An interactive 'dialog' generating a SAM Flag

The following shell script uses the dialog utility to generate a numeric Sam flag.

$ sh selectsam.sh 
      ┌───────────────────────SAM FLAGS──────────────────────────┐
      │ SELECT FLAGS                                             │  
      │ ┌──────────────────────────────────────────────────────┐ │  
      │ │ [X] 1     Read Paired                                │ │  
      │ │ [ ] 2     Read mapped in proper pair                 │ │  
      │ │ [X] 4     Read unmapped                              │ │  
      │ │ [ ] 8     Mate unmapped                              │ │  
      │ │ [ ] 16    Read reverse strand                        │ │  
      │ │ [X] 32    Mate reverse strand                        │ │  
      │ │ [ ] 64    First in pair                              │ │  
      │ │ [X] 128   Second in pair                             │ │  
      │ │ [ ] 256   Not primary alignment                      │ │  
      │ │ [ ] 512   Read fails platform/vendor quality checks  │ │  
      │ │ [ ] 1024  Read is PCR or optical duplicate           │ │  
      │ └─────↓(+)─────────────────────────────────────────────┘ │  
      │                                                          │  
      │                                                          │  
      ├──────────────────────────────────────────────────────────┤  
      │                         <  OK  >                         │  
      └──────────────────────────────────────────────────────────┘  
        
$ 165

	dialog --stdout --title "SAM FLAGS" \
	--nocancel \
	--separate-output \
	--checklist "SELECT FLAGS" 20 60 11 \
	1 "Read Paired" off \
	2 "Read mapped in proper pair" off \
	4 "Read unmapped" off \
	8 "Mate unmapped" off \
	16 "Read reverse strand" off \
	32 "Mate reverse strand" off \
	64 "First in pair" off \
	128 "Second in pair" off \
	256 "Not primary alignment" off \
	512 "Read fails platform/vendor quality checks" off \
	1024 "Read is PCR or optical duplicate" off \
	| awk 'BEGIN { i=0;} {i+=int($1);} END {printf("%s\n",i);}'

view raw samflags.sh hosted with ❤ by GitHub

Source available at: https://github.com/lindenb/samtools-utilities/blob/master/script/selectflag.sh

That's it,

Pierre