biology/htslib: Upgrade to 1.10.2

Numerous enhancements and bug fixes since 1.9, including:

Elimited refernce file size limits
SAM header API
On-the-fly indexing
Improved Amazon S3 interface

This package contains a patch for recent libcurl not in the upstream release

7 files changed, 198 insertions, 17 deletions

diff --git a/biology/htslib/Makefile b/biology/htslib/Makefile
index 03ac98ed033..c248bf75e3c 100644
--- a/biology/htslib/Makefile
+++ b/biology/htslib/Makefile
@@ -1,25 +1,30 @@
-# $NetBSD: Makefile,v 1.15 2020/05/22 10:55:57 adam Exp $
+# $NetBSD: Makefile,v 1.16 2020/07/22 14:50:14 bacon Exp $
 
-DISTNAME=	htslib-1.9
-PKGREVISION=	10
+DISTNAME=	htslib-1.10.2
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=samtools/}
-EXTRACT_SUFX=	.tar.bz2
-GITHUB_RELEASE=	${PKGVERSION_NOREV}
 
 MAINTAINER=	bacon@NetBSD.org
 HOMEPAGE=	https://www.htslib.org/
 COMMENT=	C library for high-throughput sequencing data formats
 LICENSE=	mit
 
-USE_TOOLS+=		gmake perl
+USE_TOOLS+=		autoconf automake autoreconf bash gmake perl
 GNU_CONFIGURE=		yes
+
+SUBST_CLASSES+=		version
+SUBST_STAGE.version=	pre-configure
+SUBST_SED.version=	-e "s|m4_esyscmd_s(\[./version.sh 2>/dev/null\])|[${PKGVERSION_NOREV}]|"
+SUBST_FILES.version=	configure.ac
+
+REPLACE_PERL+=		test/*.pl
+
 CONFIGURE_ARGS+=	--enable-libcurl
 PKGCONFIG_OVERRIDE=	htslib.pc.in
 TEST_TARGET=		test
 
-REPLACE_PERL+=		test/compare_sam.pl
-REPLACE_PERL+=		test/test.pl
+pre-configure:
+	cd ${WRKSRC} && autoreconf
 
 .include "../../archivers/bzip2/buildlink3.mk"
 .include "../../archivers/xz/buildlink3.mk"
diff --git a/biology/htslib/PLIST b/biology/htslib/PLIST
index ca2d06e3dda..6289cd53d5a 100644
--- a/biology/htslib/PLIST
+++ b/biology/htslib/PLIST
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.1 2018/04/30 16:51:54 bacon Exp $
+@comment $NetBSD: PLIST,v 1.2 2020/07/22 14:50:14 bacon Exp $
 bin/bgzip
 bin/htsfile
 bin/tabix
@@ -31,7 +31,7 @@ include/htslib/vcfutils.h
 lib/libhts.a
 lib/libhts.so
 lib/libhts.so.${PKGVERSION}
-lib/libhts.so.2
+lib/libhts.so.3
 lib/pkgconfig/htslib.pc
 man/man1/bgzip.1
 man/man1/htsfile.1
@@ -39,3 +39,4 @@ man/man1/tabix.1
 man/man5/faidx.5
 man/man5/sam.5
 man/man5/vcf.5
+man/man7/htslib-s3-plugin.7
diff --git a/biology/htslib/buildlink3.mk b/biology/htslib/buildlink3.mk
index 5c8a1c487be..7bb5583c741 100644
--- a/biology/htslib/buildlink3.mk
+++ b/biology/htslib/buildlink3.mk
@@ -1,11 +1,11 @@
-# $NetBSD: buildlink3.mk,v 1.2 2018/05/01 13:20:44 bacon Exp $
+# $NetBSD: buildlink3.mk,v 1.3 2020/07/22 14:50:14 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_PKGSRCDIR.htslib?=	../../biology/htslib
 
 .endif	# HTSLIB_BUILDLINK3_MK
diff --git a/biology/htslib/distinfo b/biology/htslib/distinfo
index 75982d9002f..b4938ea2013 100644
--- a/biology/htslib/distinfo
+++ b/biology/htslib/distinfo
@@ -1,6 +1,9 @@
-$NetBSD: distinfo,v 1.2 2018/11/06 10:24:14 adam Exp $
+$NetBSD: distinfo,v 1.3 2020/07/22 14:50:14 bacon Exp $
 
-SHA1 (htslib-1.9.tar.bz2) = 21be5187203df30637dda2e1133cae2e833ef050
-RMD160 (htslib-1.9.tar.bz2) = 85d5211cc197931e73a0dc7ca0673426f2ff6d89
-SHA512 (htslib-1.9.tar.bz2) = ddb0e2d970e4c2c27e203b064898f95cb7c187cd497c02fc7b4312dcea25669d0b6063d537687521e7a065f6daefa1ae897add2df4981037a187b499d08fdef7
-Size (htslib-1.9.tar.bz2) = 1178859 bytes
+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
diff --git a/biology/htslib/patches/patch-Makefile b/biology/htslib/patches/patch-Makefile
new file mode 100644
index 00000000000..d8abf1d21a3
--- /dev/null
+++ b/biology/htslib/patches/patch-Makefile
@@ -0,0 +1,76 @@
+$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 $(BUILT_PROGRAMS) plugins
+ 
+ HTSPREFIX =
+ include htslib_vars.mk
diff --git a/biology/htslib/patches/patch-cram_open__trace__file.c b/biology/htslib/patches/patch-cram_open__trace__file.c
new file mode 100644
index 00000000000..7915730995d
--- /dev/null
+++ b/biology/htslib/patches/patch-cram_open__trace__file.c
@@ -0,0 +1,18 @@
+$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
new file mode 100644
index 00000000000..b7177535ba2
--- /dev/null
+++ b/biology/htslib/patches/patch-hfile__libcurl.c
@@ -0,0 +1,78 @@
+$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;