multi-detect.should 1.61 KB
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!LAUNCH: $VIDJIL_DIR/$EXEC -g $VIDJIL_DIR/germline $VIDJIL_DATA/multi-complete.fa

$ Detect recombinations in all the seven reads
1:junction detected in 7 reads

$ Detect one read on TRA
1:TRA .* -> .* 1 

$ Detect one read on TRB
1:TRB .* -> .* 1 

$ Detect one read on TRG
1:TRG .* -> .* 1 

$ Detect one read on TRD
1:TRD .* -> .* 1 

$ Detect one read on IGH
1:IGH .* -> .* 1 

$ Detect one read on IGK
1:IGK .* -> .* 1 

$ Detect one read on IGL
1:IGL .* -> .* 1 

$ Compute the diversity. All windows have only one read, full diversity.
7: 1   1.000
1:  E = 1.000
1: Ds = 1.000

### Focusing on Ig recombinations with -g:IGH,IGK,IGL
!LAUNCH: $VIDJIL_DIR/$EXEC -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH,IGK,IGL $VIDJIL_DATA/multi-complete.fa

$ Detect the Ig recombinations
1:IGH .* -> .* 1 
1:IGK .* -> .* 1 
1:IGL .* -> .* 1 

$ Do not detect the TR recombinations
1:junction detected in 3 reads


### All loci, but shorter sequences
!LAUNCH: $VIDJIL_DIR/$EXEC -g $VIDJIL_DIR/germline $VIDJIL_DATA/multi-short.fa

$ Detect recombinations in all the seven reads
1:junction detected in 7 reads

$ Detect one read on TRA
1:TRA .* -> .* 1 

$ Detect one read on TRB
1:TRB .* -> .* 1 

$ Detect one read on TRG
1:TRG .* -> .* 1 

$ Detect one read on TRD
1:TRD .* -> .* 1 

$ Detect one read on IGH
1:IGH .* -> .* 1 

$ Detect one read on IGK
1:IGK .* -> .* 1 

$ Detect one read on IGL
1:IGL .* -> .* 1 


### Even shorter sequences
!LAUNCH: $VIDJIL_DIR/$EXEC -g $VIDJIL_DIR/germline $VIDJIL_DATA/multi-tiny.fa

$ Do not detect recombinations in any of the seven reads, they are too small
Mathieu Giraud's avatar
Mathieu Giraud committed
76 77
1:UNSEG too few .* -> .* 6
1:UNSEG only J.* -> .* 1
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