Class: Bio::Ngs::Samtools::View

Inherits:
Object
  • Object
show all
Includes:
Command::Wrapper
Defined in:
lib/bio/appl/ngs/samtools.rb

Overview

Usage: samtools view [options] <in.bam>|<in.sam> [region1 […]]

Options: -b output BAM

-h       print header for the SAM output
-H       print header only (no alignments)
-S       input is SAM
-u       uncompressed BAM output (force -b)
-1       fast compression (force -b)
-x       output FLAG in HEX (samtools-C specific)
-X       output FLAG in string (samtools-C specific)
-c       print only the count of matching records
-L FILE  output alignments overlapping the input BED FILE [null]
-t FILE  list of reference names and lengths (force -S) [null]
-T FILE  reference sequence file (force -S) [null]
-o FILE  output file name [stdout]
-R FILE  list of read groups to be outputted [null]
-f INT   required flag, 0 for unset [0]
-F INT   filtering flag, 0 for unset [0]
-q INT   minimum mapping quality [0]
-l STR   only output reads in library STR [null]
-r STR   only output reads in read group STR [null]
-?       longer help

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?