Useless use of cat reported by Annatar removed
@@ -24,8 +24,8 @@ echo "Normalizing GISAID file $GISAID_SARSCOV2_IN to $GISAID_SARSCOV2_OUT (min l
# Remove sequences shorter than minimum length
# Eliminate duplicate sequences (keep only the first seen)
-cat $GISAID_SARSCOV2_IN |
- sed 's/^>BetaCoV\//>/gi' | # remove leading BetaCo[vV]
+#cat $GISAID_SARSCOV2_IN |
+ sed 's/^>BetaCoV\//>/gi' $GISAID_SARSCOV2_IN | # remove leading BetaCo[vV]
sed 's/ //g' | # remove embedded spaces
sed 's/|.*$//' | # remove trailing metadata
awk "BEGIN{RS=\">\";FS=\"\n\"}length>$MIN_LENGTH{print \">\"\$0}" | # remove short seqs
