Commit 090afd7f authored by Mathieu Giraud's avatar Mathieu Giraud

tests: add and update

see #4425
parent 3af4db23
!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
!LAUNCH: $VIDJIL_DIR/$EXEC -r 1 -x 10 -y 5 -z 1 --out-vdjfa -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta ; cat out/Stanford_S22.vdj.fa
# Testing -x/-y/-z options
......
!LAUNCH: $VIDJIL_DIR/$EXEC -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -b out-a $VIDJIL_DATA/clones_simul.fa
!LAUNCH: $VIDJIL_DIR/$EXEC -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -b out-a --out-vdjfa $VIDJIL_DATA/clones_simul.fa
$ Output
1: out-a.vidjil
1: out-a.tsv
1: out-a.vdj.fa
!LAUNCH: $VIDJIL_DIR/$EXEC -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH --gz -b out-b $VIDJIL_DATA/clones_simul.fa
!LAUNCH: $VIDJIL_DIR/$EXEC -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH --gz -b out-b --out-vdjfa $VIDJIL_DATA/clones_simul.fa
$ Compressed output
1: out-b.vidjil.gz
......
......@@ -37,4 +37,4 @@ $ Display advanced options
: custom Cost
$ Correct number of options, including advanced options
59:^..-
60:^..-
......@@ -17,6 +17,9 @@ $ Correct output message
$ There is no clone output in individual files
0:detail, by clone
$ There is no deprecated .vdj.fa file
0:.vdj.fa
!LAUNCH: rm out/Stanford_S22.tsv ; $LAUNCHER $VIDJIL_DIR/$EXEC $EXTRA -z 0 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta > /dev/null ; touch out/Stanford_S22.tsv ; cat out/Stanford_S22.tsv
$ The AIRR .tsv file has four lines
......
!LAUNCH: $VIDJIL_DIR/$EXEC -r 1 -x 10 -y all -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 all -z 1 --out-vdjfa -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta ; cat out/Stanford_S22.vdj.fa
# Testing -x/-y/-z options
......
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