tests: update and add tests

algo/tests/bugs/bug4225.should

 !OUTPUT_FILE: out/bug4225-j.affects
-!LAUNCH: $VIDJIL_DIR/$EXEC -g $VIDJIL_DIR/germline -r 1 -1 -2 -K bug4225-j.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC -c windows -g $VIDJIL_DIR/germline -r 1 -1 -2 -K bug4225-j.fa
+
+$ Show name and sequence
+1:>igkj1 GTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC
+
+$ Display three lines per system
+3:TRG
+3:IGH\+
 
 $ Find only +k and ? affects before the stretch of _ for all loci
-16: seed .*(\+k| \?){28}( _)+$
+16:^\#.* (k|\?){28}_+$
+16:^\$.* (\+| ){28}( )+$
 
 !OUTPUT_FILE: out/chimera-fake-half.affects
-!LAUNCH: $VIDJIL_DIR/$EXEC -g $VIDJIL_DIR/germline -r 1 -4 -K ../data/chimera-fake-half.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC -c windows -g $VIDJIL_DIR/germline/homo-sapiens.g:TRB -r 1 -4 -K ../data/chimera-fake-half.fa
+
+$ Find only 48 +B affects on the TRB and unexpected lines
+2:^\#.* (_){40}(B){48}(_){10}
+2:^\$.* (\s){40}(\+){48}(\s){10}
 
-$ Find only +B and ? affects on the TRB and unexpected lines
-2: seed .* _(\+B| \?){48} _

algo/tests/should-get-tests/common-V-D.should

@@ -4,7 +4,8 @@ $ Segments the sequence
 1: SEG  .* -> .* 1 
 
 $ Find the good affects for the D segment, including a AMBIGUOUS k-mer, common with V
-1:_ _ _ \?.f.f.f.f.f.f _ _ _ _
+1:___\?ffffff____
+1:   \+\+\+\+\+\+
 
 $ The windows found by the KmerSegmenter has a fairly good position
 2: 1 163 180 220

algo/tests/should-get-tests/multi-short-affects.should

-!LAUNCH: $VIDJIL_DIR/$EXEC -r 5 -K -g $VIDJIL_DIR/germline/homo-sapiens.g:TRA,TRB,TRD,TRG,IGH,IGK,IGL $VIDJIL_DATA/multi-short.fa ; head -n 17 out/multi-short.affects
+!OUTPUT_FILE: out/multi-short.affects
+!LAUNCH: $VIDJIL_DIR/$EXEC -r 5 -K --first-reads 1 -g $VIDJIL_DIR/germline/homo-sapiens.g:TRA,TRB,TRD,TRG,IGH,IGK,IGL $VIDJIL_DATA/multi-short.fa
 # Testing .affects output (-K)
 
 $ First sequence (TRA), display sequence
-1:TCTTCATTCCTTAGTCGCTCTGATAGTTATGGTTACCTCCTTCTACAGGAGCTCCAGATGAAAGACTCTGCCTCTTACTTCTGCGCTGTGAGAGAGTATGAAAGTATTACCTCCCAGTTGCAATTTGGCAAAGGAACCAGAGTTTCCACTTCTCC
+1:>TRA.* TCTTCATTCCTTAGTCGCTCTGATAGTTATGGTTACCTCCTTCTACAGGAGCTCCAGATGAAAGACTCTGCCTCTTACTTCTGCGCTGTGAGAGAGTATGAAAGTATTACCTCCCAGTTGCAATTTGGCAAAGGAACCAGAGTTTCCACTTCTCC
 
 $ First sequence (TRA), count of k-mers
 1:129 .* TRA
 
-$ First sequence (TRA), segmentation
-1:>TRA--V1-1.01--J1.01 .* seed TRA SEG_+
+$ First sequence (TRA), detection
+1:==> TRA--V1-1.01--J1.01 .* seed TRA SEG_+
 
 
 

algo/tests/should-get-tests/revcomp.should

-!LAUNCH: $LAUNCHER $VIDJIL_DIR/$EXEC $EXTRA -k 9 -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa  -K -c clones $VIDJIL_DATA/revcomp.fa ; grep 'X.X.X' out/revcomp.affects | sed 's/[^X]//g'  | sort -u ; grep '#>'  out/revcomp.affects | sed 's/.*SEG.../e-value:/' | cut -f 1 -d' '
+!LAUNCH: $LAUNCHER $VIDJIL_DIR/$EXEC $EXTRA -k 9 -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa  -K -c clones $VIDJIL_DATA/revcomp.fa
+!NO_LAUNCHER:
+!LAUNCH: grep 'X.X.X' out/revcomp.affects | sed 's/[^X]//g'  | sort -u
+!LAUNCH: grep '==>'   out/revcomp.affects | sed 's/.*SEG.../e-value:/' | cut -f 1 -d' '
 
 $ Segments both reads, normal and reverse
 1:junction detected in 2 reads