Added HP tag to filter. Started work on sort command

.gw.ini

@@ -39,6 +39,7 @@ font_size=14
 sv_arcs=true
 mods=false
 mods_qual_threshold=50
+haplotags=0,1
 session_file=
 
 [view_thresholds]

src/menu.cpp

@@ -310,6 +310,7 @@ namespace Menu {
             else if (opts.menu_level == "low_memory") { tip = "The distance in base-pairs when using low-memory mode (reads are not buffered in this mode)"; }
             else if (opts.menu_level == "mods") { tip = "Display modified bases"; }
             else if (opts.menu_level == "mods_qual_threshold") { tip = "Threshold (>) for displaying modified bases [0-255]"; }
+            else if (opts.menu_level == "haplotags") { tip = "Comma-seperated list of haplotype tags to display, derived from the HP bam-tag"; }
             else if (opts.menu_level == "scroll_right") { tip = "Keyboard key to use for scrolling right"; }
             else if (opts.menu_level == "scroll_left") { tip = "Keyboard key to use for scrolling left"; }
             else if (opts.menu_level == "scroll_down") { tip = "Keyboard key to use for scrolling down"; }

src/parser.cpp

@@ -58,6 +58,7 @@ namespace Parse {
         opMap["AS"] = AS;
         opMap["BX"] = BX;
         opMap["RX"] = RX;
+        opMap["HP"] = HP;
 
         opMap["eq"] = EQ;
         opMap["ne"] = NE;
@@ -133,6 +134,7 @@ namespace Parse {
         permit[TC] = numeric_like;
         permit[UQ] = numeric_like;
         permit[AS] = numeric_like;
+        permit[HP] = numeric_like;
 
         permit[PATTERN] = string_like;
 
@@ -611,6 +613,9 @@ namespace Parse {
                     case AS:
                         getIntTag("AS", int_val, aln);
                         break;
+                    case HP:
+                        getIntTag("HP", int_val, aln);
+                        break;
                     case CIGAR:
                          getCigarStr(str_val, aln);
                          break;

src/parser.h

@@ -43,7 +43,7 @@ namespace Parse {
         ABS_TLEN = 3007,
         SEQ_LEN = 3008,
         NM = 3009, CM = 3010, FI = 3011, HO = 3012, MQ = 3013, SM = 3014, TC = 3015, UQ = 3016, AS = 3017,
-        TID = 3018, MID = 3019,
+        TID = 3018, MID = 3019, HP = 3020,
 
         // Patterns
         PATTERN = 3500,

src/plot_commands.cpp

@@ -1364,6 +1364,33 @@ namespace Commands {
         return Err::NONE;
     }
 
+    Err sort_command(Plot* p, std::string& command, std::vector<std::string> parts, std::ostream& out) {
+        if (parts.size() == 1) {
+
+            return Err::NONE;
+        }
+        if (parts[1] != "hap" && parts[1] != "strand") {
+            return Err::OPTION_NOT_SUPPORTED;
+        }
+
+        if (parts.size() == 2) {
+            int n_groups = 2;
+            std::vector<int> groups = {0, 1};
+        } else {
+            std::vector<int> groups;
+            for (int i=2; i < (int)parts.size(); ++i) {
+                try {
+                    groups.push_back(std::stoi(parts[i]));
+                } catch (...) {
+                    return Err::OPTION_NOT_UNDERSTOOD;
+                }
+            }
+            int n_groups = (int)groups.size();
+
+        }
+        return Err::NONE;
+    }
+
     void cache_command_or_handle_err(Plot* p, Err result, std::ostream& out,
                                     std::vector<std::string>* applied, std::string& command) {
         switch (result) {
@@ -1481,6 +1508,7 @@ namespace Commands {
                 {"colour",   PARAMS { return update_colour(p, command, parts, out); }},
                 {"color",    PARAMS { return update_colour(p, command, parts, out); }},
                 {"roi",      PARAMS { return add_roi(p, command, parts, out); }},
+                {"group",    PARAMS { return sort_command(p, command, parts, out); }},
 
                 {"count",    PARAMS { return count(p, command, out); }},
                 {"filter",   PARAMS { return addFilter(p, command, out); }},

src/plot_manager.cpp

@@ -142,6 +142,7 @@ namespace Manager {
             pool.reset(opts.threads);
         }
         triggerClose = false;
+        sortReadsBy = Manager::SortType::NONE;
     }
 
     GwPlot::~GwPlot() {

src/plot_manager.h

@@ -59,6 +59,12 @@ namespace Manager {
         SETTINGS
     };
 
+    enum SortType {
+        NONE,
+        STRAND,
+        HP
+    };
+
     class HiddenWindow {
     public:
         HiddenWindow () = default;
@@ -88,6 +94,9 @@ namespace Manager {
         bool drawLine;
 
         bool terminalOutput;  // recoverable runtime errors and output sent to terminal or outStr
+
+        SortType sortReadsBy;
+
         std::ostringstream outStr;
 
         std::vector<char> pixelMemory;

src/term_out.cpp

@@ -1351,7 +1351,7 @@ namespace Term {
     }
 
 #if !defined(__EMSCRIPTEN__)
-    const char* CURRENT_VERSION = "v0.10.0";
+    const char* CURRENT_VERSION = "v0.10.1";
 
     size_t WriteCallback(void* contents, size_t size, size_t nmemb, void* userp) {
         ((std::string*)userp)->append((char*)contents, size * nmemb);