Commit 378b9289 authored by Mikaël Salson's avatar Mikaël Salson
Browse files

algo/tests/bugs: Change parameters following new syntax for germlines

See #2147 for change in parameter syntax and #1618 for
algo/tests/bugs
parent 4455193e
!LAUNCH: ../../../vidjil -c clones -G ../../../germline/TRG -r 1 bug20130617.fa
!LAUNCH: ../../../vidjil -c clones -g ../../../germline/homo-sapiens.g:TRG -r 1 bug20130617.fa
$ Bug with J deletion being 122
......
!LAUNCH: ../../../vidjil -c segment -G ../../../germline/IGH bug20131218.fa
!LAUNCH: ../../../vidjil -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.
......
!LAUNCH: valgrind --leak-check=full ../../../vidjil -c clones -d -G ../../../germline/IGH -z 2 -r 1 bug20141024.fa 2>&1
!LAUNCH: valgrind --leak-check=full ../../../vidjil -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/IGH bug20150604.fa
!LAUNCH: ../../../vidjil -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/IGH bug20150629.fa >/dev/null && python ../../../tools/format_json.py out/bug20150629.vidjil| grep '\\"name\\"'
!LAUNCH: ../../../vidjil -c clones -r 1 -g ../../../germline/homo-sapiens.g:IGH bug20150629.fa >/dev/null && python ../../../tools/format_json.py out/bug20150629.vidjil| grep '\\"name\\"'
$ The sequence is not segmented
0:IGHV
......
!LAUNCH: ../../../vidjil -s '#####-#####' -c clones -r 1 -G ../../../germline/IGH -t 0 -e 1 bug20160121.fa
!LAUNCH: ../../../vidjil -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.
1:UNSEG only J/3' -> 2
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