Class: Bio::Ngs::Samtools::Merge

Inherits:

Object

Object
Bio::Ngs::Samtools::Merge

show all

Includes:: Command::Wrapper

Defined in:: lib/bio/appl/ngs/samtools.rb

Overview

Usage: samtools merge [-nr] [-h inh.sam] <out.bam> <in1.bam> <in2.bam> [...]

Options: -n sort by read names -r attach RG tag (inferred from file names) -u uncompressed BAM output -f overwrite the output BAM if exist -1 compress level 1 -R STR merge file in the specified region STR [all] -h FILE copy the header in FILE to <out.bam> [in1.bam]

Note: Samtools' merge does not reconstruct the @RG dictionary in the header. Users must provide the correct header with -h, or uses Picard which properly maintains the header dictionary in merging. out, in1, in2, ... inx Must be passed as arguments

Method Summary

Methods included from Command::Wrapper

#class_name, #default_options, included, #initialize, #normalize_params, #options, #options=, #output, #params, #params=, #path, #path=, #pipe_ahead, #pipe_ahead=, #pipe_ahead?, #program, #reset_params, #run, #sub_program, #thor_task, #to_cmd_ary, #use_aliases?