README.md

Setup

Each participant should choose a color which will be the name of the projects namespace. The setup consist of creating a C++ program and naming it in form of <color>_mapper, while using CMake as the build system. The program has to accept two mandatory files as floating arguments and enable options -h (--help) and --version, which are used for the help and version message (follow SemVer), respectively. Enable additional floating arguments for the case when there are multiple sequence files, and combine the sequences in memory after loading. Suggested argument parser is optarg, but this feature can be implemented independently.

The first file will contain a reference genome in FASTA format, while each following file will contain the set of fragments in either FASTA or FASTQ format. The files need to be parsed and stored in memory, and some basic statistics should be outputted to stderr for the reference and the set of all fragments, such as number of sequences, average length, N50 length, minimal and maximal length, etc. Participants can add bioparser to the project via CMake, either with FetchContent or as a git submodule (https://git-scm.com/book/en/v2/Git-Tools-Submodules), the former being preferable. Bioparser supports both needed formats and the files can also be compressed with gzip. Parsing can be implemented independently as well.

Furthermore, Googletest needs to be added via CMake's FetchContent module, accompanied with one unit test which has an always true assertion (it is used just to test Googletest integration). Every piece of code following afterwards should have its own unit tests. In order to test the code after each commit, create a GitHub Actions workflow choosing several compiler versions for both gcc and clang, and operating systems Ubuntu and macOS (can be multiple versions as well).

Usage information and compilation instructions should be put inside the README located in the root of this project. The same holds for a badge denoting the result of compilation and unit tests run via GitHub Actions.

While coding, it is suggested to follow the Google C++ Style Guide and use a linter in an IDE of choice.

The first version of the mapper can be tested on an Oxford Nanopore Technologies data set obtained by sequencing the Escherichia coli K-12 substr. MG1655 genome. The data set is available from Loman Labs here (download both MAP-006-1 and MAP-006-2 FASTA files), while the reference genome is available from NCBI here. Do not upload large files to the repository.

Example mapper runs after the setup step is completed, can be seen below:

Input:

<color>_mapper GCF_000005845.2_ASM584v2_genomic.fna MAP006-1_2D_pass.fasta

Output:

<basic statistics of reference>
<basic statistics of fragment file>

Input:

<color>_mapper GCF_000005845.2_ASM584v2_genomic.fna MAP006-1_2D_pass.fasta MAP006-2_2D_pass.fasta

Output:

<statistics of reference>
<statistics of both fragment files together>

Input:

<color>_mapper -h

Output:

<message describing how to run the tool with supported arguments>

Input:

<color>_mapper --version

Output:

v0.1.0