[med-svn] [consensuscore] 10/13: Imported Upstream version 1.0.2

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository consensuscore.

commit 5d6aec549029e891c91b6baec1c22eee724b0a2e
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Sun Jul 3 02:18:11 2016 -0700

    Imported Upstream version 1.0.2
---
 CHANGELOG.md                               |  4 ++++
 configure                                  | 23 +++++++++++++++--------
 include/ConsensusCore/Poa/RangeFinder.hpp  |  2 +-
 include/ConsensusCore/Version.hpp          |  2 +-
 setup.py                                   |  4 ++--
 src/C++/Quiver/MultiReadMutationScorer.cpp |  2 +-
 src/Tests/TestPoaConsensus.cpp             |  2 +-
 7 files changed, 25 insertions(+), 14 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index d959193..31d8a25 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,7 @@
+* Version 1.0.2
+ - Fix a rare crash that could occur during refinement if a read ended up being mapped
+   to a zero-length span of template (after lifting of reference alignment onto POA)
+
 * Version 1.0.1
   - Fix for a serious memory leak occurring on alpha/beta mating failures.  Thanks Nigel!
   - Fix for nondeterministic POA consensus
diff --git a/configure b/configure
index 9b118ec..e40668f 100755
--- a/configure
+++ b/configure
@@ -1,14 +1,7 @@
 #!/usr/bin/env bash
 
-BOOST=
-SWIG=
-SWIG_LIB=
-PYTHON_INCLUDE=
-NUMPY_INCLUDE=
-DEBUG=
 CPP_ABI=c++98
 
-
 usage ()
 {
     echo ""
@@ -26,6 +19,8 @@ usage ()
     echo
     echo "  configure --pbi                              # use PacBio perforce locations"
     echo ""
+    echo "  configure --modules                          # use PacBio GNU modules"
+    echo ""
     echo
     echo "  configure --clear                            # delete configuration"
     echo ""
@@ -47,11 +42,23 @@ configure_pbi ()
 }
 
 
+configure_modules ()
+{
+    echo "Configuring based on PacBio GNU modules"
+    echo "(assumes you have already done module load boost, module load swig (selecting your desired versions))"
+    BOOST=$BOOST_ROOT
+    SWIG=`which swig`
+}
+
+
 while test x$1 != x; do
     case $1 in
         --pbi)
             configure_pbi
             ;;
+        --modules)
+            configure_modules
+            ;;
         --boost=*)
             BOOST=`echo $1 | sed 's/--boost=//'`
             ;;
@@ -95,7 +102,7 @@ BOOST=`tools/find_boost $BOOST` || exit
 SWIG=`tools/find_swig $SWIG`  || exit
 
 if [ -z $SWIG_LIB ]; then
-    SWIG_LIB=`swig -swiglib`
+    SWIG_LIB=`$SWIG -swiglib`
 fi
 
 
diff --git a/include/ConsensusCore/Poa/RangeFinder.hpp b/include/ConsensusCore/Poa/RangeFinder.hpp
index 39c710e..f89fcc6 100644
--- a/include/ConsensusCore/Poa/RangeFinder.hpp
+++ b/include/ConsensusCore/Poa/RangeFinder.hpp
@@ -50,7 +50,7 @@ namespace detail {
 
     protected:
         virtual SdpAnchorVector FindAnchors(const std::string& consensusSequence,
-                                            const std::string& readSequence) = 0;
+                                            const std::string& readSequence) const = 0;
     };
 
 }}
diff --git a/include/ConsensusCore/Version.hpp b/include/ConsensusCore/Version.hpp
index 2c116ed..6f8bef4 100644
--- a/include/ConsensusCore/Version.hpp
+++ b/include/ConsensusCore/Version.hpp
@@ -43,7 +43,7 @@
 
 #define API_MAJOR 1
 #define API_MINOR 0
-#define API_PATCH 1
+#define API_PATCH 2
 
 namespace ConsensusCore
 {
diff --git a/setup.py b/setup.py
index 9f91a40..97158a7 100755
--- a/setup.py
+++ b/setup.py
@@ -43,7 +43,7 @@ def configure():
         die("Requires numpy >= 1.6.0")
 
     ccArgs = re.compile(r"^--(?:boost|swig|swig-lib)=?")
-    ccOpts = re.compile(r"^--(?:debug|c\+\+11|pbi)$")
+    ccOpts = re.compile(r"^--(?:debug|c\+\+11|pbi|modules)$")
 
     configArgs = []
     for arg in sys.argv[:]:
@@ -94,7 +94,7 @@ if "install" in sys.argv and not "build" in sys.argv:
     sys.argv.insert(installPos, "build")
 
 setup(name="ConsensusCore",
-      version="1.0.1",
+      version="1.0.2",
       author="Pacific Biosciences",
       author_email="devnet at pacificbiosciences.com",
       url="http://www.github.com/PacificBiosciences/ConsensusCore",
diff --git a/src/C++/Quiver/MultiReadMutationScorer.cpp b/src/C++/Quiver/MultiReadMutationScorer.cpp
index 6ce4d7a..5de2eab 100644
--- a/src/C++/Quiver/MultiReadMutationScorer.cpp
+++ b/src/C++/Quiver/MultiReadMutationScorer.cpp
@@ -66,7 +66,7 @@ namespace ConsensusCore
         if (mut.IsInsertion()) {
             return (ts < ms && me <= te);   // Insertion starts within?
         } else {
-            return (ts < me && ms < te);    // Intervals intersect?
+            return (ts < te && ts < me && ms < te);    // Intervals intersect?
         }
     }
 
diff --git a/src/Tests/TestPoaConsensus.cpp b/src/Tests/TestPoaConsensus.cpp
index 5ef7796..29a8a25 100644
--- a/src/Tests/TestPoaConsensus.cpp
+++ b/src/Tests/TestPoaConsensus.cpp
@@ -559,7 +559,7 @@ TEST(PoaConsensus, NondeterminismRegressionTest)
         "AGAGTTACTTGCGAAC";
 
     std::set<std::string> answers;
-    for (int run=0; run<1000; run++)
+    for (int run=0; run<100; run++)
     {
         const PoaConsensus* pc = PoaConsensus::FindConsensus(reads, GLOBAL);
 #if 0

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