minor_fix

Merge branch 'dev' of github.com:Sudaraka88/LDWeaver into dev

# Conflicts:
#	DESCRIPTION

CITATION.cff

@@ -1,12 +1,33 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
 cff-version: 1.2.0
-message: If you find LDWeaver helpful, please cite it as below.
-title: LDWeaver v1.1.1
-type: article
-  authors:
-    name: "Mallawaarachchi, Sudaraka et al."
-    orcid: "https://orcid.org/0000-0001-8899-3323"
-  doi: "https://doi.org/10.1101/2023.08.04.551407"
-  journal: "bioRxiv"
-  month: August
-  title: "Detecting co-selection through excess linkage disequilibrium in bacterial genomes"
-  year: 2023
+title: LDWeaver
+message: ' If you find LDWeaver helpful, please cite:'
+type: software
+authors:
+  - given-names: Sudaraka
+    family-names: Mallawa Arachchi
+    email: [email protected]
+    orcid: 'https://orcid.org/0000-0001-8899-3323'
+    affiliation: University of Oslo and University of Melbourne
+identifiers:
+  - type: doi
+    value: 10.5281/zenodo.10016711
+    description: Zenodo
+repository-code: 'https://github.com/Sudaraka88/LDWeaver/'
+abstract: >-
+  LDWeaver accepts a sequence alignment (fasta) and its
+  reference annotation (genbank or gff) as inputs and
+  identifies linkage disequilibrium (LD) between pairs of
+  variants (links) that is unusually high given the genomic
+  distance between the pair. This high LD could be the
+  result of co-selection or epistasis.
+keywords:
+  - Microbial Genomics
+  - Linkage Disequilibrium
+  - Epistasis
+  - Gene Interactions
+license: GPL-3.0-or-later
+version: v1.4
+date-released: '2024-01-04'

DESCRIPTION

@@ -1,10 +1,10 @@
 Package: LDWeaver
 Type: Package
-Title:Genomewide Epistasis Analysis on Bacteria
+Title: Genomewide Epistasis Analysis on Bacteria
 Version: 1.4
 Authors@R: person("Sudaraka", "Mallawaarachchi", email = "[email protected]", role = c("aut", "cre"))
 Maintainer: Sudaraka Mallawaarachchi <[email protected]>
-Description:Perform genomewide epistasis analysis by evaluating the LD structure in bacteria.
+Description: Perform genomewide epistasis analysis by evaluating the LD structure in bacteria.
 License: GPL (>=3) + file LICENSE
 Encoding: UTF-8
 LazyData: true

README.md

@@ -189,8 +189,10 @@ To cite LDWeaver please use: Mallawaarachchi, Sudaraka et al. Detecting co-selec
 
 The following analysis demonstrates most of the options available in
 LDWeaver. The alignment with 616 *S. pnuemoniae* genomes is available
-<a href="https://cloudstor.aarnet.edu.au/plus/s/KBRnIt1H6XZ2XFR" target="_blank">here</a>, and 
-the same sample.gbk annotation was used to generate this alignment (also available <a href="https://www.ncbi.nlm.nih.gov/nuccore/NC_011900.1?report=gbwithparts&log$=seqview" target="_blank">here</a>.
+<a href="https://uio-my.sharepoint.com/:u:/g/personal/sudarakm_uio_no/EeLNWOGYDi5Bk4PVY6JZF10BEDM2ckSCMq4nZqX8OGimJg?e=3AfBhf" target="_blank">here</a>, and 
+the same sample.gbk annotation was used to generate this alignment (also available <a href="https://www.ncbi.nlm.nih.gov/nuccore/NC_011900.1?report=gbwithparts&log$=seqview" target="_blank">here</a>).
+
+> **Note:** Alternatively, since LDWeaver v1.2, you can download and use the <a href="https://uio-my.sharepoint.com/:u:/g/personal/sudarakm_uio_no/EdQdnfYv3KRBiuYW73BEGXgBbtZR2SSdty_qiNgjJflp5w?e=vbpeEp" target="_blank">SNP-only alignment</a> with the accompanying <a href="https://uio-my.sharepoint.com/:u:/g/personal/sudarakm_uio_no/EZoekLiIyZZKuVAoHoWob1cBk2yBSOfr4MeuLp_VgKJG5g" target="_blank">positions</a> file to generate the same results.
 
 For this example, it is assumed that the current working directory is set to 
 `~/LDWeaver_run` and the