.gitignore

+# Everything generated from ./bootstrap (autoconf)
+Makefile.in
+aclocal.m4
+autom4te.cache
+compile
+config.guess
+config.sub
+configure
+depcomp
+install-sh
+io_lib/Makefile.in
+io_lib_config.h.in
+ltmain.sh
+missing
+progs/Makefile.in
+test-driver
+tests/Makefile.in
+
+# Skip local build sub-directories per OS.
+build.*

.travis.yml

+language: c
+compiler: gcc
+
+script: ./bootstrap; ./configure && make && (make check || (cat tests/test-suite.log; false))

CHANGES

+Version 1.14.11 (16th October 2018)
+---------------
+
+Updates:
+
+* CRAM: http(s) queries now honour redirects.
+  The User-Agent header is also set, which is necessary in some
+  proxies.
+
+Bug fixes:
+
+* CRAM: fix to major range query bug introduced in 1.14.10.
+
+* CRAM: more bug fixing on range queries when multi-threading (EOF
+  detection).
+
+* The test harness now works correctly in bourne shell, without
+  using bashisms.
+
+
+
+Version 1.14.10 (26th September 2018)
+---------------
+
+Updates:
+
+* BAM: Libdeflate support (https://github.com/ebiggers/libdeflate).
+  This library is significantly faster than zlib, so it is a good
+  alternative to the Cloudflare and/or Intel libraries.
+
+  Configure using --with-libdeflate=/dir/to/deflate/install
+
+* CRAM *EXPERIMENTAL*: Added custom quality and identifier codecs.
+  Also added the ability to use libbsc as a general purpose codec.
+
+  These are NOT OFFICIAL and so not enabled by default (version 3.0).
+  However as a technology demonstration only, they are available with
+  scramble -V3.1 or -V4.0 for evaluation and to promote discussion on
+  future CRAM formats.  Do not use these on production data.
+
+  Implementations of the codecs and CRAM version 4.0 layout are liable
+  to change without prior warning.
+
+* CRAM: name sorted files now automatically switch to non-ref mode.
+
+Bug fixes:
+
+* CRAM: Considerable fixes to multi-threading.
+  - Using more than 1 slice per container with threading now works.
+  - Removal of race conditions when using CRAM_OPT_REQUIRED_FIELDS.
+  - Combinations of ref and no-ref mode in adjacent containers.
+  - Other misc. threading bugs.
+
+* Corrected end-of-range check in some scenarios.
+
+* CRAM: bug fix to index creation when a slice contains exactly one
+  alignment.
+
+* SAM: fixed parsing of illegal sequence characters (eg "Z").
+  These are now treated as "N" and not "=".
+
+* BAM/SAM: protect against out of bound CIGAR operations.
+
+* CRAM: hardening of rANS codec against malicious input.
+  Also fixed a very rare frequency renormalisation case.
+
+* CRAM: fix with range queries used in conjuction with turning off
+  sequence retrieval (via CRAM_OPT_REQUIRED_FIELDS).
+
+* Improved test harness for Windows and some header file problems.
+
+* Fixed bgzip on big endian systems. (Debian bugs 876839, 876840)
+
+
+
 Version 1.14.9 (9th February 2017)
 --------------
 

MSVC_includes/sys/time.h

+//Technically this is provided by Winsock2.h
+//https://msdn.microsoft.com/en-us/library/windows/desktop/ms740560%28v=vs.85%29.aspx?f=255&MSPPError=-2147217396
+typedef struct timeval {
+  long tv_sec;
+  long tv_usec;
+} timeval;

Makefile.am

@@ -30,6 +30,7 @@
 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 # 
 AUTOMAKE_OPTIONS = foreign no-dependencies
+ACLOCAL_AMFLAGS = -I m4
 
 SUBDIRS = io_lib progs tests
 

README.md

-Io_lib:  Version 1.14.9
-=======================
+Io_lib:  Version 1.14.11
+========================
 
 Io_lib is a library of file reading and writing code to provide a general
 purpose SAM/BAM/CRAM, trace file (and Experiment File) reading
@@ -32,69 +32,136 @@ too. See the file include/Read.h for the generic 'Read' structure.
 See the CHANGES for a summary of older updates or git logs for the
 full details.
 
-Version 1.14.9 (9th February 2017)
---------------
+
+Version 1.14.11 (16th October 2018)
+---------------
 
 Updates:
 
-* BAM: Added CRC checking.  Bizarrely this was absent here and in most
-  other BAM implementations too.  Pure BAM decode of an uncompressed
-  BAM is around 9% slower and compressed BAM to compressed BAM is
-  almost identical.  The most significant hit is reading uncompressed
-  BAM (and doing nothing else) which is 120% slower as CRC dominates.
-  Options are available to disable the CRC checking incase this is an
-  issue (scramble -!).
+* CRAM: http(s) queries now honour redirects.
+  The User-Agent header is also set, which is necessary in some
+  proxies.
+
+Bug fixes:
+
+* CRAM: fix to major range query bug introduced in 1.14.10.
+
+* CRAM: more bug fixing on range queries when multi-threading (EOF
+  detection).
 
-* CRAM: Now supports bgziped fasta references.
+* The test harness now works correctly in bourne shell, without
+  using bashisms.
 
-* CRAM/SAM: Headers are now kept in the same basic type order while
-  transcoding. (Eg all @PG before all @SQ, or vice versa, depending on
-  input ordering.)
 
-* CRAM: Compression level 1 is now faster but larger. (The old -1 and
-  -2 were too similar.)
+Version 1.14.10 (26th September 2018)
+---------------
 
-* CRAM: Improved compression efficiency in some files, when switching
-  from sorted to unsorted data.
+Updates:
 
-* CRAM: Various speedups relating to memory handling,
-  multi-threaded performance and the rANS codec.
+* BAM: Libdeflate support (https://github.com/ebiggers/libdeflate).
+  This library is significantly faster than zlib, so it is a good
+  alternative to the Cloudflare and/or Intel libraries.
 
-* CRAM: Block CRC checks are now only done when the block is used,
-  speeding up multi-threading and tools that do not decode all blocks
-  (eg flagstat).
+  See below for details.
 
-* Scramble -g and -G options to generate and reuse bgzip indices when
-  reading and writing BAM files.
+* CRAM *EXPERIMENTAL*: Added custom quality and identifier codecs.
+  Also added the ability to use libbsc as a general purpose codec.
 
-* Scramble -q option to omit updating the @PG header records.
+  These are NOT OFFICIAL and so not enabled by default (version 3.0).
+  However as a technology demonstration only, they are available with
+  scramble -V3.1 or -V4.0 for evaluation and to promote discussion on
+  future CRAM formats.  Do not use these on production data.
 
-* Experimental cram_filter tool has been added, to rapidly produce
-  cram subsets.
+  Implementations of the codecs and CRAM version 4.0 layout are liable
+  to change without prior warning.
 
-* Migrated code base to git.  Use github for primary repository.
+* CRAM: name sorted files now automatically switch to non-ref mode.
 
 Bug fixes:
 
-* BAM: Fixed the bin value calculation for placed but unmapped reads.
+* CRAM: Considerable fixes to multi-threading.
+  - Using more than 1 slice per container with threading now works.
+  - Removal of race conditions when using CRAM_OPT_REQUIRED_FIELDS.
+  - Combinations of ref and no-ref mode in adjacent containers.
+  - Other misc. threading bugs.
+
+* Corrected end-of-range check in some scenarios.
+
+* CRAM: bug fix to index creation when a slice contains exactly one
+  alignment.
+
+* SAM: fixed parsing of illegal sequence characters (eg "Z").
+  These are now treated as "N" and not "=".
+
+* BAM/SAM: protect against out of bound CIGAR operations.
 
-* CRAM: Fixed file descriptor leak in refs_load_fai().
+* CRAM: hardening of rANS codec against malicious input.
+  Also fixed a very rare frequency renormalisation case.
 
-* CRAM: Fixed a crash in MD5 calculation for sequences beyond the
-  reference end.
+* CRAM: fix with range queries used in conjuction with turning off
+  sequence retrieval (via CRAM_OPT_REQUIRED_FIELDS).
 
-* CRAM: Bug fixes when encoding malformed @SQ records.
+* Improved test harness for Windows and some header file problems.
 
-* CRAM: Fixed a rare renormalisation bug in rANS codec.
+* Fixed bgzip on big endian systems. (Debian bugs 876839, 876840)
 
-* Fixed tests so make -j worked.
 
-* Removed ancient, broken and unused popen() code.
+Technology Demo: CRAM 3.1 and 4.0
+=================================
+
+The current official GA4GH CRAM version is 3.0.
+
+For purposes of *EVALUATION ONLY* this release of io_lib includes CRAM
+version 3.1, with new compression codecs (but is otherwise identical
+file layout to 3.0), and 4.0 with a few additional format
+modifications, such as 64-bit sizes.
+
+They can be turned on using e.g. scramble -V3.1 or scramble -V4.0.
+
+By default enabling either of these will also enable the new codecs,
+bar libbsc (see below for how to compile with this).  These new codecs
+are slower, but will not be used at lighter levels of compression.  So
+for example "scramble -V4.0 -4 in.bam out.cram" will only use the same
+codecs available in CRAM 3.0 bar the fast new rANS variants (rANS++).
+
+Here are some example file sizes and timings with different codecs and
+levels on 10 million NovaSeq reads, with 4 threads (-t4).  Decode
+timing is checked using "scram_flagstat -b -t4".  Tests were performed
+on an Intel i5-4570 processor at 3.2GHz.
+
+|Scramble opts.|  Size   |Enc(s)|Dec(s)|Codecs used           |
+|--------------|---------|-----:|----:|----------------------|
+|-V3.0         |224743050|  12.9|   3.8|(default)             |
+|-V3.0 -7jZ    |211734953| 105.9|   5.4|bzip2, lzma           |
+||||||
+|-V3.1 -4      |226888980|  13.2|   3.8|rANS++                |
+|-V3.1         |187238214|  35.8|  12.8|tok3,fqz,rANS++       |
+|-V3.1 -7J     |180217109|  49.2|  25.6|tok3,fqz,rANS++,libbsc|
+||||||
+|-V4.0 -4      |211515487|  15.6|   3.8|rANS++                |
+|-V4.0         |182657527|  34.9|  13.5|tok3,fqz,rANS++       |
+|-V4.0 -7J     |178819704|  46.5|  19.6|tok3,fqz,rANS++,libbsc|
+
 
 
 Building
 ========
 
+Prerequisites
+-------------
+
+You will need a C compiler, a Unix "make" program plus zlib, bzip2 and
+lzma libraries and associated development packages (including C header
+files).  The appropriate operating system package names and comands
+differ per system.  On Debian Linux derived systems use the command
+below (or build and install your own copies from source):
+
+  sudo apt-get install make zlib1g-dev libbz2-dev liblzma-dev
+
+On RedHat derived systems the package names differ:
+
+  sudo yum install make zlib-devel bzip2-devel xz-devel
+
 
 Zlib
 ----
@@ -127,6 +194,32 @@ Building io_lib with the internal CRC code disabled is done
 with ./configure --disable-own-crc (or CFLAGS=-UIOLIB_CRC).
 
 
+Libdeflate
+----------
+
+The BAM reading and writing also has optional support for the
+libdeflate library (https://github.com/ebiggers/libdeflate).  This can
+be used instead of an optimised zlib (see above), and generally is
+slightly faster.  Build using:
+
+    ./configure --with-libdeflate=/path
+
+
+Git clone
+---------
+
+We recommend building from a release tarball, which has the configure
+script already created for you.  However if you wish to build from the
+latest code and have done a "git clone" then you will need to create
+the configure script yourself using autotools:
+
+  autoreconf -i
+
+This program may not be on your system.  If it fails, then install
+autoconf, automake and libtool packages; see above for example
+OS-specific installation commands.
+
+
 Linux
 -----
 
@@ -163,22 +256,32 @@ Under Microsoft Windows we recommend the use of MSYS and MINGW as a
 build environment.
 
 These contain enough tools to build using the configure script as per
-Linux. Visit http://sourceforge.net/projects/mingw/files/ and
-download/install Automated MinGW Installer (eg MinGW-5.1.4.exe), MSYS
-Base System (eg MSYS-1.0.11.exe) and MSYS Supplementary Tools (eg
-msysDTK-1.0.1.exe).
+Linux. The latest msys can be downloaded here:
+
+   http://repo.msys2.org/distrib/msys2-x86_64-latest.exe
+
+Once installed and setup ("pacman -Syu"; close window & relaunch msys;
+"pacman -Syu" again), install mingw64 compilers via "pacman -S
+--needed man base-devel git mingw-w64-x86_64-toolchain".
+
+This should then be sufficient to configure and compile.  However note
+that you may need to use "./configure --disable-shared" for the test
+harness to work due to deficiences in the libtool wrapper script.
 
 If you wish to use Microsoft Visual Studio you may need to add the
 MSVC_includes subdirectory to your C include search path.  This
 adds several missing header files (eg unistd.h and sys/time.h) needed
-to build this software.  We do not have a MSVC project file available.
+to build this software.  We do not have a MSVC project file available
+and have not tested the build under this environment for a number of
+years.
 
 In this case you will also need to copy io_lib/os.h.in to io_lib/os.h
 and either remove the @SET_ENDIAN@ and adjacent @ lines (as these are
 normally filled out for you by autoconf) or add -DNO_AUTOCONF to your
 compiler options.
 
-The code should also build cleanly under a cross-compiler.  We use
+The code should also build cleanly under a cross-compiler.  This has
+not been tested recently, but a past successful invocation was:
 
     ./configure \
             --host=x86_64-w64-mingw32 \
@@ -194,6 +297,24 @@ with $DIST being pre-populated with already built and installed 3rd
 party dependencies, some from MSYS mentioned above.
 
 
+Libbsc
+------
+
+This is experimental, just to see what we can get with a high quality
+compression engine in CRAM.  It's hard to build right now, especially
+given it's a C++ library and our code is C.  The hacky solution now
+is (linux) e.g.:
+
+  ../configure \
+    CPPFLAGS=-I$HOME/ftp/compression/libbsc \
+    LDFLAGS="-L$HOME/ftp/compression/libbsc -fopenmp" \
+    LIBS=-lstdc++
+
+Enable it using scramble -J, but note this requires experimental CRAM
+versions 3.1 or 4.0.
+
+** Neither of these should be used for production data. **
+
 
 MacOS X
 -------

bootstrap

@@ -5,7 +5,7 @@
 set -x
 rm -rf install-sh missing mkinstalldirs depcomp aclocal.m4 config.cache config.log config.status configure autom4te.cache io_lib_config.h.in config.sub config.guess Makefile.in progs/Makefile.in progs/Makefile read/Makefile.in read/Makefile tests/Makefile tests/Makefile.in io_lib-config
 libtoolize --force --copy && \
-aclocal -I . && \
+aclocal -I . -I m4 && \
 autoheader && \
 automake --foreign --add-missing --copy && \
 autoconf

compile

-#! /bin/sh
-# Wrapper for compilers which do not understand '-c -o'.
-
-scriptversion=2012-10-14.11; # UTC
-
-# Copyright (C) 1999-2013 Free Software Foundation, Inc.
-# Written by Tom Tromey <tromey@cygnus.com>.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 2, or (at your option)
-# any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-# As a special exception to the GNU General Public License, if you
-# distribute this file as part of a program that contains a
-# configuration script generated by Autoconf, you may include it under
-# the same distribution terms that you use for the rest of that program.
-
-# This file is maintained in Automake, please report
-# bugs to <bug-automake@gnu.org> or send patches to
-# <automake-patches@gnu.org>.
-
-nl='
-'
-
-# We need space, tab and new line, in precisely that order.  Quoting is
-# there to prevent tools from complaining about whitespace usage.
-IFS=" ""	$nl"
-
-file_conv=
-
-# func_file_conv build_file lazy
-# Convert a $build file to $host form and store it in $file
-# Currently only supports Windows hosts. If the determined conversion
-# type is listed in (the comma separated) LAZY, no conversion will
-# take place.
-func_file_conv ()
-{
-  file=$1
-  case $file in
-    / | /[!/]*) # absolute file, and not a UNC file
-      if test -z "$file_conv"; then
-	# lazily determine how to convert abs files
-	case `uname -s` in
-	  MINGW*)
-	    file_conv=mingw
-	    ;;
-	  CYGWIN*)
-	    file_conv=cygwin
-	    ;;
-	  *)
-	    file_conv=wine
-	    ;;
-	esac
-      fi
-      case $file_conv/,$2, in
-	*,$file_conv,*)
-	  ;;
-	mingw/*)
-	  file=`cmd //C echo "$file " | sed -e 's/"\(.*\) " *$/\1/'`
-	  ;;
-	cygwin/*)
-	  file=`cygpath -m "$file" || echo "$file"`
-	  ;;
-	wine/*)
-	  file=`winepath -w "$file" || echo "$file"`
-	  ;;
-      esac
-      ;;
-  esac
-}
-
-# func_cl_dashL linkdir
-# Make cl look for libraries in LINKDIR
-func_cl_dashL ()
-{
-  func_file_conv "$1"
-  if test -z "$lib_path"; then
-    lib_path=$file
-  else
-    lib_path="$lib_path;$file"
-  fi
-  linker_opts="$linker_opts -LIBPATH:$file"
-}
-
-# func_cl_dashl library
-# Do a library search-path lookup for cl
-func_cl_dashl ()
-{
-  lib=$1
-  found=no
-  save_IFS=$IFS
-  IFS=';'
-  for dir in $lib_path $LIB
-  do
-    IFS=$save_IFS
-    if $shared && test -f "$dir/$lib.dll.lib"; then
-      found=yes
-      lib=$dir/$lib.dll.lib
-      break
-    fi
-    if test -f "$dir/$lib.lib"; then
-      found=yes
-      lib=$dir/$lib.lib
-      break
-    fi
-    if test -f "$dir/lib$lib.a"; then
-      found=yes
-      lib=$dir/lib$lib.a
-      break
-    fi
-  done
-  IFS=$save_IFS
-
-  if test "$found" != yes; then
-    lib=$lib.lib
-  fi
-}
-
-# func_cl_wrapper cl arg...
-# Adjust compile command to suit cl
-func_cl_wrapper ()
-{
-  # Assume a capable shell
-  lib_path=
-  shared=:
-  linker_opts=
-  for arg
-  do
-    if test -n "$eat"; then
-      eat=
-    else
-      case $1 in
-	-o)
-	  # configure might choose to run compile as 'compile cc -o foo foo.c'.
-	  eat=1
-	  case $2 in
-	    *.o | *.[oO][bB][jJ])
-	      func_file_conv "$2"
-	      set x "$@" -Fo"$file"
-	      shift
-	      ;;
-	    *)
-	      func_file_conv "$2"
-	      set x "$@" -Fe"$file"
-	      shift
-	      ;;
-	  esac
-	  ;;
-	-I)
-	  eat=1
-	  func_file_conv "$2" mingw
-	  set x "$@" -I"$file"
-	  shift
-	  ;;
-	-I*)
-	  func_file_conv "${1#-I}" mingw
-	  set x "$@" -I"$file"
-	  shift
-	  ;;
-	-l)
-	  eat=1
-	  func_cl_dashl "$2"
-	  set x "$@" "$lib"
-	  shift
-	  ;;
-	-l*)
-	  func_cl_dashl "${1#-l}"
-	  set x "$@" "$lib"
-	  shift
-	  ;;
-	-L)
-	  eat=1
-	  func_cl_dashL "$2"
-	  ;;
-	-L*)
-	  func_cl_dashL "${1#-L}"
-	  ;;
-	-static)
-	  shared=false
-	  ;;
-	-Wl,*)
-	  arg=${1#-Wl,}
-	  save_ifs="$IFS"; IFS=','
-	  for flag in $arg; do
-	    IFS="$save_ifs"
-	    linker_opts="$linker_opts $flag"
-	  done
-	  IFS="$save_ifs"
-	  ;;
-	-Xlinker)
-	  eat=1
-	  linker_opts="$linker_opts $2"
-	  ;;
-	-*)
-	  set x "$@" "$1"
-	  shift
-	  ;;
-	*.cc | *.CC | *.cxx | *.CXX | *.[cC]++)
-	  func_file_conv "$1"
-	  set x "$@" -Tp"$file"
-	  shift
-	  ;;
-	*.c | *.cpp | *.CPP | *.lib | *.LIB | *.Lib | *.OBJ | *.obj | *.[oO])
-	  func_file_conv "$1" mingw
-	  set x "$@" "$file"
-	  shift
-	  ;;
-	*)
-	  set x "$@" "$1"
-	  shift
-	  ;;
-      esac
-    fi
-    shift
-  done
-  if test -n "$linker_opts"; then
-    linker_opts="-link$linker_opts"
-  fi
-  exec "$@" $linker_opts
-  exit 1
-}
-
-eat=
-
-case $1 in
-  '')
-     echo "$0: No command.  Try '$0 --help' for more information." 1>&2
-     exit 1;
-     ;;
-  -h | --h*)
-    cat <<\EOF
-Usage: compile [--help] [--version] PROGRAM [ARGS]
-
-Wrapper for compilers which do not understand '-c -o'.
-Remove '-o dest.o' from ARGS, run PROGRAM with the remaining
-arguments, and rename the output as expected.
-
-If you are trying to build a whole package this is not the
-right script to run: please start by reading the file 'INSTALL'.
-
-Report bugs to <bug-automake@gnu.org>.
-EOF
-    exit $?
-    ;;
-  -v | --v*)
-    echo "compile $scriptversion"
-    exit $?
-    ;;
-  cl | *[/\\]cl | cl.exe | *[/\\]cl.exe )
-    func_cl_wrapper "$@"      # Doesn't return...
-    ;;
-esac
-
-ofile=
-cfile=
-
-for arg
-do
-  if test -n "$eat"; then
-    eat=
-  else
-    case $1 in
-      -o)
-	# configure might choose to run compile as 'compile cc -o foo foo.c'.
-	# So we strip '-o arg' only if arg is an object.
-	eat=1
-	case $2 in
-	  *.o | *.obj)
-	    ofile=$2
-	    ;;
-	  *)
-	    set x "$@" -o "$2"
-	    shift
-	    ;;
-	esac
-	;;
-      *.c)
-	cfile=$1
-	set x "$@" "$1"
-	shift
-	;;
-      *)
-	set x "$@" "$1"
-	shift
-	;;
-    esac
-  fi
-  shift
-done
-
-if test -z "$ofile" || test -z "$cfile"; then
-  # If no '-o' option was seen then we might have been invoked from a
-  # pattern rule where we don't need one.  That is ok -- this is a
-  # normal compilation that the losing compiler can handle.  If no
-  # '.c' file was seen then we are probably linking.  That is also
-  # ok.
-  exec "$@"
-fi
-
-# Name of file we expect compiler to create.
-cofile=`echo "$cfile" | sed 's|^.*[\\/]||; s|^[a-zA-Z]:||; s/\.c$/.o/'`
-
-# Create the lock directory.
-# Note: use '[/\\:.-]' here to ensure that we don't use the same name
-# that we are using for the .o file.  Also, base the name on the expected
-# object file name, since that is what matters with a parallel build.
-lockdir=`echo "$cofile" | sed -e 's|[/\\:.-]|_|g'`.d
-while true; do
-  if mkdir "$lockdir" >/dev/null 2>&1; then
-    break
-  fi
-  sleep 1
-done
-# FIXME: race condition here if user kills between mkdir and trap.
-trap "rmdir '$lockdir'; exit 1" 1 2 15
-
-# Run the compile.
-"$@"
-ret=$?
-
-if test -f "$cofile"; then
-  test "$cofile" = "$ofile" || mv "$cofile" "$ofile"
-elif test -f "${cofile}bj"; then
-  test "${cofile}bj" = "$ofile" || mv "${cofile}bj" "$ofile"
-fi
-
-rmdir "$lockdir"
-exit $ret
-
-# Local Variables:
-# mode: shell-script
-# sh-indentation: 2
-# eval: (add-hook 'write-file-hooks 'time-stamp)
-# time-stamp-start: "scriptversion="
-# time-stamp-format: "%:y-%02m-%02d.%02H"
-# time-stamp-time-zone: "UTC"
-# time-stamp-end: "; # UTC"
-# End:

configure.in

 dnl Process this file with autoconf to produce a configure script.
-AC_INIT(io_lib, 1.14.9)
-AC_CONFIG_HEADERS(io_lib_config.h)
+AC_INIT(io_lib, 1.14.11)
+AC_CONFIG_HEADERS([io_lib_config.h])
+AC_CONFIG_MACRO_DIR([m4])
 AM_INIT_AUTOMAKE
 AM_MAINTAINER_MODE
 
@@ -53,9 +54,9 @@ AM_MAINTAINER_MODE
 #       libstaden-read.so.1 -> libstaden-read.so.1.1.0
 #       libstaden-read.so.1.1.0
 
-VERS_CURRENT=12
-VERS_REVISION=0
-VERS_AGE=1
+VERS_CURRENT=13
+VERS_REVISION=1
+VERS_AGE=0
 AC_SUBST(VERS_CURRENT)
 AC_SUBST(VERS_REVISION)
 AC_SUBST(VERS_AGE)
@@ -100,6 +101,12 @@ AC_CHECK_LIB([lzma], [lzma_easy_buffer_encode], [
 	LIBS="-llzma $LIBS"
 	AC_DEFINE([HAVE_LIBLZMA],1,[Define to 1 if you have the liblzma library.])])
 
+AC_CHECK_LIB([bsc], [bsc_compress], [
+	LIBS="-lbsc $LIBS"
+	AC_DEFINE([HAVE_LIBBSC],1,[Define to 1 if you have the libbsc library.])])
+
+AX_LIBDEFLATE
+
 dnl Check host endian-ness
 AC_C_BIGENDIAN([SET_ENDIAN="#define SP_BIG_ENDIAN"],
 	       [SET_ENDIAN="#define SP_LITTLE_ENDIAN"],

debian/changelog

+staden-io-lib (1.14.11-1) unstable; urgency=medium
+
+  * New upstream version featuring SOVERSION bump
+  * Fix installation of docs
+    Closes: #912272
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.2.1
+
+ -- Andreas Tille <tille@debian.org>  Mon, 29 Oct 2018 20:24:24 +0100
+
 staden-io-lib (1.14.9-4) unstable; urgency=medium
 
   * Standards-Version: 4.1.2

debian/compat

-10
+11

debian/control

@@ -5,13 +5,13 @@ Uploaders: Charles Plessy <plessy@debian.org>,
            Thorsten Alteholz <debian@alteholz.de>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper (>= 11~),
                zlib1g-dev,
                libcurl4-gnutls-dev | libcurl4-nss-dev,
                d-shlibs
-Standards-Version: 4.1.2
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/staden-io-lib.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/staden-io-lib.git
+Standards-Version: 4.2.1
+Vcs-Browser: https://salsa.debian.org/med-team/staden-io-lib
+Vcs-Git: https://salsa.debian.org/med-team/staden-io-lib.git
 Homepage: https://github.com/jkbonfield/io_lib
 
 Package: staden-io-lib-utils
@@ -33,7 +33,7 @@ Description: programs for manipulating DNA sequencing files
 Package: libstaden-read-dev
 Architecture: any
 Section: libdevel
-Depends: libstaden-read11 (= ${binary:Version}),
+Depends: libstaden-read13 (= ${binary:Version}),
          ${misc:Depends}
 Description: development files for libstaden-read
  This package contains the header and development files needed to build
@@ -44,7 +44,7 @@ Description: development files for libstaden-read
  interface. It has been compiled and tested on a variety of unix systems,
  MacOS X and MS Windows.
 
-Package: libstaden-read11
+Package: libstaden-read13
 Architecture: any
 Multi-Arch: same
 Section: libs

debian/patches/0001-Bug-fix-bgzip-on-Big-Endian-systems.patch

-From: James Bonfield <jkb@sanger.ac.uk>
-Date: Thu, 28 Sep 2017 09:50:12 +0100
-Bug-Debian: 
-Origin: upstream
-Subject: Bug fix bgzip on Big Endian systems.
-
---- a/io_lib/bgzip.c
-+++ b/io_lib/bgzip.c
-@@ -186,13 +186,15 @@ int gzi_index_dump(gzi *idx, const char
- 	free(tmp);
- 
-     int i;
--    uint64_t n = idx->n;
--    if (fwrite(le_int8(&n), sizeof(n), 1, idx_f) != 1)
-+    uint64_t n = le_int8(idx->n);
-+    if (fwrite(&n, sizeof(n), 1, idx_f) != 1)
- 	goto fail;
-     for (i=0; i<idx->n; i++) {
--	if (fwrite(le_int8(&idx->c_off[i]), sizeof idx->c_off[i], 1, idx_f) != 1)
-+	n = le_int8(idx->c_off[i]);
-+	if (fwrite(&n, sizeof idx->c_off[i], 1, idx_f) != 1)
- 	    goto fail;
--	if (fwrite(le_int8(&idx->u_off[i]), sizeof idx->u_off[i], 1, idx_f) != 1)
-+	n = le_int8(idx->u_off[i]);
-+	if (fwrite(&n, sizeof idx->u_off[i], 1, idx_f) != 1)
- 	    goto fail;
-     }
-