Commit 6a9032fb authored by Antony Le Béchec's avatar Antony Le Béchec

V20210115

parent 58f6deec
......@@ -876,7 +876,7 @@ for GP_FOLDER in $GP_LIST_UNIQ; do
# cp $VCF.empty.vcf $<.tmp.fixed.vcf; \
# fi;
ln -s $< $<.tmp.fixed.vcf;
if cat $<.tmp.fixed.vcf | grep -v '^##Prioritize list is' | sed s/Number=R/Number=./g | sed s/Number=G/Number=./g | $BCFTOOLS sort -T $<.sort2. > $<.tmp.fixed2.vcf; then \
if zcat $<.tmp.fixed.vcf | grep -v '^##Prioritize list is' | sed s/Number=R/Number=./g | sed s/Number=G/Number=./g | $BCFTOOLS sort -T $<.sort2. > $<.tmp.fixed2.vcf; then \
echo '#[INFO] VCF well-formed for $VCF (sedBCFToolsSort)' ; \
else \
echo '#[ERROR] VCF not well-formed for $VCF (sedBCFToolsSort)' ; \
......
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