update ROADMAP

akikuno · Jan 17, 2024 · ce86359 · ce86359
1 parent 65030da
commit ce86359
Showing 1 changed file with 9 additions and 4 deletions.
diff --git a/docs/ROADMAP.md b/docs/ROADMAP.md
@@ -2,6 +2,7 @@
 
 <!-- TEMPLATE
 # v0.0.0 (yyyy-mm-dd)
+## 💥 Breaking Changes
 ## 📝 Documentation
 ## 🚀 New Features
 ## 🐛 Bug Fixes
@@ -11,11 +12,11 @@
 -->
 
 <!-- memo ToDo
-- macOS (Apple Silicon) でのインストール方法を追記する
-- FASTQ、VCFを出力する
+- ✅ macOS (Apple Silicon) でのインストール方法を追記する
+- Guppyの出力にあわせて、ディレクトリを指定するだけで実行できるようにする
+- ~~FASTQ~~、VCF、PDFを出力する
 
 + # 💡 Future Tasks
-+ Remove minor alleles with predicted insertion
 + Enhance the Clarity of Insertion Allele Identification.
 + Develop and Integrate Inversion Detection Capability
  -->
@@ -37,14 +38,18 @@
 
 + Update `preprocess.insertion_to_fasta` to facilitate the discrimination of Insertion alleles, the Reference for Insertion alleles has been saved in FASTA/HTML directory. [Commit Detail](https://github.com/akikuno/DAJIN2/commit/5899543077f0398863b6316d8c3e953b5f125f55)
 
++ Update `insertions_to_fasta.extract_enriched_insertions`: Previously, it calculated the presence ratio of insertion alleles separately for samples and controls, filtering at 0.5%. However, due to a threshold issue, some control insertions were narrowly missing the threshold, resulting in them being incorrectly identified as sample-specific insertions. To rectify this, the algorithm now clusters samples and controls together, excluding clusters where both types are mixed. This modification allows for the extraction of sample-specific insertion alleles. [Commit Detail](https://github.com/akikuno/DAJIN2/commit/65030daba7c56a6c3f3f685832084b71c6b2e1c3)
+
 + Updated `preprocess.insertions_to_fasta.count_insertions` of the counting method to treat similar insertions as identical. Previously, the same insertion was erroneously counted as different ones due to sequence errors. [Commit Detail](https://github.com/akikuno/DAJIN2/commit/7bc18f486253e876d51a296f64909e1c73114e79)
 
-+ Debug `clustering.merge_labels` to be able to correctly revert minor labels back to parent labels. [Commit Detail](https://github.com/akikuno/DAJIN2/commit/8127a94e042328b87e456d3748ebea66a845ba1a)
 
 + Moved the `call_sequence` function to the `cssplits_handler` module. [Commit Detail](https://github.com/akikuno/DAJIN2/commit/ef5b0bf41ab33a7e8d06d33fe7fa6c27a443742a)
 
 ## 🐛 Bug Fixes
 
++ Debug `clustering.merge_labels` to be able to correctly revert minor labels back to parent labels. [Commit Detail](https://github.com/akikuno/DAJIN2/commit/8127a94e042328b87e456d3748ebea66a845ba1a)
+
+
 + Updated `utils.input_validator.validate_genome_and_fetch_urls` to obtain `available_server` more explicitly. Previously, it relied on HTTP response codes, but there were instances where the UCSC Genome Browser showed a normal (200) response while internally being in error. Therefore, with this change, a more explicit method is employed by searching for specific keywords present in the normal HTML, to determine if the server is functioning correctly. [Commit Detail](https://github.com/akikuno/DAJIN2/commit/24a02591e8a146030012dbf564e4b6cd98d42139)
 
 + Added `config.reset_logging` to reset the logging configuration. Previously, when batch processing multiple experiment IDs (names), a bug existed where the log settings from previous experiments remained, and the log file name was not updated. However, with this change, log files are now created for each experiment ID. [Commit Detail](https://github.com/akikuno/DAJIN2/commit/b83669c627710a5e358f934212e961373203ee52)