tests: update tests

algo/tests/unit-tests/testAffectAnalyser.cpp

@@ -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;

algo/tests/unit-tests/testBugs.cpp

@@ -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, "##############");

algo/tests/unit-tests/testSegment.cpp

@@ -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, " ");
 

algo/tests/unit-tests/testTools.cpp

@@ -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);