Loading .gitignore +9 −0 Original line number Diff line number Diff line Loading @@ -55,3 +55,12 @@ pull.sh test/bamcmp test/bamtosam src/filtersam numproc.sh src/fastqtobam2 bumprun.sh src/vcffilterinfo src/vcfpatchcontigprepend src/populaterefcache src/vcfconcat src/vcfsort removespace.sh ChangeLog +205 −0 Original line number Diff line number Diff line biobambam2 (2.0.128-1) unstable; urgency=medium * remove manual page for removed kmerprob * remove bamrefdepth and bamrefdepthpeaks -- German Tischler-Höhle <germant@miltenyibiotec.de> Wed, 31 Jul 2019 14:10:27 +0200 biobambam2 (2.0.127-1) unstable; urgency=medium * add bamdepthintersect program * add bamdepth program * add DepthInterval class * remove hard coded Z_DEFAULT_COMPRESSION default and replace by DeflateDefaults::getDefaultLevel() -- German Tischler-Höhle <germant@miltenyibiotec.de> Wed, 31 Jul 2019 12:53:58 +0200 biobambam2 (2.0.126-1) unstable; urgency=medium * allow output to standard output in bamnumericalindex -- German Tischler-Höhle <germant@miltenyibiotec.de> Tue, 30 Jul 2019 11:11:47 +0200 biobambam2 (2.0.125-1) unstable; urgency=medium * add construction of numerical index from numerical indexes of input files in bamfastcat -- German Tischler-Höhle <germant@miltenyibiotec.de> Fri, 26 Jul 2019 17:17:43 +0200 biobambam2 (2.0.124-1) unstable; urgency=medium * update numerical index in bamreplacechecksums * update numerical index in bamreheader * put header and data in separate blocks in ReadHeader -- German Tischler-Höhle <germant@miltenyibiotec.de> Thu, 25 Jul 2019 15:29:48 +0200 biobambam2 (2.0.123-1) unstable; urgency=medium * avoid explicitely invoking BamDecoder class (use factory instead) * use output factory to allow SAM/BAM/CRAM output in bam12auxmerge * use input factories in bam12auxmerge to support SAM and CRAM input * add manual page for bamclipXT * remove filtersam and kmerprob -- German Tischler-Höhle <germant@miltenyibiotec.de> Thu, 25 Jul 2019 11:10:33 +0200 biobambam2 (2.0.122-1) unstable; urgency=medium * add bamnumericalindexstats -- German Tischler-Höhle <germant@miltenyibiotec.de> Wed, 24 Jul 2019 15:01:14 +0200 biobambam2 (2.0.121-1) unstable; urgency=medium * add numerical indexing in bamsormadup -- German Tischler-Höhle <germant@miltenyibiotec.de> Wed, 24 Jul 2019 14:34:22 +0200 biobambam2 (2.0.120-1) unstable; urgency=medium * add vcfsort program * remove bamclipextract * simplify bamdisthist -- German Tischler-Höhle <germant@miltenyibiotec.de> Wed, 24 Jul 2019 11:02:17 +0200 biobambam2 (2.0.119-1) unstable; urgency=medium * add manual page for bambisect * fix manual page for bamchecksort * update help message in bamauxmerge2 * remove bamcheckalignments * add manual page for bamauxmerge2 * add manual page for bamauxmerge * clean up bamauxmerge * change input order in bamalignfrac * add documentation for regex option in manual page for bamalignfrac * remove bamalignmentoffsets program * add manual page for bamalignfrac * rewrite bamalignfrac to produce more useful output -- German Tischler-Höhle <germant@miltenyibiotec.de> Tue, 23 Jul 2019 21:55:28 +0200 biobambam2 (2.0.118-1) unstable; urgency=medium * avoid writing empty BGZF blocks in ReadHeader * remove bamlastfilter * remove deprecated bamcollate program -- German Tischler-Höhle <germant@miltenyibiotec.de> Mon, 22 Jul 2019 09:36:51 +0200 biobambam2 (2.0.117-1) unstable; urgency=medium * fix breakages after libmaus2 cleanup -- German Tischler-Höhle <germant@miltenyibiotec.de> Fri, 19 Jul 2019 13:09:16 +0200 biobambam2 (2.0.116-1) unstable; urgency=medium * avoid copying inline EOF blocks in bamfastcat -- German Tischler-Höhle <germant@miltenyibiotec.de> Fri, 19 Jul 2019 12:27:19 +0200 biobambam2 (2.0.115-1) unstable; urgency=medium * add bamfiltereofblocks -- German Tischler-Höhle <germant@miltenyibiotec.de> Fri, 19 Jul 2019 11:23:28 +0200 biobambam2 (2.0.114-1) unstable; urgency=medium * bump libmaus2 version -- German Tischler-Höhle <germant@miltenyibiotec.de> Thu, 18 Jul 2019 10:55:18 +0200 biobambam2 (2.0.113-1) unstable; urgency=medium * add bamfastsplit * add multi threaded processing in bamseqchksum * add building numerical index in bamrecompress * add vcfconcat -- German Tischler-Höhle <germant@miltenyibiotec.de> Wed, 17 Jul 2019 16:19:52 +0200 biobambam2 (2.0.112-1) unstable; urgency=medium * fix bamrecompress for case of BAM input with inline empty BGZF blocks -- German Tischler-Höhle <germant@miltenyibiotec.de> Tue, 16 Jul 2019 13:57:00 +0200 biobambam2 (2.0.111-1) unstable; urgency=medium * use readFileAsStream to read text header file in bamfastcat/bamreheader/bamreplacechecksums * add tryoq flag in bamseqchksum -- German Tischler-Höhle <germant@miltenyibiotec.de> Tue, 16 Jul 2019 11:13:33 +0200 biobambam2 (2.0.110-1) unstable; urgency=medium * add headerchecksums option in bamseqchecksum -- German Tischler-Höhle <germant@miltenyibiotec.de> Mon, 15 Jul 2019 15:59:56 +0200 biobambam2 (2.0.109-1) unstable; urgency=medium * refactor bamreheader/bamfastcat and add bamreplacechecksums -- German Tischler-Höhle <germant@miltenyibiotec.de> Mon, 15 Jul 2019 13:52:29 +0200 biobambam2 (2.0.108-1) unstable; urgency=medium * add include and exclude options in normalisefasta * make sure we write an EOF block in bamfastexploderef even for "empty" output files * add bisect tool * add bamfastnumextract * add low recompression bam input/output variant of exploderef functionality * add populaterefcache program * add bamexploderef -- German Tischler-Höhle <germant@miltenyibiotec.de> Fri, 12 Jul 2019 16:34:24 +0200 biobambam2 (2.0.107-1) unstable; urgency=medium * add OQ tags in fastqtobam2 * add bamfastcat * allow multi threading input and output in bamsplit * replace usage of PosixRegex by std::regex * fixes after changes in libmaus2 * remove lasToBAM * added gzip output in vcffilterinfo * added program vcfpatchcontigprepend (prepend string to all seq ids in a VCF file) * add vcffilterinfo program (filter out all INFO fields not in a given filter list from a VCF file) * add append option in bamreheader * add bamreheader * try to avoid stalling on blocked write queue in bamauxmerge2 * refactor Reference class out of bamauxmerge2 and add cigar string rewriting in bamauxmerge2 -- German Tischler-Höhle <germant@miltenyibiotec.de> Wed, 03 Jul 2019 21:04:34 +0200 biobambam2 (2.0.106-1) unstable; urgency=medium * fix email address in version bumping script -- German Tischler-Höhle <germant@miltenyibiotec.de> Fri, 14 Jun 2019 12:39:35 +0200 biobambam2 (2.0.105-1) unstable; urgency=medium * no change version bump after fixing bumping script -- German Tischler <germant@miltenyibiotec.de> Fri, 14 Jun 2019 12:11:44 +0200 biobambam2 (2.0.104-1) unstable; urgency=medium * version bumping script test -- German Tischler <germant@miltenyibiotec.de> Fri, 14 Jun 2019 12:08:38 +0200 biobambam2 (2.0.103-1) unstable; urgency=low * bump libmaus2 version * remove bamparsort * fixes after libmaus2 changes * do not replace cigar string for unmapped reads in bamauxmerge2 -- German Tischler-Höhle <germant@miltenyibiotec.de> Thu, 14 Jun 2019 12:00:00 +0000 INSTALL +161 −159 File changed.Preview size limit exceeded, changes collapsed. Show changes Makefile.in +6 −10 Original line number Diff line number Diff line # Makefile.in generated by automake 1.15.1 from Makefile.am. # Makefile.in generated by automake 1.15 from Makefile.am. # @configure_input@ # Copyright (C) 1994-2017 Free Software Foundation, Inc. # Copyright (C) 1994-2014 Free Software Foundation, Inc. # This Makefile.in is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading Loading @@ -215,13 +215,9 @@ AUTOCONF = @AUTOCONF@ AUTOHEADER = @AUTOHEADER@ AUTOMAKE = @AUTOMAKE@ AWK = @AWK@ BAMALIGNMENTOFFSETSINSTEXP = @BAMALIGNMENTOFFSETSINSTEXP@ BAMALIGNMENTOFFSETSNOINSTEXP = @BAMALIGNMENTOFFSETSNOINSTEXP@ BAMBAM_CFLAGS = @BAMBAM_CFLAGS@ BAMBAM_LDFLAGS = @BAMBAM_LDFLAGS@ BAMBAM_LIBS = @BAMBAM_LIBS@ BAMPARSORTINSTEXP = @BAMPARSORTINSTEXP@ BAMPARSORTNOINSTEXP = @BAMPARSORTNOINSTEXP@ BAMREFDEPTHPEAKS = @BAMREFDEPTHPEAKS@ BASE64PROG = @BASE64PROG@ BASHPROG = @BASHPROG@ Loading Loading @@ -611,7 +607,7 @@ distdir: $(DISTFILES) ! -type d ! -perm -444 -exec $(install_sh) -c -m a+r {} {} \; \ || chmod -R a+r "$(distdir)" dist-gzip: distdir tardir=$(distdir) && $(am__tar) | eval GZIP= gzip $(GZIP_ENV) -c >$(distdir).tar.gz tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz $(am__post_remove_distdir) dist-bzip2: distdir Loading @@ -637,7 +633,7 @@ dist-shar: distdir @echo WARNING: "Support for shar distribution archives is" \ "deprecated." >&2 @echo WARNING: "It will be removed altogether in Automake 2.0" >&2 shar $(distdir) | eval GZIP= gzip $(GZIP_ENV) -c >$(distdir).shar.gz shar $(distdir) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).shar.gz $(am__post_remove_distdir) dist-zip: distdir Loading @@ -655,7 +651,7 @@ dist dist-all: distcheck: dist case '$(DIST_ARCHIVES)' in \ *.tar.gz*) \ eval GZIP= gzip $(GZIP_ENV) -dc $(distdir).tar.gz | $(am__untar) ;;\ GZIP=$(GZIP_ENV) gzip -dc $(distdir).tar.gz | $(am__untar) ;;\ *.tar.bz2*) \ bzip2 -dc $(distdir).tar.bz2 | $(am__untar) ;;\ *.tar.lz*) \ Loading @@ -665,7 +661,7 @@ distcheck: dist *.tar.Z*) \ uncompress -c $(distdir).tar.Z | $(am__untar) ;;\ *.shar.gz*) \ eval GZIP= gzip $(GZIP_ENV) -dc $(distdir).shar.gz | unshar ;;\ GZIP=$(GZIP_ENV) gzip -dc $(distdir).shar.gz | unshar ;;\ *.zip*) \ unzip $(distdir).zip ;;\ esac Loading aclocal.m4 +23 −23 Original line number Diff line number Diff line # generated automatically by aclocal 1.15.1 -*- Autoconf -*- # generated automatically by aclocal 1.15 -*- Autoconf -*- # Copyright (C) 1996-2017 Free Software Foundation, Inc. # Copyright (C) 1996-2014 Free Software Foundation, Inc. # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading Loading @@ -296,7 +296,7 @@ AS_VAR_COPY([$1], [pkg_cv_][$1]) AS_VAR_IF([$1], [""], [$5], [$4])dnl ])dnl PKG_CHECK_VAR # Copyright (C) 2002-2017 Free Software Foundation, Inc. # Copyright (C) 2002-2014 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading @@ -311,7 +311,7 @@ AC_DEFUN([AM_AUTOMAKE_VERSION], [am__api_version='1.15' dnl Some users find AM_AUTOMAKE_VERSION and mistake it for a way to dnl require some minimum version. Point them to the right macro. m4_if([$1], [1.15.1], [], m4_if([$1], [1.15], [], [AC_FATAL([Do not call $0, use AM_INIT_AUTOMAKE([$1]).])])dnl ]) Loading @@ -327,14 +327,14 @@ m4_define([_AM_AUTOCONF_VERSION], []) # Call AM_AUTOMAKE_VERSION and AM_AUTOMAKE_VERSION so they can be traced. # This function is AC_REQUIREd by AM_INIT_AUTOMAKE. AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION], [AM_AUTOMAKE_VERSION([1.15.1])dnl [AM_AUTOMAKE_VERSION([1.15])dnl m4_ifndef([AC_AUTOCONF_VERSION], [m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl _AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))]) # AM_AUX_DIR_EXPAND -*- Autoconf -*- # Copyright (C) 2001-2017 Free Software Foundation, Inc. # Copyright (C) 2001-2014 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading Loading @@ -386,7 +386,7 @@ am_aux_dir=`cd "$ac_aux_dir" && pwd` # AM_CONDITIONAL -*- Autoconf -*- # Copyright (C) 1997-2017 Free Software Foundation, Inc. # Copyright (C) 1997-2014 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading Loading @@ -417,7 +417,7 @@ AC_CONFIG_COMMANDS_PRE( Usually this means the macro was only invoked conditionally.]]) fi])]) # Copyright (C) 1999-2017 Free Software Foundation, Inc. # Copyright (C) 1999-2014 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading Loading @@ -608,7 +608,7 @@ _AM_SUBST_NOTMAKE([am__nodep])dnl # Generate code to set up dependency tracking. -*- Autoconf -*- # Copyright (C) 1999-2017 Free Software Foundation, Inc. # Copyright (C) 1999-2014 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading Loading @@ -684,7 +684,7 @@ AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS], # Do all the work for Automake. -*- Autoconf -*- # Copyright (C) 1996-2017 Free Software Foundation, Inc. # Copyright (C) 1996-2014 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading Loading @@ -881,7 +881,7 @@ for _am_header in $config_headers :; do done echo "timestamp for $_am_arg" >`AS_DIRNAME(["$_am_arg"])`/stamp-h[]$_am_stamp_count]) # Copyright (C) 2001-2017 Free Software Foundation, Inc. # Copyright (C) 2001-2014 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading @@ -902,7 +902,7 @@ if test x"${install_sh+set}" != xset; then fi AC_SUBST([install_sh])]) # Copyright (C) 2003-2017 Free Software Foundation, Inc. # Copyright (C) 2003-2014 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading @@ -923,7 +923,7 @@ AC_SUBST([am__leading_dot])]) # Check to see how 'make' treats includes. -*- Autoconf -*- # Copyright (C) 2001-2017 Free Software Foundation, Inc. # Copyright (C) 2001-2014 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading Loading @@ -973,7 +973,7 @@ rm -f confinc confmf # Fake the existence of programs that GNU maintainers use. -*- Autoconf -*- # Copyright (C) 1997-2017 Free Software Foundation, Inc. # Copyright (C) 1997-2014 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading Loading @@ -1014,7 +1014,7 @@ fi # Obsolete and "removed" macros, that must however still report explicit # error messages when used, to smooth transition. # # Copyright (C) 1996-2017 Free Software Foundation, Inc. # Copyright (C) 1996-2014 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading @@ -1041,7 +1041,7 @@ AU_DEFUN([fp_C_PROTOTYPES], [AM_C_PROTOTYPES]) # Helper functions for option handling. -*- Autoconf -*- # Copyright (C) 2001-2017 Free Software Foundation, Inc. # Copyright (C) 2001-2014 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading Loading @@ -1070,7 +1070,7 @@ AC_DEFUN([_AM_SET_OPTIONS], AC_DEFUN([_AM_IF_OPTION], [m4_ifset(_AM_MANGLE_OPTION([$1]), [$2], [$3])]) # Copyright (C) 1999-2017 Free Software Foundation, Inc. # Copyright (C) 1999-2014 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading Loading @@ -1117,7 +1117,7 @@ AC_LANG_POP([C])]) # For backward compatibility. AC_DEFUN_ONCE([AM_PROG_CC_C_O], [AC_REQUIRE([AC_PROG_CC])]) # Copyright (C) 2001-2017 Free Software Foundation, Inc. # Copyright (C) 2001-2014 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading @@ -1136,7 +1136,7 @@ AC_DEFUN([AM_RUN_LOG], # Check to make sure that the build environment is sane. -*- Autoconf -*- # Copyright (C) 1996-2017 Free Software Foundation, Inc. # Copyright (C) 1996-2014 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading Loading @@ -1217,7 +1217,7 @@ AC_CONFIG_COMMANDS_PRE( rm -f conftest.file ]) # Copyright (C) 2009-2017 Free Software Foundation, Inc. # Copyright (C) 2009-2014 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading Loading @@ -1277,7 +1277,7 @@ AC_SUBST([AM_BACKSLASH])dnl _AM_SUBST_NOTMAKE([AM_BACKSLASH])dnl ]) # Copyright (C) 2001-2017 Free Software Foundation, Inc. # Copyright (C) 2001-2014 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading Loading @@ -1305,7 +1305,7 @@ fi INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s" AC_SUBST([INSTALL_STRIP_PROGRAM])]) # Copyright (C) 2006-2017 Free Software Foundation, Inc. # Copyright (C) 2006-2014 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading @@ -1324,7 +1324,7 @@ AC_DEFUN([AM_SUBST_NOTMAKE], [_AM_SUBST_NOTMAKE($@)]) # Check how to create a tarball. -*- Autoconf -*- # Copyright (C) 2004-2017 Free Software Foundation, Inc. # Copyright (C) 2004-2014 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading Loading
.gitignore +9 −0 Original line number Diff line number Diff line Loading @@ -55,3 +55,12 @@ pull.sh test/bamcmp test/bamtosam src/filtersam numproc.sh src/fastqtobam2 bumprun.sh src/vcffilterinfo src/vcfpatchcontigprepend src/populaterefcache src/vcfconcat src/vcfsort removespace.sh
ChangeLog +205 −0 Original line number Diff line number Diff line biobambam2 (2.0.128-1) unstable; urgency=medium * remove manual page for removed kmerprob * remove bamrefdepth and bamrefdepthpeaks -- German Tischler-Höhle <germant@miltenyibiotec.de> Wed, 31 Jul 2019 14:10:27 +0200 biobambam2 (2.0.127-1) unstable; urgency=medium * add bamdepthintersect program * add bamdepth program * add DepthInterval class * remove hard coded Z_DEFAULT_COMPRESSION default and replace by DeflateDefaults::getDefaultLevel() -- German Tischler-Höhle <germant@miltenyibiotec.de> Wed, 31 Jul 2019 12:53:58 +0200 biobambam2 (2.0.126-1) unstable; urgency=medium * allow output to standard output in bamnumericalindex -- German Tischler-Höhle <germant@miltenyibiotec.de> Tue, 30 Jul 2019 11:11:47 +0200 biobambam2 (2.0.125-1) unstable; urgency=medium * add construction of numerical index from numerical indexes of input files in bamfastcat -- German Tischler-Höhle <germant@miltenyibiotec.de> Fri, 26 Jul 2019 17:17:43 +0200 biobambam2 (2.0.124-1) unstable; urgency=medium * update numerical index in bamreplacechecksums * update numerical index in bamreheader * put header and data in separate blocks in ReadHeader -- German Tischler-Höhle <germant@miltenyibiotec.de> Thu, 25 Jul 2019 15:29:48 +0200 biobambam2 (2.0.123-1) unstable; urgency=medium * avoid explicitely invoking BamDecoder class (use factory instead) * use output factory to allow SAM/BAM/CRAM output in bam12auxmerge * use input factories in bam12auxmerge to support SAM and CRAM input * add manual page for bamclipXT * remove filtersam and kmerprob -- German Tischler-Höhle <germant@miltenyibiotec.de> Thu, 25 Jul 2019 11:10:33 +0200 biobambam2 (2.0.122-1) unstable; urgency=medium * add bamnumericalindexstats -- German Tischler-Höhle <germant@miltenyibiotec.de> Wed, 24 Jul 2019 15:01:14 +0200 biobambam2 (2.0.121-1) unstable; urgency=medium * add numerical indexing in bamsormadup -- German Tischler-Höhle <germant@miltenyibiotec.de> Wed, 24 Jul 2019 14:34:22 +0200 biobambam2 (2.0.120-1) unstable; urgency=medium * add vcfsort program * remove bamclipextract * simplify bamdisthist -- German Tischler-Höhle <germant@miltenyibiotec.de> Wed, 24 Jul 2019 11:02:17 +0200 biobambam2 (2.0.119-1) unstable; urgency=medium * add manual page for bambisect * fix manual page for bamchecksort * update help message in bamauxmerge2 * remove bamcheckalignments * add manual page for bamauxmerge2 * add manual page for bamauxmerge * clean up bamauxmerge * change input order in bamalignfrac * add documentation for regex option in manual page for bamalignfrac * remove bamalignmentoffsets program * add manual page for bamalignfrac * rewrite bamalignfrac to produce more useful output -- German Tischler-Höhle <germant@miltenyibiotec.de> Tue, 23 Jul 2019 21:55:28 +0200 biobambam2 (2.0.118-1) unstable; urgency=medium * avoid writing empty BGZF blocks in ReadHeader * remove bamlastfilter * remove deprecated bamcollate program -- German Tischler-Höhle <germant@miltenyibiotec.de> Mon, 22 Jul 2019 09:36:51 +0200 biobambam2 (2.0.117-1) unstable; urgency=medium * fix breakages after libmaus2 cleanup -- German Tischler-Höhle <germant@miltenyibiotec.de> Fri, 19 Jul 2019 13:09:16 +0200 biobambam2 (2.0.116-1) unstable; urgency=medium * avoid copying inline EOF blocks in bamfastcat -- German Tischler-Höhle <germant@miltenyibiotec.de> Fri, 19 Jul 2019 12:27:19 +0200 biobambam2 (2.0.115-1) unstable; urgency=medium * add bamfiltereofblocks -- German Tischler-Höhle <germant@miltenyibiotec.de> Fri, 19 Jul 2019 11:23:28 +0200 biobambam2 (2.0.114-1) unstable; urgency=medium * bump libmaus2 version -- German Tischler-Höhle <germant@miltenyibiotec.de> Thu, 18 Jul 2019 10:55:18 +0200 biobambam2 (2.0.113-1) unstable; urgency=medium * add bamfastsplit * add multi threaded processing in bamseqchksum * add building numerical index in bamrecompress * add vcfconcat -- German Tischler-Höhle <germant@miltenyibiotec.de> Wed, 17 Jul 2019 16:19:52 +0200 biobambam2 (2.0.112-1) unstable; urgency=medium * fix bamrecompress for case of BAM input with inline empty BGZF blocks -- German Tischler-Höhle <germant@miltenyibiotec.de> Tue, 16 Jul 2019 13:57:00 +0200 biobambam2 (2.0.111-1) unstable; urgency=medium * use readFileAsStream to read text header file in bamfastcat/bamreheader/bamreplacechecksums * add tryoq flag in bamseqchksum -- German Tischler-Höhle <germant@miltenyibiotec.de> Tue, 16 Jul 2019 11:13:33 +0200 biobambam2 (2.0.110-1) unstable; urgency=medium * add headerchecksums option in bamseqchecksum -- German Tischler-Höhle <germant@miltenyibiotec.de> Mon, 15 Jul 2019 15:59:56 +0200 biobambam2 (2.0.109-1) unstable; urgency=medium * refactor bamreheader/bamfastcat and add bamreplacechecksums -- German Tischler-Höhle <germant@miltenyibiotec.de> Mon, 15 Jul 2019 13:52:29 +0200 biobambam2 (2.0.108-1) unstable; urgency=medium * add include and exclude options in normalisefasta * make sure we write an EOF block in bamfastexploderef even for "empty" output files * add bisect tool * add bamfastnumextract * add low recompression bam input/output variant of exploderef functionality * add populaterefcache program * add bamexploderef -- German Tischler-Höhle <germant@miltenyibiotec.de> Fri, 12 Jul 2019 16:34:24 +0200 biobambam2 (2.0.107-1) unstable; urgency=medium * add OQ tags in fastqtobam2 * add bamfastcat * allow multi threading input and output in bamsplit * replace usage of PosixRegex by std::regex * fixes after changes in libmaus2 * remove lasToBAM * added gzip output in vcffilterinfo * added program vcfpatchcontigprepend (prepend string to all seq ids in a VCF file) * add vcffilterinfo program (filter out all INFO fields not in a given filter list from a VCF file) * add append option in bamreheader * add bamreheader * try to avoid stalling on blocked write queue in bamauxmerge2 * refactor Reference class out of bamauxmerge2 and add cigar string rewriting in bamauxmerge2 -- German Tischler-Höhle <germant@miltenyibiotec.de> Wed, 03 Jul 2019 21:04:34 +0200 biobambam2 (2.0.106-1) unstable; urgency=medium * fix email address in version bumping script -- German Tischler-Höhle <germant@miltenyibiotec.de> Fri, 14 Jun 2019 12:39:35 +0200 biobambam2 (2.0.105-1) unstable; urgency=medium * no change version bump after fixing bumping script -- German Tischler <germant@miltenyibiotec.de> Fri, 14 Jun 2019 12:11:44 +0200 biobambam2 (2.0.104-1) unstable; urgency=medium * version bumping script test -- German Tischler <germant@miltenyibiotec.de> Fri, 14 Jun 2019 12:08:38 +0200 biobambam2 (2.0.103-1) unstable; urgency=low * bump libmaus2 version * remove bamparsort * fixes after libmaus2 changes * do not replace cigar string for unmapped reads in bamauxmerge2 -- German Tischler-Höhle <germant@miltenyibiotec.de> Thu, 14 Jun 2019 12:00:00 +0000
Makefile.in +6 −10 Original line number Diff line number Diff line # Makefile.in generated by automake 1.15.1 from Makefile.am. # Makefile.in generated by automake 1.15 from Makefile.am. # @configure_input@ # Copyright (C) 1994-2017 Free Software Foundation, Inc. # Copyright (C) 1994-2014 Free Software Foundation, Inc. # This Makefile.in is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading Loading @@ -215,13 +215,9 @@ AUTOCONF = @AUTOCONF@ AUTOHEADER = @AUTOHEADER@ AUTOMAKE = @AUTOMAKE@ AWK = @AWK@ BAMALIGNMENTOFFSETSINSTEXP = @BAMALIGNMENTOFFSETSINSTEXP@ BAMALIGNMENTOFFSETSNOINSTEXP = @BAMALIGNMENTOFFSETSNOINSTEXP@ BAMBAM_CFLAGS = @BAMBAM_CFLAGS@ BAMBAM_LDFLAGS = @BAMBAM_LDFLAGS@ BAMBAM_LIBS = @BAMBAM_LIBS@ BAMPARSORTINSTEXP = @BAMPARSORTINSTEXP@ BAMPARSORTNOINSTEXP = @BAMPARSORTNOINSTEXP@ BAMREFDEPTHPEAKS = @BAMREFDEPTHPEAKS@ BASE64PROG = @BASE64PROG@ BASHPROG = @BASHPROG@ Loading Loading @@ -611,7 +607,7 @@ distdir: $(DISTFILES) ! -type d ! -perm -444 -exec $(install_sh) -c -m a+r {} {} \; \ || chmod -R a+r "$(distdir)" dist-gzip: distdir tardir=$(distdir) && $(am__tar) | eval GZIP= gzip $(GZIP_ENV) -c >$(distdir).tar.gz tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz $(am__post_remove_distdir) dist-bzip2: distdir Loading @@ -637,7 +633,7 @@ dist-shar: distdir @echo WARNING: "Support for shar distribution archives is" \ "deprecated." >&2 @echo WARNING: "It will be removed altogether in Automake 2.0" >&2 shar $(distdir) | eval GZIP= gzip $(GZIP_ENV) -c >$(distdir).shar.gz shar $(distdir) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).shar.gz $(am__post_remove_distdir) dist-zip: distdir Loading @@ -655,7 +651,7 @@ dist dist-all: distcheck: dist case '$(DIST_ARCHIVES)' in \ *.tar.gz*) \ eval GZIP= gzip $(GZIP_ENV) -dc $(distdir).tar.gz | $(am__untar) ;;\ GZIP=$(GZIP_ENV) gzip -dc $(distdir).tar.gz | $(am__untar) ;;\ *.tar.bz2*) \ bzip2 -dc $(distdir).tar.bz2 | $(am__untar) ;;\ *.tar.lz*) \ Loading @@ -665,7 +661,7 @@ distcheck: dist *.tar.Z*) \ uncompress -c $(distdir).tar.Z | $(am__untar) ;;\ *.shar.gz*) \ eval GZIP= gzip $(GZIP_ENV) -dc $(distdir).shar.gz | unshar ;;\ GZIP=$(GZIP_ENV) gzip -dc $(distdir).shar.gz | unshar ;;\ *.zip*) \ unzip $(distdir).zip ;;\ esac Loading
aclocal.m4 +23 −23 Original line number Diff line number Diff line # generated automatically by aclocal 1.15.1 -*- Autoconf -*- # generated automatically by aclocal 1.15 -*- Autoconf -*- # Copyright (C) 1996-2017 Free Software Foundation, Inc. # Copyright (C) 1996-2014 Free Software Foundation, Inc. # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading Loading @@ -296,7 +296,7 @@ AS_VAR_COPY([$1], [pkg_cv_][$1]) AS_VAR_IF([$1], [""], [$5], [$4])dnl ])dnl PKG_CHECK_VAR # Copyright (C) 2002-2017 Free Software Foundation, Inc. # Copyright (C) 2002-2014 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading @@ -311,7 +311,7 @@ AC_DEFUN([AM_AUTOMAKE_VERSION], [am__api_version='1.15' dnl Some users find AM_AUTOMAKE_VERSION and mistake it for a way to dnl require some minimum version. Point them to the right macro. m4_if([$1], [1.15.1], [], m4_if([$1], [1.15], [], [AC_FATAL([Do not call $0, use AM_INIT_AUTOMAKE([$1]).])])dnl ]) Loading @@ -327,14 +327,14 @@ m4_define([_AM_AUTOCONF_VERSION], []) # Call AM_AUTOMAKE_VERSION and AM_AUTOMAKE_VERSION so they can be traced. # This function is AC_REQUIREd by AM_INIT_AUTOMAKE. AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION], [AM_AUTOMAKE_VERSION([1.15.1])dnl [AM_AUTOMAKE_VERSION([1.15])dnl m4_ifndef([AC_AUTOCONF_VERSION], [m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl _AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))]) # AM_AUX_DIR_EXPAND -*- Autoconf -*- # Copyright (C) 2001-2017 Free Software Foundation, Inc. # Copyright (C) 2001-2014 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading Loading @@ -386,7 +386,7 @@ am_aux_dir=`cd "$ac_aux_dir" && pwd` # AM_CONDITIONAL -*- Autoconf -*- # Copyright (C) 1997-2017 Free Software Foundation, Inc. # Copyright (C) 1997-2014 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading Loading @@ -417,7 +417,7 @@ AC_CONFIG_COMMANDS_PRE( Usually this means the macro was only invoked conditionally.]]) fi])]) # Copyright (C) 1999-2017 Free Software Foundation, Inc. # Copyright (C) 1999-2014 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading Loading @@ -608,7 +608,7 @@ _AM_SUBST_NOTMAKE([am__nodep])dnl # Generate code to set up dependency tracking. -*- Autoconf -*- # Copyright (C) 1999-2017 Free Software Foundation, Inc. # Copyright (C) 1999-2014 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading Loading @@ -684,7 +684,7 @@ AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS], # Do all the work for Automake. -*- Autoconf -*- # Copyright (C) 1996-2017 Free Software Foundation, Inc. # Copyright (C) 1996-2014 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading Loading @@ -881,7 +881,7 @@ for _am_header in $config_headers :; do done echo "timestamp for $_am_arg" >`AS_DIRNAME(["$_am_arg"])`/stamp-h[]$_am_stamp_count]) # Copyright (C) 2001-2017 Free Software Foundation, Inc. # Copyright (C) 2001-2014 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading @@ -902,7 +902,7 @@ if test x"${install_sh+set}" != xset; then fi AC_SUBST([install_sh])]) # Copyright (C) 2003-2017 Free Software Foundation, Inc. # Copyright (C) 2003-2014 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading @@ -923,7 +923,7 @@ AC_SUBST([am__leading_dot])]) # Check to see how 'make' treats includes. -*- Autoconf -*- # Copyright (C) 2001-2017 Free Software Foundation, Inc. # Copyright (C) 2001-2014 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading Loading @@ -973,7 +973,7 @@ rm -f confinc confmf # Fake the existence of programs that GNU maintainers use. -*- Autoconf -*- # Copyright (C) 1997-2017 Free Software Foundation, Inc. # Copyright (C) 1997-2014 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading Loading @@ -1014,7 +1014,7 @@ fi # Obsolete and "removed" macros, that must however still report explicit # error messages when used, to smooth transition. # # Copyright (C) 1996-2017 Free Software Foundation, Inc. # Copyright (C) 1996-2014 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading @@ -1041,7 +1041,7 @@ AU_DEFUN([fp_C_PROTOTYPES], [AM_C_PROTOTYPES]) # Helper functions for option handling. -*- Autoconf -*- # Copyright (C) 2001-2017 Free Software Foundation, Inc. # Copyright (C) 2001-2014 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading Loading @@ -1070,7 +1070,7 @@ AC_DEFUN([_AM_SET_OPTIONS], AC_DEFUN([_AM_IF_OPTION], [m4_ifset(_AM_MANGLE_OPTION([$1]), [$2], [$3])]) # Copyright (C) 1999-2017 Free Software Foundation, Inc. # Copyright (C) 1999-2014 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading Loading @@ -1117,7 +1117,7 @@ AC_LANG_POP([C])]) # For backward compatibility. AC_DEFUN_ONCE([AM_PROG_CC_C_O], [AC_REQUIRE([AC_PROG_CC])]) # Copyright (C) 2001-2017 Free Software Foundation, Inc. # Copyright (C) 2001-2014 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading @@ -1136,7 +1136,7 @@ AC_DEFUN([AM_RUN_LOG], # Check to make sure that the build environment is sane. -*- Autoconf -*- # Copyright (C) 1996-2017 Free Software Foundation, Inc. # Copyright (C) 1996-2014 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading Loading @@ -1217,7 +1217,7 @@ AC_CONFIG_COMMANDS_PRE( rm -f conftest.file ]) # Copyright (C) 2009-2017 Free Software Foundation, Inc. # Copyright (C) 2009-2014 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading Loading @@ -1277,7 +1277,7 @@ AC_SUBST([AM_BACKSLASH])dnl _AM_SUBST_NOTMAKE([AM_BACKSLASH])dnl ]) # Copyright (C) 2001-2017 Free Software Foundation, Inc. # Copyright (C) 2001-2014 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading Loading @@ -1305,7 +1305,7 @@ fi INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s" AC_SUBST([INSTALL_STRIP_PROGRAM])]) # Copyright (C) 2006-2017 Free Software Foundation, Inc. # Copyright (C) 2006-2014 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading @@ -1324,7 +1324,7 @@ AC_DEFUN([AM_SUBST_NOTMAKE], [_AM_SUBST_NOTMAKE($@)]) # Check how to create a tarball. -*- Autoconf -*- # Copyright (C) 2004-2017 Free Software Foundation, Inc. # Copyright (C) 2004-2014 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, Loading
