Merge pull request #28 from kcleal/gw_dev

Gw v0.10.1

.github/workflows/main.yml

@@ -5,7 +5,7 @@ on:
   pull_request:
 
 env:
-  version: 0.10.0
+  version: 0.10.1
 
 jobs:
   mingw:

.gw.ini

@@ -64,6 +64,7 @@ print_screen=PRINT_SCREEN
 find_alignments=F
 repeat_command=R
 vcf_as_tracks=false
+bed_as_tracks=true
 
 [labelling]
 number=3x3

Makefile

@@ -52,7 +52,7 @@ ifneq ($(PLATFORM), "Windows")
     else  # Darwin / Linux
     	CPPFLAGS += -I./lib/skia
         SKIA_PATH = ./lib/skia/out/Release-x64
-        LDFLAGS=
+
     endif
 endif
 

deps/gw.desktop

@@ -1,6 +1,6 @@
 [Desktop Entry]
 Encoding=UTF-8
-Version=0.10.0
+Version=0.10.1
 Type=Application
 Terminal=true
 Exec=bash -c "/usr/bin/gw"

src/drawing.cpp

@@ -61,9 +61,6 @@ namespace Drawing {
         float yOffsetAll = refSpace;
 
         for (auto &cl: collections) {
-            if (cl.skipDrawingReads && cl.skipDrawingCoverage) {
-                continue;
-            }
             cl.skipDrawingCoverage = true;
             if (cl.region->markerPos != -1) {
                 float rp = refSpace + 6 + (cl.bamIdx * cl.yPixels);
@@ -215,6 +212,7 @@ namespace Drawing {
                 }
 
                 int i = 0;
+                int refSeqLen = cl.region->refSeqLen;
                 for (const auto &mm: mmVector) {
                     float cum_h = 0;
                     float mm_h;
@@ -254,6 +252,9 @@ namespace Drawing {
                             continue;
                         }
                         const SkPaint *paint_ref;
+                        if (i >= refSeqLen) {
+                            break;
+                        }
                         switch (refSeq[i]) {
                             case 'A':
                                 paint_ref = &theme.fcA;
@@ -504,6 +505,7 @@ namespace Drawing {
         uint8_t *ptr_qual = bam_get_qual(align.delegate);
 
         const char *refSeq = region->refSeq;
+        int refSeqLen = region->refSeqLen;
 
         float precalculated_xOffset_mmPosOffset = xOffset + mmPosOffset;
 
@@ -530,6 +532,9 @@ namespace Drawing {
             size_t ref_idx = pos_start - region->start;
 
             for (size_t i=idx_start; i < (size_t)idx_end; ++i) {
+                if ((int)i >= refSeqLen) {
+                    break;
+                }
                 char ref_base = lookup_ref_base[(unsigned char)refSeq[ref_idx]];
                 char bam_base = bam_seqi(ptr_seq, i);
                 if (bam_base != ref_base) {
@@ -936,13 +941,15 @@ namespace Drawing {
                     }
                 }
 
-            } else {
+            } else if (nBlocks == 1) {
                 s = (double)a.blocks[0].start - regionBegin;
                 e = (double)a.blocks[0].end - regionBegin;
                 width = (e - s) * xScaling;
                 drawBlock(plotPointedPolygons, pointLeft, edged, (float) s * xScaling, (float) e, (float) width,
                           pointSlop, pH, yScaledOffset, xOffset, regionPixels, nBlocks, regionLen,
                           a, canvas, path, rect, faceColor, edgeColor);
+            } else {
+                continue;
             }
 
             // add soft-clip blocks
@@ -1195,8 +1202,6 @@ namespace Drawing {
         float textW = fonts.overlayWidth;
         float minLetterSize = (textW > 0) ? ((float) fb_width / (float) regions.size()) / textW : 0;
         int index = 0;
-        //h *= 0.7;
-//        h = (h - 6 < 4) ? 4 : h - 6;
         float yp = h + 2;
         for (auto &rgn: regions) {
             int size = rgn.end - rgn.start;
@@ -1403,8 +1408,14 @@ namespace Drawing {
         }
 
         if (label.i != label.ori_i) {
+
             canvas->drawRect(rect, opts.theme.lcJoins);
         }
+        if (!label.comment.empty()) {
+            bg.setXYWH(rect.right() - fonts.overlayHeight - (4*pad), rect.bottom() - fonts.overlayHeight - pad - pad - pad - pad, fonts.overlayHeight,
+                       fonts.overlayHeight);
+            canvas->drawRoundRect(bg, fonts.overlayHeight, fonts.overlayHeight, opts.theme.fcG);
+        }
     }
 
     void drawTrackBigWig(HGW::GwTrack &trk, const Utils::Region &rgn, SkRect &rect, float padX, float padY,
@@ -1868,8 +1879,8 @@ namespace Drawing {
         float regionIdx = 0;
         for (const auto& region: regions) {
 
-            float s = (float)region.start / (float)region.chromLength;
-            float e = (float)region.end / (float)region.chromLength;
+            float s = (float)region.start / (float)region.chromLen;
+            float e = (float)region.end / (float)region.chromLen;
             float w = (e - s) * drawWidth;
             if (w < 3) {
                 w = 3;
@@ -1885,8 +1896,8 @@ namespace Drawing {
             if (it != ideogram.end()) {
                 const std::vector<Themes::Band>& bands = it->second;
                 for (const auto& b : bands) {
-                    float sb = (float) b.start / (float)region.chromLength;
-                    float eb = (float) b.end / (float)region.chromLength;
+                    float sb = (float) b.start / (float)region.chromLen;
+                    float eb = (float) b.end / (float)region.chromLen;
                     float wb = (eb - sb) * drawWidth;
                     rect.setXYWH(xp + (sb * drawWidth),
                                  top + yh_one_third,

src/hts_funcs.cpp

@@ -2043,6 +2043,7 @@ namespace HGW {
     // variant id is either recorded in the filename, or else is the whole filename
     void GwVariantTrack::appendImageLabels(int startIdx, int number) {
         // rid is the file name for an image
+        std::string empty_comment;
         for (int i=startIdx; i < startIdx + number; ++i) {
             if (i < (int)multiLabels.size()) {
                 continue;
@@ -2057,7 +2058,7 @@ namespace HGW {
             if (inputLabels->contains(key)) {
                 multiLabels.push_back((*inputLabels)[key]);
             } else {
-                multiLabels.push_back(Utils::makeLabel(info.chrom, info.pos, label, labelChoices, key, info.varType, "", false, false));
+                multiLabels.push_back(Utils::makeLabel(info.chrom, info.pos, label, labelChoices, key, info.varType, "", false, false, empty_comment));
             }
         }
     }
@@ -2067,6 +2068,7 @@ namespace HGW {
         std::vector<Utils::Region> v;
         bool isTrans = chrom != chrom2;
         Utils::Region* r1; Utils::Region* r2;
+        std::string empty_comment;
         if (!isTrans && rlen <= m_opts->split_view_size) {
             v.resize(1);
             r1 = & v[0];
@@ -2094,7 +2096,7 @@ namespace HGW {
         if (inputLabels->contains(rid)) {
             multiLabels.push_back((*inputLabels)[rid]);
         } else {
-            multiLabels.push_back(Utils::makeLabel(chrom, start, label, labelChoices, rid, vartype, "", false, false));
+            multiLabels.push_back(Utils::makeLabel(chrom, start, label, labelChoices, rid, vartype, "", false, false, empty_comment));
         }
     }
 

src/main.cpp

@@ -66,6 +66,9 @@ void print_banner() {
 #endif
 }
 
+// note to developer - update version in workflows/main.yml, menu.cpp, term_out.cpp, and deps/gw.desktop, and installers .md in docs
+const char GW_VERSION [7] = "0.10.1";
+
 
 int main(int argc, char *argv[]) {
 
@@ -83,8 +86,7 @@ int main(int argc, char *argv[]) {
     static const std::vector<std::string> img_themes = { "igv", "dark", "slate" };
     static const std::vector<std::string> links = { "none", "sv", "all" };
 
-    // note to developer - update version in workflows/main.yml, menu.cpp and deps/gw.desktop, and installers .md in docs
-    argparse::ArgumentParser program("gw", "0.10.0");
+    argparse::ArgumentParser program("gw", std::string(GW_VERSION));
 
     program.add_argument("genome")
             .default_value(std::string{""}).append()
@@ -376,6 +378,8 @@ int main(int argc, char *argv[]) {
     if (program.is_used("-b")) {
         auto bam_paths_temp = program.get<std::vector<std::string>>("-b");
         for (auto &item : bam_paths_temp) {
+            bam_paths.push_back(item);
+            continue;
             if (std::filesystem::exists(item)) {
                 bam_paths.push_back(item);
                 std::cerr << item << std::endl;
@@ -529,6 +533,8 @@ int main(int argc, char *argv[]) {
                 std::exit(-1);
             }
             iopts.getOptionsFromSessionIni(iopts.seshIni);
+        } else {
+            iopts.session_file = "";
         }
         /*
          * / Gw start
@@ -659,7 +665,6 @@ int main(int argc, char *argv[]) {
             if (program.is_used("--out-labels")) {
                 plotter.setOutLabelFile(program.get<std::string>("--out-labels"));
             }
-
             plotter.addVariantTrack(img, iopts.start_index, false, true);
             if (plotter.variantTracks.back().image_glob.size() == 1) {
                 plotter.opts.number.x = 1; plotter.opts.number.y = 1;
@@ -933,6 +938,7 @@ int main(int argc, char *argv[]) {
                 std::string dateStr;
 
                 std::string fileName;
+                std::string empty_comment;
                 std::filesystem::path fsp(vcf.path);
 #if defined(_WIN32) || defined(_WIN64)
                 const wchar_t* pc = fsp.filename().c_str();
@@ -956,7 +962,7 @@ int main(int argc, char *argv[]) {
                     job.rid = vcf.rid;
                     jobs.push_back(job);
                     if (writeLabel) {
-                        Utils::Label l = Utils::makeLabel(vcf.chrom, vcf.start, vcf.label, empty_labels, vcf.rid, vcf.vartype, "", false, false);
+                        Utils::Label l = Utils::makeLabel(vcf.chrom, vcf.start, vcf.label, empty_labels, vcf.rid, vcf.vartype, "", false, false, empty_comment);
                         Utils::labelToFile(fLabels, l, dateStr, fileName);
                     }
                 }

src/menu.cpp

@@ -281,9 +281,10 @@ namespace Menu {
         }
         // write tool tip
         std::string tip;
+
         if (opts.control_level.empty()) {
             if (opts.menu_table == Themes::MenuTable::MAIN) {
-                tip = opts.ini_path + "  v0.10.0";
+                tip = opts.ini_path + "  v0.10.1";
             }
             else if (opts.menu_table == Themes::MenuTable::GENOMES) { tip = "Use ENTER key to select genome, or RIGHT_ARROW key to edit path"; }
             else if (opts.menu_table == Themes::MenuTable::SHIFT_KEYMAP) { tip = "Change characters selected when using shift+key"; }
@@ -294,7 +295,8 @@ namespace Menu {
             else if (opts.menu_level == "coverage") { tip = "Turn coverage on or off [true, false]"; }
             else if (opts.menu_level == "log2_cov") { tip = "Change the y-scale of the coverage track to log2 [true, false]"; }
             else if (opts.menu_level == "expand_tracks") { tip = "Expand overlapping track features [true, false]"; }
-            else if (opts.menu_level == "vcf_as_tracks") { tip = "Drag-and-dropped vcf/bcf files will be added as track features [true, false]"; }
+            else if (opts.menu_level == "vcf_as_tracks") { tip = "Drag-and-dropped vcf/bcf files will be added as a track if true, or image-tiles otherwise [true, false]"; }
+            else if (opts.menu_level == "bed_as_tracks") { tip = "Drag-and-dropped bed files will be added as a track if true, or image-tiles otherwise [true, false]"; }
             else if (opts.menu_level == "link") { tip = "Change which reads are linked [none, sv, all]"; }
             else if (opts.menu_level == "split_view_size") { tip = "Structural variants greater than this size will be drawn as two regions"; }
             else if (opts.menu_level == "threads") { tip = "The number of threads to use for file readings"; }
@@ -682,7 +684,7 @@ namespace Menu {
         for (const auto& v : {"scroll_speed", "tabix_track_height"}) {
             option_map[v] = Float;
         }
-        for (const auto& v : {"coverage", "log2_cov", "expand_tracks", "vcf_as_tracks", "sv_arcs", "mods"}) {
+        for (const auto& v : {"coverage", "log2_cov", "expand_tracks", "vcf_as_tracks", "bed_as_tracks", "sv_arcs", "mods"}) {
             option_map[v] = Bool;
         }
         for (const auto& v : {"scroll_right", "scroll_left", "zoom_out", "zoom_in", "scroll_down", "scroll_up", "cycle_link_mode", "print_screen", "find_alignments", "delete_labels", "enter_interactive_mode"}) {
@@ -755,6 +757,7 @@ namespace Menu {
         else if (new_opt.name == "log2_cov") { opts.log2_cov = v; }
         else if (new_opt.name == "expand_tracks") { opts.expand_tracks = v; }
         else if (new_opt.name == "vcf_as_tracks") { opts.vcf_as_tracks = v; }
+        else if (new_opt.name == "bed_as_tracks") { opts.bed_as_tracks = v; }
         else if (new_opt.name == "coverage") { opts.max_coverage = (v) ? 1410065408 : 0; }
         else if (new_opt.name == "sv_arcs") { opts.sv_arcs = v; }
         else if (new_opt.name == "mods") { opts.parse_mods = v; }

src/menu.h

@@ -49,8 +49,8 @@ namespace Menu {
 
     std::vector<std::string> getCommandTip();
 
-    constexpr std::array<const char*, 27> commandToolTip = {"ylim", "var", "tlen-y", "tags", "soft-clips", "snapshot", "sam", "remove",
-                                                            "refresh", "online", "mods", "mismatches", "mate", "mate add", "log2-cov", "link", "line", "insertions", "indel-length",
+    constexpr std::array<const char*, 28> commandToolTip = {"ylim", "var", "tlen-y", "tags", "soft-clips", "save", "sam", "remove",
+                                                            "refresh", "online", "mods", "mismatches", "mate", "mate add", "log2-cov", "load", "link", "line", "insertions", "indel-length",
                                                             "grid", "find", "filter", "expand-tracks", "edges", "cov",  "count", "add"};
 
     constexpr std::array<const char*, 16> exec = {"cov", "count", "edges", "expand-tracks", "insertions", "line", "log2-cov", "mate", "mate add", "mismatches", "mods", "tags", "soft-clips", "sam", "refresh", "tlen-y"};

src/parser.cpp

@@ -17,8 +17,8 @@
 
 namespace Parse {
 
-    constexpr std::string_view numeric_like = "eq ne gt lt ge le == != > < >= <=";
-    constexpr std::string_view string_like = "eq ne contains == != omit";
+    constexpr std::string_view numeric_like = "eq ne gt lt ge le = == != > < >= <=";
+    constexpr std::string_view string_like = "eq ne contains = == != omit";
 
     Parser::Parser(std::ostream& errOutput) : out(errOutput) {
         opMap["mapq"] = MAPQ;
@@ -66,6 +66,7 @@ namespace Parse {
         opMap["ge"] = GE;
         opMap["le"] = LE;
         opMap["=="] = EQ;
+        opMap["="] = EQ;
         opMap["!="] = NE;
         opMap[">"] = GT;
         opMap["<"] = LT;
@@ -976,6 +977,14 @@ namespace Parse {
 
     void tryTabCompletion(std::string &inputText, std::ostream& out, int& charIndex) {
         std::vector<std::string> parts = Utils::split(inputText, ' ');
+        if (parts.size() == 3) {  // chunk first two options
+            std::string tmp = parts[0];
+            std::string tmp2 = parts[1];
+            std::string tmp3 = parts[2];
+            parts[0] = tmp + " " + tmp2;
+            parts[1] = tmp3;
+            parts.resize(2);
+        }
         std::string globstr;
         if (parts.back() == "./") {
             globstr = "./*";
@@ -986,6 +995,9 @@ namespace Parse {
         std::vector<std::filesystem::path> glob_paths = glob_cpp::glob(globstr);
         if (glob_paths.size() == 1) {
             inputText = parts[0] + " " + glob_paths[0].generic_string();
+            if (std::filesystem::is_directory(glob_paths[0])) {
+                inputText += std::filesystem::path::preferred_separator;
+            }
             charIndex = inputText.size();
             return;
         }
@@ -998,6 +1010,7 @@ namespace Parse {
             return;
         }
         inputText = parts[0] + " " + lcp;
+
         charIndex = inputText.size();
         size_t width = (size_t)Utils::get_terminal_width() - 1;
         size_t i = 0;
@@ -1009,18 +1022,17 @@ namespace Parse {
             } else {
                 if (width > 6 && s.size() > 6) {
                     s.erase(s.begin() + width - 4, s.end());
-                    out << s << " ...";
+                    out << s << " ..."; out.flush();
                 }
                 break;
             }
             if (i < glob_paths.size() - 2 && width > 2) {
-                out << "  ";
+                out << "  "; out.flush();
                 width -= 2;
             } else {
                 break;
             }
         }
-        out.flush();
         return;
     }
 }