class SamtoolsIndexing

Public Class Methods

call(bam_file, job_prefix, account, debug, log_file) click to toggle source
# File lib/mutations_caller_pipeline_aws/samtools_indexing.rb, line 2
def self.call(bam_file, job_prefix, account, debug, log_file)
  cmd = "qsub -o #{log_file} -V -cwd -b y -N indexing_#{job_prefix} -l h_vmem=3G -hold_jid bwa_#{job_prefix} #{account} \
    samtools index #{bam_file}"
  puts cmd
  system(cmd) if debug == 1
end