From 1d227abaaa3a11e5a04e61e12be5c55502d00d0a Mon Sep 17 00:00:00 2001
From: Sudaraka88 <sudarakm@Sudarakas-MacBook-Pro.local>
Date: Tue, 11 Jun 2024 11:04:08 +1000
Subject: [PATCH] Add citation

---
 .github/workflows/r.yml         | 2 +-
 CITATION.cff                    | 2 +-
 README.md                       | 6 +++---
 man/LDWeaver.Rd                 | 3 ---
 man/analyse_long_range_links.Rd | 5 ++++-
 5 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/r.yml b/.github/workflows/r.yml
index caac3fc..ca27917 100644
--- a/.github/workflows/r.yml
+++ b/.github/workflows/r.yml
@@ -30,7 +30,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
 
-    steps:
+    steps:hbgvn
       - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
diff --git a/CITATION.cff b/CITATION.cff
index 1768646..bcf3648 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -29,5 +29,5 @@ keywords:
   - Epistasis
   - Gene Interactions
 license: GPL-3.0-or-later
-version: v1.4
+version: v1.5
 date-released: '2024-01-04'
diff --git a/README.md b/README.md
index 79c89c9..549d7ec 100644
--- a/README.md
+++ b/README.md
@@ -94,7 +94,7 @@ num_clusts_CDS = 2, SnpEff_Annotate = F, snp_filt_method = snp_filt_method)
 
 ## Citation
 
-Please cite LDWeaver using: Mallawaarachchi, Sudaraka et al. Detecting co-selection through excess linkage disequilibrium in bacterial genomes. bioRxiv 2023.08.04.551407; doi: https://doi.org/10.1101/2023.08.04.551407
+Please cite LDWeaver using: Mallawaarachchi, S. et al. Detecting co-selection through excess linkage disequilibrium in bacterial genomes, NAR Genomics and Bioinformatics, Volume 6, Issue 2, June 2024, lqae061, https://doi.org/10.1093/nargab/lqae061
 
 ## Detailed Workthrough using Real Data
 
@@ -103,7 +103,7 @@ LDWeaver. The alignment with 616 *S. pnuemoniae* genomes is available
 <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.
+> **Note:** Alternatively, 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
@@ -344,4 +344,4 @@ separated format
 5. Temp/X_annotated_stats.html - annotations and statistics in html
 format
 6. Temp/X_snps.vcf, Temp/X_snps_ann.vcf - input and output from the snpEff
-annotation pipeline
\ No newline at end of file
+annotation pipeline
diff --git a/man/LDWeaver.Rd b/man/LDWeaver.Rd
index 690ebe3..506f67b 100644
--- a/man/LDWeaver.Rd
+++ b/man/LDWeaver.Rd
@@ -87,9 +87,7 @@ Larger values will reduce memory usage, plotting time and ARACNE run time. If al
 
 \item{save_additional_outputs}{specify whether to save outputs such as extracted SNPs and Hamming distance weights. Recommended for very large datasets to save time on re-computation (default = F)}
 
-
 \item{mega_dset}{specify whether the datasets is megascale. This mode requires spam and spam64 packages. This is  >5 times slower, set to TRUE only if the normal analysis fails (default = F)}
-
 }
 \value{
 All generated outputs will be saved to folder <dset>.
@@ -118,6 +116,5 @@ dset <- "full_dset_spam"
 gbk_path <- system.file("extdata", "sample.gbk", package = "LDWeaver")
 aln_path <- system.file("extdata", "sample.aln.gz", package = "LDWeaver")
 LDWeaver::LDWeaver(dset = dset,  aln_path = aln_path,  gbk_path = gbk_path, validate_ref_ann_lengths = F, mega_dset = T)
-
 }
 }
diff --git a/man/analyse_long_range_links.Rd b/man/analyse_long_range_links.Rd
index fb0bbbb..b2419d6 100644
--- a/man/analyse_long_range_links.Rd
+++ b/man/analyse_long_range_links.Rd
@@ -18,7 +18,8 @@ analyse_long_range_links(
   snp.dat = NULL,
   cds_var = NULL,
   max_tophits = 500,
-  links_from_spydrpick = F
+  links_from_spydrpick = F,
+  mega_dset = F
 )
 }
 \arguments{
@@ -51,6 +52,8 @@ not required for genbank annotations if the file contains the reference sequence
 but only the top <max_tophits> will be used for visualisation (default = 500)}
 
 \item{links_from_spydrpick}{are the links computed using spydrpick (default = F)}
+
+\item{mega_dset}{set TRUE for mega scale datasets (default = F)}
 }
 \description{
 Function to analyse long range links. These links can be computed using LDWeaver or Spydrpick (faster). Spydrpick is recommended for larger datasets.