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CHANGELOG.md

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CHANGELOG

v4.0.8 (2024-07-17)

Fix

  • fix: Dummy release to generate Zenodo DOI (2c890f9)

v4.0.7 (2024-06-28)

Fix

  • fix: Remove author from init.py (2d48c4a)

Performance

  • perf: Reduce dataframe memory footprint (011f2bb)

v4.0.6 (2023-03-08)

Fix

  • fix: Fix missing fields in str conversion (4bbef95)

v4.0.5 (2023-03-06)

Fix

  • fix: Fix Python3.6 typings (5b3bdd6)

v4.0.4 (2023-03-02)

Performance

  • perf: Improve str performance (ec14074)

v4.0.3 (2023-03-02)

Performance

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

v4.0.2 (2023-02-16)

Fix

  • fix: Add init file to private module (549b7c5)

v4.0.1 (2023-02-15)

Fix

v4.0.0 (2023-02-10)

Breaking

  • fix: Match TRA to VCF specification

BREAKING CHANGE: Translocations are no longer named TRN, but TRA instead (1f7dd1e)

Feature

  • feat: Add empty_dataframe method (ebaf357)

  • feat: Add to_dataframe() method (4e666aa)

  • feat: Convert 1-length DELs to INS (ae6cd8c)

Fix

  • fix: Fix typing Python3.6 (1d72f80)

  • fix: Fix typing for Python3.6 (1648bb7)

  • fix: Rename to breakend notation (2d86782)

  • fix: Print format values in the correct order (ee3d399)

  • fix: Fix float .2f VCF representation (ed34a40)

  • fix: Trim extra \t (ef55c36)

  • fix: Prioritize MATEID over coords for matching breakends (c6d21bf)

  • fix: Unify different filters for paired breakends (2407216)

  • fix: Change SNV length to 1 (dfe6463)

Unknown

  • fix: Fix wrong SAMPLEs in multiallelic variants (7fc170f)

v3.1.0 (2022-06-14)

Feature

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

Fix

  • fix: Remove 'None' from sample field (23bc5f3)

  • fix: Correctly display flag INFO values (bd83771)

  • fix: Fix permutation of SV variant (d1cad92)

  • fix: Add missing END to info str (3606000)

  • fix: Remove complex indel normalization (65c5007)

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

v3.0.0 (2022-04-25)

Breaking

  • feat: Switch to VariantExtractor iterations through iter

BREAKING CHANGE: read_vcf() method no longer exists. Iterating through the VariantExtractor instance have the same effect. (b7d8e58)

  • feat: read_vcf() returns a lazy generator

BREAKING CHANGE: VariantExtractor constructor parameter only_pass renamed to pass_only

BREAKING CHANGE: read_vcf() no longer returns a list, but a lazy generator (cd7decf)

Feature

  • feat: Add str method to VariantRecord (7f3aa7d)

Fix

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

v2.1.0 (2022-04-20)

Feature

  • feat: Include all information in VariantRecord (894763e)

  • feat: Infer TRN brackets from pair (6cd0ede)

  • feat: Add support for multiallelic variants (c763b97)

  • feat: Divide compound indels (96f72e5)

Fix

  • fix: Fix imprecise breakends handling (b2cab22)

  • fix: Switch regex to fullmatch (c554b52)

  • fix: Fix multiallelic record handling (0e1620f)

  • fix: SVLEN not set now defaults to 0 (6afbb0d)

  • fix: Fix mate_id referenced before assignment (5efdeca)

v2.0.0 (2022-04-04)

Breaking

  • feat: Change alts to alt

BREAKING CHANGE: VariantRecord.alts no longer contains a list, it has been changed to VariantRecord.alt (8e1dd86)

  • feat: Include variant_type in VariantRecord

BREAKING CHANGE: read_vcf() no longer returns a tuple of VariantType and VariantRecord. It now returns a list of just VariantRecord (2fe8b37)

  • feat: Remove INDEL_DEL and INDEL_INS

BREAKING CHANGE: Now INDEL_DEL and INDEL_INS are treated like DEL and INS (e7bbd40)

Feature

  • feat: Add length field to VariantRecord (9a0e446)

  • feat: Add qual field (4d23686)

  • feat: Add only_pass parameter (39d7b41)

  • feat: Add support for SGLs (#1) (f3621c0)

  • feat: Import implementation (8a676e7)

Fix

  • fix: Divide INV into bracket notation (c18a40c)

  • fix: Fix SGL regex (b58c867)

  • fix: Complete the documentation (fbe5c4d)

  • fix: Add support for dots in bracket notation (e4dc00b)

  • fix: Fix import path (a9db147)