.gitignore

@@ -64,3 +64,4 @@ src/populaterefcache
 src/vcfconcat
 src/vcfsort
 removespace.sh
+src/filtergtf
\ No newline at end of file

ChangeLog

+biobambam2 (2.0.137-1) unstable; urgency=medium
+
+  * add manual page for bamfeaturecount
+  * add manual page for filtergtf
+  * add filtergtf program
+  * implement simplified transcript level analysis in bamfeaturecount
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Wed, 28 Aug 2019 10:04:09 +0200
+
+biobambam2 (2.0.136-1) unstable; urgency=medium
+
+  * add bamfixpairinfo program
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Thu, 22 Aug 2019 14:44:39 +0200
+
+biobambam2 (2.0.135-1) unstable; urgency=medium
+
+  * add UniqueInterval class in bamfeaturecount
+  * add readgroup and program header lines in bamconsensus
+  * fix border check in bamrecalculatecigar
+  * fix computation of MD/NM fields in bamconsensus
+  * make exclude flags user settable in bamconsensus
+  * change default verbose setting in bamfillquery
+  * update synopsis in bamconsensus help message
+  * make bamconsensus output BAM file containing alignments of consensus with the reference instead of just the consensus as FastA
+  * construct fasta index in bamrecalculatecigar if needed
+  * add unmapped option for bamfilterlength
+  * add bamconsensus to list of installed programs and add documentation
+  * improve scaling in bamconsensus
+  * make running dot optional in bamconsensus
+
+ -- German Tischler-Höhle <germant@miltenyibiotec.de>  Thu, 22 Aug 2019 10:47:00 +0200
+
 biobambam2 (2.0.134-1) unstable; urgency=medium
 
   * bump libmaus2 version

INSTALL

-Installation Instructions
-*************************
-
-Copyright (C) 1994-1996, 1999-2002, 2004-2013 Free Software Foundation,
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-==================
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compile

-#! /bin/sh
-# Wrapper for compilers which do not understand '-c -o'.
-
-scriptversion=2012-10-14.11; # UTC
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-# <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
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-func_file_conv ()
-{
-  file=$1
-  case $file in
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-      if test -z "$file_conv"; then
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-	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=$file
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-    lib_path="$lib_path;$file"
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-  linker_opts="$linker_opts -LIBPATH:$file"
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-# func_cl_dashl library
-# Do a library search-path lookup for cl
-func_cl_dashl ()
-{
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-      lib=$dir/$lib.dll.lib
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-      found=yes
-      lib=$dir/$lib.lib
-      break
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-      lib=$dir/lib$lib.a
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-  IFS=$save_IFS
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-  if test "$found" != yes; then
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-	  # configure might choose to run compile as 'compile cc -o foo foo.c'.
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-	      func_file_conv "$2"
-	      set x "$@" -Fo"$file"
-	      shift
-	      ;;
-	    *)
-	      func_file_conv "$2"
-	      set x "$@" -Fe"$file"
-	      shift
-	      ;;
-	  esac
-	  ;;
-	-I)
-	  eat=1
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-	  set x "$@" -I"$file"
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-	  func_file_conv "$1" mingw
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-	eat=1
-	case $2 in
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-	    ofile=$2
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-	  *)
-	    set x "$@" -o "$2"
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-	cfile=$1
-	set x "$@" "$1"
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-if test -z "$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.ac

-AC_INIT(biobambam2,2.0.134,[tischler@mpi-cbg.de],[biobambam2],[http://www.sanger.ac.uk])
+AC_INIT(biobambam2,2.0.137,[tischler@mpi-cbg.de],[biobambam2],[http://www.sanger.ac.uk])
 AC_CANONICAL_SYSTEM
 AC_PROG_LIBTOOL
 
@@ -165,9 +165,9 @@ if test ! -z "${with_libmaus2}" ; then
 	fi
 fi
 
-PKG_CHECK_MODULES([libmaus2],[libmaus2 >= 2.0.657])
-PKG_CHECK_MODULES([libmaus2digests],[libmaus2digests >= 2.0.657])
-PKG_CHECK_MODULES([libmaus2seqchksumsfactory],[libmaus2seqchksumsfactory >= 2.0.657])
+PKG_CHECK_MODULES([libmaus2],[libmaus2 >= 2.0.663])
+PKG_CHECK_MODULES([libmaus2digests],[libmaus2digests >= 2.0.663])
+PKG_CHECK_MODULES([libmaus2seqchksumsfactory],[libmaus2seqchksumsfactory >= 2.0.663])
 
 if test ! -z "${with_libmaus2}" ; then
 	if test ! -z "${PKGCONFIGPATHSAVE}" ; then
@@ -302,7 +302,7 @@ if test "${have_libmaus2_irods}" = "yes" ; then
 		fi
 	fi
 
-	PKG_CHECK_MODULES([libmaus2irods],[libmaus2irods >= 2.0.657])
+	PKG_CHECK_MODULES([libmaus2irods],[libmaus2irods >= 2.0.663])
 
 	LIBMAUS2IRODSCPPFLAGS="${libmaus2irods_CFLAGS}"
 	LIBMAUS2IRODSLIBS="${libmaus2irods_LIBS}"

debian/changelog

+biobambam2 (2.0.137+dfsg-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream version
+  * Removed autogenerated files from source tree
+
+ -- Steffen Moeller <moeller@debian.org>  Wed, 28 Aug 2019 14:49:00 +0200
+
 biobambam2 (2.0.134-1) unstable; urgency=medium
 
   * New upstream version

debian/control

@@ -5,7 +5,7 @@ Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 12),
                pkg-config,
-               libmaus2-dev (>= 2.0.657)
+               libmaus2-dev (>= 2.0.663)
 Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/biobambam2
 Vcs-Git: https://salsa.debian.org/med-team/biobambam2.git

debian/copyright

 Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: biobambam2
 Source: https://gitlab.com/german.tischler/biobambam2/tags
+Files-Excluded:
+ ltmain.sh
+ install-sh
+ Makefile.in
+ INSTALL
+ depcomp
+ aclocal.m4
+ missing
+ configure
+ compile
+ src/Makefile.in
+ m4/libtool.m4
+ test/Makefile.in
+ autom4te.cache
+ autom4te.cache/traces.2
+ autom4te.cache/requests
+ autom4te.cache/traces.0
+ autom4te.cache/output.1
+ autom4te.cache/output.2
+ autom4te.cache/traces.1
+ autom4te.cache/output.0
+
 
 Files: *
 Copyright: 2013-2019 German Tischler <tischler@mpi-cbg.de>

debian/lintian-overrides

-# see https://lists.debian.org/debian-med/2018/06/msg00043.html
-#PKGNAME#: script-with-language-extension usr/bin/*.*

debian/rules

@@ -6,3 +6,7 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 
 %:
 	dh $@
+
+override_dh_auto_clean:
+	dh_auto_clean
+	rm -f config.log