Resolve VERSION

.devcontainer/devcontainer.json

@@ -0,0 +1,5 @@
+{
+  "build": {
+    "dockerfile": "../Dockerfile"
+  }
+}

.github/workflows/cmake-multi-platform.yml

@@ -0,0 +1,64 @@
+# This starter workflow is for a CMake project running on multiple platforms. There is a different starter workflow if you just want a single platform.
+# See: https://github.com/actions/starter-workflows/blob/main/ci/cmake-single-platform.yml
+name: CMake on multiple platforms
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      # Set fail-fast to false to ensure that feedback is delivered for all matrix combinations. Consider changing this to true when your workflow is stable.
+      fail-fast: false
+
+      # Set up a matrix to run the following 3 configurations:
+      # 1. <Linux, Release, latest GCC compiler toolchain on the default runner image, default generator>
+      # 2. <Linux, Release, latest Clang compiler toolchain on the default runner image, default generator>
+      #
+      # To add more build types (Release, Debug, RelWithDebInfo, etc.) customize the build_type list.
+      matrix:
+        os: [ubuntu-latest]
+        build_type: [Release]
+        c_compiler: [gcc, clang]
+        include:
+          - os: ubuntu-latest
+            c_compiler: gcc
+            cpp_compiler: g++
+          - os: ubuntu-latest
+            c_compiler: clang
+            cpp_compiler: clang++
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Set reusable strings
+      # Turn repeated input strings (such as the build output directory) into step outputs. These step outputs can be used throughout the workflow file.
+      id: strings
+      shell: bash
+      run: |
+        echo "build-output-dir=${{ github.workspace }}/build" >> "$GITHUB_OUTPUT"
+
+    - name: Configure CMake
+      # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
+      # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
+      run: >
+        cmake -B ${{ steps.strings.outputs.build-output-dir }}
+        -DCMAKE_CXX_COMPILER=${{ matrix.cpp_compiler }}
+        -DCMAKE_C_COMPILER=${{ matrix.c_compiler }}
+        -DCMAKE_BUILD_TYPE=${{ matrix.build_type }}
+        -S ${{ github.workspace }}
+
+    - name: Build
+      # Build your program with the given configuration. Note that --config is needed because the default Windows generator is a multi-config generator (Visual Studio generator).
+      run: cmake --build ${{ steps.strings.outputs.build-output-dir }} --config ${{ matrix.build_type }}
+
+    - name: Test
+      working-directory: ${{ steps.strings.outputs.build-output-dir }}
+      # Execute tests defined by the CMake configuration. Note that --build-config is needed because the default Windows generator is a multi-config generator (Visual Studio generator).
+      # See https://cmake.org/cmake/help/latest/manual/ctest.1.html for more detail
+      run: ctest --build-config ${{ matrix.build_type }}

.gitignore

@@ -11,3 +11,4 @@ tn93
 validate_fasta
 tn93-cluster
 fasta_diff
+seqdiff

Dockerfile

@@ -0,0 +1,12 @@
+# Docker image for a tn93 development environment
+FROM oraclelinux:8
+
+# Set up environment and install dependencies
+RUN yum -y update && \
+    yum install -y cmake gcc-c++ gcc-toolset-10 git make oracle-epel-release-el8 && \
+    echo 'source /opt/rh/gcc-toolset-10/enable' > ~/.bashrc && \
+    source ~/.bashrc
+
+# To compile tn93 within the development environment:
+#   cmake .
+#   make

VERSION.txt

@@ -1 +1 @@
-v1.0.14
+v1.0.14

src/TN93.cpp

@@ -421,7 +421,7 @@ int main(int argc, const char *argv[]) {
                               HISTOGRAM_SLICE, HISTOGRAM_BINS, weighted_count);
 
 
-        if (thisD >= -1.e-10 && thisD <= args.distance) {
+        if (thisD >= args.min_distance && thisD <= args.distance) {
           local_links_found += weighted_count;
           // char *s2 = stringText(sequences, seqLengths, seq1);
           if (!args.do_count) {

src/argparse.cpp

@@ -20,6 +20,7 @@ namespace argparse
   "[-v] "
   "[-o OUTPUT] "
   "[-t THRESHOLD] "
+  "[-w MIN_THRESHOLD] "
   "[-a AMBIGS] "
   "[-g FRACTION] "
   "[-l OVERLAP] "
@@ -43,6 +44,7 @@ namespace argparse
   "  -v, --version            show tn93 version \n"
   "  -o OUTPUT                direct the output to a file named OUTPUT (default=stdout)\n"
   "  -t THRESHOLD             only report (count) distances below this threshold (>=0, default=" TO_STR (DEFAULT_DISTANCE)")\n"
+  "  -w MINIMUM THRESHOLD     report distances above minimum threshold \n"
   "  -a AMBIGS                handle ambigous nucleotides using one of the following strategies (default=" TO_STR( DEFAULT_AMBIG ) ")\n"
   "                           resolve: resolve ambiguities to minimize distance (e.g.R matches A);\n"
   "                           average: average ambiguities (e.g.R-A is 0.5 A-A and 0.5 G-A);\n"
@@ -118,6 +120,7 @@ namespace argparse
   input1( stdin ),
   input2( NULL ),
   distance( DEFAULT_DISTANCE ),
+  min_distance( DEFAULT_MIN_DISTANCE ),
   ambig( DEFAULT_AMBIG ),
   format ( DEFAULT_FORMAT ),
   overlap ( DEFAULT_OVERLAP ),
@@ -149,6 +152,7 @@ namespace argparse
         else if (  arg[1] == 'v' ) version();
         else if (  arg[1] == 'o' ) parse_output( next_arg (i, argc, argv) );
         else if (  arg[1] == 't' ) parse_distance ( next_arg (i, argc, argv) );
+        else if (  arg[1] == 'w' ) parse_min_distance ( next_arg (i, argc, argv) );
         else if (  arg[1] == 'l')  parse_overlap( next_arg (i, argc, argv) );
         else if (  arg[1] == 'f')  parse_format( next_arg (i, argc, argv) );
         else if (  arg[1] == 'a')  parse_ambig( next_arg (i, argc, argv) );
@@ -234,6 +238,15 @@ namespace argparse
       ERROR( "genetic distance threshold must be in [0,1], had: %s", str );
   }
 
+  void args_t::parse_min_distance ( const char * str )
+  {
+    min_distance = atof( str );
+
+    if ( min_distance < 0.0 || min_distance > 1.0)
+      ERROR( "genetic minimum distance threshold must be in [0,1], had: %s", str );
+  }
+
+
   void args_t::parse_fraction ( const char * str )
   {
     resolve_fraction = atof( str );

src/argparse.hpp

@@ -9,6 +9,7 @@
 #define DEFAULT_FORMAT            csv
 #define DEFAULT_FRACTION          1.0
 #define DEFAULT_DISTANCE          0.015
+#define DEFAULT_MIN_DISTANCE      -1.e-10
 #define DEFAULT_COUNTS_IN_NAME    ':'
 #define DEFAULT_OVERLAP           100
 #define DEFAULT_INCLUDE_PROB      1.0
@@ -44,6 +45,7 @@ namespace argparse
                         * input2;
 
         double          distance;
+        double          min_distance;
         ambig_t         ambig;
         format_t        format;
         unsigned long   overlap;
@@ -69,6 +71,7 @@ namespace argparse
         void parse_second_in( const char * );
         void parse_output   ( const char * );
         void parse_distance ( const char * );
+        void parse_min_distance ( const char * );
         void parse_overlap  ( const char * );
         void parse_format   ( const char * );
         void parse_ambig    ( const char * );

src/tn93_shared.cc

@@ -129,7 +129,6 @@ const  double   resolutionsCount[] = { 1.f,
   1./2.f, // R
   1./2.f, // Y
   1./2.f, // S
-  1./2.f, // S
   1./2.f, // W
   1./2.f, // K
   1./2.f, // M