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vidjil
vidjil
Commits
556d8b0b
Commit
556d8b0b
authored
Feb 12, 2019
by
Mathieu Giraud
Browse files
tests: update
parent
cb50a85d
Changes
5
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algo/tests/bugs/bug20141024.should-get
View file @
556d8b0b
!NO_LAUNCHER:
!LAUNCH: valgrind --suppressions=gzstream_cpp.supp --suppressions=libstdc++_leak.supp --leak-check=full $VIDJIL_DIR/$EXEC -c clones -d -g ../../../germline/homo-sapiens.g:IGH -z 2 -r 1 bug20141024.fa 2>&1
!LAUNCH: valgrind --suppressions=gzstream_cpp.supp --suppressions=libstdc++_leak.supp --leak-check=full $VIDJIL_DIR/$EXEC
--clean-memory
-c clones -d -g ../../../germline/homo-sapiens.g:IGH -z 2 -r 1 bug20141024.fa 2>&1
!REQUIRES: which valgrind
$ No invalid read with short sequences
...
...
algo/tests/should-get-tests/large-r.should-get
View file @
556d8b0b
!LAUNCH: (i=1; while [ $i -le 100000 ]; do echo '>read' ; echo ccgtgtattactgtgcgagagagctgaatacttccagcactg ; i=$((i+1)); done ;) > same-igh-100k.fa ; $LAUNCHER $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -r 5000 -w 15 same-igh-100k.fa; rm -f same-igh-100k.fa
!LAUNCH: (i=1; while [ $i -le 100000 ]; do echo '>read' ; echo ccgtgtattactgtgcgagagagctgaatacttccagcactg ; i=$((i+1)); done ;) > same-igh-100k.fa ; $LAUNCHER $VIDJIL_DIR/$EXEC
$EXTRA
$VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -r 5000 -w 15 same-igh-100k.fa; rm -f same-igh-100k.fa
$ Find a unique clone with all reads
1:>clone-001--IGH--0100000--100.--window
...
...
algo/tests/should-get-tests/revcomp.should-get
View file @
556d8b0b
!LAUNCH: $LAUNCHER $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -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
$VIDJIL_DEFAULT_OPTIONS -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' '
$ Segments both reads, normal and reverse
1:junction detected in 2 reads
...
...
algo/tests/should-get-tests/stanford-germlines.should-get
View file @
556d8b0b
!LAUNCH: ($LAUNCHER $VIDJIL_DIR/$EXEC $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 -t 100 -s '######-######' $VIDJIL_DATA/Stanford_S22.fasta)
$ number of reads and kmers
1:13153 reads, 3020179 kmers
...
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algo/tests/should-get-tests/vidjil-help-advanced.should-get
View file @
556d8b0b
...
...
@@ -17,4 +17,4 @@ $ Display advanced options
: custom Cost
$ Correct number of options
B
49
:^ -
B
50
:^ -
Mathieu Giraud
@magiraud
mentioned in commit
694f786d
·
Mar 05, 2019
mentioned in commit
694f786d
mentioned in commit 694f786dd1e2ec83afdfe131e8ecba0f666e360a
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