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biology/htslib: Upgrade to 1.11.0

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Numerous bug fixes, new features and performance improvements since 1.10
https://github.com/samtools/htslib/releases/tag/1.11

Reported by:    portscout
This commit is contained in:
Jason W. Bacon 2020-11-05 20:30:50 +00:00
parent 4842225b41
commit 6fd02632f0
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=554155
7 changed files with 51 additions and 103 deletions
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2
biology/htslib/Makefile
View File

@ -2,7 +2,7 @@
# $FreeBSD$
PORTNAME= htslib
DISTVERSION= 1.10.2
DISTVERSION= 1.11.0
CATEGORIES= biology devel
MAINTAINER= jwb@FreeBSD.org

6
biology/htslib/distinfo
View File

@ -1,3 +1,3 @@
TIMESTAMP = 1595116892
SHA256 (samtools-htslib-1.10.2_GH0.tar.gz) = b352eabed6392869dbdea0fe6db10a736a226d1f90036a724a49798f7e81cab7
SIZE (samtools-htslib-1.10.2_GH0.tar.gz) = 1452177
TIMESTAMP = 1602982298
SHA256 (samtools-htslib-1.11.0_GH0.tar.gz) = 55356e78f25a20194488d94308335f409c3757101398961388caf38d3cce12dd
SIZE (samtools-htslib-1.11.0_GH0.tar.gz) = 1485848

41
biology/htslib/files/patch-Makefile
View File

@ -1,31 +1,7 @@
--- Makefile.orig 2020-08-02 22:52:13 UTC
--- Makefile.orig 2020-10-18 00:44:56 UTC
+++ Makefile
@@ -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
+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
@@ -40,7 +40,8 @@ EXTRA_CFLAGS_PIC = -fpic
LDFLAGS = -fvisibility=hidden
LIBS = $(htslib_default_libs)
-prefix = /usr/local
@ -34,7 +10,7 @@
exec_prefix = $(prefix)
bindir = $(exec_prefix)/bin
includedir = $(prefix)/include
@@ -53,13 +54,13 @@ man5dir = $(mandir)/man5
@@ -53,13 +54,14 @@ man5dir = $(mandir)/man5
man7dir = $(mandir)/man7
pkgconfigdir= $(prefix)/libdata/pkgconfig
@ -47,6 +23,7 @@
-INSTALL_PROGRAM = $(INSTALL)
+# Use ports BSD_INSTALL_PROGRAM to strip if WITH_DEBUG is not set
+MKDIR_P = mkdir -p
+INSTALL = install -p
+INSTALL_DATA = ${BSD_INSTALL_DATA}
+INSTALL_DIR = $(MKDIR_P)
+INSTALL_LIB = ${BSD_INSTALL_LIB}
@ -55,12 +32,12 @@
# Set by config.mk if plugins are enabled
plugindir =
@@ -98,7 +99,7 @@ BUILT_THRASH_PROGRAMS = \
@@ -100,7 +102,7 @@ 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
-all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS) \
+all: lib-static lib-shared $(BUILT_PROGRAMS) plugins \
htslib_static.mk htslib-uninstalled.pc
HTSPREFIX =
include htslib_vars.mk

82
biology/htslib/files/patch-hfile__libcurl.c
View File

@ -1,74 +1,24 @@
--- hfile_libcurl.c.orig 2019-12-19 09:54:30 UTC
--- hfile_libcurl.c.orig 2020-09-22 12:15:49 UTC
+++ hfile_libcurl.c
@@ -74,6 +74,10 @@ typedef struct {
unsigned int size;
} hdrlist;
@@ -22,6 +22,10 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR O
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE. */
+#ifndef ENOTRECOVERABLE
+#define ENOTRECOVERABLE EIO
+#endif
+
#define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h
#include <config.h>
@@ -73,6 +77,10 @@ typedef struct {
unsigned int num;
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, 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;

10
biology/htslib/files/patch-hts.c Normal file
View File

@ -0,0 +1,10 @@
--- hts.c.orig 2020-10-18 00:49:42 UTC
+++ hts.c
@@ -39,6 +39,7 @@ DEALINGS IN THE SOFTWARE. */
#include <time.h>
#include <sys/stat.h>
#include <assert.h>
+#include <unistd.h> // R_OK
#include "htslib/hts.h"
#include "htslib/bgzf.h"

10
biology/htslib/files/patch-sam.c Normal file
View File

@ -0,0 +1,10 @@
--- sam.c.orig 2020-10-18 00:50:46 UTC
+++ sam.c
@@ -35,6 +35,7 @@ DEALINGS IN THE SOFTWARE. */
#include <assert.h>
#include <signal.h>
#include <inttypes.h>
+#include <unistd.h> // usleep()
// Suppress deprecation message for cigar_tab, which we initialise
#include "htslib/hts_defs.h"

3
biology/htslib/pkg-plist
View File

@ -16,6 +16,7 @@ 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
@ -29,7 +30,7 @@ include/htslib/vcf_sweep.h
include/htslib/vcfutils.h
lib/libhts.a
lib/libhts.so
lib/libhts.so.%%PORTVERSION%%
lib/libhts.so.1.11
lib/libhts.so.3
libdata/pkgconfig/htslib.pc
man/man1/bgzip.1.gz