feature-va-left-align: implementation of left align normalisation in VA CLI started
@@ -378,8 +378,11 @@ public class CliOptionsParser {
required = false, arity = 0)
public boolean benchmark;
- @Parameter(names = {"--reference-fasta"}, description = "To use only with the --benchmark flag. Full path to a "
- + " fasta file containing the reference genome.",
+ @Parameter(names = {"--reference-fasta"}, description = "Enables left-alignment normalisation: set this parameter"
+ + " to the full path to a fasta (not fasta.gz!) file containing the reference sequence if you want to enable"
+ + " lef-alignment during the normalisation process. If not set (default), left-alignment step will be skipped"
+ + " during normalisation. **NOTE**: this parameter is mandatory if the --benchmark flag is enabled (in "
+ + " this case fasta.gz files are allowed)",
required = false, arity = 1)
public String referenceFasta;
