cleanup

.github/workflows/build.yml

@@ -27,7 +27,7 @@ jobs:
       run: |
         sudo apt-get update
         sudo apt-get install cmake wget build-essential
-        ./install_dependencies.sh linux
+        ./install_dependencies.sh
     - name: Compile and test
       run: |
         mkdir build && cd build && cmake -G "Unix Makefiles" -DCMAKE_CXX_COMPILER=${{ matrix.config.cxx }} -DCMAKE_C_COMPILER=${{ matrix.config.cc }} -DSTATIC_BUILD=1 ..
@@ -67,7 +67,6 @@ jobs:
       run: |
         #brew update
         HOMEBREW_NO_AUTO_UPDATE=1 brew install boost automake
-        ./install_dependencies.sh osx
     - name: Compile and test
       run: |
         mkdir build && cd build && cmake -G "Unix Makefiles" -DCMAKE_CXX_COMPILER=${{ matrix.config.cxx }} -DCMAKE_C_COMPILER=${{ matrix.config.cc }} ..
@@ -107,7 +106,6 @@ jobs:
       run: |
         #brew update
         HOMEBREW_NO_AUTO_UPDATE=1 brew install boost automake libtool
-        ./install_dependencies.sh osx
     - name: Compile and test
       run: |
         mkdir build && cd build && cmake -G "Unix Makefiles" -DCMAKE_CXX_COMPILER=${{ matrix.config.cxx }} -DCMAKE_C_COMPILER=${{ matrix.config.cc }} ..

README.md

@@ -134,15 +134,15 @@ Boost* | \>=1.65 | manual or automatic
 If you are using Ubuntu 16, you can prepare all dependencies and compile the Validation Suite with these commands:
 ```
 sudo apt-get install cmake wget build-essential
-./install_dependencies.sh linux
+./install_dependencies.sh
 mkdir build && cd build && cmake -G "Unix Makefiles" -DSTATIC_BUILD=1 ..
 make
 ```
 
 The VCF Validation Suite binaries will be created in the `build/bin` subfolder. Optionally, read below for the explanation of the previous commands.
 
 ##### CMake and automatic installation
-The automatic install **requires** CMake and wget to be installed before running the script (as zlib require them to be installed). Also, the script will compile some dependencies so a compilation environment is needed. If you are using Ubuntu, you can install all that with the command `sudo apt-get install cmake wget build-essential`. After installing that, use the command `./install_dependencies.sh linux`.
+The automatic install **requires** CMake and wget to be installed before running the script (as zlib require them to be installed). Also, the script will compile some dependencies so a compilation environment is needed. If you are using Ubuntu, you can install all that with the command `sudo apt-get install cmake wget build-essential`. After installing that, use the command `./install_dependencies.sh`.
 
 A subfolder named `dependencies` will be created, with all the required libraries copied into it. 
 
@@ -177,7 +177,7 @@ Boost | \>=1.65 | manual
 
 You can prepare all dependencies and compile the Validation Suite with these commands:
 ```
-brew install cmake boost sqlite3
+brew install cmake boost
 mkdir build && cd build && cmake -G "Unix Makefiles" ..
 make
 ```
@@ -188,8 +188,6 @@ The VCF Validation Suite binaries will be created in the `build/bin` subfolder.
 
 The automatic install requires CMake and wget to be installed before running the script (as zlib require them to be installed). In order to set up the environment to compile the dependencies, first you need to run `brew install cmake boost`.
 
-A subfolder named `osx_dependencies` will be created, with all the required libraries copied into it.
-
 #### Compile
 
 In order to create the build scripts, please run `cmake` with your preferred generator. For instance, `mkdir build && cd build && cmake -G "Unix Makefiles" ..` will create Makefiles, and to build the binaries, you will need to run `make`.
@@ -222,15 +220,12 @@ bootstrap
 In order to create the build scripts and compile vcf-validator, please run the following commands from the project root folder:
 
 ```
-cmake -DCMAKE_BUILD_TYPE=Release -G "NMake Makefiles" /path/to/CMakeLists.txt
+cmake -DCMAKE_BUILD_TYPE=Release -DSTATIC_BUILD=1 -G "NMake Makefiles" /path/to/CMakeLists.txt
 nmake
 ```
 
 Binaries will be created in the `bin` subfolder.
 
-In order to run those binaries, you will need to add the `lib/windows_specific` directory to the `PATH`. This will allow the dll files inside that directory to be found.
-
-
 ## Deliverables
 
 The following binaries are be created after successful build:

appveyor.yml

@@ -24,8 +24,5 @@ artifacts:
   - path: bin\vcf_validator.exe
     name: vcf_validator_win.exe
 
-  - path: bin\vcf_debugulator.exe
-    name: vcf_debugulator_win.exe
-
   - path: bin\vcf_assembly_checker.exe
     name: vcf_assembly_checker_win.exe

docs/developer-guide.md

@@ -11,11 +11,11 @@ into the programming technical details.
 
 ## Build process overview
 
-This is a C++ project that produces 3 binaries: vcf-validator,
-vcf-assembly-checker and vcf-debugulator. The build is done with CMake (file
+This is a C++ project that produces 2 binaries: vcf-validator and
+vcf-assembly-checker. The build is done with CMake (file
 [CMakeLists.txt](../CMakeLists.txt)) for Linux, Windows and macOS. There are
 scripts to help installing the dependencies
-([install_dependencies.sh](../install_dependencies.sh)) for Linux and macOS, and
+([install_dependencies.sh](../install_dependencies.sh)) for Linux and
 [install_dependencies.bat](../install_dependencies.bat) for Windows).
 
 We also use TravisCI ([.travis.yml](../.travis.yml)) and AppVeyor
@@ -79,11 +79,7 @@ VCF (including the metadata section), and `Error` classes (related among
 themselves by hierarchical inheritance) are used to represent different types of
 possible errors.
 
-Based on those `Error`s, the program can produce human-readable reports and a
-machine-readable report that the VCF Debugulator can read to fix some basic
-errors. Later, this machine-readable report and Debugulator support were removed
-to make build, packaging and installation simpler.
-
+Based on those `Error`s, the program can produce human-readable reports.
 The level of checks can be configured, from doing just a quick syntax check, to
 raise warnings of suspicious details.
 
@@ -179,25 +175,9 @@ of polymorphism when we catch those exceptions in vcf.ragel (again, search for
 
 If the policy to report the errors is in use, the parser has the list of
 report writers the user requested. These can be any combination of
-[simple report](../inc/vcf/record.hpp), [summary
-report](../inc/vcf/summary_report_writer.hpp), and [ODB
-report](../inc/vcf/odb_report.hpp).
-
-ODB is a library for Object Relational Mapping. In other words, we use it to
-serialize the class data of errors, so that the debugulator can deserialize
-the error details directly into variables and classes without parsing.
-
-We use ODB mostly in [inc/vcf/Error.hpp](../inc/vcf/error.hpp), through some
-pragmas. The way ODB works is parsing the C++ classes that have ODB pragmas and
-outputs C++ code that serializes the class instance information into a SQL
-database. We chose Sqlite as database backend, which means that the DB reports
-can actually be opened with a Sqlite client.
-
-The debugulator had very minimal functionality and limited usage. To reduce the
-build, packaging and installation complexities, a few of the dependencies were
-removed and ODB is one among them. Along with ODB, debugulator was also removed
-from build as it is fully dependent on ODB. The sources and part of
-documentation retained for future reference.
+[simple report](../inc/vcf/record.hpp) and
+[summaryreport](../inc/vcf/summary_report_writer.hpp).
+
 
 ### VCF assembly checker
 
@@ -222,31 +202,9 @@ There's also limited support to use assembly reports
 and translate between synonym contig names/accessions in case the nomenclature
 in the VCF and in the FASTA don't match.
 
-### VCF Debugulator
-
-At the beginning of the project we expected there would be interesting
-situations were we could use the ODB report to fix automatically wrong VCFs.
-Sadly, it turned out that there's not much an automated program can do, really.
-
-The fixes are implemented in [inc/vcf/fixer.hpp](../inc/vcf/fixer.hpp) and 
-[src/vcf/fixer.cpp](../src/vcf/fixer.cpp), and basically consist on removing
-duplicate variants and dropping entire fields that are non-conforming with the
-spec.
-
-The debugulator had very minimal functionality and limited usage. To reduce the
-build, packaging and installation complexities, a few of the dependencies were
-removed and ODB is one among them. Along with ODB, debugulator was also removed
-from build as it is fully dependent on ODB. The sources and part of
-documentation retained for future reference.
-
 ## Testing
 
 Testing is performed with [Catch](https://github.com/catchorg/Catch2) in the
 [`test/`](../test/) folder. The folders test/vcf/, test/fasta/ and
 test/assembly_report/ contain test source code, and test/input_files contain a
-medium-sized set of correct and wrong VCFs that are used in the tests.
-
-## ODB dependency
-
-ODB was in use earlier and it has now been removed. Debugulator was also removed
-along with it as it depends on ODB.
+medium-sized set of correct and wrong VCFs that are used in the tests.