Use htslib

.github/workflows/c-cpp.yml

@@ -0,0 +1,28 @@
+name: C/C++ CI
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }}
+    strategy:
+      matrix:
+        os: [ ubuntu-latest, ubuntu-latest-arm, macos-15 ]
+
+    steps:
+    - uses: actions/checkout@v4
+#    - name: configure
+#      run: ./configure
+    - name: make
+      run: make
+    - name: make check
+      run: make check
+#    - name: make distcheck
+#      run: make distcheck
+

.github/workflows/main.yml

@@ -0,0 +1,27 @@
+name: Main C/C++ CI
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+  workflow_dispatch:
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: clone repo
+      uses: actions/checkout@v4
+    - name: make
+      run: make
+    - name: make check
+      run: make check
+
+#    - name: make distcheck
+#      run: make distcheck
+#    - name: configure
+#      run: ./configure
+

.gitignore

@@ -1,6 +1,10 @@
 build/
+tmp_*
 *.swp
 *.swo
 *~
 *.DS_Store
 *.vscode/
+scratch/
+data/
+tags

CLAUDE.md

@@ -0,0 +1,40 @@
+# Purpose
+- Compute the genetic similarity matrix from genetic data stored in the 
+vcf, vcf.gz, and bcf files.
+- Use htslib C library to query / read genentic data.
+- Write data to a binary file with a header and payload.
+    * header data must include all information that is
+    required to reproduce the calculation.
+    * payload consists of the computed values
+- Easy to use command line interface
+
+
+# External libraries
+- htslib, code available on github at: https://github.com/samtools/htslib
+- argparse, code available on github at: https://github.com/robert-vogel/argparse
+
+
+# Code style
+- variable, function, class, etc. names:
+    * should be descriptive (self-documenting) and short.
+    * classes and structs use Upper camel case
+    * functions and variables use snake case
+    - global constants use all upper case
+- keep orthogonal services of the code in distinct modules
+- module header files 
+    * written to the 'include' directory.
+    * API documentation should be on line(s) proceeding the entities they
+    describe.
+- implementation files in the 'src' directory, make sure to describe the
+purpose / design of complex code blocks in the comments
+- Unit tests should be written in the 'tests' directory and use Google
+test and mock frameworks
+
+
+# File and directory structure
+- 'scratch' directory is not tracked by version control and is for testing
+ideas by implementing in small programs
+- 'build' directory is the target path for program and unit test builds
+and should not be tracked by version control.
+- 'include' directory for header files
+- 'src' directory for 'main.cpp' file and module implementation files