Commit a2901340 authored by Mathieu Giraud's avatar Mathieu Giraud

tests: add tests, dumping and reading 'config' sections in .vidjil

Opens #3837.
parent a2455f80
{
"config": {
"first-reads": 10,
"min-reads": "1",
"max-consensus": "1",
"cdr3": true
}
}
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH --config ../data/config.vidjil $VIDJIL_DATA/Stanford_S22.fasta
$ Analyze 10 reads (--first-reads)
: in 10 reads
$ Report a clone with one read (--min-reads)
1: Clone #001 .* 1 read
$ Compute a CDR3 (--cdr3)
1:CARVGSSWS#MLLIIW
$ Report only one clone (--max-consensus)
1: Clone #
......@@ -13,3 +13,14 @@ $ Segment two reads on IgVC/IgJC (second -g option)
1: IgVC .* -> .* 1
1: IgJC .* -> .* 1
!LAUNCH: cat out/isotypes.vidjil
$ Both germlines are in .vidjil
1: /germline"
1: /homo-sapiens-isotypes.g"
$ Check that some options are correctly reported
1: "max-consensus": "100"
1: "plain-index": false
1: "cdr3": false
......@@ -13,5 +13,10 @@ $ 1 clone is fully analyzed, and not more (-z 1)
2:clone-.* IGHV
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS --config out/Stanford_S22.vidjil $VIDJIL_DATA/Stanford_S22.fasta ; cat out/Stanford_S22.vdj.fa
$ Same tests than before, options taken from 'out/StanfordS22.vidjil' that was just generated
1: ==> 10 clones
2:clone-005--.* bp
1:clone-006--.*--window
2:clone-.* IGHV
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