tests: testing options -a, -o, -u, -U, -v

algo/tests/stanford-debug.should_get

+!LAUNCH: ../../vidjil -d -r 5 -o out2 -u -U -v -G ../../germline/IGH ../../data/Stanford_S22.fasta ; tail out2/Stanford_S22.segmented.vdj.fa out2/Stanford_S22.unsegmented.fa
+# Testing uncommon and debug options 
+
+$ verbose (-v)
+2:auditioned sequences
+
+$ segmented.fa (-U)
+1:>lcl.FLN1FA001BCDD7.1. .* seed
+
+$ unsegmented.fa (-u)
+1:>lcl.FLN1FA002PX5D6.1.
+

algo/tests/stanford-detailed.should_get

+!LAUNCH: ../../vidjil -d -r 5 -a -G ../../germline/IGH ../../data/Stanford_S22.fasta ; cat out/seq/clone.fa-2
+# Testing detailed clone output (-a)
+
+$ Detailed clone output (out/seq/clone.fa-2), germline
+1:>IGHV1-8.01
+1:>IGHD3-22.01
+1:>IGHJ6.03
+
+$ Detailed clone output (out/seq/clone.fa-2), reads
+1:>lcl.FLN1FA002TBW9H.1
+1:>lcl.FLN1FA002TAWKB.1
+1:>lcl.FLN1FA001EFSW3.1
+1:>lcl.FLN1FA001ENA4H.1
+1:>lcl.FLN1FA001B2WWF.1
+