NEWS

-Noteworthy changes in release a.b
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Noteworthy changes in release 1.10.2 (19th December 2019)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This is a release fix that corrects minor inconsistencies discovered in
+previous deliverables.
+
 
 Noteworthy changes in release 1.10.1 (17th December 2019)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

bgzip.1

-.TH bgzip 1 "6 December 2019" "htslib-1.10" "Bioinformatics tools"
+.TH bgzip 1 "19 December 2019" "htslib-1.10.2" "Bioinformatics tools"
 .SH NAME
 .PP
 bgzip \- Block compression/decompression utility

configure

 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.68 for HTSlib 1.10.1.
+# Generated by GNU Autoconf 2.68 for HTSlib 1.10.2.
 #
 # Report bugs to <samtools-help@lists.sourceforge.net>.
 #
@@ -565,8 +565,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='HTSlib'
 PACKAGE_TARNAME='htslib'
-PACKAGE_VERSION='1.10.1'
-PACKAGE_STRING='HTSlib 1.10.1'
+PACKAGE_VERSION='1.10.2'
+PACKAGE_STRING='HTSlib 1.10.2'
 PACKAGE_BUGREPORT='samtools-help@lists.sourceforge.net'
 PACKAGE_URL='http://www.htslib.org/'
 
@@ -1245,7 +1245,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures HTSlib 1.10.1 to adapt to many kinds of systems.
+\`configure' configures HTSlib 1.10.2 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1306,7 +1306,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of HTSlib 1.10.1:";;
+     short | recursive ) echo "Configuration of HTSlib 1.10.2:";;
    esac
   cat <<\_ACEOF
 
@@ -1413,7 +1413,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-HTSlib configure 1.10.1
+HTSlib configure 1.10.2
 generated by GNU Autoconf 2.68
 
 Copyright (C) 2010 Free Software Foundation, Inc.
@@ -1742,7 +1742,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by HTSlib $as_me 1.10.1, which was
+It was created by HTSlib $as_me 1.10.2, which was
 generated by GNU Autoconf 2.68.  Invocation command line was
 
   $ $0 $@
@@ -5804,7 +5804,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by HTSlib $as_me 1.10.1, which was
+This file was extended by HTSlib $as_me 1.10.2, which was
 generated by GNU Autoconf 2.68.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -5867,7 +5867,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-HTSlib config.status 1.10.1
+HTSlib config.status 1.10.2
 configured by $0, generated by GNU Autoconf 2.68,
   with options \\"\$ac_cs_config\\"
 

debian/changelog

+htslib (1.10.2-1) unstable; urgency=medium
+
+  * New upstream version
+  * debian/source/options: ignore changes to aclocal.m4 config.h.in configure
+  * debian/control: remove libhts-private-dev (Closes: #947066)
+
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Fri, 20 Dec 2019 09:57:05 -0800
+
 htslib (1.10.1-2) unstable; urgency=medium
 
   * Fix binary-arch vs binary-indep builds

debian/control

@@ -60,30 +60,9 @@ Description: development files for the HTSlib
  This package contains development files for the HTSlib: headers, static
  library, manual pages, etc.
 
-Package: libhts-private-dev
-Architecture: all
-Section: libdevel
-Depends: libhts-dev (>= 1.5-5),
-         ${misc:Depends}
-Breaks: libhts-dev (<= 1.5-4)
-Description: private development files for the HTSlib (use with care)
- HTSlib is an implementation of a unified C library for accessing common file
- formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call
- Format), used for high-throughput sequencing data, and is the core library
- used by samtools and bcftools. HTSlib only depends on zlib. It is known to be
- compatible with gcc, g++ and clang.
- .
- HTSlib implements a generalized BAM (binary SAM) index, with file extension
- ‘csi’ (coordinate-sorted index). The HTSlib file reader first looks for the
- new index and then for the old if the new index is absent.
- .
- This package contains private header files for the HTSlib.  They are *not*
- intended for general use but libseqlib needs these files.
-
 Package: htslib-test
 Architecture: all
-Depends: libhts-private-dev,
-         ${misc:Depends},
+Depends: ${misc:Depends},
          ${perl:Depends}
 Description: Test data for HTSlib
  HTSlib is an implementation of a unified C library for accessing common file

debian/libhts-private-dev.install

-cram/*.h				usr/include/htslib/cram
-header.h				usr/include/htslib/cram

debian/patches/no_git_version

 Author: Michael R. Crusoe <michael.crusoe@gmail.com>
 Description: Don't check git tags for versioning
---- a/version.sh
-+++ b/version.sh
+--- htslib.orig/version.sh
++++ htslib/version.sh
 @@ -27,11 +27,11 @@
- VERSION=1.10.1
+ VERSION=1.10.2
  
  # If we have a git clone, then check against the current tag
 -if [ -e .git ]

debian/rules

@@ -78,13 +78,6 @@ override_dh_installdocs:
 override_dh_installchangelogs:
 	dh_installchangelogs NEWS
 
-override_dh_link-indep:
-	dh_link --indep
-	# for some very strange reason /usr/include/htslib/cram/cram.h is using the private interface header.h
-	# this is provided now in the libhts-private-dev package rather than htslib-test so we need a symlink here
-	find debian/htslib-test -name header.h
-	dh_link --indep -phtslib-test usr/include/htslib/cram/header.h	usr/share/htslib-test/header.h
-
 override_dh_fixperms:
 	dh_fixperms
 	find debian -name simple_test_driver.sh -exec chmod +x \{\} \;

debian/source/options

 single-debian-patch
-extend-diff-ignore = "^(\.travis\.yml|README.md)$"
+extend-diff-ignore = "^(\.travis\.yml|README.md|aclocal.m4|config.h.in|configure)$"

htsfile.1

-.TH htsfile 1 "6 December 2019" "htslib-1.10" "Bioinformatics tools"
+.TH htsfile 1 "19 December 2019" "htslib-1.10.2" "Bioinformatics tools"
 .SH NAME
 htsfile \- identify high-throughput sequencing data files
 .\"

htslib-s3-plugin.7

-.TH htslib-s3-plugin 7 "6 December 2019" "htslib-1.10" "Bioinformatics tools"
+.TH htslib-s3-plugin 7 "19 December 2019" "htslib-1.10.2" "Bioinformatics tools"
 .SH NAME
 s3 plugin \- htslib AWS S3 plugin
 .\"

htslib/hts.h

@@ -421,7 +421,7 @@ const char *hts_version(void);
 // Immediately after release, bump ZZ to 90 to distinguish in-development
 // Git repository builds from the release; you may wish to increment this
 // further when significant features are merged.
-#define HTS_VERSION 101001
+#define HTS_VERSION 101002
 
 /*!
   @abstract    Determine format by peeking at the start of a file

tabix.1

-.TH tabix 1 "6 December 2019" "htslib-1.10" "Bioinformatics tools"
+.TH tabix 1 "19 December 2019" "htslib-1.10.2" "Bioinformatics tools"
 .SH NAME
 .PP
 tabix \- Generic indexer for TAB-delimited genome position files

version.sh

@@ -24,7 +24,7 @@
 # DEALINGS IN THE SOFTWARE.
 
 # Master version, for use in tarballs or non-git source copies
-VERSION=1.10.1
+VERSION=1.10.2
 
 # If we have a git clone, then check against the current tag
 if [ -e .git ]