[med-svn] [bambamc] 01/04: Imported Upstream version 0.0.50

[Roland Fehrenbacher]

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rfehren-guest pushed a commit to branch master
in repository bambamc.

commit b1e2877d94490e28eef3f0499b743e3200c7b4a7
Author: Roland Fehrenbacher <rf at q-leap.de>
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,[gt1 at sanger.ac.uk],[bambamc],[http://www.sanger.ac.uk])
-LIBRARY_VERSION=0:49:0
+AC_INIT(bambamc,0.0.50,[gt1 at sanger.ac.uk],[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 );

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