tests: remove $VIDJIL_DEFAULT_OPTIONS when it is it in the first place

see #3762

algo/tests/should-get-tests/3344-bad-filtering.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -c designations -g $VIDJIL_DIR/germline/homo-sapiens.g $VIDJIL_DATA/3344-bad-filtering.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC -c designations -g $VIDJIL_DIR/germline/homo-sapiens.g $VIDJIL_DATA/3344-bad-filtering.fa
 
 $ Check that proper filtering is used
 1: IGHV4-31.02

algo/tests/should-get-tests/airr-S22.should

-!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
+!LAUNCH: $VIDJIL_DIR/$EXEC -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:

algo/tests/should-get-tests/airr-X5.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -c clones -z 2 -2 -3 -r 1 -g $VIDJIL_DIR/germline/homo-sapiens.g ../should-vdj-tests/Demo-X5.should-vdj.fa  > /dev/null ; cat out/Demo-X5.should-vdj.tsv
+!LAUNCH: $VIDJIL_DIR/$EXEC -c clones -z 2 -2 -3 -r 1 -g $VIDJIL_DIR/germline/homo-sapiens.g ../should-vdj-tests/Demo-X5.should-vdj.fa  > /dev/null ; cat out/Demo-X5.should-vdj.tsv
  
 $ There are 15 = 1 + 14 lines, all with tabs
 15:

algo/tests/should-get-tests/algo-then-fuse.should

 !REQUIRES: python $VIDJIL_DIR/tools/check_python_version.py
-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -r 1 -z 0 -w 60 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta ; python $VIDJIL_DIR/tools/fuse.py out/Stanford_S22.vidjil out/Stanford_S22.vidjil -o out/fused.data ; cat out/fused.data | python $VIDJIL_DIR/tools/format_json.py -1
+!LAUNCH: $VIDJIL_DIR/$EXEC -r 1 -z 0 -w 60 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta ; python $VIDJIL_DIR/tools/fuse.py out/Stanford_S22.vidjil out/Stanford_S22.vidjil -o out/fused.data ; cat out/fused.data | python $VIDJIL_DIR/tools/format_json.py -1
 
 $ Points list
 1:"original_names": \[".*data//Stanford_S22.fasta", ".*data//Stanford_S22.fasta"\]

algo/tests/should-get-tests/algo-then-vidjil-to-fasta.should

 !REQUIRES: python $VIDJIL_DIR/tools/check_python_version.py
-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -x 100 -r 1 -z 5 -w 60 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta ; python $VIDJIL_DIR/tools/vidjil-to-fasta.py  -o out/S22.fasta out/Stanford_S22.vidjil ;
+!LAUNCH: $VIDJIL_DIR/$EXEC -x 100 -r 1 -z 5 -w 60 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta ; python $VIDJIL_DIR/tools/vidjil-to-fasta.py  -o out/S22.fasta out/Stanford_S22.vidjil ;
 !OUTPUT_FILE: out/S22.fasta
 
 $ 5 representative sequences in the FASTA output file

algo/tests/should-get-tests/alternative-genes.should

 !REQUIRES: python $VIDJIL_DIR/tools/check_python_version.py
-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS --alternative-genes 3 -c designations -x 1 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta > /dev/null ; cat out/Stanford_S22.vidjil | python $VIDJIL_DIR/tools/format_json.py -1
+!LAUNCH: $VIDJIL_DIR/$EXEC --alternative-genes 3 -c designations -x 1 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta > /dev/null ; cat out/Stanford_S22.vidjil | python $VIDJIL_DIR/tools/format_json.py -1
 
 $ Presence of alternative:
 1: "3alt"

algo/tests/should-get-tests/analysis-S22.should

 
-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -e 10 -z 0 -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -D $VIDJIL_DIR/germline/homo-sapiens/IGHD.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -s "######-######" $VIDJIL_DATA/Stanford_S22.fasta
+!LAUNCH: $VIDJIL_DIR/$EXEC -e 10 -z 0 -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -D $VIDJIL_DIR/germline/homo-sapiens/IGHD.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -s "######-######" $VIDJIL_DATA/Stanford_S22.fasta
 
 $ Germlines are custom
 1: custom germlines

algo/tests/should-get-tests/analysis-cost.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS --analysis-cost '1, 2, 3, 4, 5' $VIDJIL_DATA/Stanford_S22.fasta
+!LAUNCH: $VIDJIL_DIR/$EXEC --analysis-cost '1, 2, 3, 4, 5' $VIDJIL_DATA/Stanford_S22.fasta
 !EXIT_CODE: 1
 
 $Check that correct custom cost is used

algo/tests/should-get-tests/analysis-erg.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens-isoforms.g -r 1 -e 0.1 $VIDJIL_DATA/erg_debre.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC -g $VIDJIL_DIR/germline/homo-sapiens-isoforms.g -r 1 -e 0.1 $VIDJIL_DATA/erg_debre.fa
 
 
 $ All sequences have been seen as different ERG recombinations

algo/tests/should-get-tests/analysis-ikaros.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens-isoforms.g -r 1 -e 0.1 $VIDJIL_DATA/ikaros_debre.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC -g $VIDJIL_DIR/germline/homo-sapiens-isoforms.g -r 1 -e 0.1 $VIDJIL_DATA/ikaros_debre.fa
 
 
 $ All sequences have been seen as unique clone

algo/tests/should-get-tests/analysis-lec.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g -c clones --all -3 $VIDJIL_DATA/segment_lec.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC -g $VIDJIL_DIR/germline/homo-sapiens.g -c clones --all -3 $VIDJIL_DATA/segment_lec.fa
 
 $ Extract up to 50bp windows (TRG)
 1:windows up to 50bp

algo/tests/should-get-tests/cd-no.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -e 1e-2 -y 0 -g $VIDJIL_DIR/germline/homo-sapiens-cd.g $VIDJIL_DATA/Stanford_S22.fasta
+!LAUNCH: $VIDJIL_DIR/$EXEC -e 1e-2 -y 0 -g $VIDJIL_DIR/germline/homo-sapiens-cd.g $VIDJIL_DATA/Stanford_S22.fasta
 
 $ Do not segment any read with SEG_METHOD_ONE on homo-sapiens-cd.g
 1: CD .* -> .* 0 .* 0

algo/tests/should-get-tests/cdr3-stopcodon.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -c designations -3 -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG $VIDJIL_DATA/cdr3-stopcodon.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC -c designations -3 -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG $VIDJIL_DATA/cdr3-stopcodon.fa
 !OUTPUT_FILE: out/cdr3-stopcodon.vidjil
 
 $ Two identical junctions in JSON

algo/tests/should-get-tests/cdr3-vdj-fa.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -c designations -3 -E 1.0 -g $VIDJIL_DIR/germline ../should-vdj-tests/Demo-X5.should-vdj.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC -c designations -3 -E 1.0 -g $VIDJIL_DIR/germline ../should-vdj-tests/Demo-X5.should-vdj.fa
 
 $ Detects a CDR3 on regular V(D)J recombinations
 1: IGH SEG.* [{].*[}]

algo/tests/should-get-tests/chimera-2549.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline --all -2 $VIDJIL_DATA/2549.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC -g $VIDJIL_DIR/germline --all -2 $VIDJIL_DATA/2549.fa
 
 $ The KmerSegmenter segments the chimera on xxx germline (-2)
 1:unexpected .* -> .* 1

algo/tests/should-get-tests/chimera-fake-2.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS --all -g $VIDJIL_DIR/germline -2 $VIDJIL_DATA/chimera-fake.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC --all -g $VIDJIL_DIR/germline -2 $VIDJIL_DATA/chimera-fake.fa
 
 $ The KmerSegmenter segments the three chimera reads on PSEUDO_MAX12 germline (-2)
 1:unexpected .* -> .* 3

algo/tests/should-get-tests/chimera-fake-D.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS --all -g $VIDJIL_DIR/germline -2 $VIDJIL_DATA/chimera-fake-D.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC --all -g $VIDJIL_DIR/germline -2 $VIDJIL_DATA/chimera-fake-D.fa
 
 $ The KmerSegmenter segments the chimera reads on PSEUDO_MAX12 germline (-2)
 f1:unexpected .* -> .* 2

algo/tests/should-get-tests/chimera-fake-VJ-germlines-trim.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS --all -g $VIDJIL_DATA/chimera-fake-VJ-trim.g $VIDJIL_DATA/chimera-fake-VJ.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC --all -g $VIDJIL_DATA/chimera-fake-VJ-trim.g $VIDJIL_DATA/chimera-fake-VJ.fa
 # Testing a custom (fake) .g with special parameters for the algorithm
 
 $ The KmerSegmenter segments no read in Y because of the parameter

algo/tests/should-get-tests/chimera-fake-VJ-germlines.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS --all -g $VIDJIL_DATA/chimera-fake-VJ.g $VIDJIL_DATA/chimera-fake-VJ.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC --all -g $VIDJIL_DATA/chimera-fake-VJ.g $VIDJIL_DATA/chimera-fake-VJ.fa
 # Testing a custom (fake) germlines.data
 
 $ Report the species

algo/tests/should-get-tests/chimera-fake-VJ.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS --all -g $VIDJIL_DIR/germline -2 $VIDJIL_DATA/chimera-fake-VJ.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC --all -g $VIDJIL_DIR/germline -2 $VIDJIL_DATA/chimera-fake-VJ.fa
 
 $ The KmerSegmenter segments the five chimera reads on PSEUDO_MAX12 germline (-2)
 1:unexpected .* -> .* 5

algo/tests/should-get-tests/chimera-fake-half.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -e 100 --all -g $VIDJIL_DIR/germline -4 $VIDJIL_DATA/chimera-fake-half.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC -e 100 --all -g $VIDJIL_DIR/germline -4 $VIDJIL_DATA/chimera-fake-half.fa
 # TODO: a more precise modeling should give a e-value computation that could make this work even with -e 1
 
 $ The KmerSegmenter segments the six chimera reads on PSEUDO_MAX1U germline (-4)

algo/tests/should-get-tests/chimera-fake.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -e 1e-2 -g $VIDJIL_DIR/germline $VIDJIL_DATA/chimera-fake.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC -e 1e-2 -g $VIDJIL_DIR/germline $VIDJIL_DATA/chimera-fake.fa
 
 $ Do not segment on any germline, even incomplete
 1:junction detected in 0 reads

algo/tests/should-get-tests/chimera.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS --all -uU -g $VIDJIL_DIR/germline $VIDJIL_DATA/chimera-trg.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC --all -uU -g $VIDJIL_DIR/germline $VIDJIL_DATA/chimera-trg.fa
 
 $ Do not segment on IG/TR by chance
 12:(IG|TR).* -> .* 0

algo/tests/should-get-tests/cluster-epsilon.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -k 14 -w 50 -c clones -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -y 3 -z 1 -r 1 $VIDJIL_DATA/clones_simul.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC -k 14 -w 50 -c clones -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -y 3 -z 1 -r 1 $VIDJIL_DATA/clones_simul.fa
 
 $ Junction extractions
 1:found 25 windows in 66 reads
@@ -16,7 +16,7 @@ $ Clone 3 output (sequencing error)
 1:Clone #003 .* 1 reads
 
 
-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -k 14 -w 50 -c clones -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -y 3 -z 0 -r 1 --cluster-epsilon 5 $VIDJIL_DATA/clones_simul.fa ; cat out/clones_simul.vidjil
+!LAUNCH: $VIDJIL_DIR/$EXEC -k 14 -w 50 -c clones -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -y 3 -z 0 -r 1 --cluster-epsilon 5 $VIDJIL_DATA/clones_simul.fa ; cat out/clones_simul.vidjil
 
 $ Window extractions
 1:windows up to 50bp

algo/tests/should-get-tests/colinear-D7-27--J1.should

 
-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -K --all  -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH+  -r 4  -b co  $VIDJIL_DATA/D7-27--J1.fa  ; cat out/co.vidjil
+!LAUNCH: $VIDJIL_DIR/$EXEC -K --all  -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH+  -r 4  -b co  $VIDJIL_DATA/D7-27--J1.fa  ; cat out/co.vidjil
 
 # Test D7-27 0/92/0 J1 non-recombination
 

algo/tests/should-get-tests/combo-grep-reads.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -x 2000 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH --grep-reads GAGAGGTTACTATGATAGTAGTGGTTATTACGGGGTAGGGCAGTACTACT $VIDJIL_DATA/Stanford_S22.fasta ; cat out/seq/clone.fa-1
+!LAUNCH: $VIDJIL_DIR/$EXEC -x 2000 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH --grep-reads GAGAGGTTACTATGATAGTAGTGGTTATTACGGGGTAGGGCAGTACTACT $VIDJIL_DATA/Stanford_S22.fasta ; cat out/seq/clone.fa-1
 
 # See also label-grep-reads.should-get
 

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

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -K --all -z 0 -s 10s -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -D $VIDJIL_DIR/germline/homo-sapiens/IGHD.fa   $VIDJIL_DATA/common-V-D.fa  ; cat out/common-V-D.affects
+!LAUNCH: $VIDJIL_DIR/$EXEC -K --all -z 0 -s 10s -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -D $VIDJIL_DIR/germline/homo-sapiens/IGHD.fa   $VIDJIL_DATA/common-V-D.fa  ; cat out/common-V-D.affects
 
 $ Segments the sequence
 1: SEG  .* -> .* 1 

algo/tests/should-get-tests/config-read.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH --config ../data/config.vidjil $VIDJIL_DATA/Stanford_S22.fasta
+!LAUNCH: $VIDJIL_DIR/$EXEC -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH --config ../data/config.vidjil $VIDJIL_DATA/Stanford_S22.fasta
 
 $ Analyze 10 reads (--first-reads)
 : in 10 reads

algo/tests/should-get-tests/config-write-then-read.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -r 1 -x 10 -y 5 -z 1 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta ; cat out/Stanford_S22.vdj.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC -r 1 -x 10 -y 5 -z 1 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta ; cat out/Stanford_S22.vdj.fa
 
 # Testing -x/-y/-z options
 
@@ -13,7 +13,7 @@ $ 1 clone is fully analyzed, and not more (-z 1)
 2:clone-.* IGHV
 
 
-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS --config out/Stanford_S22.vidjil $VIDJIL_DATA/Stanford_S22.fasta ; cat out/Stanford_S22.vdj.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC --config out/Stanford_S22.vidjil $VIDJIL_DATA/Stanford_S22.fasta ; cat out/Stanford_S22.vdj.fa
 
 $ Same tests than before, options taken from 'out/StanfordS22.vidjil' that was just generated
 1: ==> 10 clones

algo/tests/should-get-tests/consensus-N.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS --all -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG ../should-vdj-tests/ext-nucleotides-N.should-vdj.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC --all -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG ../should-vdj-tests/ext-nucleotides-N.should-vdj.fa
 
 $ Segments on TRG
 1: TRG .* -> .* 1

algo/tests/should-get-tests/consensus-ambigous-2.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS --all -c clones -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/test_representatives.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC --all -c clones -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/test_representatives.fa
 
 $ Three clones should be found
 1:3 clones

algo/tests/should-get-tests/consensus-ambigous.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -r 1 -k 4 -w 20 -z 0 -c clones -V $VIDJIL_DATA/toy_V.fa -J $VIDJIL_DATA/toy_J.fa $VIDJIL_DATA/ambiguous_representative.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC -r 1 -k 4 -w 20 -z 0 -c clones -V $VIDJIL_DATA/toy_V.fa -J $VIDJIL_DATA/toy_J.fa $VIDJIL_DATA/ambiguous_representative.fa
 
 $ Short reads properly segmented
 1:SEG_+.* -> .* 4

algo/tests/should-get-tests/consensus-min-cover.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -r 5 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/representative-few-reads.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC -r 5 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/representative-few-reads.fa
 
 $ Consensus sequence should span on the whole sequence
 1: clone.*99% of 243

algo/tests/should-get-tests/consensus-random-read-chooser.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -w 20 -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG $VIDJIL_DATA/test-random-consensus.fa.gz > consensus-default.log
-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -w 20 -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG --consensus-on-random-sample $VIDJIL_DATA/test-random-consensus.fa.gz > consensus-random.log
+!LAUNCH: $VIDJIL_DIR/$EXEC -w 20 -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG $VIDJIL_DATA/test-random-consensus.fa.gz > consensus-default.log
+!LAUNCH: $VIDJIL_DIR/$EXEC -w 20 -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG --consensus-on-random-sample $VIDJIL_DATA/test-random-consensus.fa.gz > consensus-random.log
 !NO_LAUNCHER:
 !LAUNCH: diff consensus-default.log consensus-random.log
 !EXIT_CODE: 1

algo/tests/should-get-tests/debug.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS --header-sep FA -k 16 -z 0 -w 60 -r 5 -o out2 -uuu -U -v -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa   $VIDJIL_DATA/Stanford_S22.fasta ; tail out2/Stanford_S22.segmented.vdj.fa ; grep UNSEG out2/Stanford_S22.unsegmented.vdj.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC --header-sep FA -k 16 -z 0 -w 60 -r 5 -o out2 -uuu -U -v -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa   $VIDJIL_DATA/Stanford_S22.fasta ; tail out2/Stanford_S22.segmented.vdj.fa ; grep UNSEG out2/Stanford_S22.unsegmented.vdj.fa
 # Testing uncommon and debug options 
 
 $ verbose (-v)

algo/tests/should-get-tests/designations-D-read-number.should

@@ -7,9 +7,9 @@
 # other reads. This is what is tested, we first put 10 sequences, then 5 and
 # finally just the sequence of interest alone.
 
-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -d -r 1 -w 60 -z 100 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/buggy-D.fa \
-; $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -d -r 1 -w 60 -z 100 -x 6 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/buggy-D.fa \
-; $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -d -r 1 -w 60 -z 100 -x 1 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/buggy-D.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC -d -r 1 -w 60 -z 100 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/buggy-D.fa \
+; $VIDJIL_DIR/$EXEC -d -r 1 -w 60 -z 100 -x 6 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/buggy-D.fa \
+; $VIDJIL_DIR/$EXEC -d -r 1 -w 60 -z 100 -x 1 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/buggy-D.fa
 
 $ Three times the same window
 3: TGTGCGGGATCTTCGTCCTCTTATCATAATAATGGTTTTTTGGCGGGGGAGTCATGGGGC

algo/tests/should-get-tests/designations-simul.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -v -g $VIDJIL_DIR/germline -c designations $VIDJIL_DATA/segment_simul.fa | grep '^[>#]'
+!LAUNCH: $VIDJIL_DIR/$EXEC -v -g $VIDJIL_DIR/germline -c designations $VIDJIL_DATA/segment_simul.fa | grep '^[>#]'
 
 
 $ First sequence, easy segmentation (no error, few deletions at the windows, small N)

algo/tests/should-get-tests/designations.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -c designations $VIDJIL_DATA/segment_S22.fa | grep '^>' ; cat out/segment_S22.vidjil | python $VIDJIL_DIR/tools/format_json.py -1
+!LAUNCH: $VIDJIL_DIR/$EXEC -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -c designations $VIDJIL_DATA/segment_S22.fa | grep '^>' ; cat out/segment_S22.vidjil | python $VIDJIL_DIR/tools/format_json.py -1
 
 $ First sequence Stanford
 #                            164        175                 195     203

algo/tests/should-get-tests/error-deprecated-options.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -c segment -aAtl reads 2>&1
+!LAUNCH: $VIDJIL_DIR/$EXEC -c segment -aAtl reads 2>&1
 !EXIT_CODE: 1
 
 $ Deprecated options

algo/tests/should-get-tests/error-unknown-option.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS --hello reads 2>&1
+!LAUNCH: $VIDJIL_DIR/$EXEC --hello reads 2>&1
 !EXIT_CODE: 109
 
 $ Unknown option

algo/tests/should-get-tests/filter.should

 
-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS --analysis-filter 10 --all -x 30 -v -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta
+!LAUNCH: $VIDJIL_DIR/$EXEC --analysis-filter 10 --all -x 30 -v -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta
 
 $ Clone 13 is correctly analyzed
 1:FLN1FA001EP9M2.* IGHV2-26.* 2/GAT.*GCC/8 IGHJ2

algo/tests/should-get-tests/first-reads.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -c designations -x 2 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta
+!LAUNCH: $VIDJIL_DIR/$EXEC -c designations -x 2 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta
 
 $ Segments the good number of sequences in Stanford S22 
 2: >lcl

algo/tests/should-get-tests/first-sampled-reads.should

 
-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -y 0 -x 100 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta
+!LAUNCH: $VIDJIL_DIR/$EXEC -y 0 -x 100 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta
 
 $ Analyze the good number of sequences in Stanford S22 
 1: found .* of 100 reads
 
 
-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -y 0 -X 100 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta
+!LAUNCH: $VIDJIL_DIR/$EXEC -y 0 -X 100 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta
 
 $ Skip the good number of reads
 1:Processing every 131th read

algo/tests/should-get-tests/germlines-error-no-germline.should

 !NO_LAUNCHER:
-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS $VIDJIL_DATA/Stanford_S22.fasta 2>&1
+!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DATA/Stanford_S22.fasta 2>&1
 !EXIT_CODE: 1
 
 $ Error, no germlines

algo/tests/should-get-tests/germlines-error.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/Makefile $VIDJIL_DATA/Stanford_S22.fasta 2>&1
+!LAUNCH: $VIDJIL_DIR/$EXEC -g $VIDJIL_DIR/germline/Makefile $VIDJIL_DATA/Stanford_S22.fasta 2>&1
 !EXIT_CODE: 1
 
 $ Error, incorrect *.g

algo/tests/should-get-tests/germlines-several.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline -g $VIDJIL_DIR/germline/homo-sapiens-isotypes.g $VIDJIL_DATA/isotypes.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC -g $VIDJIL_DIR/germline -g $VIDJIL_DIR/germline/homo-sapiens-isotypes.g $VIDJIL_DATA/isotypes.fa
 
 $ Report the correct species
 1: Homo sapiens .9606.

algo/tests/should-get-tests/gzip.should

 !NO_LAUNCHER:
-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/clones_simul.fa > out-fa ;  $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -b clones_simul $VIDJIL_DATA/clones_simul.fa.gz > out-fa-gz ; diff -s -I '\#' -I 'index' -I 'Command line' out-fa out-fa-gz ; echo 'Diff: '$?; wc -l out-fa-gz
+!LAUNCH: $VIDJIL_DIR/$EXEC -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/clones_simul.fa > out-fa ;  $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -b clones_simul $VIDJIL_DATA/clones_simul.fa.gz > out-fa-gz ; diff -s -I '\#' -I 'index' -I 'Command line' out-fa out-fa-gz ; echo 'Diff: '$?; wc -l out-fa-gz
 
 $ Identical output
 1:Diff: 0

algo/tests/should-get-tests/help.should

 !NO_LAUNCHER:
-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -h
+!LAUNCH: $VIDJIL_DIR/$EXEC -h
 
 $ License
 1:vidjil-algo is free software
@@ -19,7 +19,7 @@ $ Correct number of regular options
 
 
 !NO_LAUNCHER:
-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -H
+!LAUNCH: $VIDJIL_DIR/$EXEC -H
 
 $ License
 1:vidjil-algo is free software

algo/tests/should-get-tests/json-limits.should

 !REQUIRES: python $VIDJIL_DIR/tools/check_python_version.py
-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -3 --max-clones 10 -y 5 -z 1 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH  -r 4  -b limits  $VIDJIL_DATA/Stanford_S22.fasta > /dev/null ; cat out/limits.vidjil
+!LAUNCH: $VIDJIL_DIR/$EXEC -3 --max-clones 10 -y 5 -z 1 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH  -r 4  -b limits  $VIDJIL_DATA/Stanford_S22.fasta > /dev/null ; cat out/limits.vidjil
 
 # Test limits in the .vidjil json output
 

algo/tests/should-get-tests/json-quality.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -c clones --all -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG $VIDJIL_DATA/segment_lec.fq > /dev/null ; cat out/segment_lec.vidjil
+!LAUNCH: $VIDJIL_DIR/$EXEC -c clones --all -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG $VIDJIL_DATA/segment_lec.fq > /dev/null ; cat out/segment_lec.vidjil
 
 $ Window
 1:"id": "GGGGTCTATTACTGTGCCACCTGGGCCTTATTATAAGAAACTCTTTGGCA"

algo/tests/should-get-tests/json.should

 !REQUIRES: python $VIDJIL_DIR/tools/check_python_version.py
-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -3 -z 1 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -w 60 -r 5 -e 10 -b data  $VIDJIL_DATA/Stanford_S22.fasta > /dev/null ; cat out/data.vidjil | python $VIDJIL_DIR/tools/format_json.py -1
+!LAUNCH: $VIDJIL_DIR/$EXEC -3 -z 1 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -w 60 -r 5 -e 10 -b data  $VIDJIL_DATA/Stanford_S22.fasta > /dev/null ; cat out/data.vidjil | python $VIDJIL_DIR/tools/format_json.py -1
 
 $ From homo-sapiens.g
 1:"ref": "http://www.vidjil.org/germlines/germline-.*.tar.gz"

algo/tests/should-get-tests/k-14.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -y 0 -k 14 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta
+!LAUNCH: $VIDJIL_DIR/$EXEC -y 0 -k 14 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta
 
 $ Find the good number of windows in Stanford S22 (contiguous seed 14)
 1: found 10796 windows in 13152 reads

algo/tests/should-get-tests/label-file.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -z 0 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -x 100 -r 5 --label-file $VIDJIL_DATA/Stanford_S22.label $VIDJIL_DATA/Stanford_S22.fasta ; cat out/Stanford_S22.vidjil
+!LAUNCH: $VIDJIL_DIR/$EXEC -z 0 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -x 100 -r 5 --label-file $VIDJIL_DATA/Stanford_S22.label $VIDJIL_DATA/Stanford_S22.fasta ; cat out/Stanford_S22.vidjil
 
 $ Some clone has only one read, bypassing the -r 5 option, and the good label
 1: clone-00..*0001-.* my-clone

algo/tests/should-get-tests/label-sequences.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -e 10 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH --label ACCGGTATTACT --label CAGCTGCTCCCC --label TGGGCCACTC --label ATCAACGCTGGCAATGGTAACACTAAATATTCACAGAAGTTCCAGGGCAGAGTCACCATTACCAGGGACACATACGCGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAAGACACGGCTCTGTATTACTGTGCGAGAGTGCGCAGCAGCTGGTCTGATGCTTTTGATTATCTGG $VIDJIL_DATA/clones_simul.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC -e 10 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH --label ACCGGTATTACT --label CAGCTGCTCCCC --label TGGGCCACTC --label ATCAACGCTGGCAATGGTAACACTAAATATTCACAGAAGTTCCAGGGCAGAGTCACCATTACCAGGGACACATACGCGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAAGACACGGCTCTGTATTACTGTGCGAGAGTGCGCAGCAGCTGGTCTGATGCTTTTGATTATCTGG $VIDJIL_DATA/clones_simul.fa
 
 $ ACCGGTATTACT is found (in window and representative and in the command line)
 3:ACCGGTATTACT

algo/tests/should-get-tests/label.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -x 100 -z 0 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -r 5 --label ACTGTGCGAGAGTTGGAATTAGTAGTGGCTGGCCTGATTCCTGGGGCCAG $VIDJIL_DATA/Stanford_S22.fasta ; cat out/Stanford_S22.vidjil
+!LAUNCH: $VIDJIL_DIR/$EXEC -x 100 -z 0 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -r 5 --label ACTGTGCGAGAGTTGGAATTAGTAGTGGCTGGCCTGATTCCTGGGGCCAG $VIDJIL_DATA/Stanford_S22.fasta ; cat out/Stanford_S22.vidjil
 
 $ Some clone has only one read, bypassing the -r 5 option, and the good label
 1: clone-00..*0001-.* --label

algo/tests/should-get-tests/labels-grep-reads.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -x 2000 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH --out-reads --label-filter --label GAGAGGTTACTATGATAGTAGTGGTTATTACGGGGTAGGGCAGTACTACT $VIDJIL_DATA/Stanford_S22.fasta ; cat out/seq/clone.fa-1
+!LAUNCH: $VIDJIL_DIR/$EXEC -x 2000 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH --out-reads --label-filter --label GAGAGGTTACTATGATAGTAGTGGTTATTACGGGGTAGGGCAGTACTACT $VIDJIL_DATA/Stanford_S22.fasta ; cat out/seq/clone.fa-1
 
 # See also combo-grep-reads.should-get
 

algo/tests/should-get-tests/labels-json.should

 
-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH --max-consensus 0 --first-reads 10 --label-json ../data/labels-json.vidjil $VIDJIL_DATA/Stanford_S22.fasta
+!LAUNCH: $VIDJIL_DIR/$EXEC -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH --max-consensus 0 --first-reads 10 --label-json ../data/labels-json.vidjil $VIDJIL_DATA/Stanford_S22.fasta
 
 $ Labels are taken into account
 : 2 labels

algo/tests/should-get-tests/large-N.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -r 1 $VIDJIL_DATA/large_N.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -r 1 $VIDJIL_DATA/large_N.fa
 
 $ Find a huge insertion in the segmentation
 1:>clone-001.*/[ACGT]{100}

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

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline $VIDJIL_DATA/multi-complete.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC -g $VIDJIL_DIR/germline $VIDJIL_DATA/multi-complete.fa
 
 $ Segment all the seven reads
 1:junction detected in 7 reads
@@ -30,7 +30,7 @@ $ Compute the diversity. All windows have only one read, full diversity.
 1: Ds = 1.000
 
 
-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline $VIDJIL_DATA/multi-short.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC -g $VIDJIL_DIR/germline $VIDJIL_DATA/multi-short.fa
 
 $ Segment all the seven reads
 1:junction detected in 7 reads

algo/tests/should-get-tests/multi-segment.should

-!LAUNCH: $VIDJIL_DIR/$EXEC -c designations $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH,IGK,IGL $VIDJIL_DATA/multi-complete.fa ; cat out/multi-complete.vidjil | python $VIDJIL_DIR/tools/format_json.py -1
+!LAUNCH: $VIDJIL_DIR/$EXEC -c designations -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH,IGK,IGL $VIDJIL_DATA/multi-complete.fa ; cat out/multi-complete.vidjil | python $VIDJIL_DIR/tools/format_json.py -1
 
 $ Segment the Ig recombinations
 1:IGH SEG

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

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -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
+!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
 # Testing .affects output (-K)
 
 $ First sequence (TRA), display sequence

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

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens-cd.g -g $VIDJIL_DIR/germline/homo-sapiens.g:TRA,TRB,TRG,TRD,IGH,IGK,IGL $VIDJIL_DATA/multi-short.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC -g $VIDJIL_DIR/germline/homo-sapiens-cd.g -g $VIDJIL_DIR/germline/homo-sapiens.g:TRA,TRB,TRG,TRD,IGH,IGK,IGL $VIDJIL_DATA/multi-short.fa
 
 $ Segment all the seven reads
 1:junction detected in 7 reads

algo/tests/should-get-tests/multi-tiny-segment.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -c designations -g $VIDJIL_DIR/germline $VIDJIL_DATA/multi-tiny.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC -c designations -g $VIDJIL_DIR/germline $VIDJIL_DATA/multi-tiny.fa
 
 $ Do not segment any of the seven reads
 7:UNSEG

algo/tests/should-get-tests/no-cdr3-json.should

 # The sequences are on TRG, no CDR3 should be found with IGH
 
-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -c designations -3 -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -D $VIDJIL_DIR/germline/homo-sapiens/IGHD.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa ../should-vdj-tests/cdr3-indels.should-vdj.fa; cat out/cdr3-indels.should-vdj.vidjil
+!LAUNCH: $VIDJIL_DIR/$EXEC -c designations -3 -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -D $VIDJIL_DIR/germline/homo-sapiens/IGHD.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa ../should-vdj-tests/cdr3-indels.should-vdj.fa; cat out/cdr3-indels.should-vdj.vidjil
 
 $ No CDR3 should be found
 0:TRGV.* [{].*[}]

algo/tests/should-get-tests/no-cdr3.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -c designations -3 -g $VIDJIL_DIR/germline $VIDJIL_DATA/no-cdr3.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC -c designations -3 -g $VIDJIL_DIR/germline $VIDJIL_DATA/no-cdr3.fa
 
 $ No CDR3 should be found
 0:seq1.* IGH SEG.* [{].*[}]

algo/tests/should-get-tests/out-reads.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -z 2 -r 5 --out-reads -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta ; cat out/seq/clone.fa-2
+!LAUNCH: $VIDJIL_DIR/$EXEC -z 2 -r 5 --out-reads -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta ; cat out/seq/clone.fa-2
 # Testing detailed clone output (--out-reads)
 
 $ Detailed clone output (out/seq/clone.fa-2), germline

algo/tests/should-get-tests/overlap-stdout.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -c designations -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH --all $VIDJIL_DATA/overlap-d-j.fa | grep -v out | tail -4 | tr -d '\n' | wc -c
+!LAUNCH: $VIDJIL_DIR/$EXEC -c designations -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH --all $VIDJIL_DATA/overlap-d-j.fa | grep -v out | tail -4 | tr -d '\n' | wc -c
 
 $ Exported sequence has all the bases
 1:116

algo/tests/should-get-tests/revcomp-S22.should

-!LAUNCH: $LAUNCHER $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -z 1 -k 9 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH --ratio 0.001 -r 2 -x 1000 -y 1 -c clones $VIDJIL_DATA/Stanford_S22.fasta | sed 's/--IGH--.*VDJ\\(.*\\).$/\\1/' | sed 's/IGH SEG_./IGH SEG_X/' > vidjil_s22.log
-!LAUNCH: $LAUNCHER $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -z 1 -k 9 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH --ratio 0.001 -r 2 -x 1000 -y 1 -c clones $VIDJIL_DATA/Stanford_S22.rc.fasta | sed 's/--IGH--.*VDJ\\(.*\\).$/\\1/' |  sed 's/IGH SEG_./IGH SEG_X/' > vidjil_s22_rc.log
+!LAUNCH: $LAUNCHER $VIDJIL_DIR/$EXEC -z 1 -k 9 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH --ratio 0.001 -r 2 -x 1000 -y 1 -c clones $VIDJIL_DATA/Stanford_S22.fasta | sed 's/--IGH--.*VDJ\\(.*\\).$/\\1/' | sed 's/IGH SEG_./IGH SEG_X/' > vidjil_s22.log
+!LAUNCH: $LAUNCHER $VIDJIL_DIR/$EXEC -z 1 -k 9 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH --ratio 0.001 -r 2 -x 1000 -y 1 -c clones $VIDJIL_DATA/Stanford_S22.rc.fasta | sed 's/--IGH--.*VDJ\\(.*\\).$/\\1/' |  sed 's/IGH SEG_./IGH SEG_X/' > vidjil_s22_rc.log
 !LAUNCH: diff out/Stanford_S22{,.rc}.vidjil | grep GGG && diff vidjil_s22.log vidjil_s22_rc.log
 !EXIT_CODE: 1
 

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

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/ -r 1 -c clones $VIDJIL_DATA/revcomp-VdJa.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC -g $VIDJIL_DIR/germline/ -r 1 -c clones $VIDJIL_DATA/revcomp-VdJa.fa
 
 $ Just one window found
 1:==> found 1 windows

algo/tests/should-get-tests/species-mus-musculus.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -3 -c designations -g $VIDJIL_DIR/germline/mus-musculus.g $VIDJIL_DATA/example_mouse.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC -3 -c designations -g $VIDJIL_DIR/germline/mus-musculus.g $VIDJIL_DATA/example_mouse.fa
 
 $ Segment sequence on IGK
 1:segIGK.*IGKV.*IGKJ

algo/tests/should-get-tests/tabs-in-output.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -2 -c designations -g $VIDJIL_DIR/germline  $VIDJIL_DATA/segment-or-not.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC -2 -c designations -g $VIDJIL_DIR/germline  $VIDJIL_DATA/segment-or-not.fa
 
 $ Check that output has one tab for each sequence
 3:^>.*\t
\ No newline at end of file

algo/tests/should-get-tests/trb-only-VJ.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS --all -g $VIDJIL_DIR/germline/homo-sapiens.g:TRB $VIDJIL_DATA/trb-only-VJ.fa ; cat out/trb-only-VJ.vidjil
+!LAUNCH: $VIDJIL_DIR/$EXEC --all -g $VIDJIL_DIR/germline/homo-sapiens.g:TRB $VIDJIL_DATA/trb-only-VJ.fa ; cat out/trb-only-VJ.vidjil
 
 $ Segments the read on TRB (the information is given twice, stdout + .vidjil)
 2: TRB .* -> .* 1

algo/tests/should-get-tests/trd-dd2-dd3-complete.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS --all -g $VIDJIL_DIR/germline/homo-sapiens.g:TRD $VIDJIL_DATA/trd-dd2-dd3.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC --all -g $VIDJIL_DIR/germline/homo-sapiens.g:TRD $VIDJIL_DATA/trd-dd2-dd3.fa
 
 $ Segment only 2 reads, because we do not look for incomplete recombinations
 1:junction detected in 2 reads

algo/tests/should-get-tests/trd-dd2-dd3-incomplete.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -w 10 -e 10 --all -g $VIDJIL_DIR/germline $VIDJIL_DATA/trd-dd2-dd3.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC -w 10 -e 10 --all -g $VIDJIL_DIR/germline $VIDJIL_DATA/trd-dd2-dd3.fa
 
 $ Segment 6 reads, thanks to -i
 1:junction detected in 6 reads

algo/tests/should-get-tests/trd-dd2-dd3.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -K --all -e 10 -k 8 -w 20 -V $VIDJIL_DIR/germline/homo-sapiens/TRDV.fa -V $VIDJIL_DIR/germline/homo-sapiens/TRDD2+up.fa -J $VIDJIL_DIR/germline/homo-sapiens/TRDD3+down.fa -J $VIDJIL_DIR/germline/homo-sapiens/TRDJ.fa $VIDJIL_DATA/trd-dd2-dd3.fa ; cat out/trd-dd2-dd3.affects
+!LAUNCH: $VIDJIL_DIR/$EXEC -K --all -e 10 -k 8 -w 20 -V $VIDJIL_DIR/germline/homo-sapiens/TRDV.fa -V $VIDJIL_DIR/germline/homo-sapiens/TRDD2+up.fa -J $VIDJIL_DIR/germline/homo-sapiens/TRDD3+down.fa -J $VIDJIL_DIR/germline/homo-sapiens/TRDJ.fa $VIDJIL_DATA/trd-dd2-dd3.fa ; cat out/trd-dd2-dd3.affects
 
 $ Segment all 8 reads, thanks to TRDD2 and TRDD3
 1: junction detected in 8 reads .100..

algo/tests/should-get-tests/trim.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -y 0 --trim 1 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -x 100 $VIDJIL_DATA/Stanford_S22.fasta
+!LAUNCH: $VIDJIL_DIR/$EXEC -y 0 --trim 1 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -x 100 $VIDJIL_DATA/Stanford_S22.fasta
 
 $ No read segmented as we have no germline because of the --trim
 1: UNSEG too few V/J ->      100

algo/tests/should-get-tests/unsegmentation-causes.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:TRA,TRB,TRD,TRG,IGH,IGK,IGL -uuu $VIDJIL_DATA/segmentation-2.fa ; cat out/segmentation-2.unsegmented.vdj.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC -g $VIDJIL_DIR/germline/homo-sapiens.g:TRA,TRB,TRD,TRG,IGH,IGK,IGL -uuu $VIDJIL_DATA/segmentation-2.fa ; cat out/segmentation-2.unsegmented.vdj.fa
 
 $ Only one sequence is segmented, but it is too small for a window (too short w)
 1: junction detected in 1 reads
@@ -24,7 +24,7 @@ $ The proper unsegmentation cause is given in the .unsegmented.vdj.fa file (-uuu
 
 
 
-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:TRA,TRB,TRD,TRG,IGH,IGK,IGL -u $VIDJIL_DATA/segmentation-2.fa ; cat ./out///segmentation-2.UNSEG_ambiguous.fa ; cat ./out///segmentation-2.UNSEG_too_few_V_J.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC -g $VIDJIL_DIR/germline/homo-sapiens.g:TRA,TRB,TRD,TRG,IGH,IGK,IGL -u $VIDJIL_DATA/segmentation-2.fa ; cat ./out///segmentation-2.UNSEG_ambiguous.fa ; cat ./out///segmentation-2.UNSEG_too_few_V_J.fa
 
 $ The proper unsegmentation cause is given
 1: UNSEG too short   -> .* 1

algo/tests/should-get-tests/w-100-short-shift.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -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
+!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

algo/tests/should-get-tests/w-all.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -w all -r 1 -y 15 -z 0 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta
+!LAUNCH: $VIDJIL_DIR/$EXEC -w all -r 1 -y 15 -z 0 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta
 
 # Testing '-w all' option
 

algo/tests/should-get-tests/w-small-error.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -x 1 -w -10 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta 2>&1
+!LAUNCH: $VIDJIL_DIR/$EXEC -x 1 -w -10 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta 2>&1
 !EXIT_CODE: 1
 
 $ Error, too small -w

algo/tests/should-get-tests/w-small.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -x 100 -r 1 -y 1 -z 0 -w 10 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta 2>&1
+!LAUNCH: $VIDJIL_DIR/$EXEC -x 100 -r 1 -y 1 -z 0 -w 10 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta 2>&1
 !OUTPUT_FILE: out/seq/clone.fa-1
 ### !EXIT_CODE: 1
 

algo/tests/should-get-tests/warning-all.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS --all -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/toy_V.fa ; cat out/toy_V.vidjil | python $VIDJIL_DIR/tools/format_json.py -1
+!LAUNCH: $VIDJIL_DIR/$EXEC --all -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/toy_V.fa ; cat out/toy_V.vidjil | python $VIDJIL_DIR/tools/format_json.py -1
 
 $ Warning, --all
 1:WARNING

algo/tests/should-get-tests/warning-similar.should

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS --all -w all -g $VIDJIL_DIR/germline/homo-sapiens.g $VIDJIL_DATA/s-somatic.fa ; cat out/s-somatic.vidjil | python $VIDJIL_DIR/tools/format_json.py -1
+!LAUNCH: $VIDJIL_DIR/$EXEC --all -w all -g $VIDJIL_DIR/germline/homo-sapiens.g $VIDJIL_DATA/s-somatic.fa ; cat out/s-somatic.vidjil | python $VIDJIL_DIR/tools/format_json.py -1