CHANGELOG

v4.0.10 (2025-03-26)

Bug Fixes

  • Add pysam missing dependency (0660910)

  • Reduce dataframe memory footprint (d81bcd9)

v4.0.9 (2025-03-26)

Bug Fixes

  • Allow for numbers in shorthand SVs (8feb749)

v4.0.8 (2024-07-17)

Bug Fixes

  • Dummy release to generate Zenodo DOI (2c890f9)

v4.0.7 (2024-06-28)

Bug Fixes

  • Remove author from init.py (2d48c4a)

Performance Improvements

  • Reduce dataframe memory footprint (011f2bb)

v4.0.6 (2023-03-08)

Bug Fixes

  • Fix missing fields in str conversion (4bbef95)

v4.0.5 (2023-03-06)

Bug Fixes

v4.0.4 (2023-03-02)

Performance Improvements

  • Improve str performance (ec14074)

v4.0.3 (2023-03-02)

Performance Improvements

  • Improve I/O speed by lazy loading fields (93782fc)

v4.0.2 (2023-02-16)

Bug Fixes

  • Add init file to private module (549b7c5)

v4.0.1 (2023-02-15)

Bug Fixes

v4.0.0 (2023-02-10)

Bug Fixes

  • Change SNV length to 1 (dfe6463)

  • Fix float .2f VCF representation (ed34a40)

  • Fix typing for Python3.6 (1648bb7)

  • Fix typing Python3.6 (1d72f80)

  • Match TRA to VCF specification (1f7dd1e)

BREAKING CHANGE: Translocations are no longer named TRN, but TRA instead

  • Print format values in the correct order (ee3d399)

  • Prioritize MATEID over coords for matching breakends (c6d21bf)

  • Rename to breakend notation (2d86782)

  • Trim extra \t (ef55c36)

  • Unify different filters for paired breakends (2407216)

Features

  • Add empty_dataframe method (ebaf357)

  • Add to_dataframe() method (4e666aa)

  • Convert 1-length DELs to INS (ae6cd8c)

Breaking Changes

  • Translocations are no longer named TRN, but TRA instead

v3.1.0 (2022-06-14)

Bug Fixes

  • Add missing END to info str (3606000)

  • Correctly display flag INFO values (bd83771)

  • Fix permutation of SV variant (d1cad92)

  • Remove ‘None’ from sample field (23bc5f3)

  • Remove complex indel normalization (65c5007)

  • Set dot for None values in sample field (43e4c83)

Features

  • Replace N with correct nucleotide if possible (8a260e1)

v3.0.0 (2022-04-25)

Bug Fixes

  • Add dot if info is not defined (70fa09b)

Features

  • Add str method to VariantRecord (7f3aa7d)

  • Read_vcf() returns a lazy generator (cd7decf)

BREAKING CHANGE: VariantExtractor constructor parameter only_pass renamed to pass_only

BREAKING CHANGE: read_vcf() no longer returns a list, but a lazy generator

  • Switch to VariantExtractor iterations through iter (b7d8e58)

BREAKING CHANGE: read_vcf() method no longer exists. Iterating through the VariantExtractor instance have the same effect.

Breaking Changes

  • Read_vcf() method no longer exists. Iterating through the VariantExtractor instance have the same effect.

v2.1.0 (2022-04-20)

Bug Fixes

  • Fix imprecise breakends handling (b2cab22)

  • Fix mate_id referenced before assignment (5efdeca)

  • Fix multiallelic record handling (0e1620f)

  • Svlen not set now defaults to 0 (6afbb0d)

  • Switch regex to fullmatch (c554b52)

Features

  • Add support for multiallelic variants (c763b97)

  • Divide compound indels (96f72e5)

  • Include all information in VariantRecord (894763e)

  • Infer TRN brackets from pair (6cd0ede)

v2.0.0 (2022-04-04)

Bug Fixes

  • Add support for dots in bracket notation (e4dc00b)

  • Complete the documentation (fbe5c4d)

  • Divide INV into bracket notation (c18a40c)

  • Fix import path (a9db147)

  • Fix SGL regex (b58c867)

Features

BREAKING CHANGE: VariantRecord.alts no longer contains a list, it has been changed to VariantRecord.alt

  • Import implementation (8a676e7)

  • Include variant_type in VariantRecord (2fe8b37)

BREAKING CHANGE: read_vcf() no longer returns a tuple of VariantType and VariantRecord. It now returns a list of just VariantRecord

  • Remove INDEL_DEL and INDEL_INS (e7bbd40)

BREAKING CHANGE: Now INDEL_DEL and INDEL_INS are treated like DEL and INS