message: test: adjust gene extraction tests to the new stripping logic
diff: +#include "../src/translate/extractGene.h"
  +
  #include <gtest/gtest.h>
  #include <nextalign/nextalign.h>
  #include <string_view>
  #include <vector>
  -#include "../src/translate/extractGene.h"
  #include "../src/translate/mapCoordinates.h"
  @@ -42,7 +43,7 @@ TEST(extractGeneQuery, ExtractsQueryGene) {
  // const std::string ref_aligned = "ACTCCG---TGCGCTGCTG";
  const std::string query_aligned = "ACTGGTCTA---GCA";
  // const std::string expected_gene_ref = "TCCGTGCGCTGC";
  - const std::string expected_gene_query = "TGGTCTAGC";
  + const std::string expected_gene_query = "TGGTCTA---GC";
  // clang-format on
  const Gene gene = {
  @@ -59,53 +60,3 @@ TEST(extractGeneQuery, ExtractsQueryGene) {
  EXPECT_EQ(toString(*gene_query.result), expected_gene_query);
  }
  -
  -
  -TEST(extractGeneQuery, ExtractsQueryGeneCorrectlyStripped) {
  - // clang-format off
  - // 6 18
  - // | | | | |
  - const std::string ref = "ATGTGA" "ATGAATGGCCCG" "AAAAAA";
  - const std::string query_aligned = "------" "-TGAATGGCC--" "------";
  - const std::string expected_gene_query = "NTGAATGGCCNN" ;
  - // clang-format on | | | | |
  -
  - const Gene gene = {
  - .geneName = "Hello",
  - .start = 6,
  - .end = 18,
  - .strand = "+",
  - .frame = 0,
  - .length = 12,
  - };
  -
  - const auto coordMap = mapCoordinates(toNucleotideSequence(ref));
  - const auto gene_query = extractGeneQuery(toNucleotideSequence(query_aligned), gene, coordMap);
  -
  - EXPECT_EQ(toString(*gene_query.result), expected_gene_query);
  -}
  -
  -TEST(extractGeneQuery, ExtractsQueryGeneCorrectlyStrippedWithGaps) {
  - // clang-format off
  - // 6 18
  - // | | | | |
  - const std::string ref = "ATGTGA" "ATGAATGGCCCG" "AAAAAA";
  - const std::string query_aligned = "------" "-T---TGGCC--" "------";
  - const std::string expected_gene_query = "NT" "TGGCCNN" ;
  - // clang-format on | | | | |
  -
  - const Gene gene = {
  - .geneName = "Hello",
  - .start = 6,
  - .end = 18,
  - .strand = "+",
  - .frame = 0,
  - .length = 12,
  - };
  -
  - const auto coordMap = mapCoordinates(toNucleotideSequence(ref));
  - const auto gene_query = extractGeneQuery(toNucleotideSequence(query_aligned), gene, coordMap);
  -
  - EXPECT_EQ(toString(*gene_query.result), expected_gene_query);
  -}
  -
  