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.

algo/tests/should-get-tests/chimera-fake-VJ-germlines-trim.should-get

+!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/Makefile

-DATA=Stanford_S22.fasta Stanford_S22_rc.fasta
+DATA=Stanford_S22.fasta Stanford_S22_rc.fasta chimera-fake-VJ-trim.g
 
-all: 
+all: chimera-fake-VJ-trim.g
 	sh get-sequences
 
+chimera-fake-VJ-trim.g: chimera-fake-VJ.g
+	sed '/"13s"/ s/$$/, "trim_sequences": 1/' $^ > $@
+
 clean:
 	$(RM) -f $(DATA)