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vidjil
vidjil
Commits
44d74052
Commit
44d74052
authored
Apr 24, 2015
by
Mathieu Giraud
Browse files
tests: update tests for .affects debug output (-K)
parent
6aef087f
Changes
2
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algo/tests/multi-short-affects.should_get
View file @
44d74052
!LAUNCH: ../../vidjil -r 5 -K -g ../../germline ../../data/multi-short.fa ; head -n 1
5
out/multi-short.affects
!LAUNCH: ../../vidjil -r 5 -K -g ../../germline ../../data/multi-short.fa ; head -n 1
7
out/multi-short.affects
# Testing .affects output (-K)
$ First sequence (TRA), display sequence
1:TCTTCATTCCTTAGTCGCTCTGATAGTTATGGTTACCTCCTTCTACAGGAGCTCCAGATGAAAGACTCTGCCTCTTACTTCTGCGCTGTGAGAGAGTATGAAAGTATTACCTCCCAGTTGCAATTTGGCAAAGGAACCAGAGTTTCCACTTCTCC
$ First sequence (TRA), count of k-mers
1:
.TRA .* 129
1:
129 .* TRA
$ First sequence (TRA), segmentation
1:>TRA--V1-1.01--J1.01 .* seed TRA SEG_+
...
...
algo/tests/revcomp.should_get
View file @
44d74052
!LAUNCH: $LAUNCHER ../../vidjil -k 9 -G ../../germline/IGH -K -c clones ../../data/revcomp.fa ; grep '
#IGH
' out/revcomp.affects | sed 's/[^X]//g' | awk '{ print length }'
!LAUNCH: $LAUNCHER ../../vidjil -k 9 -G ../../germline/IGH -K -c clones ../../data/revcomp.fa ; grep '
X.X.X
' out/revcomp.affects | sed 's/[^X]//g' | awk '{ print length }'
$ Segments both reads, normal and reverse
1:junction detected in 2 reads
...
...
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