!LAUNCH: $VIDJIL_DIR/$EXEC -K -e 10 -r 1 -y 0 -s '#####-#####' -w 100 -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -D $VIDJIL_DIR/germline/homo-sapiens/IGHD.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -b stanford-w100 $VIDJIL_DATA/Stanford_S22.fasta ; grep 'w.*/.* seed' out/stanford-w100.affects; grep -v 'UNSEG strand' out/stanford-w100.vidjil

$ Look for windows up to 100bp
1:windows up to 100bp

$ Find the good number of "too short sequences" for windows of size 100
1: UNSEG too short w ->      0

$ Some reads have shortened or shifted windows
1: SEG changed w -> 1370

$ Most changed windows are just shifted
915: w100/-5
360: w100/-10

$ Some changed windows are lighlty shortened
63: w95/-10
29: w90/-10

$ Find the good number of segmented sequences (including "too short sequences")
1: junction detected in 13153 reads .100%.

$ Find the good number of windows in Stanford S22
1: found 11836 windows in 13153 reads

$ Find the correct number of clones with shifted of shortened windows
1245: "Short or shifted window"
1245: "W50"