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Merge Haploflow into master

Status: Draft (not ready).

cfe-lab/MiCallnumber 1015

#1015 In cfe-lab/MiCall;

· Donaim opened on Sep 15, 2023

Consider replacing Gotoh alignment algorithm

enhancement

Status: Open.

#556 In cfe-lab/MiCall;

· donkirkby opened on Apr 17, 2020

Write <code>conseq_ins_csv</code> to the output directory

enhancement

Status: Open.

#1085 In cfe-lab/MiCall;

· Donaim opened on Apr 26, 2024

Low-prevalance nucleotide mutations

Status: Open.

#628 In cfe-lab/MiCall;

· donkirkby opened on Oct 19, 2020

Proviral upload into QAI fails

Status: Open.

#886 In cfe-lab/MiCall;

· CBeelen opened on Nov 7, 2022

Improve coordinate concordance

Status: Open.

#965 In cfe-lab/MiCall;

· CBeelen opened on May 19, 2023

Add insertion sequence to nuc.csv and amino.csv

Status: Open.

#768 In cfe-lab/MiCall;

· CBeelen opened on Nov 10, 2021

Insertion counts for small insertions that change the reading frame

Status: Open.

#836 In cfe-lab/MiCall;

· CBeelen opened on May 10, 2022

Summarize insertions

enhancement

Status: Open.

#390 In cfe-lab/MiCall;

· donkirkby opened on May 2, 2017