Release 1.15

Author: daviesrob

.appveyor.yml

@@ -27,7 +27,7 @@ install:
   - set MSYSTEM=MINGW64
   - set PATH=C:/msys64/usr/bin;C:/msys64/mingw64/bin;%PATH%
   - set MINGWPREFIX=x86_64-w64-mingw32
-  - "sh -lc \"pacman -S --noconfirm --needed base-devel mingw-w64-x86_64-toolchain mingw-w64-x86_64-zlib mingw-w64-x86_64-bzip2 mingw-w64-x86_64-xz mingw-w64-x86_64-curl\""
+  - "sh -lc \"pacman -S --noconfirm --needed base-devel mingw-w64-x86_64-toolchain mingw-w64-x86_64-autotools mingw-w64-x86_64-zlib mingw-w64-x86_64-bzip2 mingw-w64-x86_64-xz mingw-w64-x86_64-curl mingw-w64-x86_64-tools-git\""
 
 build_script:
   - set HOME=.

.cirrus.yml

@@ -117,11 +117,11 @@ ubuntu_task:
   << : *TEST
 
 
-# CentOS
-centos_task:
-  name: centos-gcc
+# Rocky Linux
+rocky_task:
+  name: rockylinux-gcc
   container:
-    image: centos:latest
+    image: rockylinux:latest
     cpu: 2
     memory: 1G
 
@@ -146,7 +146,7 @@ centos_task:
 macosx_task:
   name: macosx + clang
   osx_instance:
-    image: catalina-base
+    image: monterey-base
 
   environment:
     CC: clang

INSTALL

@@ -53,11 +53,9 @@ library is used.  Systems that do not have CCHmac will get this from
 libcrypto.  libcrypto is part of OpenSSL or one of its derivatives (LibreSSL
 or BoringSSL).
 
-On Microsoft Windows we recommend use of Mingw64/Msys2.  Note that
-currently for the test harness to work you will need to override the
-test temporary directory with e.g.: make check TEST_OPTS="-t C:/msys64/tmp/_"
-Whilst the code may work on Windows with other environments, these have
-not been verified.
+On Microsoft Windows we recommend use of Mingw64/Msys2.  Whilst the
+code may work on Windows with other environments, these have not been
+verified.  Use of the configure script is a requirement too.
 
 Update htscodecs submodule
 ==========================
@@ -259,13 +257,37 @@ RedHat / CentOS
 
 sudo yum install autoconf automake make gcc perl-Data-Dumper zlib-devel bzip2 bzip2-devel xz-devel curl-devel openssl-devel
 
+Note: On some versions perl FindBin will need to be installed to make the tests work.
+
+sudo yum install perl-FindBin
+
 Alpine Linux
 ------------
 
-sudo apk update  # Ensure the package list is up to date
-sudo apk add autoconf automake make gcc musl-dev perl bash zlib-dev bzip2-dev xz-dev curl-dev libressl-dev
+doas apk update  # Ensure the package list is up to date
+doas apk add autoconf automake make gcc musl-dev perl bash zlib-dev bzip2-dev xz-dev curl-dev libressl-dev
 
 OpenSUSE
 --------
 
 sudo zypper install autoconf automake make gcc perl zlib-devel libbz2-devel xz-devel libcurl-devel libopenssl-devel
+
+Windows MSYS2/MINGW64
+---------------------
+
+The configure script must be used as without it the compilation will
+likely fail.
+
+Follow MSYS2 installation instructions at
+https://www.msys2.org/wiki/MSYS2-installation/
+
+Then relaunch to MSYS2 shell using the "MSYS2 MinGW x64" executable.
+Once in that environment (check $MSYSTEM equals "MINGW64") install the
+compilers using pacman -S and the following package list:
+
+base-devel mingw-w64-x86_64-toolchain
+mingw-w64-x86_64-libdeflate mingw-w64-x86_64-zlib mingw-w64-x86_64-bzip2
+mingw-w64-x86_64-xz mingw-w64-x86_64-curl mingw-w64-x86_64-autotools
+mingw-w64-x86_64-tools-git
+
+(The last is only needed for building libraries compatible with MSVC.)

LICENSE

@@ -3,7 +3,7 @@ according to the terms of the following MIT/Expat license.]
 
 The MIT/Expat License
 
-Copyright (C) 2012-2021 Genome Research Ltd.
+Copyright (C) 2012-2022 Genome Research Ltd.
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
@@ -29,7 +29,7 @@ according to the terms of the following Modified 3-Clause BSD license.]
 
 The Modified-BSD License
 
-Copyright (C) 2012-2020 Genome Research Ltd.
+Copyright (C) 2012-2022 Genome Research Ltd.
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:

Makefile

@@ -1,6 +1,6 @@
 # Makefile for htslib, a C library for high-throughput sequencing data formats.
 #
-#    Copyright (C) 2013-2021 Genome Research Ltd.
+#    Copyright (C) 2013-2022 Genome Research Ltd.
 #
 #    Author: John Marshall <jm18@sanger.ac.uk>
 #
@@ -131,8 +131,8 @@ LIBHTS_SOVERSION = 3
 # is not strictly necessary and should be removed the next time
 # LIBHTS_SOVERSION is bumped (see #1144 and
 # https://developer.apple.com/library/archive/documentation/DeveloperTools/Conceptual/DynamicLibraries/100-Articles/DynamicLibraryDesignGuidelines.html#//apple_ref/doc/uid/TP40002013-SW23)
-MACH_O_COMPATIBILITY_VERSION = 3.1.14
-MACH_O_CURRENT_VERSION = 3.1.14
+MACH_O_COMPATIBILITY_VERSION = 3.1.15
+MACH_O_CURRENT_VERSION = 3.1.15
 
 # $(NUMERIC_VERSION) is for items that must have a numeric X.Y.Z string
 # even if this is a dirty or untagged Git working tree.
@@ -282,10 +282,10 @@ SHLIB_FLAVOUR = cygdll
 lib-shared: cyghts-$(LIBHTS_SOVERSION).dll
 else ifeq "$(findstring MSYS,$(PLATFORM))" "MSYS"
 SHLIB_FLAVOUR = dll
-lib-shared: hts-$(LIBHTS_SOVERSION).dll
+lib-shared: hts-$(LIBHTS_SOVERSION).dll hts-$(LIBHTS_SOVERSION).def hts-$(LIBHTS_SOVERSION).lib
 else ifeq "$(findstring MINGW,$(PLATFORM))" "MINGW"
 SHLIB_FLAVOUR = dll
-lib-shared: hts-$(LIBHTS_SOVERSION).dll
+lib-shared: hts-$(LIBHTS_SOVERSION).dll hts-$(LIBHTS_SOVERSION).def hts-$(LIBHTS_SOVERSION).lib
 else
 SHLIB_FLAVOUR = so
 lib-shared: libhts.so
@@ -330,6 +330,41 @@ cyghts-$(LIBHTS_SOVERSION).dll libhts.dll.a: $(LIBHTS_OBJS)
 hts-$(LIBHTS_SOVERSION).dll hts.dll.a: $(LIBHTS_OBJS)
 	$(CC) -shared -Wl,--out-implib=hts.dll.a -Wl,--enable-auto-import -Wl,--exclude-all-symbols $(LDFLAGS) -o $@ -Wl,--whole-archive $(LIBHTS_OBJS) -Wl,--no-whole-archive $(LIBS) -lpthread
 
+hts-$(LIBHTS_SOVERSION).def: hts-$(LIBHTS_SOVERSION).dll
+	gendef hts-$(LIBHTS_SOVERSION).dll
+
+hts-$(LIBHTS_SOVERSION).lib: hts-$(LIBHTS_SOVERSION).def
+	dlltool -m i386:x86-64 -d hts-$(LIBHTS_SOVERSION).def -l hts-$(LIBHTS_SOVERSION).lib
+
+# Bundling libraries, binaries, dll dependencies, and licenses into a
+# single directory.  NB: This is not needed for end-users, but a test bed
+# for maintainers building binary distributions.
+#
+# NOTE: only tested on the supported MSYS2/MINGW64 environment.
+dist-windows: DESTDIR=
+dist-windows: prefix=dist-windows
+dist-windows: install
+	cp hts-$(LIBHTS_SOVERSION).def hts-$(LIBHTS_SOVERSION).lib dist-windows/lib
+	cp `ldd hts-$(LIBHTS_SOVERSION).dll| awk '/mingw64/ {print $$3}'` dist-windows/bin
+	mkdir -p dist-windows/share/licenses/htslib
+	-cp -r /mingw64/share/licenses/mingw-w64-libraries \
+	      /mingw64/share/licenses/brotli \
+	      /mingw64/share/licenses/bzip2 \
+	      /mingw64/share/licenses/gcc-libs \
+	      /mingw64/share/licenses/libdeflate \
+	      /mingw64/share/licenses/libpsl \
+	      /mingw64/share/licenses/libtre \
+	      /mingw64/share/licenses/libwinpthread \
+	      /mingw64/share/licenses/openssl \
+	      /mingw64/share/licenses/xz \
+	      /mingw64/share/licenses/zlib \
+	      /mingw64/share/licenses/zstd \
+	      dist-windows/share/licenses/
+	-cp -r /usr/share/licenses/curl \
+	      dist-windows/share/licenses/
+	cp LICENSE dist-windows/share/licenses/htslib/
+
+
 # Target to allow htslib.mk to build all the object files before it
 # links the shared and static libraries.
 hts-object-files: $(LIBHTS_OBJS)

NEWS

@@ -1,3 +1,86 @@
+Noteworthy changes in release 1.15 (21st February 2022)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Features and Updates
+--------------------
+
+* Bgzip now has a --keep option to not remove the input file after
+  compressing. (PR#1331)
+
+* Improved file format detection so some BED files are no longer
+  detected as FASTQ or FASTA. (PR#1350, thanks to John Marshall)
+
+* Added xz (lzma), zstd and D4 formats to the file type detection
+  functions.  We don't actively support reading these data types, but
+  function calls and htsfile can detect them. (PR#1340, thanks to
+  John Marshall)
+
+* CRAM now also uses libdeflate for read-names if the libdeflate
+  version is new enough (1.9 onwards).  Previously we used zlib for
+  this due to poor performance of libdeflate.  This gives a slight
+  speed up and reduction in file size. (PR#1383)
+
+* The VCF and BCF readers will now issue a warning if contig, INFO
+  or FORMAT IDs do not match the formats described in the VCFv4.3
+  specification. Note that while the invalid names will mostly still
+  be accepted, future updates will convert the warnings to errors
+  causing files including invalid names to be rejected.  (PR#1389)
+
+Build changes
+-------------
+
+These are compiler, configuration and makefile based changes.
+
+* HTSlib now uses libhtscodecs release 1.2.1.
+
+* Improved support for compiling and linking against HTSlib with
+  Microsoft Visual Studio. (PR#1380, #1377, #1375.  Thanks to
+  Aidan Bickford and John Marshall)
+
+* Various internal CI improvements.
+
+Bug fixes
+---------
+
+* Fixed CRAM index queries for HTSJDK output (PR#1388, reported by
+  Chris Norman).  Note this also fixes writing CRAM writing, to match
+  the specification (and HTSJDK), from version 3.1 onwards.
+
+* Fixed CRAM index queries when required-fields settings are selected
+  to ignore CIGARs (PR#1372, reported by Giulio Genovese).
+
+* Unmapped but placed (having chr/pos) are now included in the BAM
+  indices. (PR#1352, thanks to John Marshall)
+
+* CRAM now honours the filename##idx##index nomenclature for
+  specifying non-standard index locations. (PR#1360, reported by
+  Michael Cariaso)
+
+* Minor CRAM v1.0 read-group fix (PR#1349, thanks to John Marshall)
+
+* Permit .fa and .fq file type detection as synonyms for FASTA and
+  FASTQ. (PR#1386).
+
+* Empty VCF format fields are now output ":.:" as instead of "::".
+  (PR#1370)
+
+* Repeated bcf_sr_seek calls now work. (PR#1363, reported by
+  Giulio Genovese)
+
+* Bcf_remove_allele_set now works on unpacked BCF records. (PR#1358,
+  reported by Brent Pedersen).
+
+* The hts_parse_decimal() function used to read numbers in region lists
+  is now better at rejecting non-numeric values.  In particular it
+  now rejects a lone 'G' instead of interpreting it as '0G', i.e. zero.
+  (PR#1396, PR#1400, reported by SSSimon Yang; thanks to John Marshall).
+
+* Improve support for GPU issues listed by -Wdouble-promotion.
+  (PR#1365, reported by David Seisert)
+
+* Fix example code in header file documentation. (PR#1381, Thanks to
+  Aidan Bickford)
+
 Noteworthy changes in release 1.14 (22nd October 2021)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 

bgzip.1

@@ -1,4 +1,4 @@
-.TH bgzip 1 "22 October 2021" "htslib-1.14" "Bioinformatics tools"
+.TH bgzip 1 "21 February 2022" "htslib-1.15" "Bioinformatics tools"
 .SH NAME
 .PP
 bgzip \- Block compression/decompression utility

bgzip.c

@@ -173,7 +173,7 @@ int main(int argc, char **argv)
         case 1:
             printf(
 "bgzip (htslib) %s\n"
-"Copyright (C) 2021 Genome Research Ltd.\n", hts_version());
+"Copyright (C) 2022 Genome Research Ltd.\n", hts_version());
             return EXIT_SUCCESS;
         case 'h': return bgzip_main_usage(stdout, EXIT_SUCCESS);
         case '?': return bgzip_main_usage(stderr, EXIT_FAILURE);

cram/cram_decode.c

@@ -1,5 +1,5 @@
 /*
-Copyright (c) 2012-2020 Genome Research Ltd.
+Copyright (c) 2012-2020, 2022 Genome Research Ltd.
 Author: James Bonfield <jkb@sanger.ac.uk>
 
 Redistribution and use in source and binary forms, with or without
@@ -1777,7 +1777,7 @@ static int cram_decode_seq(cram_fd *fd, cram_container *c, cram_slice *s,
     }
 
     cr->ncigar = ncigar - cr->cigar;
-    cr->aend = ref_pos;
+    cr->aend = ref_pos > cr->apos ? ref_pos : cr->apos;
 
     //printf("2: %.*s %d .. %d\n", cr->name_len, DSTRING_STR(name_ds) + cr->name, cr->apos, ref_pos);
 
@@ -3228,15 +3228,17 @@ static cram_slice *cram_next_slice(cram_fd *fd, cram_container **cp) {
                     }
 
                     // position beyond end of range; bail out
-                    if (c_next->ref_seq_start > fd->range.end) {
+                    if (fd->range.refid != -1 &&
+                        c_next->ref_seq_start > fd->range.end) {
                         cram_free_container(c_next);
                         fd->ctr_mt = NULL;
                         fd->ooc = 1;
                         break;
                     }
 
                     // before start of range; skip to next container
-                    if (c_next->ref_seq_start + c_next->ref_seq_span-1 <
+                    if (fd->range.refid != -1 &&
+                        c_next->ref_seq_start + c_next->ref_seq_span-1 <
                         fd->range.start) {
                         c_next->curr_slice_mt = c_next->max_slice;
                         cram_seek(fd, c_next->length, SEEK_CUR);
@@ -3301,15 +3303,17 @@ static cram_slice *cram_next_slice(cram_fd *fd, cram_container **cp) {
                 }
 
                 // position beyond end of range; bail out
-                if (s_next->hdr->ref_seq_start > fd->range.end) {
+                if (fd->range.refid != -1 &&
+                    s_next->hdr->ref_seq_start > fd->range.end) {
                     fd->ooc = 1;
                     cram_free_slice(s_next);
                     c_next->slice = s_next = NULL;
                     break;
                 }
 
                 // before start of range; skip to next slice
-                if (s_next->hdr->ref_seq_start + s_next->hdr->ref_seq_span-1 <
+                if (fd->range.refid != -1 &&
+                    s_next->hdr->ref_seq_start + s_next->hdr->ref_seq_span-1 <
                     fd->range.start) {
                     cram_free_slice(s_next);
                     c_next->slice = s_next = NULL;