Nous avons procédé ce jeudi matin 08 avril 2021 à une MAJ de sécurité urgente. Nous sommes passé de la version 13.9.3 à la version 13.9.5 les releases notes correspondantes sont ici:
https://about.gitlab.com/releases/2021/03/17/security-release-gitlab-13-9-4-released/
https://about.gitlab.com/releases/2021/03/31/security-release-gitlab-13-10-1-released/

Commit 1fb59b9b authored by marc duez's avatar marc duez Committed by Mathieu Giraud

aligner_test : muteSubstitutonString

parent e8c7966c
......@@ -239,13 +239,15 @@ Sequence.prototype = {
}
}
if (typeof cdr3.start != "undefined") {
start = cdr3.start;
stop = cdr3.stop;
cdr3aa = cdr3.aa;
}else if (cdr3.constructor === String){
start = clone.sequence.indexOf(cdr3);
stop = start + cdr3.length;
if (typeof cdr3 != "undefined" ){
if (typeof cdr3.start != "undefined") {
start = cdr3.start;
stop = cdr3.stop;
cdr3aa = cdr3.aa;
}else if (cdr3.constructor === String){
start = clone.sequence.indexOf(cdr3);
stop = start + cdr3.length;
}
}
......
......@@ -273,14 +273,20 @@ json_data_align = {
"reads" : [20] ,
"top" : 1,
"germline" : "TRG",
"seg" : {
"cdr3" : {"start": 1, "stop": 11, "aa": "W#WA", "seq": "atcatgatgcta"}
}
},
{
"sequence" : "ATGCATGCATGCATGCCCCCCCCCCCCCCCCCCAAATTTTTTTTGATCGATCGATCGATCGAT",
"sequence" : "ATTCATGCATGCATGCCCCCCCCCCCCCCCCCCAAATTTTTTTTGATCGATCGATCGATCGAT",
"name" : "testalign2",
"id" : "id1",
"reads" : [25],
"top" : 2,
"germline" : "IGH",
"germline" : "IGH",
"seg" : {
"cdr3" : {"start": 1, "stop": 11, "aa": "W#WA", "seq": "atcatgatgcta"}
}
}
]
};
......
......@@ -262,7 +262,7 @@ QUnit.test("align", function (assert) {
assert.ok(aligned_sequence2.includes(""), "aligned sequence should contains '–'" + aligned_sequence2 )
var nucleo2 = seq2.nucleoString();
assert.equal( nucleo2, "ATGCATGCATGCATGCCCCCCCCCCCCCCCCCCAAA–––––––––––TTTTTTTTGATCGAT–CGATCGATCGAT",
assert.equal( nucleo2, "ATTCATGCATGCATGCCCCCCCCCCCCCCCCCCAAA–––––––––––TTTTTTTTGATCGAT–CGATCGATCGAT",
nucleo2.toUpperCase() + " reference sequence spaced");
var nucleo1 = seq1.nucleoString();
......@@ -281,6 +281,12 @@ QUnit.test("align", function (assert) {
assert.equal( insert1.replace(/(?=\s)[^\r\n\t]/g, ' '), " TTTTTTTTTTT C ",
insert1.toUpperCase().replace(/(?=\s)[^\r\n\t]/g, '_') + " inserted nucleotide");
var amino1 = seq1.aminoString();
var aminosplit1 = seq1.aminoSplitString();
var mute1 = seq1.muteSubstitutionString();
assert.equal( mute1.replace(/(?=\s)[^\r\n\t]/g, ' '), " _ _ ",
mute1.toUpperCase().replace(/(?=\s)[^\r\n\t]/g, '_') + " mute substitution");
segment.resetAlign()
done()
}, delay+=step)
......
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