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

4 files changed, 21 insertions, 49 deletions

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
+