Class: BwaCaller

Inherits:
Object
  • Object
show all
Defined in:
lib/mutations_caller_pipeline_aws/bwa_caller.rb

Class Method Summary collapse

Class Method Details

.call_aln(read, index, out_file, log_file, bwa, job_prefix, account, debug, direction) ⇒ Object 



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# File 'lib/mutations_caller_pipeline_aws/bwa_caller.rb', line 12

def self.call_aln(read, index, out_file, log_file, bwa, job_prefix, ,debug,direction)
  cmd = "qsub -pe DJ 8 -o #{log_file} -e #{log_file}_bwa_aln_errors_#{direction} -V -cwd -b y -N bwa_aln_#{job_prefix} -l h_vmem=4G #{} \
         #{bwa} aln -t 8 -f #{out_file} #{index} #{read} "
  puts cmd
  system(cmd) if debug == 1
end

.call_paired_end(r1, r2, sai1, sai2, sam_file, index, log_file, bwa, samtools, job_prefix, account, debug) ⇒ Object 



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# File 'lib/mutations_caller_pipeline_aws/bwa_caller.rb', line 3

def self.call_paired_end(r1, r2, sai1, sai2,  sam_file, index, log_file, bwa, samtools, job_prefix,, debug)
  dummy = "\\\\\\"
  cmd = "qsub -o #{log_file} -e #{log_file}_bwa_sampe_errors -hold_jid bwa_aln_#{job_prefix} -V -cwd -b y -N bwa_#{job_prefix} -l h_vmem=6G  #{}\
         #{bwa} sampe  #{index}   \
        #{sai1} #{sai2}  #{r1} #{r2} -f #{sam_file}"
  puts cmd
  system('bash','-c', cmd) if debug == 1
end