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Fix missing exit(0) when phasing is skipped #170

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Fix missing exit(0) when phasing is skipped #170

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6 changes: 5 additions & 1 deletion R/battenberg.R
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Original file line number Diff line number Diff line change
Expand Up @@ -314,7 +314,7 @@ battenberg = function(analysis="paired",
ismale = gender == "male"
}


if (!skip_phasing[sampleidx]) {

# if external phasing data is provided (as a vcf), split into chromosomes for use in haplotype reconstruction
Expand Down Expand Up @@ -406,6 +406,10 @@ battenberg = function(analysis="paired",
inputfile.postfix="_heterozygousMutBAFs_haplotyped.txt",
outputfile=paste(samplename[sampleidx], "_heterozygousMutBAFs_haplotyped.txt", sep=""),
chr_names=chrom_names)
} else{
# If skip_phasing, we just end the script here and return exit status 0, as the downstream steps of Battenberg can be run with the output of the previous steps as input
print("Phasing and haplotype reconstruction is skipped as requested, exiting with status 0")
q(save="no", status=0)
}

# Segment the phased and haplotyped BAF data
Expand Down
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