Merge pull request #2514 from smehringer/main

[FIX] mason_variator: Fix StructuralVariantRecord::endPosition() for deletions.
seqan · Mar 28, 2024 · 45fa07b · 45fa07b
2 parents 77c2180 + 97d57e5
commit 45fa07b
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Showing 5 changed files with 16 additions and 11 deletions.
diff --git a/.github/workflows/ci_win.yml b/.github/workflows/ci_win.yml
@@ -52,9 +52,17 @@ jobs:
 
       - name: Setup conda
         uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: ""
+          auto-activate-base: true
+          auto-update-conda: false
 
       - name: Install conda dependencies
-        run: conda install -c conda-forge boost-cpp bzip2 libxml2 zlib
+        run: |
+          conda install -c conda-forge boost-cpp bzip2 libxml2 zlib
+          $CONDA_BASE = conda info --base
+          "$CONDA_BASE\Library\include" | Out-File -FilePath $env:GITHUB_PATH -Append
+          "$CONDA_BASE\Library\lib" | Out-File -FilePath $env:GITHUB_PATH -Append
 
       - name: Configure tests
         run: |

diff --git a/apps/mason2/README b/apps/mason2/README
@@ -86,12 +86,6 @@ VCF file:
 3. Reference and Contact
 ------------------------------------------------------------------------------
 
-In case of questions and problems please contact the mailing list
-
-  https://lists.fu-berlin.de/listinfo/seqan-dev
-
-or file a bug at
-
-  https://trac.seqan.de/newticket
-
+In case of questions and problems please contact us on
 
+https://github.com/seqan/seqan
diff --git a/apps/mason2/genomic_variants.cpp b/apps/mason2/genomic_variants.cpp
@@ -59,7 +59,7 @@ int StructuralVariantRecord::endPosition() const
             if (size > 0)
                 return pos;
             else
-                return pos + size;
+                return pos - size; // for deletions, size is negative!
         case INVERSION:
             return pos + size;
         case TRANSLOCATION:

diff --git a/include/seqan/graph_types/graph_impl_hmm.h b/include/seqan/graph_types/graph_impl_hmm.h
@@ -740,6 +740,9 @@ getTransitionProbability(Graph<Hmm<TAlphabet, TCargo, TSpec> > const& g,
     typedef Graph<Hmm<TAlphabet, TCargo, TSpec> > const TGraph;
     typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
     TEdgeDescriptor e = findEdge(g, state1, state2);
+#ifdef __INTEL_LLVM_COMPILER
+    asm volatile("" : : "r,m"(e) : "memory"); // Kindly request IntelLLVM (2024.1) to not optimize result away.
+#endif
     if (e == 0) return 0.0;
     else return cargo(e);
 }

diff --git a/util/bin/demo_checker.py b/util/bin/demo_checker.py
@@ -44,7 +44,7 @@ def fuzzyEqual(pattern, text):
                 print('Line %s is different between expected and actual outputs.' % (i), file=sys.stderr)
                 return False
             else:
-                P = (re.escape(P)).replace('\\[VAR\\]', "[+-]?(\d+(\.\d*)?|\.\d+)([eE][+-]?\d+)?")
+                P = (re.escape(P)).replace('\\[VAR\\]', r'[+-]?(\d+(\.\d*)?|\.\d+)([eE][+-]?\d+)?')
                 r = re.compile(P)
                 if re.match(r, T) == None:
                     print('Line %s is different (REGEX) between expected and actual outputs.' % (i), file=sys.stderr)