Variant-extractor

Fix

* fix: Add __init__ file to private module ([`549b7c5`](https://github.com/EUCANCan/variant-extractor/commit/549b7c53fcd6c8ede96c177c4f65e414b260c7f5))

Fix

* fix: Add PyPI docs ([`fd3b89c`](https://github.com/EUCANCan/variant-extractor/commit/fd3b89c995810834c13389f1ee16d0b9333f43ba))

Breaking

* fix: Match TRA to VCF specification

BREAKING CHANGE: Translocations are no longer named TRN, but TRA instead ([`1f7dd1e`](https://github.com/EUCANCan/variant-extractor/commit/1f7dd1eb99f425e787a6d0cfb75c1641316c5b8c))

Feature

* feat: Add empty_dataframe method ([`ebaf357`](https://github.com/EUCANCan/variant-extractor/commit/ebaf357f40f3dd1ac2e5bbd6c74615385e668e12))

* feat: Add to_dataframe() method ([`4e666aa`](https://github.com/EUCANCan/variant-extractor/commit/4e666aa6821f58b887feb8f013afc76060d1aaff))

* feat: Convert 1-length DELs to INS ([`ae6cd8c`](https://github.com/EUCANCan/variant-extractor/commit/ae6cd8ca66205a40e5e39bef06ede0949a20a0aa))

Fix

* fix: Fix typing Python3.6 ([`1d72f80`](https://github.com/EUCANCan/variant-extractor/commit/1d72f80f54ffb3e6db4769f4e2f3388ba96f825b))

* fix: Fix typing for Python3.6 ([`1648bb7`](https://github.com/EUCANCan/variant-extractor/commit/1648bb744ed911b72d421ad9340570493d8baec8))

* fix: Rename to breakend notation ([`2d86782`](https://github.com/EUCANCan/variant-extractor/commit/2d86782a4870376d6ab2985ff477ce72eed6dd96))

* fix: Print format values in the correct order ([`ee3d399`](https://github.com/EUCANCan/variant-extractor/commit/ee3d399a68601d37da9391e91261feb2d0cffc8d))

* fix: Fix float .2f VCF representation ([`ed34a40`](https://github.com/EUCANCan/variant-extractor/commit/ed34a40bafce79c49be4b46fe9c032478106233b))

* fix: Trim extra \t ([`ef55c36`](https://github.com/EUCANCan/variant-extractor/commit/ef55c36f05e3c8c3793a5d8b6989c5d304a640f2))

* fix: Prioritize MATEID over coords for matching breakends ([`c6d21bf`](https://github.com/EUCANCan/variant-extractor/commit/c6d21bf51246315adca68ed4763c831742d844a2))

* fix: Unify different filters for paired breakends ([`2407216`](https://github.com/EUCANCan/variant-extractor/commit/24072160ac4f05d8d89928df00c4fa00125bf766))

* fix: Change SNV length to 1 ([`dfe6463`](https://github.com/EUCANCan/variant-extractor/commit/dfe6463e018a1d0368668e091be26a27f4dcdda7))

Unknown

* fix: Fix wrong SAMPLEs in multiallelic variants ([`7fc170f`](https://github.com/EUCANCan/variant-extractor/commit/7fc170fd535b2483f8d344428a5e567148e8b4c6))

Feature

* feat: Replace N with correct nucleotide if possible ([`8a260e1`](https://github.com/EUCANCan/variant-extractor/commit/8a260e10bc0f01f268a27dba3e4ed85adbc0f042))

Fix

* fix: Remove &39;None&39; from sample field ([`23bc5f3`](https://github.com/EUCANCan/variant-extractor/commit/23bc5f3caca4fc5114299480362f23bc6284ecb5))

* fix: Correctly display flag INFO values ([`bd83771`](https://github.com/EUCANCan/variant-extractor/commit/bd8377159d70eb6c75b181b0c35a04bd4508d102))

* fix: Fix permutation of SV variant ([`d1cad92`](https://github.com/EUCANCan/variant-extractor/commit/d1cad92800dc6e603a90800943449180700b2d09))

* fix: Add missing END to info str ([`3606000`](https://github.com/EUCANCan/variant-extractor/commit/36060003088c8240c4d02c733a124785822a922b))

* fix: Remove complex indel normalization ([`65c5007`](https://github.com/EUCANCan/variant-extractor/commit/65c5007f4c5314abeb3baadd899ac0fd334f2740))

* fix: Set dot for None values in sample field ([`43e4c83`](https://github.com/EUCANCan/variant-extractor/commit/43e4c831f5eaddb5ed2233b3d544070941be805d))

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`](https://github.com/EUCANCan/variant-extractor/commit/b7d8e5846979c696dd587ec2e747f782d0c8360c))

* 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`](https://github.com/EUCANCan/variant-extractor/commit/cd7decf68e18f0bf73568db7ac3e5b0b317ef65d))

Feature

* feat: Add __str__ method to VariantRecord ([`7f3aa7d`](https://github.com/EUCANCan/variant-extractor/commit/7f3aa7d312c99c3654ac22b071c2468cb7432c6b))

Fix

* fix: Add dot if info is not defined ([`70fa09b`](https://github.com/EUCANCan/variant-extractor/commit/70fa09b7d7b9eef63a826db0f1749fc850a04e8d))

Feature

* feat: Include all information in VariantRecord ([`894763e`](https://github.com/EUCANCan/variant-extractor/commit/894763e38b5ca34abe3d909fe1cc2e738133d4f0))

* feat: Infer TRN brackets from pair ([`6cd0ede`](https://github.com/EUCANCan/variant-extractor/commit/6cd0edef719d8c817b071331c9a3af598925a3e4))

* feat: Add support for multiallelic variants ([`c763b97`](https://github.com/EUCANCan/variant-extractor/commit/c763b97b613e9cb85a98401e09888f4d5322040e))

* feat: Divide compound indels ([`96f72e5`](https://github.com/EUCANCan/variant-extractor/commit/96f72e51dbea136b2f1c638b6d686a57a294e187))

Fix

* fix: Fix imprecise breakends handling ([`b2cab22`](https://github.com/EUCANCan/variant-extractor/commit/b2cab22f1dc476c9e703537f389a66b94f5a7a4c))

* fix: Switch regex to fullmatch ([`c554b52`](https://github.com/EUCANCan/variant-extractor/commit/c554b5247621d95a4a81470683ee668311bdfea3))

* fix: Fix multiallelic record handling ([`0e1620f`](https://github.com/EUCANCan/variant-extractor/commit/0e1620f4dd4d08bda18399418aa7e6dcc26feaee))

* fix: SVLEN not set now defaults to 0 ([`6afbb0d`](https://github.com/EUCANCan/variant-extractor/commit/6afbb0df1410859043e5645b80680763cf0f5310))

* fix: Fix mate_id referenced before assignment ([`5efdeca`](https://github.com/EUCANCan/variant-extractor/commit/5efdeca18f742a4c6453eb91916954ec600a78e6))