diff --git a/CHANGES b/CHANGES index ad26256..4fcd648 100644 --- a/CHANGES +++ b/CHANGES @@ -1,3 +1,46 @@ +Version 1.14.14 (17th March 2021) +--------------- + +This is primarily a bug fix release. + +Updates: + +* Bumped htscodecs submodule to 1.0. This is mainly security + hardening. This now means for the first time Io_lib and HTSlib + share the same code for the CRAM codecs. + +* Cram_filter now copies with CRAM 3.1 and 4.0 files. + +* Added Power support(ppc64le) to CI. (Author: Arumugam) + +* Added int64_t as a HashTable key type. + +* Improved configure script handling of lzma and bzip2, which are now + on by default. + +* Improved support for hurd_i386 by defining PATH_MAX (with thanks to + Michael Crusoe). + +Bug fixes: + +* The CRAM_IO_CUSTOM_BUFFERING code is now enabled correctly. This is + required for biobambam2 / libmaus2 integration. (Thanks to German + Tischler-Hohle) + +* Fixed a recent bug in the cram_open_by_callbacks function used by + Biobambam. (#39. Thanks to German Tischler-Hohle) + +* Fixed cram_codec_decoder2encoder handling of CRAM 4 encodings. + +* Fixed an uninitialised memory access added during 1.14.13 (harmless + as it was then immediately replaced again, but it triggered valgrind + warnings). + +* Fixed configure --disable-custom-buffering + +* Typo fixes, courtesy of Debian lintian. + + Version 1.14.13 (3rd July 2020) --------------- diff --git a/README.md b/README.md index eceaf27..e165711 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -Io_lib: Version 1.14.13 +Io_lib: Version 1.14.14 ======================== Io_lib is a library of file reading and writing code to provide a general @@ -33,6 +33,12 @@ See the CHANGES for a summary of older updates or git logs for the full details. +Version 1.14.14 (17th March 2021) +--------------- + +This is simply a bug fix release. It also updates to the latest +htscodecs submodule, now at an official 1.0 release. + Version 1.14.13 (3rd July 2020) --------------- diff --git a/configure.ac b/configure.ac index 48910f4..c55d9dd 100644 --- a/configure.ac +++ b/configure.ac @@ -1,5 +1,5 @@ dnl Process this file with autoconf to produce a configure script. -AC_INIT(io_lib, 1.14.13) +AC_INIT(io_lib, 1.14.14) IOLIB_VERSION=$PACKAGE_VERSION IOLIB_VERSION_MAJOR=`expr "$PACKAGE_VERSION" : '\([[0-9]]*\)'` IOLIB_VERSION_MINOR=`expr "$PACKAGE_VERSION" : '[[0-9]]*\.\([[0-9]]*\)'` @@ -69,7 +69,7 @@ AX_SUBDIRS_CONFIGURE([htscodecs],[[--disable-shared],[--with-pic]]) # libstaden-read.so.1.1.0 VERS_CURRENT=15 -VERS_REVISION=0 +VERS_REVISION=1 VERS_AGE=1 AC_SUBST(VERS_CURRENT) AC_SUBST(VERS_REVISION) diff --git a/progs/scramble.c b/progs/scramble.c index 94967c9..70b2bb9 100644 --- a/progs/scramble.c +++ b/progs/scramble.c @@ -184,7 +184,7 @@ static int filter_tags(bam_seq_t *s, char *aux_filter, int keep) { static void usage(FILE *fp) { fprintf(fp, " -=- sCRAMble -=- version %s\n", IOLIB_VERSION); - fprintf(fp, "Author: James Bonfield, Wellcome Trust Sanger Institute. 2013-2020\n\n"); + fprintf(fp, "Author: James Bonfield, Wellcome Trust Sanger Institute. 2013-2021\n\n"); fprintf(fp, "Usage: scramble [options] [input_file [output_file]]\n");