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Commit 75b95db4 authored by Mikaël Salson's avatar Mikaël Salson

chimera-fake-VJ-germlines-trim.should-get: Test parameters in .g

Check that they are correctly taken into account.

For this test we start from an existing .g used for testing purpose and
slightly modify it to add the trim_sequences parameter for one locus.
parent 00cfe3ba
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/data/chimera-fake-VJ-trim.g $VIDJIL_DIR/data/chimera-fake-VJ.fa
# Testing a custom (fake) .g with special parameters for the algorithm
$ The KmerSegmenter segments no read in Y because of the parameter
1:Y-.* -> .* 0
1:UNSEG too few V/J -> 1
$ The KmerSegmenter segments correctly in Z (no parameter)
1:Z-.* -> .* 2
DATA=Stanford_S22.fasta Stanford_S22_rc.fasta
DATA=Stanford_S22.fasta Stanford_S22_rc.fasta chimera-fake-VJ-trim.g
all: chimera-fake-VJ-trim.g
sh get-sequences
chimera-fake-VJ-trim.g: chimera-fake-VJ.g
sed '/"13s"/ s/$$/, "trim_sequences": 1/' $^ > $@
$(RM) -f $(DATA)
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