Merge branch 'feature-a/3295-option-names-and-help' into 'dev'

Feature a/3295 option names and help

Closes #3785 and #3295

See merge request !434

algo/tests/bugs/bug20150604.should-get

-!LAUNCH: $VIDJIL_DIR/$EXEC -KA -k 16 -z 0 -g ../../../germline/homo-sapiens.g:IGH bug20150604.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC -K --all -k 16 -z 0 -g ../../../germline/homo-sapiens.g:IGH bug20150604.fa
 
 $ Bug on some architectures, not segmented
 1: junction detected in 1 reads

algo/tests/bugs/bug20160121.should-get

-!LAUNCH: $VIDJIL_DIR/$EXEC -s '#####-#####' -c clones -r 1 -g ../../../germline/homo-sapiens.g:IGH -t 0 -e 1e-2 bug20160121.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC -s '#####-#####' -c clones -r 1 -g ../../../germline/homo-sapiens.g:IGH -e 1e-2 bug20160121.fa
 
 $ Sequences should not be segmented since they only contain J.
 1:UNSEG only J/3' -> 2

algo/tests/should-get-tests/ambiguous_representative2.should-get

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -A -c clones -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/test_representatives.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS --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/cd-trimmed.should-get

-!LAUNCH: $VIDJIL_DIR/$EXEC -a -g $VIDJIL_DIR/germline/homo-sapiens-cd.g -A $VIDJIL_DATA/cd-19-trimmed.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC --all --out-reads -g $VIDJIL_DIR/germline/homo-sapiens-cd.g $VIDJIL_DATA/cd-19-trimmed.fa
 
 $ Load CD-sorting.fa
 1:homo-sapiens/CD-sorting.fa .* 28 sequences

algo/tests/should-get-tests/cd.should-get

-!LAUNCH: $VIDJIL_DIR/$EXEC -K -g $VIDJIL_DIR/germline/homo-sapiens-cd.g -A $VIDJIL_DATA/cd-4-19.fa ; grep 'seed' out/cd-4-19.affects
+!LAUNCH: $VIDJIL_DIR/$EXEC -K -g $VIDJIL_DIR/germline/homo-sapiens-cd.g --all $VIDJIL_DATA/cd-4-19.fa ; grep 'seed' out/cd-4-19.affects
 
 $ Load CD-sorting.fa
 1:homo-sapiens/CD-sorting.fa .* 28 sequences

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

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline -A -2 $VIDJIL_DATA/2549.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -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-get

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -A -t 0 -g $VIDJIL_DIR/germline -2 $VIDJIL_DATA/chimera-fake.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS --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-get

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline -2 $VIDJIL_DATA/chimera-fake-D.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS --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-get

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DATA/chimera-fake-VJ-trim.g $VIDJIL_DATA/chimera-fake-VJ.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS --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-get

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DATA/chimera-fake-VJ.g $VIDJIL_DATA/chimera-fake-VJ.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS --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-get

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline -2 $VIDJIL_DATA/chimera-fake-VJ.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS --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-get

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -e 100 -A -t 0 -g $VIDJIL_DIR/germline -4 $VIDJIL_DATA/chimera-fake-half.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -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.should-get

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -A -uU -g $VIDJIL_DIR/germline $VIDJIL_DATA/chimera-trg.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS --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/clones_lec.should-get

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g -c clones -A -3 $VIDJIL_DATA/segment_lec.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -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/clones_simul_cluster.should-get

-!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 -n 5 $VIDJIL_DATA/clones_simul.fa ; cat out/clones_simul.vidjil
+!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
 
 $ Window extractions
 1:windows up to 50bp

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

 
-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -KA  -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 $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
 
 # Test D7-27 0/92/0 J1 non-recombination
 

algo/tests/should-get-tests/stanford-labels-FaW.should-get → algo/tests/should-get-tests/combo-grep-reads.should-get

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -x 2000 -t 0 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -FaW GAGAGGTTACTATGATAGTAGTGGTTATTACGGGGTAGGGCAGTACTACT $VIDJIL_DATA/Stanford_S22.fasta ; cat out/seq/clone.fa-1
+!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
+
+# See also label-grep-reads.should-get
 
 $ Keep only one windows, the one given by -W, with only 2 reads in the first 2000 reads (it is actually the second clone in Stanford_S22.fasta)
 1: keep 1 windows in 2 reads

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

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -KA -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 $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
 
 $ Segments the sequence
 1: SEG  .* -> .* 1 

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

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -c segment reads 2>&1
+!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -c segment -aAtl reads 2>&1
 !EXIT_CODE: 1
 
-$ Deprecated option
-1:is deprecated
+$ Deprecated options
+5:is deprecated
  
 $ Advice on usage
 1:-c designations
-
+1:--trim
+1:--all
+1:--label
+1:--out-reads

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

@@ -5,5 +5,5 @@ $ Unknown option
 1:error.* --hello
  
 $ Refer to online help and documentation
-1:run with -h
+1:run with --help
 1:see doc/vidjil-algo.md

algo/tests/should-get-tests/stanford-Z.should-get → algo/tests/should-get-tests/filter.should-get

 
-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -Z 10 -A -x 30 -v -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta
+!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
 
 $ Clone 13 is correctly analyzed
 1:FLN1FA001EP9M2.* IGHV2-26.* 2/GAT.*GCC/8 IGHJ2
 
 $ Statistics on -Z
 1:Statistics on clone analysis
-rb1: IGH 3[0-2][0-9]{2}/ 1[0-2][0-9]{3} 28..%
+rb1: IGH 3[0-2][0-9]{2}/ 1[0-2][0-9]{3} 28..%
\ No newline at end of file

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

+!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -x 2000 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH --out-reads --label-filter --label GAGAGGTTACTATGATAGTAGTGGTTATTACGGGGTAGGGCAGTACTACT $VIDJIL_DATA/Stanford_S22.fasta ; cat out/seq/clone.fa-1
+
+# See also combo-grep-reads.should-get
+
+$ Keep only one windows, the one given by -W, with only 2 reads in the first 2000 reads (it is actually the second clone in Stanford_S22.fasta)
+1: keep 1 windows in 2 reads
+
+$ Tbere are the three IGHV/D/J genes in out/seq/clone.fa-1
+3:>IGH
+
+$ There are 2 reads in out/seq/clone.fa-1
+2:>lcl

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

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

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

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

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

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

algo/tests/should-get-tests/sequences_of_interest.should-get

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

algo/tests/should-get-tests/somatic.should-get

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -A -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 $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
 
 $ No clustering due to -w all
 1: considering all analyzed reads as windows

algo/tests/should-get-tests/stanford-detailed.should-get

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -z 2 -r 5 -a -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta ; cat out/seq/clone.fa-2
-# Testing detailed clone output (-a)
+!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
+# Testing detailed clone output (--out-reads)
 
 $ Detailed clone output (out/seq/clone.fa-2), germline
 # IGHV1-8*01 could also be detected

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

-!LAUNCH: ($LAUNCHER $VIDJIL_DIR/$EXEC $EXTRA $VIDJIL_DEFAULT_OPTIONS -c germlines -g $VIDJIL_DIR/germline/homo-sapiens.g:TRA,TRB,TRD,TRG,IGH,IGK,IGL -t 100 -s '######-######' $VIDJIL_DATA/Stanford_S22.fasta)
+!LAUNCH: ($LAUNCHER $VIDJIL_DIR/$EXEC $EXTRA $VIDJIL_DEFAULT_OPTIONS -c germlines -g $VIDJIL_DIR/germline/homo-sapiens.g:TRA,TRB,TRD,TRG,IGH,IGK,IGL --trim 100 -s '######-######' $VIDJIL_DATA/Stanford_S22.fasta)
 
 $ number of reads and kmers
 1:13153 reads, 3020179 kmers

algo/tests/should-get-tests/stanford-labels-W.should-get

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

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

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -z 0 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -x 100 -r 5 -l $VIDJIL_DATA/Stanford_S22.label $VIDJIL_DATA/Stanford_S22.fasta ; cat out/Stanford_S22.vidjil
+!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
 
 $ 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/stanford-t1.should-get

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

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

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline/homo-sapiens.g:TRB $VIDJIL_DATA/trb-only-VJ.fa ; cat out/trb-only-VJ.vidjil
+!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
 
 $ 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-get

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline/homo-sapiens.g:TRD $VIDJIL_DATA/trd-dd2-dd3.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS --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-get

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -w 10 -e 10 -A -g $VIDJIL_DIR/germline $VIDJIL_DATA/trd-dd2-dd3.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -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-get

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -K -A -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 $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
 
 $ Segment all 8 reads, thanks to TRDD2 and TRDD3
 1: junction detected in 8 reads .100..

algo/tests/should-get-tests/vidjil-custom-cost.should-get

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -f '1, 2, 3, 4, 5' $VIDJIL_DATA/Stanford_S22.fasta
+!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS --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/vidjil-help-advanced.should-get

@@ -5,7 +5,7 @@ $ License
 1:vidjil-algo is free software
 
 $ Check default costs
-1:segmenter .* "4, -6, -10, -1, -10"
+1:analysis.* "4, -6, -10, -1, -10"
 1:clustering .* "1, -4, -4, 0, 0"
 
 $ Show seeds
@@ -17,4 +17,4 @@ $ Display advanced options
 : custom Cost
 
 $ Correct number of options
-B51:^  -
+B52:^  -

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

@@ -7,12 +7,12 @@ $ License
 $ Check default filtering options
 1: =5 .* minimal number of reads supporting a clone
 1: =0 .* minimal percentage of reads supporting a clone
-1: =100 .* maximal number of clones computed with a consensus sequence
-1: =100 .* maximal number of clones to be analyzed
+1: =100 .*maximal number of clones computed with a consensus sequence
+1: max-designations .*=100
 
 $ Do not display advanced options
 0: , experimental options
 0: custom Cost
 
 $ Correct number of regular options
-B25:^  -
+B24:^  -

algo/tests/should-get-tests/vidjil-warning-A.should-get → algo/tests/should-get-tests/warning-all.should-get

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -A -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 $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
 
-$ Warning, -A
+$ Warning, --all
 1:WARNING
 
 $ Warning in json output

server/web2py/applications/vidjil/models/task.py

@@ -234,7 +234,7 @@ def run_vidjil(id_file, id_config, id_data, grep_reads,
 
     if grep_reads:
         # TODO: security, assert grep_reads XXXX
-        vidjil_cmd += ' -FaW "%s" ' % grep_reads
+        vidjil_cmd += ' --grep-reads "%s" ' % grep_reads
     
     os.makedirs(out_folder)
     out_log = out_folder+'/'+output_filename+'.vidjil.log'