Commit bb3a5cfc authored by Mathieu Giraud's avatar Mathieu Giraud

tests: update tests

parent c568f70e
......@@ -342,8 +342,8 @@ void testGetMaximum() {
*/
template<template <class> class T>
void testBugAffectAnalyser() {
Fasta seqV("../../germline/IGHV.fa", 2);
Fasta seqJ("../../germline/IGHJ.fa", 2);
Fasta seqV("../../germline/homo-sapiens/IGHV.fa", 2);
Fasta seqJ("../../germline/homo-sapiens/IGHJ.fa", 2);
Fasta data("../../data/bug-revcomp.fa", 1, " ");
int k = 9;
......
......@@ -9,8 +9,8 @@ using namespace std;
void testSegmentationBug1(IndexTypes index, int delta_min) {
string buggy_sequences = "bugs/kmersegment.fa";
Fasta seqV("../../germline/TRGV.fa");
Fasta seqJ("../../germline/TRGJ.fa");
Fasta seqV("../../germline/homo-sapiens/TRGV.fa");
Fasta seqJ("../../germline/homo-sapiens/TRGJ.fa");
Germline *germline ;
germline = new Germline("custom", 'x', seqV, seqV, seqJ, delta_min, "##############");
......
......@@ -44,9 +44,9 @@ void testOverlap()
void testFineSegment(IndexTypes index)
{
Fasta seqV("../../germline/IGHV.fa", 2);
Fasta seqD("../../germline/IGHD.fa", 2);
Fasta seqJ("../../germline/IGHJ.fa", 2);
Fasta seqV("../../germline/homo-sapiens/IGHV.fa", 2);
Fasta seqD("../../germline/homo-sapiens/IGHD.fa", 2);
Fasta seqJ("../../germline/homo-sapiens/IGHJ.fa", 2);
OnlineFasta data("../../data/Stanford_S22.fasta", 1, " ");
data.next();
......@@ -99,8 +99,8 @@ void testFineSegment(IndexTypes index)
*/
void testSegmentOverlap(IndexTypes index)
{
Fasta seqV("../../germline/TRGV.fa", 2);
Fasta seqJ("../../germline/TRGJ.fa", 2);
Fasta seqV("../../germline/homo-sapiens/TRGV.fa", 2);
Fasta seqJ("../../germline/homo-sapiens/TRGJ.fa", 2);
Fasta data("../../data/bug-segment-overlap.fa", 1, " ");
......@@ -135,8 +135,8 @@ void testSegmentOverlap(IndexTypes index)
}
void testSegmentationCause(IndexTypes index) {
Fasta seqV("../../germline/TRGV.fa", 2);
Fasta seqJ("../../germline/TRGJ.fa", 2);
Fasta seqV("../../germline/homo-sapiens/TRGV.fa", 2);
Fasta seqJ("../../germline/homo-sapiens/TRGJ.fa", 2);
Fasta data("../../data/segmentation.fasta", 1, " ");
......@@ -248,8 +248,8 @@ void testSegmentationCause(IndexTypes index) {
}
void testExtractor(IndexTypes index) {
Fasta seqV("../../germline/TRGV.fa", 2);
Fasta seqJ("../../germline/TRGJ.fa", 2);
Fasta seqV("../../germline/homo-sapiens/TRGV.fa", 2);
Fasta seqJ("../../germline/homo-sapiens/TRGJ.fa", 2);
OnlineFasta data("../../data/segmentation.fasta", 1, " ");
......
......@@ -49,9 +49,9 @@ void testOnlineFastaMaxNth() {
void testFastaNbSequences() {
TAP_TEST(nb_sequences_in_fasta("../../germline/IGHV.fa") == 350, TEST_FASTA_NB_SEQUENCES, "ccc");
TAP_TEST(nb_sequences_in_fasta("../../germline/homo-sapiens/IGHV.fa") == 350, TEST_FASTA_NB_SEQUENCES, "ccc");
int a1 = approx_nb_sequences_in_fasta("../../germline/IGHV.fa");
int a1 = approx_nb_sequences_in_fasta("../../germline/homo-sapiens/IGHV.fa");
TAP_TEST(a1 >= 345 && a1 <= 355, TEST_FASTA_NB_SEQUENCES, "");
int a2 = nb_sequences_in_fasta("../../data/Stanford_S22.fasta", true);
......
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