Fix madc2vcf_all() "invalid substring arguments" error on off-target alleles

NEWS.md

@@ -1,3 +1,7 @@
+# BIGr (development version)
+
+- Fixed `madc2vcf_all()` error "invalid substring arguments" that occurred with `add_others = TRUE` when an off-target ("Other") allele aligned to the reference with no mismatch positions remaining after the target SNP position was removed. The reference/alternate base lookups for off-target alleles are now guarded by the existing non-empty check, matching how the off-target Match alleles are already handled.
+
 # BIGr 0.7.2
 
 - Fixed manual text errors

R/madc2vcf_all.R

@@ -652,10 +652,11 @@ compare <- function(one_tag, botloci, alignment_score_thr = 40, mi_df = NULL, ad
               pos_alt_idx <- pos_alt_idx[-rm_target_other]
             }
           }
-          other_ref_base <- substring(ref_seq, pos_ref_idx, pos_ref_idx)
-          other_alt_base <- substring(others_seq[j,]$AlleleSequence, pos_alt_idx, pos_alt_idx)
           # Cases found where the AltMatch is another alternative for the target SNP - they are discarted
           if(length(pos_ref_idx) >0){
+            # Compute bases only when mismatch positions remain; substring() errors on integer(0) indices
+            other_ref_base <- substring(ref_seq, pos_ref_idx, pos_ref_idx)
+            other_alt_base <- substring(others_seq[j,]$AlleleSequence, pos_alt_idx, pos_alt_idx)
             # If Match sequences have N, do not consider as polymorphism
             if(any(!other_alt_base %in% c("A", "T", "C", "G"))) {
               other_ref_base <- other_ref_base[-which(!other_alt_base %in% c("A", "T", "C", "G"))]

README.md

@@ -21,8 +21,13 @@ BIGr is an R package developed by [Breeding Insight](https://breedinginsight.org
 
 ## Installation
 
-To install BIGr, you'll need to have `BiocManager` installed.
+The stable version of BIGr is now available on CRAN. To install from the R terminal:
+```R
+install.packages("BIGr")
+```
 
+
+To install the development version of BIGr, you'll need to have `BiocManager` installed. Then, install from GitHub.
 ```R
 if (!require("BiocManager", quietly = TRUE))
     install.packages("BiocManager")
@@ -31,9 +36,11 @@ if (!require("BiocManager", quietly = TRUE))
 BiocManager::install("Breeding-Insight/BIGr", dependencies = TRUE)
 library(BIGr)
 ```
+> Note: This GitHub version of BIGr is in development. So, there could be bugs present, and the stable version of BIGr on CRAN should be viewed as more reliable.
+
 ## Funding
 
-BIGr development is supported by [Breeding Insight](https://breedinginsight.org/), a USDA-funded initiative based at Cornell University.
+BIGr development is supported by [Breeding Insight](https://breedinginsight.org/), a USDA-funded initiative based at the University of Florida - IFAS.
 
 ## Citation