Commit 2d665349 authored by Steffen Möller's avatar Steffen Möller
Browse files

New upstream version 2.0.147+dfsg

parent a0e14aaa

ChangeLog

+66 −0
Original line number Diff line number Diff line 
biobambam2 (2.0.147-1) unstable; urgency=medium



  * fix heap comparisons in bamconsensus



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Tue, 05 Nov 2019 10:19:07 +0100



biobambam2 (2.0.146-1) unstable; urgency=medium



  * add explicit flush in bamtofastq

  * bump libmaus2 version

  * explicitely call flush on BamToFastqOutputFileSet objects in bamtofastq (try to avoid triggering exceptions in object destructor)

  * allow disabling adapter detection/clipping in fastqtobam2

  * use dynamic scheduling in bamfilterk



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Wed, 30 Oct 2019 10:48:48 +0100



biobambam2 (2.0.145-1) unstable; urgency=medium



  * refactor vcfsort

  * add kmer end position on reference in bamconsensus

  * fixes after libmaus2 changes



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Fri, 11 Oct 2019 12:46:33 +0200



biobambam2 (2.0.144-1) unstable; urgency=medium



  * update list of uncommon programs



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Fri, 27 Sep 2019 13:37:44 +0200



biobambam2 (2.0.143-1) unstable; urgency=medium



  * fix newline issue in Makefile



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Fri, 27 Sep 2019 13:11:19 +0200



biobambam2 (2.0.142-1) unstable; urgency=medium



  * add install-uncommon configure option to deselect some programs from standard installation



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Fri, 27 Sep 2019 12:58:23 +0200



biobambam2 (2.0.141-1) unstable; urgency=medium



  * bump libmaus2 version



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Fri, 27 Sep 2019 11:24:14 +0200



biobambam2 (2.0.140-1) unstable; urgency=medium



  * update libmaus2 version



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Fri, 27 Sep 2019 08:57:03 +0200



biobambam2 (2.0.139-1) unstable; urgency=medium



  * add bamheap3 program



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Thu, 19 Sep 2019 14:09:13 +0200



biobambam2 (2.0.138-1) unstable; urgency=medium



  * add exportcdna option in bamfeaturecount



 -- German Tischler-Höhle <germant@miltenyibiotec.de>  Wed, 28 Aug 2019 15:50:12 +0200



biobambam2 (2.0.137-1) unstable; urgency=medium



  * add manual page for bamfeaturecount

configure.ac

+22 −7
Original line number Diff line number Diff line 
AC_INIT(biobambam2,2.0.137,[tischler@mpi-cbg.de],[biobambam2],[http://www.sanger.ac.uk])

AC_INIT(biobambam2,2.0.147,[germant@miltenyibiotec.de],[biobambam2],[https://gitlab.com/german.tischler/biobambam2])

AC_CANONICAL_SYSTEM

AC_PROG_LIBTOOL
@@ -165,9 +165,7 @@ if test ! -z "${with_libmaus2}" ; then 
	fi

fi



PKG_CHECK_MODULES([libmaus2],[libmaus2 >= 2.0.663])

PKG_CHECK_MODULES([libmaus2digests],[libmaus2digests >= 2.0.663])

PKG_CHECK_MODULES([libmaus2seqchksumsfactory],[libmaus2seqchksumsfactory >= 2.0.663])

PKG_CHECK_MODULES([libmaus2],[libmaus2 >= 2.0.683])



if test ! -z "${with_libmaus2}" ; then

	if test ! -z "${PKGCONFIGPATHSAVE}" ; then
@@ -175,8 +173,8 @@ if test ! -z "${with_libmaus2}" ; then 
	fi

fi



LIBMAUS2CPPFLAGS="${libmaus2_CFLAGS} ${libmaus2seqchksumsfactory_CFLAGS} ${libmaus2digests_CFLAGS}"

LIBMAUS2LIBS="${libmaus2_LIBS} ${libmaus2seqchksumsfactory_LIBS} ${libmaus2digests_LIBS}"

LIBMAUS2CPPFLAGS="${libmaus2_CFLAGS}"

LIBMAUS2LIBS="${libmaus2_LIBS}"



CPPFLAGS_SAVE="${CPPFLAGS}"

LDFLAGS_SAVE="${LDFLAGS}"
@@ -302,7 +300,7 @@ if test "${have_libmaus2_irods}" = "yes" ; then 
		fi

	fi



	PKG_CHECK_MODULES([libmaus2irods],[libmaus2irods >= 2.0.663])

	PKG_CHECK_MODULES([libmaus2irods],[libmaus2irods >= 2.0.683])



	LIBMAUS2IRODSCPPFLAGS="${libmaus2irods_CFLAGS}"

	LIBMAUS2IRODSLIBS="${libmaus2irods_LIBS}"
@@ -461,6 +459,19 @@ else 
	BLASTXMLTOBAMNOINSTEXP=${BLASTNXMLTOBAM}

fi



AC_ARG_ENABLE(install_uncommon,

        AS_HELP_STRING([--enable-install-uncommon],[enable installation of some uncommon programs (default no)]),

        [install_uncommon=${enableval}],[install_uncommon=no])



UNCOMMON="bamfilter bamfixmatecoordinates bamfixmatecoordinatesnamesorted bamtoname bamdisthist fastabgzfextract bamheap bamfrontback bamrandomtag bamheap2 bamheap3 bamtagconversion fastqtobampar bambisect vcffilterinfo vcfpatchcontigprepend vcfconcat vcfsort filtergtf bamconsensus"

UNCOMMONINSTALLED=

UNCOMMONUNINSTALLED=

if test "${install_uncommon}" = "yes" ; then

	UNCOMMONINSTALLED="${UNCOMMON}"

else

	UNCOMMONUNINSTALLED="${UNCOMMON}"

fi



AC_MSG_NOTICE([Using flags ${CFLAGS} for C compiler ${CC}])

AC_MSG_NOTICE([Using flags ${CXXFLAGS} for C++ compiler ${CXX}])
@@ -497,4 +508,8 @@ AC_SUBST([GMPLIBS]) 
AC_SUBST([HAVE_PTHREAD_MUTEX_RECURSIVE_NP])

AC_SUBST([HAVE_PTHREAD_MUTEX_RECURSIVE])

#

AC_SUBST([UNCOMMON])

AC_SUBST([UNCOMMONINSTALLED])

AC_SUBST([UNCOMMONUNINSTALLED])

#

AC_OUTPUT(Makefile src/Makefile test/Makefile src/biobambam2/BamBamConfig.hpp)

src/Makefile.am

+35 −19
Original line number Diff line number Diff line
@@ -39,7 +39,12 @@ man_MANS = ${MANPAGES} 


EXTRA_DIST = ${MANPAGES}



bin_PROGRAMS = bamtofastq bammarkduplicates bamsort bammaskflags bamrecompress \

bin_PROGRAMS = \

	bamtofastq \

	bammarkduplicates \

	bamsort \

	bammaskflags \

	bamrecompress \

	bamadapterfind \

	bamfilteraux \

	bamauxsort \
@@ -77,7 +82,6 @@ bin_PROGRAMS = bamtofastq bammarkduplicates bamsort bammaskflags bamrecompress \ 
	bamintervalcomment \

	bamintervalcommenthist \

	bamstreamingmarkduplicates \

	bamheap2 \

	bamalignfrac \

	bamfilternames \

	bamsormadup \
@@ -85,9 +89,7 @@ bin_PROGRAMS = bamtofastq bammarkduplicates bamsort bammaskflags bamrecompress \ 
	bamexploderef \

	bamfastexploderef \

	bamfastnumextract \

    	fastqtobampar \

	bamranksort \

	bamtagconversion \

	fastaexplod \

	bamrecalculatecigar \

	bamfiltermc \
@@ -106,28 +108,37 @@ bin_PROGRAMS = bamtofastq bammarkduplicates bamsort bammaskflags bamrecompress \ 
	bamreheader \

	bamreplacechecksums \

	bamfastcat \

	vcffilterinfo \

	vcfpatchcontigprepend \

	populaterefcache \

	bambisect \

	vcfconcat \

	vcfsort \

	bamfiltereofblocks \

	bamdepth \

	bamdepthintersect \

	bamfilterk \

	bamconsensus \

	bamfixpairinfo \

	filtergtf \

	bamfeaturecount \

	@BLASTXMLTOBAMINSTEXP@



noinst_PROGRAMS = bamfilter bamfixmatecoordinates bamfixmatecoordinatesnamesorted bamtoname \

	bamdisthist fastabgzfextract @BAMREFDEPTHPEAKS@ \

	bamheap bamfrontback  \

	@BLASTXMLTOBAMNOINSTEXP@ bamrandomtag

	

EXTRA_PROGRAMS = blastnxmltobam

	bamfeaturecount @BLASTXMLTOBAMINSTEXP@ @UNCOMMONINSTALLED@



noinst_PROGRAMS = @BAMREFDEPTHPEAKS@ @BLASTXMLTOBAMNOINSTEXP@ @UNCOMMONUNINSTALLED@

	

EXTRA_PROGRAMS = blastnxmltobam \

	bamfilter \

	bamfixmatecoordinates \

	bamfixmatecoordinatesnamesorted \

	bamtoname \

	bamdisthist \

	fastabgzfextract \

	bamheap \

	bamfrontback \

	bamrandomtag \

	bamheap2 \

	bamheap3 \

	bamtagconversion \

	fastqtobampar \

	bambisect \

	bamconsensus \

	vcffilterinfo \

	vcfpatchcontigprepend \

	vcfconcat \

	vcfsort \

	filtergtf



populaterefcache_SOURCES = programs/populaterefcache.cpp biobambam2/Licensing.cpp

populaterefcache_LDADD = ${LIBMAUS2LIBS}
@@ -459,6 +470,11 @@ bamheap2_LDADD = ${LIBMAUS2LIBS} 
bamheap2_LDFLAGS = ${AM_CPPFLAGS} ${LIBMAUS2CPPFLAGS} ${LIBMAUS2LDFLAGS} ${AM_LDFLAGS}

bamheap2_CPPFLAGS = ${AM_CPPFLAGS} ${LIBMAUS2CPPFLAGS}



bamheap3_SOURCES = programs/bamheap3.cpp biobambam2/Licensing.cpp

bamheap3_LDADD = ${LIBMAUS2LIBS}

bamheap3_LDFLAGS = ${AM_CPPFLAGS} ${LIBMAUS2CPPFLAGS} ${LIBMAUS2LDFLAGS} ${AM_LDFLAGS}

bamheap3_CPPFLAGS = ${AM_CPPFLAGS} ${LIBMAUS2CPPFLAGS}



bamalignfrac_SOURCES = programs/bamalignfrac.cpp biobambam2/Licensing.cpp

bamalignfrac_LDADD = ${LIBMAUS2LIBS}

bamalignfrac_LDFLAGS = ${AM_CPPFLAGS} ${LIBMAUS2CPPFLAGS} ${LIBMAUS2LDFLAGS} ${AM_LDFLAGS}

src/programs/bamconsensus.cpp

+341 −139

File changed.

Preview size limit exceeded, changes collapsed.

src/programs/bamfeaturecount.1

+38 −0
Original line number Diff line number Diff line
@@ -74,6 +74,44 @@ given in column 6 of the transcript output). 
maximum fraction of bases allowed to be uncovered in the unique region of a transcript so the

transcript will be reported (i.e. minimum value allowed for the first number

given in column 4 of the transcript output).

.PP

.B exclude=<SECONDARY>:

Do not include reads in the output that have any of the given flags set. The

flags are given separated by commas. Valid flags are:

.IP PAIRED:

read was paired in sequencing

.IP PROPER_PAIR:

read has been mapped as part of a proper pair

.IP UNMAP:

read was not mapped

.IP MUNMAP:

mate of read was not mapped

.IP REVERSE:

read was mapped to the reverse strand

.IP MREVERSE:

mate of read was mapped to the reverse strand

.IP READ1:

read was first read of a pair during sequencing

.IP READ2:

read was second read of a pair during sequencing

.IP SECONDARY:

alignment is secondary, i.e. an alternative mapping to the primary alignment in the same file

.IP QCFAIL:

read as marked as having failed quality control

.IP DUP:

read is marked as a duplicate of another read in the same file (see bammarkduplicates)

.IP SUPPLEMENTARY:

read is marked as supplementary alignment

.PP

.B exportcdna=<0>:

instead of feature counting generate a FastA file containing the CDNA as

designated by the GTF annotation file. The second parameter (BAM file) needs

to be specified, but will not be read. This option requires a reference

FastA file suitable for the GTF file to be provided via the reference

key.

.PP

.B reference=<>:

name of a reference FastA file. This is required for the exportcdna option.

.SH AUTHOR

Written by German Tischler-Höhle.

.SH "REPORTING BUGS"