Changeset 3561

Timestamp:

Jan 4, 2017, 1:55:10 AM (6 years ago)

Author:

Peter

Message:

Merged release 0.13.1 into trunk

Location:

trunk

Files:

• . (modified) (1 prop)
• NEWS (modified) (1 diff)
• configure.ac (modified) (3 diffs)
• doc/first_page.doxygen.in (modified) (2 diffs)
• m4/version.m4 (modified) (2 diffs)
• yat/statistics/Fisher.h (modified) (1 diff)

trunk/NEWS

@@ -19 +19 @@
 
 yat 0.13.x series from http://dev.thep.lu.se/yat/svn/branches/0.13-stable
+
+version 0.13.1 (released 4 January 2017)
+  - fixed bug in pkg-config file 'yat.pc' (bug #850)
+  - improved detection of boost thread detection (bug #863)
+
+  A complete list of closed tickets can be found here [[br]]
+  http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.13
 
 version 0.13 (released 20 November 2015)

trunk/configure.ac

@@ -247 +247 @@
 # skip boost link tests if boost is not wanted (--without-boost)
 AS_IF([test x"$want_boost" = x"yes"],[
+  AX_BOOST_SYSTEM
+  LIBS="$BOOST_SYSTEM_LIB $LIBS"
   AX_BOOST_THREAD
-  AX_BOOST_SYSTEM
   YAT_CPP_ADD_FLAG([CPPFLAGS], [$BOOST_CPPFLAGS])
   YAT_LD_ADD_FLAG([LDFLAGS], [$BOOST_LDFLAGS])
-  # boost tests above only test compilation, so let's try link in the libs
-  LIBS="$LIBS $BOOST_THREAD_LIB $BOOST_SYSTEM_LIB"
+  LIBS="$BOOST_THREAD_LIB $LIBS"
+  # linking tests in AX_BOOST_SYSTEM occasionaly miss to detect
+  # missing lib (see ticket #719), so link specifically here to catch
+  # that case.
   AC_MSG_CHECKING([for boost::thread_specific_ptr])
   AC_LINK_IFELSE([AC_LANG_PROGRAM([@%:@include <boost/thread/tss.hpp>],
@@ -533 +536 @@
 AS_IF([test x$with_htslib != x"no"], [
   # htslib comes with a pc file, so we can require htslib in yat.pc
-  AS_IF([test x$with_hts = x"yes"], [
+  AS_IF([test x$have_hts = x"yes"], [
     YAT_VAR_REMOVE([YAT_PC_LIBS_PRIVATE], [$BAM_LIBS -lz])
     YAT_SET_CONTAINS([$yat_libyat_la_LIBADD], [-lhts], [
@@ -544 +547 @@
     # require zlib
     YAT_VAR_REMOVE([YAT_PC_LIBS_PRIVATE], [-lz])
-    YAT_PC_REQUIRES="$YAT_PC_REQUIRES zlib"
     YAT_SET_CONTAINS([$yat_libyat_la_LIBADD], [-lz], [
       YAT_PC_REQUIRES_PRIVATE="$YAT_PC_REQUIRES_PRIVATE zlib"

trunk/doc/first_page.doxygen.in

@@ -5 +5 @@
   Copyright (C) 2003, 2004 Jari Häkkinen
   Copyright (C) 2005, 2006, 2007, 2008 Jari Häkkinen, Peter Johansson
-  Copyright (C) 2010, 2013, 2014 Peter Johansson
+  Copyright (C) 2010, 2013, 2014, 2015 Peter Johansson
 
   This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -54 +54 @@
 
    <li> Wrapper classes for <a
-   href="http://samtools.sourceforge.net/">samtools</a> allowing
+   href="http://www.htslib.org//">htslib</a> allowing
    handling BAM reads with <a
    href="http://www.sgi.com/tech/stl/table_of_contents.html">Standard

trunk/m4/version.m4

@@ -2 +2 @@
 #
 # Copyright (C) 2008, 2009 Jari Häkkinen, Peter Johansson
-# Copyright (C) 2010, 2011, 2012, 2013, 2014, 2015 Peter Johansson
+# Copyright (C) 2010, 2011, 2012, 2013, 2014, 2015, 2017 Peter Johansson
 #
 # This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -80 +80 @@
 # yat-0.12.2 9:2:0
 # yat-0.13   10:0:0
+# yat-0.13.1 10:1:0
 #
 # *Accidently, the libtool number was not updated for yat 0.5

trunk/yat/statistics/Fisher.h

@@ -73 +73 @@
     /// chi-squared calculation
     ///
+    /// \since Constructor with argument was introduced in yat 0.13
+    ///
     Fisher(bool yates=false);