Commit d793efe2 authored by Mathieu Giraud's avatar Mathieu Giraud

tests: breaking change in should, put !EXIT_CODE before commands

parent 1c54c254
!LAUNCH: $VIDJIL_DIR/$EXEC --analysis-cost '1, 2, 3, 4, 5' $VIDJIL_DATA/Stanford_S22.fasta
!EXIT_CODE: 1
!LAUNCH: $VIDJIL_DIR/$EXEC --analysis-cost '1, 2, 3, 4, 5' $VIDJIL_DATA/Stanford_S22.fasta
$Check that correct custom cost is used
1:use custom Cost "1, 2, 3, 4, 5"
!LAUNCH: $VIDJIL_DIR/$EXEC -w 20 -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG --consensus-on-longest-sequences $VIDJIL_DATA/test-random-consensus.fa.gz > consensus-longest.log
!LAUNCH: $VIDJIL_DIR/$EXEC -w 20 -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG $VIDJIL_DATA/test-random-consensus.fa.gz > consensus-random.log
!NO_LAUNCHER:
!LAUNCH: diff consensus-longest.log consensus-random.log
!EXIT_CODE: 1
!LAUNCH: diff consensus-longest.log consensus-random.log
$ Output should differ: ReadQualityScore gives a consensus of 52bp (with the spurious insertion)
# Appears twice in the header of the consensus sequence and in the similarity matrix
......
!LAUNCH: $VIDJIL_DIR/$EXEC -c segment -aAtl reads 2>&1
!EXIT_CODE: 1
!LAUNCH: $VIDJIL_DIR/$EXEC -c segment -aAtl reads 2>&1
$ Deprecated options
5:is deprecated
......
!LAUNCH: $VIDJIL_DIR/$EXEC --hello reads 2>&1
!EXIT_CODE: 109
!LAUNCH: $VIDJIL_DIR/$EXEC --hello reads 2>&1
$ Unknown option
1:error.* --hello
......
!NO_LAUNCHER:
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DATA/Stanford_S22.fasta 2>&1
!EXIT_CODE: 1
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DATA/Stanford_S22.fasta 2>&1
$ Error, no germlines
1:error.* one germline must be given
......
!LAUNCH: $VIDJIL_DIR/$EXEC -g $VIDJIL_DIR/germline/Makefile $VIDJIL_DATA/Stanford_S22.fasta 2>&1
!EXIT_CODE: 1
!LAUNCH: $VIDJIL_DIR/$EXEC -g $VIDJIL_DIR/germline/Makefile $VIDJIL_DATA/Stanford_S22.fasta 2>&1
$ Error, incorrect *.g
1:error.* cannot properly read
......
!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
!LAUNCH: diff out/Stanford_S22{,.rc}.vidjil | grep GGG && diff vidjil_s22.log vidjil_s22_rc.log
$ Same number detected
0:==> detected
......
!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
!LAUNCH: $VIDJIL_DIR/$EXEC -x 1 -w -10 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta 2>&1
$ Error, too small -w
1:error.* Too small -w
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