@ -59,12 +59,11 @@ pluginpath  = $(plugindir)
- misc_bindir = $(bindir)
+@@ -60,11 +60,11 @@ 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)
@@ -57,12 +21,3 @@ $NetBSD: patch-Makefile,v 1.1 2020/07/27 00:29:04 bacon Exp $
  
  PROGRAMS = bcftools
  MISC_SCRIPTS = \
-@@ -78,7 +77,7 @@ TEST_PROGRAMS = test/test-rbuf test/test
- 
- ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS)
- ALL_LDFLAGS  = $(HTSLIB_LDFLAGS) $(LDFLAGS)
--ALL_LIBS     = -lz $(DL_LIBS) $(LIBS)
-+ALL_LIBS     = -lz $(LIBS)
- 
- all: $(PROGRAMS) $(TEST_PROGRAMS) plugins
- 
diff --git a/biology/bcftools/patches/patch-misc_run-roh.pl b/biology/bcftools/patches/patch-misc_run-roh.pl
deleted file mode 100644
index e4a5aac3032..00000000000
--- a/biology/bcftools/patches/patch-misc_run-roh.pl
+++ /dev/null
@@ -1,24 +0,0 @@
-$NetBSD: patch-misc_run-roh.pl,v 1.1 2020/07/27 00:29:04 bacon Exp $
-
-# bash path
-
---- misc/run-roh.pl.orig	2019-12-19 09:57:32.000000000 +0000
-+++ misc/run-roh.pl
-@@ -110,7 +110,7 @@ sub cmd
- 
-     if ( $args{verbose} ) { print STDERR $cmd,"\n"; }
- 
--    # Why not to use backticks? Perl calls /bin/sh, which is often bash. To get the correct
-+    # Why not to use backticks? Perl calls bash, which is often bash. To get the correct
-     #   status of failing pipes, it must be called with the pipefail option.
- 
-     my $kid_io;
-@@ -127,7 +127,7 @@ sub cmd
-     else 
-     {      
-         # child
--        exec('/bin/bash', '-o','pipefail','-c', $cmd) or error("Failed to run the command [/bin/sh -o pipefail -c $cmd]: $!");
-+        exec('bash', '-c', $cmd) or error("Failed to run the command [bash -c $cmd]: $!");
-     }
- 
-     if ( exists($args{exit_on_error}) && !$args{exit_on_error} ) { return @out; }
diff --git a/biology/htslib/Makefile b/biology/htslib/Makefile
index 39cb0734bfa..1103edec029 100644
--- a/biology/htslib/Makefile
+++ b/biology/htslib/Makefile
@@ -1,9 +1,10 @@
-# $NetBSD: Makefile,v 1.18 2020/08/31 18:06:39 wiz Exp $
+# $NetBSD: Makefile,v 1.19 2021/03/20 18:17:07 bacon Exp $
 
-DISTNAME=	htslib-1.10.2
-PKGREVISION=	2
+DISTNAME=	htslib-1.12
 CATEGORIES=	biology
-MASTER_SITES=	${MASTER_SITE_GITHUB:=samtools/}
+# Github-generated distfiles are incomplete, use custom tarballs instead
+MASTER_SITES=	https://github.com/samtools/htslib/releases/download/${PKGVERSION_NOREV}/
+EXTRACT_SUFX=	.tar.bz2
 
 MAINTAINER=	bacon@NetBSD.org
 HOMEPAGE=	https://www.htslib.org/
@@ -23,6 +24,7 @@ REPLACE_PERL+=		test/*.pl
 CONFIGURE_ARGS+=	--enable-libcurl
 PKGCONFIG_OVERRIDE=	htslib.pc.in
 TEST_TARGET=		test
+MAKE_ENV+=		BUILT_TEST_PROGRAMS=''
 
 pre-configure:
 	cd ${WRKSRC} && autoreconf -if
diff --git a/biology/htslib/PLIST b/biology/htslib/PLIST
index 6289cd53d5a..423d488e12a 100644
--- a/biology/htslib/PLIST
+++ b/biology/htslib/PLIST
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.2 2020/07/22 14:50:14 bacon Exp $
+@comment $NetBSD: PLIST,v 1.3 2021/03/20 18:17:07 bacon Exp $
 bin/bgzip
 bin/htsfile
 bin/tabix
@@ -9,6 +9,7 @@ include/htslib/hfile.h
 include/htslib/hts.h
 include/htslib/hts_defs.h
 include/htslib/hts_endian.h
+include/htslib/hts_expr.h
 include/htslib/hts_log.h
 include/htslib/hts_os.h
 include/htslib/kbitset.h
@@ -17,6 +18,7 @@ include/htslib/khash.h
 include/htslib/khash_str2int.h
 include/htslib/klist.h
 include/htslib/knetfile.h
+include/htslib/kroundup.h
 include/htslib/kseq.h
 include/htslib/ksort.h
 include/htslib/kstring.h
diff --git a/biology/htslib/buildlink3.mk b/biology/htslib/buildlink3.mk
index 2cd4c3791e1..ebe0413f6dc 100644
--- a/biology/htslib/buildlink3.mk
+++ b/biology/htslib/buildlink3.mk
@@ -1,11 +1,11 @@
-# $NetBSD: buildlink3.mk,v 1.4 2020/07/22 15:36:55 bacon Exp $
+# $NetBSD: buildlink3.mk,v 1.5 2021/03/20 18:17:07 bacon Exp $
 
 BUILDLINK_TREE+=	htslib
 
 .if !defined(HTSLIB_BUILDLINK3_MK)
 HTSLIB_BUILDLINK3_MK:=
 
-BUILDLINK_API_DEPENDS.htslib+=	htslib>=1.8
+BUILDLINK_API_DEPENDS.htslib+=	htslib>=1.10.2
 BUILDLINK_ABI_DEPENDS.htslib+=	htslib>=1.10.2
 BUILDLINK_PKGSRCDIR.htslib?=	../../biology/htslib
 
diff --git a/biology/htslib/distinfo b/biology/htslib/distinfo
index b4938ea2013..ca1df5ff799 100644
--- a/biology/htslib/distinfo
+++ b/biology/htslib/distinfo
@@ -1,9 +1,6 @@
-$NetBSD: distinfo,v 1.3 2020/07/22 14:50:14 bacon Exp $
+$NetBSD: distinfo,v 1.4 2021/03/20 18:17:07 bacon Exp $
 
-SHA1 (htslib-1.10.2.tar.gz) = 0ac4b86e49556d7dcaa89d4cce2661c9ca706631
-RMD160 (htslib-1.10.2.tar.gz) = 6d8b6a362297345420dc9acc544029276ce4b1b6
-SHA512 (htslib-1.10.2.tar.gz) = 7a91c15ca1de35653d068dc57ae511ad791ae0bd8504867d4e60c46e813e58b441409541197cde3b2a37840e60331336aebc627ecbf5c64fca1af63dd05f8f9e
-Size (htslib-1.10.2.tar.gz) = 1452177 bytes
-SHA1 (patch-Makefile) = e13333dd97ecd6c6753d14c1b738d6e5934a2911
-SHA1 (patch-cram_open__trace__file.c) = 49b47e13786317e652a8ec810cc91f10d21bb8ea
-SHA1 (patch-hfile__libcurl.c) = 2a143818f1099ef01c57a3c904060a76abb63f14
+SHA1 (htslib-1.12.tar.bz2) = 8cab518f97bbdf43165320c3a4bdef1e9a42893a
+RMD160 (htslib-1.12.tar.bz2) = 3d93d91db8c382f42b8ad0843609cabd3b502b46
+SHA512 (htslib-1.12.tar.bz2) = a810c646561f5c8b3a19b73ac22ec5f25b04d4e88e1314988881a8120c54106591d1d65aa708bbe2608f0065ca8abe92bdd70ef59a0dd0cdf63ff45c10957092
+Size (htslib-1.12.tar.bz2) = 4094458 bytes
diff --git a/biology/htslib/patches/patch-Makefile b/biology/htslib/patches/patch-Makefile
deleted file mode 100644
index d8abf1d21a3..00000000000
--- a/biology/htslib/patches/patch-Makefile
+++ /dev/null
@@ -1,76 +0,0 @@
-$NetBSD: patch-Makefile,v 1.1 2020/07/22 14:50:14 bacon Exp $
-
-# Respect pkgsrc env
-
---- Makefile.orig	2019-12-19 09:54:30.000000000 +0000
-+++ Makefile
-@@ -22,44 +22,43 @@
- # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
- # DEALINGS IN THE SOFTWARE.
- 
--CC     = gcc
--AR     = ar
--RANLIB = ranlib
-+CC     ?= gcc
-+AR     ?= ar
-+RANLIB ?= ranlib
- 
- # Default libraries to link if configure is not used
- htslib_default_libs = -lz -lm -lbz2 -llzma -lcurl
- 
--CPPFLAGS =
-+# CPPFLAGS =
- # TODO: make the 64-bit support for VCF optional via configure, for now add -DVCF_ALLOW_INT64
- #       to CFLAGS manually, here or in config.mk if the latter exists.
- # TODO: probably update cram code to make it compile cleanly with -Wc++-compat
- # For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600
- #CFLAGS   = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600
--CFLAGS   = -g -Wall -O2 -fvisibility=hidden
-+CFLAGS   ?= -g -Wall -O2 -fvisibility=hidden
- EXTRA_CFLAGS_PIC = -fpic
--LDFLAGS  = -fvisibility=hidden
-+LDFLAGS  ?= -fvisibility=hidden
- LIBS     = $(htslib_default_libs)
- 
--prefix      = /usr/local
--exec_prefix = $(prefix)
-+PREFIX      ?= /usr/local
-+exec_prefix = $(PREFIX)
- bindir      = $(exec_prefix)/bin
--includedir  = $(prefix)/include
-+includedir  = $(PREFIX)/include
- libdir      = $(exec_prefix)/lib
- libexecdir  = $(exec_prefix)/libexec
--datarootdir = $(prefix)/share
-+datarootdir = $(PREFIX)/share
- mandir      = $(datarootdir)/man
- man1dir     = $(mandir)/man1
- man5dir     = $(mandir)/man5
- man7dir     = $(mandir)/man7
- pkgconfigdir= $(libdir)/pkgconfig
- 
--MKDIR_P = mkdir -p
--INSTALL = install -p
--INSTALL_DATA    = $(INSTALL) -m 644
--INSTALL_DIR     = $(MKDIR_P) -m 755
--INSTALL_LIB     = $(INSTALL_DATA)
--INSTALL_MAN     = $(INSTALL_DATA)
--INSTALL_PROGRAM = $(INSTALL)
-+MKDIR_P         = mkdir -p
-+INSTALL_DATA    = ${BSD_INSTALL_DATA}
-+INSTALL_DIR     = $(MKDIR_P)
-+INSTALL_LIB     = ${BSD_INSTALL_LIB}
-+INSTALL_MAN     = ${BSD_INSTALL_MAN}
-+INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM}
- 
- # Set by config.mk if plugins are enabled
- plugindir =
-@@ -98,7 +97,7 @@ BUILT_THRASH_PROGRAMS = \
- 	test/thrash_threads6 \
- 	test/thrash_threads7
- 
--all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS)
-+all: lib-static lib-shared $(BUILT_PROGRAMS) plugins
- 
- HTSPREFIX =
- include htslib_vars.mk
diff --git a/biology/htslib/patches/patch-cram_open__trace__file.c b/biology/htslib/patches/patch-cram_open__trace__file.c
deleted file mode 100644
index 7915730995d..00000000000
--- a/biology/htslib/patches/patch-cram_open__trace__file.c
+++ /dev/null
@@ -1,18 +0,0 @@
-$NetBSD: patch-cram_open__trace__file.c,v 1.1 2020/07/22 14:50:14 bacon Exp $
-
-# Enhance error message
-
---- cram/open_trace_file.c.orig	2019-12-19 09:54:30.000000000 +0000
-+++ cram/open_trace_file.c
-@@ -204,8 +204,9 @@ mFILE *find_file_url(const char *file, c
-             goto fail;
-         }
-     }
--    if (hclose(hf) < 0 || len < 0) {
--        hts_log_warning("Failed to read reference \"%s\": %s", path, strerror(errno));
-+    int close_status = hclose(hf);
-+    if (close_status < 0 || len < 0) {
-+        hts_log_warning("Failed to read reference \"%s\": %s  close_status = %d len = %ld", path, strerror(errno));
-         goto fail;
-     }
- 
diff --git a/biology/htslib/patches/patch-hfile__libcurl.c b/biology/htslib/patches/patch-hfile__libcurl.c
deleted file mode 100644
index b7177535ba2..00000000000
--- a/biology/htslib/patches/patch-hfile__libcurl.c
+++ /dev/null
@@ -1,78 +0,0 @@
-$NetBSD: patch-hfile__libcurl.c,v 1.1 2020/07/22 14:50:14 bacon Exp $
-
-# recent libcurl compatibility
-
---- hfile_libcurl.c.orig	2019-12-19 09:54:30.000000000 +0000
-+++ hfile_libcurl.c
-@@ -74,6 +74,10 @@ typedef struct {
-     unsigned int size;
- } hdrlist;
- 
-+#ifndef ENOTRECOVERABLE
-+#define ENOTRECOVERABLE EIO
-+#endif
-+
- typedef struct {
-     hdrlist fixed;                   // List of headers supplied at hopen()
-     hdrlist extra;                   // List of headers from callback
-@@ -218,6 +222,8 @@ static int easy_errno(CURL *easy, CURLco
-         return EEXIST;
- 
-     default:
-+        hts_log_error("Libcurl reported error %d (%s)", (int) err,
-+                      curl_easy_strerror(err));
-         return EIO;
-     }
- }
-@@ -238,6 +244,8 @@ static int multi_errno(CURLMcode errm)
-         return ENOMEM;
- 
-     default:
-+        hts_log_error("Libcurl reported error %d (%s)", (int) errm,
-+                      curl_multi_strerror(errm));
-         return EIO;
-     }
- }
-@@ -797,9 +805,13 @@ static ssize_t libcurl_read(hFILE *fpv, 
-         fp->buffer.ptr.rd = buffer;
-         fp->buffer.len = nbytes;
-         fp->paused = 0;
--        err = curl_easy_pause(fp->easy, CURLPAUSE_CONT);
--        if (err != CURLE_OK) { errno = easy_errno(fp->easy, err); return -1; }
--
-+	if (! fp->finished) {
-+            err = curl_easy_pause(fp->easy, CURLPAUSE_CONT);
-+            if (err != CURLE_OK) {
-+		errno = easy_errno(fp->easy, err);
-+		return -1;
-+	    }
-+	}
-         while (! fp->paused && ! fp->finished) {
-             if (wait_perform(fp) < 0) return -1;
-         }
-@@ -1003,12 +1015,6 @@ static int restart_from_position(hFILE_l
-     }
-     temp_fp.nrunning = ++fp->nrunning;
- 
--    err = curl_easy_pause(temp_fp.easy, CURLPAUSE_CONT);
--    if (err != CURLE_OK) {
--        save_errno = easy_errno(temp_fp.easy, err);
--        goto error_remove;
--    }
--
-     while (! temp_fp.paused && ! temp_fp.finished)
-         if (wait_perform(&temp_fp) < 0) {
-             save_errno = errno;
-@@ -1084,8 +1090,10 @@ static int libcurl_close(hFILE *fpv)
-     fp->buffer.len = 0;
-     fp->closing = 1;
-     fp->paused = 0;
--    err = curl_easy_pause(fp->easy, CURLPAUSE_CONT);
--    if (err != CURLE_OK) save_errno = easy_errno(fp->easy, err);
-+    if (! fp->finished) {
-+        err = curl_easy_pause(fp->easy, CURLPAUSE_CONT);
-+        if (err != CURLE_OK) save_errno = easy_errno(fp->easy, err);
-+    }
- 
-     while (save_errno == 0 && ! fp->paused && ! fp->finished)
-         if (wait_perform(fp) < 0) save_errno = errno;
diff --git a/biology/samtools/Makefile b/biology/samtools/Makefile
index 997c3925e1c..b9786953fff 100644
--- a/biology/samtools/Makefile
+++ b/biology/samtools/Makefile
@@ -1,7 +1,6 @@
-# $NetBSD: Makefile,v 1.10 2020/12/04 20:45:00 nia Exp $
+# $NetBSD: Makefile,v 1.11 2021/03/20 18:17:07 bacon Exp $
 
-DISTNAME=	samtools-1.10
-PKGREVISION=	2
+DISTNAME=	samtools-1.12
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=samtools/}
 
@@ -26,7 +25,7 @@ SUBST_FILES.bash+=	test/test.pl
 
 REPLACE_PERL+=		misc/*.pl
 REPLACE_PERL+=		test/*.pl
-REPLACE_PERL+=		misc/plot-bamstats
+REPLACE_PERL+=		misc/plot-bamstats misc/plot-ampliconstats
 REPLACE_LUA+=		misc/*.lua
 
 CONFIGURE_ARGS+=	--with-htslib=system
diff --git a/biology/samtools/PLIST b/biology/samtools/PLIST
index 01cac0afb68..d8b3d51a4e0 100644
--- a/biology/samtools/PLIST
+++ b/biology/samtools/PLIST
@@ -1,14 +1,16 @@
-@comment $NetBSD: PLIST,v 1.2 2020/07/26 23:30:29 bacon Exp $
+@comment $NetBSD: PLIST,v 1.3 2021/03/20 18:17:07 bacon Exp $
 bin/ace2sam
 bin/blast2sam.pl
 bin/bowtie2sam.pl
 bin/export2sam.pl
+bin/fasta-sanitize.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
@@ -20,10 +22,13 @@ bin/wgsim
 bin/wgsim_eval.pl
 bin/zoom2sam.pl
 man/man1/samtools-addreplacerg.1
+man/man1/samtools-ampliconclip.1
+man/man1/samtools-ampliconstats.1
 man/man1/samtools-bedcov.1
 man/man1/samtools-calmd.1
 man/man1/samtools-cat.1
 man/man1/samtools-collate.1
+man/man1/samtools-coverage.1
 man/man1/samtools-depad.1
 man/man1/samtools-depth.1
 man/man1/samtools-dict.1
diff --git a/biology/samtools/distinfo b/biology/samtools/distinfo
index 07f9aabbe1b..32a52179ee4 100644
--- a/biology/samtools/distinfo
+++ b/biology/samtools/distinfo
@@ -1,7 +1,7 @@
-$NetBSD: distinfo,v 1.3 2020/07/26 23:30:29 bacon Exp $
+$NetBSD: distinfo,v 1.4 2021/03/20 18:17:07 bacon Exp $
 
-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-1.12.tar.gz) = f46eb3a18885fb352d8746d51a206f7f34916232
+RMD160 (samtools-1.12.tar.gz) = 511ba541e9f3dbbab333d4a24a83f63c628b5b18
+SHA512 (samtools-1.12.tar.gz) = 7f468a4740610c2fdc42d8f020d3082e5b2b2e73b0c2dfc19b212ca259d703f34f7df0922e409a94500ccc0357d4d46306035be29c23a523ef6e959022f9d1db
+Size (samtools-1.12.tar.gz) = 4528460 bytes
+SHA1 (patch-Makefile) = 3fc1f1d67167c8ca8eff1ed17f7a084ec3d4579d
diff --git a/biology/samtools/patches/patch-Makefile b/biology/samtools/patches/patch-Makefile
index 59adadc7690..700832db503 100644
--- a/biology/samtools/patches/patch-Makefile
+++ b/biology/samtools/patches/patch-Makefile
@@ -1,56 +1,24 @@
-$NetBSD: patch-Makefile,v 1.1 2020/07/26 23:30:30 bacon Exp $
+$NetBSD: patch-Makefile,v 1.2 2021/03/20 18:17:07 bacon Exp $
 
 # Respect pkgsrc env
 
---- Makefile.orig	2020-07-21 20:20:56.996788479 +0000
+--- Makefile.orig	2021-03-19 17:48:34.572594186 +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)
+@@ -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
+ 
-- 
cgit v1.2.3