Develop 0.4.3

[akikuno]

v0.4.3 (2024-03-29)

📝 Documentation

• Update example dataset and a description of README.md/README_JP.md Commit Detail

🐛 Bug Fixes

• Update preprocess.genome_fetcher_fetch_seq_coordinates to accurately verify that the entire length of the input sequence is present within the reference sequence. Previously, partial 100% matches were inadvertently accepted; this revision aims to ensure the full alignment of the input sequence with the reference. Commit Detail

• Update report.bam_exporter to be case-sensitive and consistent with directory names. This is to avoid errors caused by the difference between report/bam and report/BAM on Ubuntu, which is case-sensitive to directory names. Commit Detail

  • Thank you @takeiga for reporting the issue two more errors in execution (one fixed) #24 !

🔧 Maintenance

• Change threshold_readnumber at labem_merger.merge_labels from 10 to 5 to capture 1% alleles from 500 total reads. Commit Detail

• Update the requirements.txt to install a newer version of the library. Commit Detail

• Update report.report_bam and rename to report.bam_exporter: Commit Detail

  • Use UUID instead of random number for the temporary file name.
  • Rename realign to recalculate_sam_coodinates_to_reference for the readability of the function name.
  • Add convert_pos_to_one_indexed to convert the 0-based position to 1-based position and suppress samtools warning.
    • Warning: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped
  • Add tests for the write_sam_to_bam function

• Move read_sam function from sam_handler to io module. Commit Detail

• Rename report.report_mutation, report.report_files to report.mutation_exporter and report.sequence_exporter to be more explicit. Commit Detail