chimera-fake-VJ.should-get 791 Bytes
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!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline -2 $VIDJIL_DATA/chimera-fake-VJ.fa
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$ The KmerSegmenter segments the five chimera reads on PSEUDO_MAX12 germline (-2)
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1:unexpected .* -> .* 5
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$ The FineSegmenter gives the locus information (-2)
1:Unexpected [+]TRBV/[+]TRGJ
1:Unexpected [+]TRDV/[+]IGHJ
1:Unexpected [+]TRDV/[-]IGKV
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1:Unexpected [-]IGLJ.down/[+]TRGJ
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$ The FineSegmenter gives the locus information (-2) and takes the best strand
1:Unexpected [+]IGKV/[+]IGLJ

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$ The FineSegmenter correclty segments the three sequences (-2)
1:IGKV1-12.01 0//0 IGLJ1.01
1:TRBV1.01 0//0 TRGJ1.01
1:TRDV1.01 0//0 IGHJ1.01
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$ The FineSegmenter correclty segments the two sequences with either V or J reversed (-2)
1:TRDV1.01 0//0 IGKV1-12.01
1:IGLJ1.01 0//0 TRGJ1.01