Changeset 4316

Timestamp:

Feb 17, 2023, 2:40:50 AM (3 months ago)

Author:

Peter

Message:

Merged release 0.20.2 into trunk

Location:

trunk

Files:

• . (modified) (1 prop)
• NEWS (modified) (1 diff)
• m4/version.m4 (modified) (1 diff)
• test/vcf.cc (modified) (3 diffs)
• yat/omic/VCF.h (modified) (6 diffs)

trunk/NEWS

@@ -11 +11 @@
 
 yat 0.20.x series from http://dev.thep.lu.se/yat/svn/branches/0.20-stable
+
+version 0.20.2 (released 17 February 2023)
+  - Fixed bug in VCF::Info::set(2) (bug #995)
+
+  A complete list of closed tickets can be found here [[br]]
+  http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.20.2
 
 version 0.20.1 (released 10 February 2023)

trunk/m4/version.m4

@@ -102 +102 @@
 # yat-0.20   17:0:0
 # yat-0.20.1 17:1:0
+# yat-0.20.2 17:2:0
 #
 # *Accidently, the libtool number was not updated for yat 0.5

trunk/test/vcf.cc

@@ -1 +1 @@
 // $Id$
 //
-// Copyright (C) 2018, 2020, 2022 Peter Johansson
+// Copyright (C) 2018, 2020, 2022, 2023 Peter Johansson
 //
 // This program is free software; you can redistribute it and/or modify
@@ -32 +32 @@
 using namespace theplu::yat;
 
+template<typename T>
+void equal_vec(test::Suite& suite, std::vector<T> x, std::vector<T> y)
+{
+  if (x != y) {
+    suite.add(false);
+    if (x.size() != y.size())
+      suite.err() << "error: vectors not the same\n"
+                  << "x size: " << x.size() << "\n"
+                  << "y size: " << y.size() << "\n";
+    else
+      for (size_t i=0; i<x.size(); ++i)
+        std::cerr << "'" << x[i] << "' : '" << y[i] << "'\n";
+  }
+}
+
+
+template<typename T1, typename T2>
+void equal(test::Suite& suite, T1 x, T2 y)
+{
+  if (x != y) {
+    suite.add(false);
+    suite.err() << "error: " << x << " != " << y << "\n";
+  }
+}
+
+
+void test_info(test::Suite& suite, omic::VCF::Info info)
+{
+  std::string value;
+  info.add("FOO", "foo");
+  info.get(value, "FOO");
+  equal(suite, value, "foo");
+
+  info.set("FOO", "foo2");
+  info.get(value, "FOO");
+  equal(suite, value, "foo2");
+
+  int x;
+  info.add("X", "1");
+  info.get(x, "X");
+  equal(suite, x, 1);
+
+  info.set("X", 2);
+  info.get(x, "X");
+  equal(suite, x, 2);
+
+  std::vector<std::string> values;
+  std::vector<std::string> foos(2, "fu");
+  info.add("FOOS", foos);
+  info.get(values, "FOOS");
+  equal_vec(suite, values, foos);
+  info.set("FOOS", foos);
+  info.get(value, "FOOS");
+  equal_vec(suite, values, foos);
+
+  std::vector<int> y;
+  std::vector<int> bars(2, 13);
+  info.add("BARS", bars);
+  info.get(y, "BARS");
+  equal_vec(suite, y, bars);
+  info.set("BARS", bars);
+  info.get(y, "BARS");
+  equal_vec(suite, y, bars);
+}
+
+
 int main(int argc, char* argv[])
 {
@@ -104 +170 @@
 
     suite.out() << "test info\n";
+    test_info(suite, vcf.info());
     suite.add(vcf.info().str() == "");
     vcf.info().set("SNV");

trunk/yat/omic/VCF.h

@@ -5 +5 @@
 
 /*
-  Copyright (C) 2018, 2019, 2020, 2022 Peter Johansson
+  Copyright (C) 2018, 2019, 2020, 2022, 2023 Peter Johansson
 
   This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -221 +221 @@
       /**
          Add entry \a key to semicolon-delimited list of entries.
+
+         If \a key is already present, the behaviour is undefined.
        */
       void add(const std::string& key);
@@ -227 +229 @@
          T is either string or numeric or a std::vector with strings
          or numerics.
+
+         If \a key is already present, the behaviour is undefined.
        */
       template<typename T>
@@ -242 +246 @@
 
       /**
-        get value corresponding to \a key
+        get value corresponding to \a key. If \a key is not present,
+        result is as value is empty string.
 
         T is string, numeric, vector<string> or vector<numeric>
@@ -270 +275 @@
 
       /**
+         If \a key is absent, equivalent to call add(key, value). If
+         \a key present, erase its value and set to \a value.
+
          T is either string or numeric or a std::vector with strings
          or numerics.
@@ -685 +693 @@
     str_ = "";
     auto it = map_.lower_bound(key);
-    if (it==map_.end() && it->first!=key) {
+    if (it==map_.end() || it->first!=key) {
       keys_.push_back(key);
       it = map_.insert(it, std::make_pair(key, ""));
     }
+    else
+      it->second.clear();
     detail::Appender<T> append(',');
     append(it->second, value);