Added test for amino acid translation taking strand into account

data/test.strand.pileup

@@ -0,0 +1,20 @@
+test	1	G	20	GGGGGGGGGGGGGGGGGGGG	????????????????????
+test	2	A	20	AAAAAAAAAAAAAAAAAAAA	????????????????????
+test	3	G	20	GGGGGGGGGGGGGGGGGGGG	????????????????????
+test	4	G	20	GGGGGGGGGGGGGGGGGGGG	????????????????????
+test	5	C	20	CCCCCCCCCCTTTTTTTTTT	????????????????????
+test	6	T	20	TTTTTTTTTTTTTTTTTTTT	????????????????????
+test	7	G	20	GGGGGGGGGGGGGGGGGGGG	????????????????????
+test	8	C	20	CCCCCCCCCCCCCCCCCCCC	????????????????????
+test	9	C	20	CCCCCCCCCCCCCCCCCCCC	????????????????????
+test	10	A	20	AAAAAAAAAAAAAAAAAAAA	????????????????????
+test	11	G	20	GGGGGGGGGGGGGGGGGGGG	????????????????????
+test	12	C	20	CCCCCCCCCCCCCCCCCCCC	????????????????????
+test	13	C	20	CCCCCCCCCCCCCCCCCCCC	????????????????????
+test	14	G	20	GGGGGGGGGGGGGGGGGGGG	????????????????????
+test	15	G	20	GGGGGGGGGGCCCCCCCCCC	????????????????????
+test	16	A	20	AAAAAAAAAAAAAAAAAAAA	????????????????????
+test	17	C	20	CCCCCCCCCCCCCCCCCCCC	????????????????????
+test	18	T	20	TTTTTTTTTTTTTTTTTTTT	????????????????????
+test	19	T	20	TTTTTTTTTTTTTTTTTTTT	????????????????????
+test	20	C	20	CCCCCCCCCCCCCCCCCCCC	????????????????????

data/test_strand.gff

@@ -0,0 +1,3 @@
+## GFF3 file format
+test	Genbank	CDS	1	9	.	+	.	ID=test1;Note=positiveStrand;gene=A;
+test	Genbank	CDS	11	20	.	-	.	ID=test2;Note=negativeStrand;gene=B;

tests/Makefile.am

@@ -2,8 +2,8 @@ LIBS = -lhts -lz -lpthread
 
 CXXFLAGS = -g -std=c++11 -Wall -Wextra -Werror
 
-TESTS = check_primer_trim check_trim check_quality_trim check_consensus check_allele_depth check_consensus_threshold check_consensus_min_depth check_consensus_seq_id check_primer_bed check_getmasked check_removereads check_variants check_common_variants check_unpaired_trim check_primer_trim_edge_cases check_isize_trim check_interval_tree check_amplicon_search check_consensus_min_insert_threshold
-check_PROGRAMS = check_primer_trim check_trim check_quality_trim check_consensus check_allele_depth check_consensus_threshold check_consensus_min_depth check_consensus_seq_id check_primer_bed check_getmasked check_removereads check_variants check_common_variants check_unpaired_trim check_primer_trim_edge_cases check_isize_trim check_interval_tree check_amplicon_search check_consensus_min_insert_threshold
+TESTS = check_primer_trim check_trim check_quality_trim check_consensus check_allele_depth check_consensus_threshold check_consensus_min_depth check_consensus_seq_id check_primer_bed check_getmasked check_removereads check_variants check_common_variants check_unpaired_trim check_primer_trim_edge_cases check_isize_trim check_interval_tree check_amplicon_search check_consensus_min_insert_threshold check_strand_variants
+check_PROGRAMS = check_primer_trim check_trim check_quality_trim check_consensus check_allele_depth check_consensus_threshold check_consensus_min_depth check_consensus_seq_id check_primer_bed check_getmasked check_removereads check_variants check_common_variants check_unpaired_trim check_primer_trim_edge_cases check_isize_trim check_interval_tree check_amplicon_search check_consensus_min_insert_threshold check_strand_variants
 check_primer_trim_SOURCES = test_primer_trim.cpp ../src/trim_primer_quality.cpp ../src/primer_bed.cpp ../src/interval_tree.cpp
 check_trim_SOURCES = test_trim.cpp ../src/trim_primer_quality.cpp ../src/primer_bed.cpp ../src/interval_tree.cpp
 check_quality_trim_SOURCES = check_quality_trim.cpp ../src/trim_primer_quality.cpp ../src/primer_bed.cpp ../src/interval_tree.cpp
@@ -23,3 +23,4 @@ check_primer_trim_edge_cases_SOURCES = test_primer_trim_edge_cases.cpp ../src/tr
 check_isize_trim_SOURCES = test_isize_trim.cpp ../src/trim_primer_quality.cpp ../src/primer_bed.cpp ../src/interval_tree.cpp
 check_interval_tree_SOURCES = test_interval_tree.cpp ../src/primer_bed.cpp ../src/interval_tree.cpp
 check_amplicon_search_SOURCES = test_amplicon_search.cpp ../src/trim_primer_quality.cpp ../src/primer_bed.cpp ../src/interval_tree.cpp
+check_strand_variants_SOURCES = test_variants_reverse_strand.cpp ../src/call_variants.cpp ../src/allele_functions.cpp ../src/parse_gff.cpp ../src/ref_seq.cpp

tests/test_variants_reverse_strand.cpp

@@ -0,0 +1,45 @@
+#include <fstream>
+#include <iostream>
+#include <string>
+
+#include "../src/allele_functions.h"
+#include "../src/call_variants.h"
+
+int call_var_check_outfile(std::string prefix, uint8_t min_qual,
+                           uint8_t min_depth, double min_threshold,
+                           std::string out[], int len) {
+  std::string path = "../data/test.strand.pileup";
+  std::ifstream mplp(path);
+  call_variants_from_plup(mplp, prefix, min_qual, min_threshold, min_depth,
+                          "../data/db/test_ref.fa", "../data/test_strand.gff");
+  std::ifstream outFile(prefix + ".tsv");
+  std::string l;
+  getline(outFile, l);  // Ignore first line
+  int comp = 0, ctr = 0;
+
+  while (ctr < len) {
+    getline(outFile, l);
+    std::cout << l << std::endl;
+    std::cout << out[ctr] << " -> CORRECT" << std::endl;
+    comp += l.compare(out[ctr]);
+    std::cout << l.compare(out[ctr]) << "\n";
+    ctr++;
+  }
+  return comp;
+}
+
+int main() {
+  int num_success = 0;
+  // Quality threshold 20. Frequency threshold: 0.03. Total_DP = 3. Indel passes
+  // filters with total_depth 4. Has two lines.
+  std::string expected_out[2] = {
+      "test\t5\tC\tT\t10\t0\t30\t10\t0\t30\t0.5\t20\t0.000290613\tTRUE\tA:test1\tGCT\tA\tGTT\tV\t2",
+      "test\t15\tG\tC\t10\t0\t30\t10\t0\t30\t0.5\t20\t0.000290613\tTRUE\tB:test2\tGTC\tV\tGTG\tV\t2"
+      };
+  num_success =
+      call_var_check_outfile("../data/test_strand", 20, 0, 0.03, expected_out, 2);
+  std::cout << num_success << std::endl;
+
+  if (num_success == 0) return 0;
+  return -1;
+}