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Commits on Feb 16, 2026

• Automatically run "extract_cb_umi_as_fastq_from_sra_file.sh" script from "sra_file_to_fastqs.sh" when needed.

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• Add script to extract CB and UMI (10X sc/snRNA) from "LINKAGE_GROUP" field of SRA file and convert to FASTQ.

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• Get SRR number from SRA filename earlier in "sra_file_to_fastqs".

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• Check if needed executables are available in PATH for "sra_file_to_fastqs.sh".

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Commits on Feb 11, 2026

• Add "sra_file_to_fastqs.sh" script to convert SRA file to multiple FASTQ files.

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Commits on Dec 19, 2025

• Add support for sc/snRNA barcode correction in `correct_barcode_from_fastq`

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• Rename "auto_reverse_comp" to "auto_rev_comp".

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Commits on Dec 18, 2025

• Use __new__ constructor in CorrectedBC for different type than the default.

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• Add "bc_start_idx" option to "read_barcode_whitelist_from_file".

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Commits on Dec 16, 2025

• Only support Codon in barcode extraction and correction scripts.

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• Rename "*.seq" scripts to "*.codon" and "seq_lib" dir to "barcode_extraction_and_correction".

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Commits on Dec 15, 2025

• Move scripts than manipulate FASTQ files to a subfolder.

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• Move scripts for barcode extraction and correction to a subfolder.

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Commits on Dec 11, 2025

• Allow comma separated chromosome names for "--chroms" option in split_bams_per_cluster(_htslib).

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• Improve long help output of split_bams_per_cluster(_htslib).

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Commits on Dec 10, 2025

• Add extract_and_correct_hydrop_rna_barcode_from_fastq for extracting and correcting HyDrop RNA barcodes from R1 read.

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• Fix adding bc_suffix to cell barcodes in extract_and_correct_hydrop_atac_barcode_from_fastq.

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• Add script to convert fragments file to cut sites file.

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• Use new "update_aux" function instead of removing and re-adding an aux tag.

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Commits on Aug 6, 2025

• Run `rustfmt` on `create_parsebio_per_sample_bams.rs`.

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Commits on Jun 30, 2025

• Fix typo in help of split_bams_per_cluster and split_bams_per_cluster_htslib.

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Commits on Jun 26, 2025

• Update split_bams_per_cluster so it works with noodles v0.99.0.

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• Update dependencies.

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• Run `rustfmt` for split_bams_per_cluster_htslib.

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Commits on Jan 6, 2025

• Allow only retaining reads for specific chromosomes in split_bams_per_cluster_htslib.

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• Check if BAM files are coordinate sorted in a more robust way.

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• Add `--ignore_mate_mapping_quality` option to split_bams_per_cluster_htslib.

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Commits on Dec 12, 2024

• Expose chunk_size as command line argument in split_bams_per_cluster.

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• Add needed column names for input files to help output of split_bams_per_cluster_htslib.

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• Include reads at the end of the chromosome and expose chunk_size as command line argument in split_bams_per_cluster_htslib.

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• Add "cargo +nightly fmt" changes.

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• Update bgzf::MultithreadedWriter usage in create_fragments_file to noodles 0.85.

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• Update noodles and enable libdeflate again in rust-htslib.

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Commits on Dec 11, 2024

• Update some dependencies.

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Commits on Dec 10, 2024

• Skip unwanted reads quicker in split_bams_per_cluster.

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