hello Dr. Guo
I have a problem when I used snboxplot module in Candihap.
the error message is "Insufficient values in manual scale. 6 needed but only 4 provided". it seems something wrong which ggplot2 packages, but i dont know how to deal with this problem .

Because I want to change hap to ovl in the origin code, therefore it occurs the new error about the test data. I only want use the package to draw the gene structure and SNP. Can you help me to solve it?

Kai，
您好，最近用了CandiHap做单倍型分析，看了运行出来的结果，对hap_result的结果有一些地方不是很明白。如下截图，截得是CandiHap文章里的。红色框里的Hap信息，为什么都是两个碱基的，比如T/T G/G等，而且文章中有一个类似的表格，甚至两个碱基还不一样。我理解的单倍型是位于同一条染色体的，应该是一连串单碱基的，我觉得是我没有理解这个文件，在您不忙时，能不能帮我解答一下，万分感谢。

The function snp2hap exit with the following error:
Error in gr[x][, c("REF", "ALT", hapind[[x]])] :
'j' cannot mix between and within metadata column names

The command is as follows:
my.hap <- snp2hap(my.pheno,my.ovl)

The object my.pheno is:

my.pheno

A tibble: 462 × 2

sample test

1 WB-001 1
2 WB-002 2
3 WB-003 3
4 WB-004 4
5 WB-005 5
6 WB-006 6
7 WB-007 7
8 WB-008 8
9 WB-009 9
10 WB-010 10

while the object my.ovl was created with the followinf two functions:

my.hmp <-read_hmp("haplotypes.hmp", comment = "&")
my.ovl <- findover(my.gr,my.hmp)

want to extract results (For V0.0.15)

Hap_results <- results(hap, gene="Si9g49990")

Plot Gene LDheatmap

if (! require("LDheatmap")) install.packages("LDheatmap")
if (! require("genetics")) install.packages("genetics")
LDsnp <- Hap_results[, !names(Hap_results) %in% c("sample","Info")]
LDsnp = LDsnp[,-ncol(LDsnp)]
NAs <- LDsnp == "N/N"
is.na(LDsnp)[NAs] <- TRUE
LDsnp[NAs] <- NA
LDsnp = LDsnp[-1,]
Dist = as.numeric(LDsnp[1,])
LDsnp = LDsnp[-c(1:6),]
num<-ncol(LDsnp) 
for(i in 1:num){
    LDsnp[,i]<-as.genotype(LDsnp[,i]) 
}
rgb.palette <- colorRampPalette(rev(c("#1F77B4", "#AEC7E8", "#FF7F0E")), space = "rgb")
LDheatmap(LDsnp, genetic.distances = Dist, flip = TRUE, color=rgb.palette(40))

Error in S4Vectors:::normarg_names(value, class(x), length(x)): attempt to set too many names (242) on GroupedIRanges object of length 241
I try many ways to solve it, such as the trait sample name is consistent with vcf name;and one step by step running the code,when I run ss <- bplapply(sequence, function(x)as.DNAbin(muscle(x, quiet =TRUE)),BPPARAM=BPPARAM), it will happen this error.Can you help me to solve this problem

Dear CandiHap team:

Is the CandiHap software no longer supported on windows_X64? Thank you very much

I get this error: when using the snp2hap funtion hap <- snp2hap(pheno,ovl, hapname="Hap")
Error in which(unlist(lapply(sequence, function(x) max(width(x)) > 5))) :
argument to 'which' is not logical