This is an automated email from the git hooks/post-receive script. rfehren-guest pushed a commit to branch master in repository bambamc.
commit b1e2877d94490e28eef3f0499b743e3200c7b4a7 Author: Roland Fehrenbacher <[email protected]> Date: Mon May 19 11:50:31 2014 +0200 Imported Upstream version 0.0.50 --- .gitignore | 9 ++++++++- ChangeLog | 4 ++++ configure.in | 4 ++-- release.sh | 17 +++++++++++++++++ src/bambamc/BamBam_BamAlignmentPut.c | 13 +++++++++++-- src/test/bamwritertest.c | 17 +++++++++++++++++ 6 files changed, 59 insertions(+), 5 deletions(-) diff --git a/.gitignore b/.gitignore index b06d403..a2d3ec6 100644 --- a/.gitignore +++ b/.gitignore @@ -32,4 +32,11 @@ m4/lt~obsolete.m4 maccombined.sh src/.deps/ stamp-h1 - +ubuntu.sh +src/*.lo +src/*.la +src/bambamc/BamBam_Config.h +bambamc.pc +src/bamreadertest +src/bamwritertest +src/.libs/ diff --git a/ChangeLog b/ChangeLog index e69de29..b9b4f47 100644 --- a/ChangeLog +++ b/ChangeLog @@ -0,0 +1,4 @@ +bambamc (0.0.50) + + * add support for null quality pointers when constructing alignments using + PutAlignment diff --git a/configure.in b/configure.in index 5c06857..23197c9 100644 --- a/configure.in +++ b/configure.in @@ -1,5 +1,5 @@ -AC_INIT(bambamc,0.0.49,[[email protected]],[bambamc],[http://www.sanger.ac.uk]) -LIBRARY_VERSION=0:49:0 +AC_INIT(bambamc,0.0.50,[[email protected]],[bambamc],[http://www.sanger.ac.uk]) +LIBRARY_VERSION=0:50:0 AC_CANONICAL_SYSTEM AC_PROG_LIBTOOL diff --git a/release.sh b/release.sh new file mode 100644 index 0000000..96d4151 --- /dev/null +++ b/release.sh @@ -0,0 +1,17 @@ +#! /bin/bash +VERSION=`grep <configure.in "AC_INIT" | perl -p -e "s/.*AC_INIT\(//" | awk -F ',' '{print $2}'` +DATE=`date +"%Y%m%d%H%M%S"` +RELEASE=${VERSION}-release-${DATE} +# echo $VERSION $DATE $RELEASE +git checkout master +git checkout -b ${RELEASE}-branch master +PATH=/software/hpag/autotools/bin:${PATH} autoreconf -i -f +ADDFILES="INSTALL Makefile.in aclocal.m4 autom4te.cache compile config.guess config.h.in config.sub configure depcomp install-sh ltmain.sh m4/libtool.m4 m4/ltoptions.m4 m4/ltsugar.m4 m4/ltversion.m4 m4/lt~obsolete.m4 missing src/Makefile.in" +mv .gitignore .gitignore_ +git add ${ADDFILES} +git commit -m "Release ${RELEASE}" +mv .gitignore_ .gitignore +git tag ${RELEASE} +git push origin ${RELEASE} +git checkout master +git branch -D ${RELEASE}-branch diff --git a/src/bambamc/BamBam_BamAlignmentPut.c b/src/bambamc/BamBam_BamAlignmentPut.c index f4ebca9..f2fd782 100644 --- a/src/bambamc/BamBam_BamAlignmentPut.c +++ b/src/bambamc/BamBam_BamAlignmentPut.c @@ -241,8 +241,17 @@ int BamBam_CharBuffer_PutAlignmentC( return ret; /* encode quality */ - for ( i = 0; i < quallen && ret >= 0; ++i ) - BamBam_CharBuffer_PushCharQuick(buffer,qual[i]-33,ret); + if ( qual ) + { + for ( i = 0; i < quallen && ret >= 0; ++i ) + BamBam_CharBuffer_PushCharQuick(buffer,qual[i]-33,ret); + } + /* no quality given */ + else + { + for ( i = 0; i < quallen && ret >= 0; ++i ) + BamBam_CharBuffer_PushCharQuick(buffer,255,ret); + } if ( ret < 0 ) return ret; diff --git a/src/test/bamwritertest.c b/src/test/bamwritertest.c index 36d8b6c..0a569d2 100644 --- a/src/test/bamwritertest.c +++ b/src/test/bamwritertest.c @@ -59,6 +59,23 @@ int testLibBamFree(char const * filename) r = BamBam_BamWriter_Commit(writer); assert ( r >= 0 ); + + r = BamBam_BamWriter_PutAlignment( + writer, + 0, + 0, + 5000, + -1, + 0, + "readname_noqual", + "ACGTTGCA", + 0, + "8M", + 60, + 100); + assert ( r >= 0 ); + r = BamBam_BamWriter_Commit(writer); + assert ( r >= 0 ); BamBam_BamWriter_Delete(writer,&status); assert ( status >= 0 ); -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bambamc.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
