bin/reference_data.py
def validate_data(self):
        """
        Validate that the reference data conforms to some expectations such as:
          - The vcf file ran through GATK ValidateVariants without error.
        """
        if self.reference_variation:
            if 'faidx' in self.procs:
                self.procs['faidx'].wait()
            self.procs['CreateSequenceDictionary'].wait()

            self.procs['ValidateVariants'] = self.run_background(
                'java -Xmx20G -jar %s -T ValidateVariants -V %s -R %s -warnOnErrors' % (
                    self.tools['gatk'], self.reference_variation, self.reference_fasta),
                '%s.validate_variants.log' % self.reference_variation
            )

        Validate that the reference data conforms to some expectations such as:
          - The vcf file ran through GATK ValidateVariants without error.
        
Validate that the reference data conforms to some expectations such as:
The vcf file ran through GATK ValidateVariants without error.
Validate that the reference data conforms to some expectations such as : The vcf file ran through GATK ValidateVariants without error .
def validate_data(self):
        if self.reference_variation:
            if 'faidx' in self.procs:
                self.procs['faidx'].wait()
            self.procs['CreateSequenceDictionary'].wait()
            self.procs['ValidateVariants'] = self.run_background(
                'java -Xmx20G -jar %s -T ValidateVariants -V %s -R %s -warnOnErrors' % (
                    self.tools['gatk'], self.reference_variation, self.reference_fasta),
                '%s.validate_variants.log' % self.reference_variation
            )
def validate_data ( self ) : if self . reference_variation : if 'faidx' in self . procs : self . procs [ 'faidx' ] . wait ( ) self . procs [ 'CreateSequenceDictionary' ] . wait ( ) self . procs [ 'ValidateVariants' ] = self . run_background ( 'java -Xmx20G -jar %s -T ValidateVariants -V %s -R %s -warnOnErrors' % ( self . tools [ 'gatk' ] , self . reference_variation , self . reference_fasta ) , '%s.validate_variants.log' % self . reference_variation )
Validate that the reference data conforms to some expectations such as:
 The vcf file ran through GATK ValidateVariants without error.
Validate that the reference data conforms to some expectations such as : The vcf file ran through GATK ValidateVariants without error .
"""
        Validate that the reference data conforms to some expectations such as:
          - The vcf file ran through GATK ValidateVariants without error.
        """
self