From 49b236f17aaa95ffa7d21ac3f01c7e8ba491199b Mon Sep 17 00:00:00 2001 From: Adam English Date: Wed, 5 Feb 2025 09:38:29 -0500 Subject: [PATCH] version bump --- README.md | 2 +- repo_utils/answer_key/help.txt | 2 +- truvari/__init__.py | 2 +- truvari/variant_record.py | 4 ++-- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index f889883f..13c05faa 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ [![pylint](imgs/pylint.svg)](https://github.com/acenglish/truvari/actions/workflows/pylint.yml) [![FuncTests](https://github.com/acenglish/truvari/actions/workflows/func_tests.yml/badge.svg?branch=develop&event=push)](https://github.com/acenglish/truvari/actions/workflows/func_tests.yml) [![coverage](imgs/coverage.svg)](https://github.com/acenglish/truvari/actions/workflows/func_tests.yml) -[![develop](https://img.shields.io/github/commits-since/acenglish/truvari/v5.0.0)](https://github.com/ACEnglish/truvari/compare/v5.0.0...develop) +[![develop](https://img.shields.io/github/commits-since/acenglish/truvari/v5.1.1)](https://github.com/ACEnglish/truvari/compare/v5.1.1...develop) [![Downloads](https://static.pepy.tech/badge/truvari)](https://pepy.tech/project/truvari) ![Logo](https://raw.githubusercontent.com/ACEnglish/truvari/develop/imgs/BoxScale1_DarkBG.png) diff --git a/repo_utils/answer_key/help.txt b/repo_utils/answer_key/help.txt index 0fdc9aed..3f67d903 100644 --- a/repo_utils/answer_key/help.txt +++ b/repo_utils/answer_key/help.txt @@ -1,6 +1,6 @@ usage: truvari [-h] CMD ... -Truvari v5.1.1 Structural Variant Benchmarking and Annotation +Truvari v5.1.2-dev Structural Variant Benchmarking and Annotation Available commands: bench Performance metrics from comparison of two VCFs diff --git a/truvari/__init__.py b/truvari/__init__.py index 77121047..f129dd96 100644 --- a/truvari/__init__.py +++ b/truvari/__init__.py @@ -67,7 +67,7 @@ :data:`truvari.SZBINTYPE` """ -__version__ = '5.1.1' +__version__ = '5.1.2-dev' from truvari.bench import ( diff --git a/truvari/variant_record.py b/truvari/variant_record.py index 993212c1..0c949fdc 100644 --- a/truvari/variant_record.py +++ b/truvari/variant_record.py @@ -710,7 +710,7 @@ def same_type(self, other): b_type = truvari.SV.INS return a_type == b_type - def seqsim(self, other, roll=True): + def seqsim(self, other): """ Calculate sequence similarity of two entries. If reference is not None, compare their shared reference context. Otherwise, use the unroll technique. @@ -741,7 +741,7 @@ def seqsim(self, other, roll=True): b_seq = b_seq.upper() st_dist, ed_dist = self.distance(other) - if not roll or st_dist == 0 or ed_dist == 0: + if not self.params.no_roll or st_dist == 0 or ed_dist == 0: return truvari.seqsim(a_seq, b_seq) # Return best of rolled, unrolled from both ends, and direct similarity