Commit 43218e8e authored by Marc Duez's avatar Marc Duez
Browse files

c++ test : fix germline/clusters change

parent 54a565cc
......@@ -15,7 +15,7 @@ void testSegmentationBug1(int delta_min, int delta_max) {
Fasta seqJ("../../germline/TRGJ.fa");
Germline *germline ;
germline = new Germline(seqV, seqV, seqJ, "##############", delta_min, delta_max);
germline = new Germline("custom", 'x', seqV, seqV, seqJ, "##############", delta_min, delta_max);
MultiGermline *multi ;
multi = new MultiGermline();
......
......@@ -47,8 +47,10 @@ void testCluster() {
windows.add("CCCCCCCCCCCCCCCCCCCCCCCCCGGGGGGTCTAGGGGG", seq, 0, 0);
windows.add("CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCATGCCCCCC", seq, 0, 0);
windows.sort();
list<pair <junction, int> > sort_clones = windows.getSortedList();
comp_matrix comp=comp_matrix(windows);
comp_matrix comp=comp_matrix(sort_clones);
//create matrix using junctions
comp.compare( cout, Cluster);
......
......@@ -20,7 +20,7 @@ void testFineSegment()
Fasta data("../../data/Stanford_S22.fasta", 1, " ");
Germline *germline ;
germline = new Germline(seqV, seqD, seqJ, "####", 0, 50);
germline = new Germline("IGH", 'G', seqV, seqD, seqJ, "####", 0, 50);
Sequence seq = data.read(2);
......@@ -70,9 +70,9 @@ void testSegmentOverlap()
Fasta data("../../data/bug-segment-overlap.fa", 1, " ");
Germline *germline1 ;
germline1 = new Germline(seqV, seqV, seqJ, "##########", -50, 50);
germline1 = new Germline("TRG", 'G', seqV, seqV, seqJ, "##########", -50, 50);
Germline *germline2 ;
germline2 = new Germline(seqV, seqV, seqJ, "##########", -50, 50);
germline2 = new Germline("TRG2", 'G', seqV, seqV, seqJ, "##########", -50, 50);
MultiGermline *multi1 ;
multi1 = new MultiGermline();
......@@ -103,7 +103,7 @@ void testSegmentationCause() {
Fasta data("../../data/segmentation.fasta", 1, " ");
Germline *germline ;
germline = new Germline(seqV, seqV, seqJ, "##########", 0, 10);
germline = new Germline("TRG", 'G', seqV, seqV, seqJ, "##########", 0, 10);
MultiGermline *multi ;
multi = new MultiGermline();
......@@ -197,7 +197,7 @@ void testExtractor() {
OnlineFasta data("../../data/segmentation.fasta", 1, " ");
Germline *germline ;
germline = new Germline(seqV, seqV, seqJ, "##########", 0, 10);
germline = new Germline("TRG", 'G', seqV, seqV, seqJ, "##########", 0, 10);
MultiGermline *multi ;
multi = new MultiGermline();
......
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