From 903a3669cb7b19b816c8fd7935d583eed90fded5 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Sat, 15 Jun 2024 13:29:18 -0400 Subject: [PATCH] fix(call): fix VCF output for alts with no common suffix --- strkit/call/output/vcf.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/strkit/call/output/vcf.py b/strkit/call/output/vcf.py index abed0db..5a14c22 100644 --- a/strkit/call/output/vcf.py +++ b/strkit/call/output/vcf.py @@ -2,6 +2,7 @@ import logging import pathlib import pysam + from os.path import commonprefix from typing import Optional @@ -123,10 +124,10 @@ def output_contig_vcf_lines( call = result["call"] seq_alleles_raw: tuple[Optional[str], ...] = (ref_seq, *(seq_alts or (None,))) if call is not None else (".",) - seq_alleles: list[str] = [ref_start_anchor + ref_seq[:common_suffix_idx]] + seq_alleles: list[str] = [ref_start_anchor + (ref_seq[:common_suffix_idx] if common_suffix_idx else ref_seq)] if call is not None and seq_alts: - seq_alleles.extend(ref_start_anchor + a[:common_suffix_idx] for a in seq_alts) + seq_alleles.extend(ref_start_anchor + (a[:common_suffix_idx] if common_suffix_idx else a) for a in seq_alts) else: seq_alleles.append(".")