Changeset 4308

Timestamp:

Feb 10, 2023, 3:40:22 AM (4 months ago)

Author:

Peter

Message:

merge release 0.20.1 into trunk.

Location:

trunk

Files:

• . (modified) (1 prop)
• NEWS (modified) (2 diffs)
• m4/version.m4 (modified) (2 diffs)
• test/Makefile.am (modified) (2 diffs)
• test/needleman_wunsch.cc (copied) (copied from branches/0.20-stable/test/needleman_wunsch.cc)
• test/vcf_header.cc (modified) (3 diffs)
• yat/omic/VcfCompare.h (modified) (2 diffs)
• yat/omic/VcfHeader.cc (modified) (3 diffs)
• yat/utility/Aligner.cc (modified) (2 diffs)

trunk/NEWS

@@ -11 +11 @@
 
 yat 0.20.x series from http://dev.thep.lu.se/yat/svn/branches/0.20-stable
+
+version 0.20.1 (released 10 February 2023)
+  - Aligner::needleman_wunsch and NeedlemanWunsch functions were
+    previously buggy for non-zero gap penalties (bug #993)
+  - VcfHeaer::add_program_command now outputs Date (bug #994)
+
+  A complete list of closed tickets can be found here [[br]]
+  http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.20.1
 
 version 0.20 (released 18 November 2022)
@@ -598 +606 @@
 Copyright (C) 2010, 2011 Peter Johansson
 Copyright (C) 2012 Jari Häkkinen, Peter Johansson
-Copyright (C) 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 Peter Johansson
+Copyright (C) 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 Peter Johansson
 
 This file is part of yat library, http://dev.thep.lu.se/yat

trunk/m4/version.m4

@@ -2 +2 @@
 #
 # Copyright (C) 2008, 2009 Jari Häkkinen, Peter Johansson
-# Copyright (C) 2010, 2011, 2012, 2013, 2014, 2015, 2017, 2018, 2019, 2020, 2021, 2022 Peter Johansson
+# Copyright (C) 2010, 2011, 2012, 2013, 2014, 2015, 2017, 2018, 2019, 2020, 2021, 2022, 2023 Peter Johansson
 #
 # This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -101 +101 @@
 # yat-0.19.2 16:2:0
 # yat-0.20   17:0:0
+# yat-0.20.1 17:1:0
 #
 # *Accidently, the libtool number was not updated for yat 0.5

trunk/test/Makefile.am

@@ -5 +5 @@
 # Copyright (C) 2005 Jari Häkkinen, Peter Johansson
 # Copyright (C) 2006, 2007, 2008 Jari Häkkinen, Peter Johansson, Markus Ringnér
-# Copyright (C) 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 Peter Johansson
+# Copyright (C) 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 Peter Johansson
 #
 # This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -108 +108 @@
   test/nbc.test \
   test/ncc.test \
+  test/needleman_wunsch.test \
   test/negative_binomial.test \
   test/negative_binomial_mixture.test \

trunk/test/vcf_header.cc

@@ -2 +2 @@
 
 /*
-  Copyright (C) 2018, 2020 Peter Johansson
+  Copyright (C) 2018, 2020, 2023 Peter Johansson
 
   This program is free software; you can redistribute it and/or modify
@@ -23 +23 @@
 
 #include "yat/omic/VcfHeader.h"
+
+#include "yat/utility/split.h"
+#include "yat/utility/utility.h"
 
 #include <iostream>
@@ -83 +86 @@
   suite.out() << hdr.line(4) << "\n";
 
+  // test VcfHeader::add_program_command
+  suite.out() << "test ::add_program_command:\n";
+  hdr.add_program_command(argc, argv);
+  bool found_command=false;
+  for (size_t i=0; i<hdr.size(); ++i) {
+    if (utility::contains(hdr.line(i), "vcf_header.testCommand")) {
+      suite.out() << hdr.line(i) << "\n";
+      std::vector<std::string> vec;
+      utility::split(vec, hdr.line(i), ';');
+      for (size_t j=0; j<vec.size(); ++j) {
+        if (utility::contains(vec[j], "Date")) {
+          found_command = true;
+          suite.out() << "date: '" << vec[j] << "'\n";
+          if (vec[j].size() < 20) {
+            suite.err() << "date value too short\n";
+            suite.add(false);
+          }
+        }
+      }
+    }
+  }
+  suite.add(found_command);
+
   return suite.return_value();
 }

trunk/yat/omic/VcfCompare.h

@@ -5 +5 @@
 
 /*
-  Copyright (C) 2018 Peter Johansson
+  Copyright (C) 2018, 2023 Peter Johansson
 
   The yat library is free software; you can redistribute it and/or
@@ -58 +58 @@
 
        The following criteria are used to compare the two objects:
-       1) chromosome (as defined din constructor)
+       1) chromosome (as defined in constructor)
        2) position \c POS
        3) reference allele \c REF

trunk/yat/omic/VcfHeader.cc

@@ -2 +2 @@
 
 /*
-  Copyright (C) 2018, 2020, 2021 Peter Johansson
+  Copyright (C) 2018, 2020, 2021, 2023 Peter Johansson
 
   The yat library is free software; you can redistribute it and/or
@@ -28 +28 @@
 #include <algorithm>
 #include <cassert>
+#include <ctime>
 #include <istream>
 #include <iterator>
@@ -142 +143 @@
   {
     std::string key = utility::basename(argv[0]) + "Command";
-    std::string val;
+    std::stringstream ss;
+
     for (int i=1; i<argc; ++i) {
       if (i!=1)
-        val += ' ';
-      val += argv[i];
-    }
-    val += "; Date=";
-    //    val += current_time("%a %b %e %H:%M:%S %Y");
+        ss << ' ';
+      ss << argv[i];
+    }
+    ss << "; Date=";
+    std::time_t time = std::time(nullptr);
+    ss << std::asctime(std::localtime(&time));
+
+    std::string val;
+    getline(ss, val);
+
     add(key, val);
   }

trunk/yat/utility/Aligner.cc

@@ -2 +2 @@
 
 /*
-  Copyright (C) 2012, 2014, 2016, 2019, 2020, 2022 Peter Johansson
+  Copyright (C) 2012, 2014, 2016, 2019, 2020, 2022, 2023 Peter Johansson
 
   This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -57 +57 @@
     // Init upper and left border of matrix
     for (size_t i=1; i<m.rows(); i++)
-      m(i,0) = -i * vertical_gap_ - open_vertical_gap_;
+      m(i,0) = - (i * vertical_gap_ + open_vertical_gap_);
     for (size_t i=1; i<m.columns(); i++)
-      m(0,i) = -i * horizon_gap_ - open_horizon_gap_;
+      m(0,i) = - (i * horizon_gap_ + open_horizon_gap_);
     (*this)(s, m);
     // return lower right corner element