Mercurial > repos > iuc > snpfreqplot
diff snpEffExtract.R @ 2:dc51db22310c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"
author | iuc |
---|---|
date | Fri, 18 Dec 2020 23:48:01 +0000 |
parents | 1062d6ad6503 |
children |
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--- a/snpEffExtract.R Thu Dec 10 13:41:29 2020 +0000 +++ b/snpEffExtract.R Fri Dec 18 23:48:01 2020 +0000 @@ -5,6 +5,12 @@ tsv_eff_from_vcf <- function(input_vcf, output_tab) { read_vcf <- readVcf(input_vcf) # nolint + if (!nrow(read_vcf@fixed)) { + # no variants in file -> just write a valid header line + write(c("CHROM", "POS", "REF", "ALT", "AF", "EFF[*].GENE", "EFF[*].EFFECT"), + ncolumns = 7, file = output_tab, sep = "\t") + return() + } chrom_pos <- data.frame(read_vcf@rowRanges)[, c("seqnames", "start")] ref_alt_filter <- read_vcf@fixed[, c("REF", "ALT", "FILTER")] dp_af <- read_vcf@info[c("DP", "AF")]