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Length zero fix #1030

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Length zero fix #1030

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019454e
ensure concordant_snps handles cases with zero length
eolaniru Jun 11, 2024
bab3173
check to avoid errors if concordant_snps have fewer elements
eolaniru Jun 11, 2024
096e022
code polishing
eolaniru Jun 12, 2024
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16 changes: 11 additions & 5 deletions R/sample_swap.R
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Original file line number Diff line number Diff line change
Expand Up @@ -110,9 +110,9 @@ sampleSwaps = function(bams = NULL, build = "hg19", prefix = NULL, add = TRUE, m
data.table::data.table(
X_bam = names(rc_af)[idx],
Y_bam = names(rc_af)[rest_idx],
concordant_snps = concordant_snps[[1]],
discordant_snps = concordant_snps[[2]],
fract_concordant_snps = prop.table(concordant_snps)[[1]],
concordant_snps = ifelse(length(concordant_snps) > 0, concordant_snps[[1]], 0),
discordant_snps = ifelse(length(concordant_snps) > 1, concordant_snps[[2]], 0),
fract_concordant_snps = ifelse(length(concordant_snps) > 0, prop.table(concordant_snps)[[1]], 0),
cor_coef = cor_coef
)
})
Expand All @@ -126,8 +126,14 @@ sampleSwaps = function(bams = NULL, build = "hg19", prefix = NULL, add = TRUE, m
sample_matches = sample_matches[1:(length(sample_matches)-1)]

pos_mathces = lapply(sample_matches, function(sample_pair){
if(nrow(sample_pair) > 0){
unique(unlist(sample_pair[XY_possibly_paired == "Yes", .(X_bam, Y_bam)], use.names = FALSE))
if (all(c("XY_possibly_paired", "X_bam", "Y_bam") %in% colnames(sample_pair))) {
# Filter out rows where X_bam or Y_bam have length zero
valid_rows <- sapply(sample_pair$X_bam, nchar) > 0 & sapply(sample_pair$Y_bam, nchar) > 0
filtered_sample_pair <- sample_pair[valid_rows, ]

if(nrow(filtered_sample_pair) > 0){
unique(unlist(filtered_sample_pair[XY_possibly_paired == "Yes", .(X_bam, Y_bam)], use.names = FALSE))
}
}
})
pos_mathces = pos_mathces[which(lapply(pos_mathces, function(x) length(x) > 0) == TRUE)]

@ShixiangWang ShixiangWang Jun 12, 2024

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It should be better to use pos_mathces[sapply(pos_mathces, function(x) length(x) > 0)]?

@eolaniru eolaniru Jun 12, 2024

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Yes, you are right. That works as well

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