Commit 677948d3 authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

tests: update unit tests, germline index handling

parent d43c6c96
......@@ -15,7 +15,8 @@ void testSegmentationBug1(int delta_min, int delta_max) {
Fasta seqJ("../../germline/TRGJ.fa");
Germline *germline ;
germline = new Germline("custom", 'x', seqV, seqV, seqJ, "##############", delta_min, delta_max);
germline = new Germline("custom", 'x', seqV, seqV, seqJ, delta_min, delta_max);
germline->new_index("##############");
MultiGermline *multi ;
multi = new MultiGermline();
......
......@@ -20,7 +20,8 @@ void testFineSegment()
Fasta data("../../data/Stanford_S22.fasta", 1, " ");
Germline *germline ;
germline = new Germline("IGH", 'G', seqV, seqD, seqJ, "####", 0, 50);
germline = new Germline("IGH", 'G', seqV, seqD, seqJ, 0, 50);
germline->new_index("####");
Sequence seq = data.read(2);
......@@ -70,9 +71,12 @@ void testSegmentOverlap()
Fasta data("../../data/bug-segment-overlap.fa", 1, " ");
Germline *germline1 ;
germline1 = new Germline("TRG", 'G', seqV, seqV, seqJ, "##########", -50, 50);
germline1 = new Germline("TRG", 'G', seqV, seqV, seqJ, -50, 50);
germline1->new_index("##########");
Germline *germline2 ;
germline2 = new Germline("TRG2", 'G', seqV, seqV, seqJ, "##########", -50, 50);
germline2 = new Germline("TRG2", 'G', seqV, seqV, seqJ, -50, 50);
germline2->new_index("##########");
MultiGermline *multi1 ;
multi1 = new MultiGermline();
......@@ -103,7 +107,8 @@ void testSegmentationCause() {
Fasta data("../../data/segmentation.fasta", 1, " ");
Germline *germline ;
germline = new Germline("TRG", 'G', seqV, seqV, seqJ, "##########", 0, 10);
germline = new Germline("TRG", 'G', seqV, seqV, seqJ, 0, 10);
germline->new_index("##########");
MultiGermline *multi ;
multi = new MultiGermline();
......@@ -197,8 +202,9 @@ void testExtractor() {
OnlineFasta data("../../data/segmentation.fasta", 1, " ");
Germline *germline ;
germline = new Germline("TRG", 'G', seqV, seqV, seqJ, "##########", 0, 10);
germline = new Germline("TRG", 'G', seqV, seqV, seqJ, 0, 10);
germline->new_index("##########");
MultiGermline *multi ;
multi = new MultiGermline();
multi->insert(germline);
......
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