class BwaCaller
Public Class Methods
call_aln(read, index, out_file, log_file, bwa, job_prefix, account,debug,direction)
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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, account,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 #{account} \ #{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)
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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,account, 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 #{account}\ #{bwa} sampe #{index} \ #{sai1} #{sai2} #{r1} #{r2} -f #{sam_file}" puts cmd system('bash','-c', cmd) if debug == 1 end