biology/htslib: Upgrade to 1.10.2

Numerous bug fixes and enhancements since 1.9:
https://github.com/samtools/htslib/tags

Bump PORTREVISION on dependents that don't require additional patching

PR:             248089

12 files changed, 113 insertions, 43 deletions

diff --git a/biology/bcftools/Makefile b/biology/bcftools/Makefile
index 0ae73933e5d2..73e4a9fef542 100644
--- a/biology/bcftools/Makefile
+++ b/biology/bcftools/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	bcftools
 PORTVERSION=	1.9
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	biology
 
 MAINTAINER=	cartwright@asu.edu
@@ -16,8 +16,6 @@ BUILD_DEPENDS=	htslib>=1.6:biology/htslib
 LIB_DEPENDS=	libhts.so:biology/htslib
 TEST_DEPENDS=	bash:shells/bash
 
-CONFLICTS_BUILD=openssl
-
 USES=		autoreconf gmake localbase \
 		perl5 python:env shebangfix
 
diff --git a/biology/cufflinks/Makefile b/biology/cufflinks/Makefile
index 275b60f9a467..c3232d9a414a 100644
--- a/biology/cufflinks/Makefile
+++ b/biology/cufflinks/Makefile
@@ -3,6 +3,7 @@
 PORTNAME=	cufflinks
 DISTVERSIONPREFIX=	v
 DISTVERSION=	2.2.1-89
+PORTREVISION=	1
 DISTVERSIONSUFFIX=	-gdc3b0cb
 CATEGORIES=	biology
 
diff --git a/biology/htslib/Makefile b/biology/htslib/Makefile
index 18b7acf4735d..11927a423710 100644
--- a/biology/htslib/Makefile
+++ b/biology/htslib/Makefile
@@ -2,28 +2,28 @@
 # $FreeBSD$
 
 PORTNAME=	htslib
-DISTVERSION=	1.9
+DISTVERSION=	1.10.2
 CATEGORIES=	biology devel
 
-MAINTAINER=	cartwright@asu.edu
+MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	C library for high-throughput sequencing data formats
 
 LICENSE=	BSD3CLAUSE MIT
 LICENSE_COMB=	multi
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
+LIB_DEPENDS=	libdeflate.so:archivers/libdeflate
 TEST_DEPENDS=	bash:shells/bash
 
-USES=		autoreconf gmake localbase \
-		pathfix perl5 shebangfix
+USES=		autoreconf gmake localbase pathfix perl5 shebangfix
 USE_GITHUB=	yes
-GH_ACCOUNT=	samtools
 USE_PERL5=	test
 USE_LDCONFIG=	yes
-GNU_CONFIGURE=	yes
+
+GH_ACCOUNT=		samtools
+GNU_CONFIGURE=		yes
 PATHFIX_MAKEFILEIN=	Makefile
-SHEBANG_FILES=		test/compare_sam.pl \
-			test/test.pl
+SHEBANG_FILES=		test/*.pl
 
 OPTIONS_DEFINE=		CURL
 OPTIONS_DEFAULT=	CURL
diff --git a/biology/htslib/distinfo b/biology/htslib/distinfo
index 6748afa34d04..c27d7e91533c 100644
--- a/biology/htslib/distinfo
+++ b/biology/htslib/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1532906408
-SHA256 (samtools-htslib-1.9_GH0.tar.gz) = d2e3cde77b8f874b37453c63390cd992901266336e9f70e871ef42402510467f
-SIZE (samtools-htslib-1.9_GH0.tar.gz) = 1285580
+TIMESTAMP = 1595116892
+SHA256 (samtools-htslib-1.10.2_GH0.tar.gz) = b352eabed6392869dbdea0fe6db10a736a226d1f90036a724a49798f7e81cab7
+SIZE (samtools-htslib-1.10.2_GH0.tar.gz) = 1452177
diff --git a/biology/htslib/files/patch-Makefile b/biology/htslib/files/patch-Makefile
index f01cc74714db..c2b011767521 100644
--- a/biology/htslib/files/patch-Makefile
+++ b/biology/htslib/files/patch-Makefile
@@ -1,46 +1,52 @@
---- Makefile.orig	2017-10-18 08:03:33 UTC
+--- Makefile.orig	2020-08-02 22:52:13 UTC
 +++ Makefile
-@@ -22,41 +22,26 @@
+@@ -22,25 +22,26 @@
  # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
  # DEALINGS IN THE SOFTWARE.
  
 -CC     = gcc
 -AR     = ar
 -RANLIB = ranlib
--
--# Default libraries to link if configure is not used
--htslib_default_libs = -lz -lm -lbz2 -llzma
--
++CC     ?= gcc
++AR     ?= ar
++RANLIB ?= ranlib
+ 
+ # Default libraries to link if configure is not used
+ htslib_default_libs = -lz -lm -lbz2 -llzma -lcurl
+ 
 -CPPFLAGS =
--# 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 -D__FUNCTION__=__func__
--CFLAGS   = -g -Wall -O2
++# 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  =
--LIBS     = $(htslib_default_libs)
+-LDFLAGS  = -fvisibility=hidden
++LDFLAGS  ?= -fvisibility=hidden
+ LIBS     = $(htslib_default_libs)
  
 -prefix      = /usr/local
-+prefix      = ${PREFIX}
++PREFIX      ?= /usr/local
++prefix      = $(PREFIX)
  exec_prefix = $(prefix)
  bindir      = $(exec_prefix)/bin
  includedir  = $(prefix)/include
- libdir      = $(exec_prefix)/lib
- libexecdir  = $(exec_prefix)/libexec
- datarootdir = $(prefix)/share
--mandir      = $(datarootdir)/man
-+mandir      = $(prefix)/man
- man1dir     = $(mandir)/man1
- man5dir     = $(mandir)/man5
+@@ -53,13 +54,13 @@ man5dir     = $(mandir)/man5
+ man7dir     = $(mandir)/man7
  pkgconfigdir= $(prefix)/libdata/pkgconfig
  
- MKDIR_P = mkdir -p
+-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)
++# Use ports BSD_INSTALL_PROGRAM to strip if WITH_DEBUG is not set
++MKDIR_P         = mkdir -p
 +INSTALL_DATA    = ${BSD_INSTALL_DATA}
 +INSTALL_DIR     = $(MKDIR_P)
 +INSTALL_LIB     = ${BSD_INSTALL_LIB}
@@ -49,9 +55,9 @@
  
  # Set by config.mk if plugins are enabled
  plugindir =
-@@ -87,7 +72,7 @@ BUILT_THRASH_PROGRAMS = \
- 	test/thrash_threads5 \
- 	test/thrash_threads6
+@@ -98,7 +99,7 @@ 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
diff --git a/biology/htslib/files/patch-hfile__libcurl.c b/biology/htslib/files/patch-hfile__libcurl.c
index 6b6ebb6e48d9..e4cd8745a18e 100644
--- a/biology/htslib/files/patch-hfile__libcurl.c
+++ b/biology/htslib/files/patch-hfile__libcurl.c
@@ -1,6 +1,6 @@
---- hfile_libcurl.c.orig	2017-09-28 11:20:23 UTC
+--- hfile_libcurl.c.orig	2019-12-19 09:54:30 UTC
 +++ hfile_libcurl.c
-@@ -49,6 +49,10 @@ typedef struct {
+@@ -74,6 +74,10 @@ typedef struct {
      unsigned int size;
  } hdrlist;
  
@@ -11,3 +11,64 @@
  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, CURLcode err)
+         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, void *bufferv,
+         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_libcurl *fp, of
+     }
+     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/htslib/pkg-plist b/biology/htslib/pkg-plist
index 2143ba6be014..dd5727097944 100644
--- a/biology/htslib/pkg-plist
+++ b/biology/htslib/pkg-plist
@@ -30,7 +30,7 @@ include/htslib/vcfutils.h
 lib/libhts.a
 lib/libhts.so
 lib/libhts.so.%%PORTVERSION%%
-lib/libhts.so.2
+lib/libhts.so.3
 libdata/pkgconfig/htslib.pc
 man/man1/bgzip.1.gz
 man/man1/htsfile.1.gz
@@ -38,3 +38,4 @@ man/man1/tabix.1.gz
 man/man5/faidx.5.gz
 man/man5/sam.5.gz
 man/man5/vcf.5.gz
+man/man7/htslib-s3-plugin.7.gz
diff --git a/biology/jellyfish/Makefile b/biology/jellyfish/Makefile
index d8f05aaa0c97..16592d4754b3 100644
--- a/biology/jellyfish/Makefile
+++ b/biology/jellyfish/Makefile
@@ -3,7 +3,7 @@
 PORTNAME=		Jellyfish
 DISTVERSIONPREFIX=	v
 DISTVERSION=		2.2.10
-PORTREVISION=		8
+PORTREVISION=		9
 CATEGORIES=		biology
 
 MAINTAINER=	jwb@FreeBSD.org
diff --git a/biology/pbbam/Makefile b/biology/pbbam/Makefile
index 85cc82fbedd8..0b68e2c346d0 100644
--- a/biology/pbbam/Makefile
+++ b/biology/pbbam/Makefile
@@ -2,7 +2,7 @@
 
 PORTNAME=	pbbam
 DISTVERSION=	0.18.0 # Test with biology/unanimity before upgrading!
-PORTREVISION=	4
+PORTREVISION=	5
 CATEGORIES=	biology
 
 # As of March 2018, unanimity is no longer open source.
diff --git a/biology/samtools/Makefile b/biology/samtools/Makefile
index 602b6f949228..45ac92975918 100644
--- a/biology/samtools/Makefile
+++ b/biology/samtools/Makefile
@@ -3,6 +3,7 @@
 
 PORTNAME=	samtools
 DISTVERSION=	1.9
+PORTREVISION=	1
 CATEGORIES=	biology
 
 MAINTAINER=	cartwright@asu.edu
diff --git a/biology/tabixpp/Makefile b/biology/tabixpp/Makefile
index 70ec51ab5f14..83413d207c85 100644
--- a/biology/tabixpp/Makefile
+++ b/biology/tabixpp/Makefile
@@ -3,6 +3,7 @@
 PORTNAME=	tabixpp
 DISTVERSIONPREFIX=	v
 DISTVERSION=	1.0.0-10
+PORTREVISION=	1
 DISTVERSIONSUFFIX=	-g6bbe690
 CATEGORIES=	biology
 
diff --git a/biology/vcflib/Makefile b/biology/vcflib/Makefile
index a5a9de773fe3..f66def256f3b 100644
--- a/biology/vcflib/Makefile
+++ b/biology/vcflib/Makefile
@@ -3,6 +3,7 @@
 PORTNAME=		vcflib
 DISTVERSIONPREFIX=	v
 DISTVERSION=		1.0.0-rc1-130
+PORTREVISION=	1
 DISTVERSIONSUFFIX=	-g7e3d806
 CATEGORIES=		biology