Changeset 3439

Timestamp:

Nov 20, 2015, 6:41:52 AM (7 years ago)

Author:

Peter

Message:

merge release 0.13 into trunk

Location:

trunk

Files:

• . (modified) (1 prop)
• NEWS (modified) (1 diff)
• README (modified) (2 diffs)
• configure.ac (modified) (1 diff)
• test/Suite.cc (modified) (1 diff)
• test/Suite.h (modified) (3 diffs)
• test/pileup.cc (modified) (3 diffs)
• test/roc.cc (modified) (2 diffs)
• yat/omic/config_bam.h (modified) (1 diff)
• yat/statistics/ROC.cc (modified) (2 diffs)
• yat/statistics/ROC.h (modified) (2 diffs)
• yat/utility/config_public.h.in (modified) (1 diff)

trunk/NEWS

@@ -10 +10 @@
 yat 0.13.x series from http://dev.thep.lu.se/yat/svn/branches/0.13-stable
 
-version 0.13 (released NOT YET)
+version 0.13 (released 20 November 2015)
+  - added support for htslib (see ticket #794)
+      - macro `YAT_HAVE_LIBBAM` is #defined if linking against either libbam
+        or libhts. Use #if defined YAT_HAVE_LIBBAM && !defined
+        (YAT_HAVE_HTSLIB) to check that building against libbam.
+      - macro `YAT_BAM_HEADER` is only #defined when building against libbam
   - utility::get separates types in map and passed key (ticket #799)
   - utility::Range is deprecated (ticket #786)
   - AveragerWeighted::n(void) now return 0, when object is empty (ticket #802)
-  - added support for htslib (see ticket #794)
   - Container2DIterator is now tagged with
     boost::random_access_traversal_tag (see ticket #803, r3393)

trunk/README

@@ -113 +113 @@
 compiler with `./configure CPPFLAGS=-I<include dir>` when header files
 are found in directory `<include dir>`. Configure detects whether
-header files are from htslib or old samtools and looks for either libhts or libbam accordingly. If library is installed outside linker's search path, in `<lib
-dir>`, you can run `./configure LDFLAGS=-L<lib dir>`. You can build
-yat without bam support by running `./configure --without-samtools`.
-
-The samtools program is needed for some tests realted to bam
+header files are from htslib or old samtools and looks for either
+libhts or libbam accordingly. If library is installed outside linker's
+search path, in `<libdir>`, you can run `./configure LDFLAGS=-L<lib
+dir>`. You can build yat without bam support by running `./configure
+--without-samtools`.
+
+The samtools program is needed for some tests related to bam
 functionality. If samtools is not found by configure, these tests will
 be skipped. If you have samtools available outside PATH, you can help
@@ -186 +188 @@
 Copyright (C) 2004 Jari Häkkinen
 Copyright (C) 2006, 2007, 2008 Jari Häkkinen, Peter Johansson
-Copyright (C) 2009, 2010, 2011, 2012, 2013, 2014 Peter Johansson
+Copyright (C) 2009, 2010, 2011, 2012, 2013, 2014, 2015 Peter Johansson
 
 This file is part of yat library, http://dev.thep.lu.se/yat

trunk/configure.ac

@@ -371 +371 @@
   ], [$LIBZ $user_LIBS], [$LIBZ], [YAT_STATIC_LIBS])
 
-  # Check if htslib is available. If no check if samtools API is available
+  # Check if htslib is available. If not, check if samtools API is available
   YAT_CHECK_HTS([
     AC_MSG_CHECKING([htslib])

trunk/test/Suite.cc

@@ -46 +46 @@
     if (require_bam) {
 #ifndef YAT_HAVE_LIBBAM
-      out() << "no libbam\n";
+      out() << "no bam support\n";
       exit (EXIT_SKIP);
 #endif

trunk/test/Suite.h

@@ -6 +6 @@
 /*
   Copyright (C) 2008 Jari Häkkinen, Peter Johansson
-  Copyright (C) 2009, 2010, 2011, 2013, 2014 Peter Johansson
+  Copyright (C) 2009, 2010, 2011, 2013, 2014, 2015 Peter Johansson
 
   This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -24 +24 @@
 */
 
+// ensure that config.h always is included first
+#ifndef YAT_VERSION
+#error header 'config.h' not included
+#endif
+
+#include <yat/utility/config_public.h>
+
 #define YAT_TEST_PROLOGUE "\n=== " << __func__ << " ===\n"
 
@@ -30 +37 @@
 
 // SKIP_BAM_TEST is defined if we should skip bam tests
-#ifndef HAVE_LIBBAM
-#define SKIP_BAM_TEST
-#endif
-#ifndef HAVE_SAMTOOLS
+#if !defined (YAT_HAVE_LIBBAM) || !defined (HAVE_SAMTOOLS_EXECUTABLE)
 #define SKIP_BAM_TEST
 #endif

trunk/test/pileup.cc

@@ -23 +23 @@
 
 #include "Suite.h"
+
+#include <yat/utility/config_public.h>
 
 #ifdef YAT_HAVE_LIBBAM
@@ -50 +52 @@
 
 
-#ifdef YAT_HAVE_LIBBAM
 char seq_nt16(size_t x)
 {
@@ -59 +60 @@
 #else
   std::string table = "=ACMGRSVTWYHKDBN";
-  return table[c];
+  return table[x];
 #endif
 }
 
+#ifdef YAT_HAVE_LIBBAM
 void test1(test::Suite& suite, const std::string& fn)
 {

trunk/test/roc.cc

@@ -3 +3 @@
 /*
   Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson
-  Copyright (C) 2011, 2012, 2013 Peter Johansson
+  Copyright (C) 2011, 2012, 2013, 2015 Peter Johansson
 
   This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -230 +230 @@
     suite.err() << "error: expected p-value>0.5\n  found: "
                 << roc.p_right() << "\n";
+  }
+  if (roc.p_value() > 1.0) {
+    suite.err() << "error: expected p-value <= 1\n    found: "
+                << roc.p_value() << "\n";
+    suite.add(false);
   }
 }

trunk/yat/omic/config_bam.h

@@ -49 +49 @@
 #ifndef YAT_SAM_HEADER
 #error This file requires samtools header files and cannot be used when \
-yat was configured with switch '--without-samtools'.
+yat was configured with switch '--without-htslib'.
 #endif
 

trunk/yat/statistics/ROC.cc

@@ -4 +4 @@
   Copyright (C) 2004, 2005 Peter Johansson
   Copyright (C) 2006, 2007, 2008 Jari Häkkinen, Peter Johansson
-  Copyright (C) 2011, 2012, 2013 Peter Johansson
+  Copyright (C) 2011, 2012, 2013, 2015 Peter Johansson
 
   This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -228 +228 @@
       return std::min(p, 1.0);
     }
-    return 2*get_p_approx(area());
+    return 2*get_p_approx(std::max(area(), 1-area()));
   }
 

trunk/yat/statistics/ROC.h

@@ -7 +7 @@
   Copyright (C) 2004 Peter Johansson
   Copyright (C) 2005, 2006, 2007, 2008 Jari Häkkinen, Peter Johansson
-  Copyright (C) 2011, 2012, 2013 Peter Johansson
+  Copyright (C) 2011, 2012, 2013, 2015 Peter Johansson
 
   This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -96 +96 @@
 
        Threshold deciding whether p-value is computed using exact
-       method or a Gaussian approximation. If both number of positive
-       samples, n_pos(void), and number of negative samples,
+       method or a Gaussian approximation. If either number of positive
+       samples, n_pos(void), or number of negative samples,
        n_neg(void), are smaller than minimum_size the exact method is
        used.

trunk/yat/utility/config_public.h.in

@@ -44 +44 @@
 #undef YAT_HAVE_HTS_H
 
-/// Define to 1 if yat is build with bam support
+/// Define to 1 if yat is built with bam support
 #undef YAT_HAVE_LIBBAM