Make release 1.14.14

Author: jkbonfield

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)
 ---------------
 

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)
 ---------------
 

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)

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");