Commit 5972737b authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

tests/bugs: update

parent a6e67abb
!LAUNCH: ../../../vidjil -c clones -g ../../../germline/homo-sapiens.g:TRG -r 1 bug20130617.fa
!LAUNCH: $VIDJIL_DIR/$EXEC -c clones -g ../../../germline/homo-sapiens.g:TRG -r 1 bug20130617.fa
$ Bug with J deletion being 122
......
!LAUNCH: ../../../vidjil -c segment -g ../../../germline/homo-sapiens.g:IGH bug20131218.fa
!LAUNCH: $VIDJIL_DIR/$EXEC -c segment -g ../../../germline/homo-sapiens.g:IGH bug20131218.fa
# The number of deletions in the D is larger than the D length itself.
$ Bug with the number of deletions in the D.
......
!NO_LAUNCHER:
!LAUNCH: valgrind --suppressions=gzstream_cpp.supp --suppressions=libstdc++_leak.supp --leak-check=full ../../../vidjil -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 -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
......
!LAUNCH: ../../../vidjil -KA -k 16 -z 0 -g ../../../germline/homo-sapiens.g:IGH bug20150604.fa
!LAUNCH: $VIDJIL_DIR/$EXEC -KA -k 16 -z 0 -g ../../../germline/homo-sapiens.g:IGH bug20150604.fa
$ Bug on some architectures, not segmented
1: junction detected in 1 reads
......
!LAUNCH: ../../../vidjil -c clones -r 1 -g ../../../germline/homo-sapiens.g:IGH bug20150629.fa >/dev/null && python ../../../tools/format_json.py out/bug20150629.vidjil| sed -n '/\\"name\\"/p'
!LAUNCH: $VIDJIL_DIR/$EXEC -c clones -r 1 -g ../../../germline/homo-sapiens.g:IGH bug20150629.fa >/dev/null && python ../../../tools/format_json.py out/bug20150629.vidjil| sed -n '/\\"name\\"/p'
$ The sequence is not segmented
0:IGHV
......
!LAUNCH: ../../../vidjil -s '#####-#####' -c clones -r 1 -g ../../../germline/homo-sapiens.g:IGH -t 0 -e 1 bug20160121.fa
!LAUNCH: $VIDJIL_DIR/$EXEC -s '#####-#####' -c clones -r 1 -g ../../../germline/homo-sapiens.g:IGH -t 0 -e 1 bug20160121.fa
$ Sequences should not be segmented since they only contain J.
f1:UNSEG only J/3' -> 2
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -e 1e-3 -r 1 -y 0 -z 0 -g $VIDJIL_DIR/germline/homo-sapiens.g ./bug2107.fa
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -e 1e-3 -r 1 -y 0 -z 0 -g $VIDJIL_DIR/germline/homo-sapiens.g ./bug2107.fa
# No sequences are segmented
1: junction detected in 0 reads
......
!LAUNCH: $VIDJIL_DIR/vidjil -E 1 -d -g $VIDJIL_DIR/germline -c segment bug2249.fa
!LAUNCH: $VIDJIL_DIR/$EXEC -E 1 -d -g $VIDJIL_DIR/germline -c segment bug2249.fa
$ Should not have a TRDD2 (length 9) with 8 deletions (first seq)
fe0:7 TRDD2*01 1
......
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