Merge pull request #157 from Irallia/FEATURE/add_verbose_option

[FEATURE] Add verbose option

include/iGenVar.hpp

@@ -4,6 +4,8 @@
 
 #include "variant_detection/method_enums.hpp"           // for enum detection_methods, clustering_methods and refinement_methods
 
+inline bool gVerbose{false};
+
 struct cmd_arguments
 {
 // Input:
@@ -16,7 +18,7 @@ struct cmd_arguments
     /* -b */ std::filesystem::path clusters_file_path{};
 // Others:
     /* -h - help - not part of the args struct */
-    /* -v - verbose - not implementet yet */
+    /* -v - verbose - global variable gVerbose */
     /* -t */ int16_t threads = 1;
 // Methods:
     /* -d */ std::vector<detection_methods> methods{cigar_string, split_read, read_pairs, read_depth}; // default: all

src/iGenVar.cpp

@@ -49,6 +49,9 @@ void initialize_argument_parser(seqan3::argument_parser & parser, cmd_arguments
     parser.add_option(args.threads, 't', "threads",
                       "Specify the number of decompression threads used for reading BAM files.",
                       seqan3::option_spec::standard);
+    parser.add_flag(gVerbose, 'v', "verbose",
+                    "If you set this flag, we provide additional details about what iGenVar does. The detailed output "
+                    "is printed in the standard error.");
 
     // Options - Optional output:
     parser.add_option(args.junctions_file_path, 'a', "junctions",

src/modules/clustering/hierarchical_clustering_method.cpp

@@ -1,3 +1,4 @@
+#include "iGenVar.hpp"                                            // for global variable gVerbose
 #include "modules/clustering/hierarchical_clustering_method.hpp"
 
 #include <limits>                                                 // for infinity
@@ -134,15 +135,18 @@ std::vector<Cluster> hierarchical_clustering_method(std::vector<Junction> const
         }
         if (partition_size > max_partition_size)
         {
-            seqan3::debug_stream << "A partition exceeds the maximum size ("
-                                 << partition_size
-                                 << ">"
-                                 << max_partition_size
-                                 << ") and has to be subsampled. Representative partition member:\n["
-                                 << partition[0].get_mate1()
-                                 << "] -> ["
-                                 << partition[0].get_mate2()
-                                 << "]\n";
+            if (gVerbose)
+            {
+                seqan3::debug_stream << "A partition exceeds the maximum size ("
+                                    << partition_size
+                                    << ">"
+                                    << max_partition_size
+                                    << ") and has to be subsampled. Representative partition member:\n["
+                                    << partition[0].get_mate1()
+                                    << "] -> ["
+                                    << partition[0].get_mate2()
+                                    << "]\n";
+            }
             partition = subsample_partition(partition, max_partition_size);
             partition_size = max_partition_size;
         }

src/modules/sv_detection_methods/analyze_cigar_method.cpp

@@ -3,6 +3,7 @@
 #include <seqan3/core/debug_stream.hpp>
 #include <seqan3/io/sequence_file/output.hpp>
 
+#include "iGenVar.hpp"              // for global variable gVerbose
 #include "structures/breakend.hpp"  // for class Breakend
 #include "structures/junction.hpp"  // for class Junction
 
@@ -43,7 +44,8 @@ void analyze_cigar(std::string const & read_name,
                                       inserted_bases,
                                       tandem_dup_count,
                                       read_name};
-                seqan3::debug_stream << "INS: " << new_junction << "\n";
+                if (gVerbose)
+                    seqan3::debug_stream << "INS: " << new_junction << "\n";
                 junctions.push_back(std::move(new_junction));
             }
             pos_read += length;
@@ -58,7 +60,8 @@ void analyze_cigar(std::string const & read_name,
                                       ""_dna5,
                                       tandem_dup_count,
                                       read_name};
-                seqan3::debug_stream << "DEL: " << new_junction << "\n";
+                if (gVerbose)
+                    seqan3::debug_stream << "DEL: " << new_junction << "\n";
                 junctions.push_back(std::move(new_junction));
             }
             pos_ref += length;

src/modules/sv_detection_methods/analyze_split_read_method.cpp

@@ -1,3 +1,4 @@
+#include "iGenVar.hpp"              // for global variable gVerbose
 #include "modules/sv_detection_methods/analyze_split_read_method.hpp"
 
 #include <seqan3/core/debug_stream.hpp>
@@ -119,7 +120,8 @@ void analyze_aligned_segments(std::vector<AlignedSegment> const & aligned_segmen
                                                                                 next.get_query_start());
                     junctions.emplace_back(mate1, mate2, inserted_bases, tandem_dup_count, read_name);
                 }
-                seqan3::debug_stream << "BND: " << junctions.back() << "\n";
+                if (gVerbose)
+                    seqan3::debug_stream << "BND: " << junctions.back() << "\n";
             }
         }
     }

test/api/clustering_test.cpp

@@ -1,5 +1,6 @@
 #include <gtest/gtest.h>
 
+#include "iGenVar.hpp"                                              // for global variable gVerbose
 #include "modules/clustering/simple_clustering_method.hpp"          // for the simple clustering method
 #include "modules/clustering/hierarchical_clustering_method.hpp"    // for the hierarchical clustering method
 #include "structures/cluster.hpp"                                   // for class Cluster
@@ -448,6 +449,8 @@ TEST(hierarchical_clustering, clustering_25)
 
 TEST(hierarchical_clustering, subsampling)
 {
+    gVerbose = true;
+
     std::vector<Junction> input_junctions;
     for (int32_t i = 0; i < 300; ++i)
     {

test/cli/iGenVar_cli_test.cpp

@@ -48,6 +48,9 @@ std::string const help_page_part_1
     "    -t, --threads (signed 16 bit integer)\n"
     "          Specify the number of decompression threads used for reading BAM\n"
     "          files. Default: 1.\n"
+    "    -v, --verbose\n"
+    "          If you set this flag, we provide additional details about what\n"
+    "          iGenVar does. The detailed output is printed in the standard error.\n"
 };
 
 std::string const help_page_part_2
@@ -162,10 +165,6 @@ std::string expected_res_empty
 std::string expected_err_default_no_err
 {
     "Detect junctions in long reads...\n"
-    "INS: chr21\t41972615\tForward\tchr21\t41972616\tForward\t1681\t0\tm2257/8161/CCS\n"
-    "BND: chr21\t41972615\tReverse\tchr22\t17458415\tReverse\t2\t0\tm41327/11677/CCS\n"
-    "BND: chr21\t41972616\tReverse\tchr22\t17458416\tReverse\t0\t0\tm21263/13017/CCS\n"
-    "BND: chr21\t41972616\tReverse\tchr22\t17458416\tReverse\t0\t0\tm38637/7161/CCS\n"
     "Start clustering...\n"
     "Done with clustering. Found 2 junction clusters.\n"
     "No refinement was selected.\n"
@@ -188,14 +187,23 @@ TEST_F(iGenVar_cli_test, no_options)
 // TODO (irallia): There is an open Issue, if we want to add the verbose option https://github.com/seqan/iGenVar/issues/20
 TEST_F(iGenVar_cli_test, test_verbose_option)
 {
-    cli_test_result result = execute_app("iGenVar", "-v");
+    cli_test_result result = execute_app("iGenVar", "-j", data(default_alignment_long_reads_file_path), "--verbose");
     std::string expected_err
     {
-        "[Error] Unknown option -v. In case this is meant to be a non-option/argument/parameter, please specify "
-        "the start of non-options with '--'. See -h/--help for program information.\n"
+        "Detect junctions in long reads...\n"
+        "INS: chr21\t41972615\tForward\tchr21\t41972616\tForward\t1681\t0\tm2257/8161/CCS\n"
+        "The read depth method for long reads is not yet implemented.\n"
+        "BND: chr21\t41972615\tReverse\tchr22\t17458415\tReverse\t2\t0\tm41327/11677/CCS\n"
+        "The read depth method for long reads is not yet implemented.\n"
+        "BND: chr21\t41972616\tReverse\tchr22\t17458416\tReverse\t0\t0\tm21263/13017/CCS\n"
+        "The read depth method for long reads is not yet implemented.\n"
+        "BND: chr21\t41972616\tReverse\tchr22\t17458416\tReverse\t0\t0\tm38637/7161/CCS\n"
+        "The read depth method for long reads is not yet implemented.\n"
+        "Start clustering...\n"
+        "Done with clustering. Found 2 junction clusters.\nNo refinement was selected.\n"
     };
-    EXPECT_EQ(result.exit_code, 65280);
-    EXPECT_EQ(result.out, std::string{});
+    EXPECT_EQ(result.exit_code, 0);
+    EXPECT_EQ(result.out, expected_res_default);
     EXPECT_EQ(result.err, expected_err);
 }
 
@@ -351,13 +359,9 @@ TEST_F(iGenVar_cli_test, with_default_arguments)
     std::string expected_err
     {
         "Detect junctions in long reads...\n"
-        "INS: chr21\t41972615\tForward\tchr21\t41972616\tForward\t1681\t0\tm2257/8161/CCS\n"
         "The read depth method for long reads is not yet implemented.\n"
-        "BND: chr21\t41972615\tReverse\tchr22\t17458415\tReverse\t2\t0\tm41327/11677/CCS\n"
         "The read depth method for long reads is not yet implemented.\n"
-        "BND: chr21\t41972616\tReverse\tchr22\t17458416\tReverse\t0\t0\tm21263/13017/CCS\n"
         "The read depth method for long reads is not yet implemented.\n"
-        "BND: chr21\t41972616\tReverse\tchr22\t17458416\tReverse\t0\t0\tm38637/7161/CCS\n"
         "The read depth method for long reads is not yet implemented.\n"
         "Start clustering...\n"
         "Done with clustering. Found 2 junction clusters.\n"
@@ -442,10 +446,6 @@ TEST_F(iGenVar_cli_test, test_direct_methods_input)
     std::string expected_err
     {
         "Detect junctions in long reads...\n"
-        "INS: chr21\t41972615\tForward\tchr21\t41972616\tForward\t1681\t0\tm2257/8161/CCS\n"
-        "BND: chr21\t41972615\tReverse\tchr22\t17458415\tReverse\t2\t0\tm41327/11677/CCS\n"
-        "BND: chr21\t41972616\tReverse\tchr22\t17458416\tReverse\t0\t0\tm21263/13017/CCS\n"
-        "BND: chr21\t41972616\tReverse\tchr22\t17458416\tReverse\t0\t0\tm38637/7161/CCS\n"
         "Start clustering...\n"
         "Done with clustering. Found 3 junction clusters.\n"
         "No refinement was selected.\n"
@@ -534,6 +534,7 @@ TEST_F(iGenVar_cli_test, dataset_single_end_mini_example)
 {
     cli_test_result result = execute_app("iGenVar",
                                          "-j", data("single_end_mini_example.sam"),
+                                         "--verbose",
                                          "--method cigar_string --method split_read "
                                          "--min_var_length 8 --max_var_length 400");