airr-S22.should-get 1001 Bytes
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!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -c clones -z 2 -3 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta  > /dev/null ; cat out/Stanford_S22.tsv

$ There are four lines, all with tabs
4:
4:\t

$ The required AIRR fields are present
:v_call	d_call j_call
:sequence_id
:sequence	
:sequence_alignment	
:germline_alignment
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:v_cigar d_cigar	j_cigar	
:junction
:junction_aa
:productive
:rev_comp
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$ Three clones on IGH
3:IGH

$ One clone has 8 reads, two clones have 5 reads
1:IGH 8
2:IGH 5

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$ Two clones are productive, no clone is labeled as non-productive
2:\tT\t
0:\tF\t

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$ v_call for 2 clones (-z 2)
2:IGHV

$ First clone window appears third times (clone_id, sequence_id, sequence)
w3:TATTACTGTACCCGGGAGGAACAATATAGCAGCTGGTACTTTGACTTCTG

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$ Junction of the first clone appears once, but CDR3 twice (it is also included in the junction)
1:CTREEQYSSWYFDFW		
w2:TREEQYSSWYFDF

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$ The first clone has three warnings
1:W51 W69 W69

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$ No spurious character
0:"
0:@
0:\\