v1.1.1 Added .pdf and .svg to snapshot command. Simplified pdf/png sa…

…ving from CLI

.github/workflows/main.yml

@@ -5,7 +5,7 @@ on:
   pull_request:
 
 env:
-  version: 1.1.0
+  version: 1.1.1
 
 jobs:
   mingw:

deps/build_skia.sh

@@ -42,7 +42,6 @@ if [ "$OS" = "Darwin" ]; then
     echo "SDK_PATH ${SDK_PATH}"
     EXTRA_CFLAGS=$(echo "$EXTRA_CFLAGS" | sed 's/\]$//')
     EXTRA_CFLAGS+=", \"-mmacosx-version-min=10.15\", \"-isysroot\", \"${SDK_PATH}\"]"
-
     EXTRA_LDFLAGS=$(echo "$EXTRA_LDFLAGS" | sed 's/\]$//')
     EXTRA_LDFLAGS+=", \"-mmacosx-version-min=10.15\", \"-isysroot\", \"${SDK_PATH}\"]"
 

deps/gw.desktop

@@ -1,6 +1,6 @@
 [Desktop Entry]
 Encoding=UTF-8
-Version=1.1.0
+Version=1.1.1
 Type=Application
 Terminal=true
 Exec=bash -c "/usr/bin/gw"

src/main.cpp

@@ -59,7 +59,7 @@ void print_banner() {
 }
 
 // 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] = "1.1.0";
+const char GW_VERSION [7] = "1.1.1";
 
 
 bool str_is_number(const std::string &s) {
@@ -736,28 +736,32 @@ int main(int argc, char *argv[]) {
 
             plotter.opts.theme.setAlphas();
 
-            if (program.is_used("--fmt") && (program.get<std::string>("--fmt") == "pdf" || program.get<std::string>("--fmt") == "svg" )) {
-                std::string format_str = program.get<std::string>("--fmt");
+            std::filesystem::path fname;
+            std::filesystem::path out_path;
+            std::string format_str = ".png";
+            if (program.is_used("--file")) {
+                fname = program.get<std::string>("--file");
+                format_str = fname.extension().generic_string();
+            } else if (program.is_used("--fmt") && program.get<std::string>("--fmt") != "png") {
+                format_str = "." + program.get<std::string>("--fmt");
+            }
+
+            if (format_str != ".png") {
                 if (regions.empty()) {
                     std::cerr << "Error: --fmt is only supported by providing a --region\n";
                     std::exit(-1);
                 }
 
-                std::filesystem::path fname;
-                std::filesystem::path out_path;
-
-                if (program.is_used("--file")) {
-                    fname = program.get<std::string>("--file");
-                    out_path = fname;
-                } else {
-                    if (outdir.empty()) {
+                if (fname.empty()) {
+                    if (fname.empty()) {
                         std::cerr << "Error: please provide an output directory using --outdir, or direct to --file\n";
                         std::exit(-1);
                     }
                     fname = regions[0].chrom + "_" + std::to_string(regions[0].start) + "_" +
-                            std::to_string(regions[0].end) + "." + format_str;
-                    out_path = outdir / fname;
+                            std::to_string(regions[0].end) + format_str;
+
                 }
+                out_path = outdir / fname;
 
 #if defined(_WIN32) || defined(_WIN64)
                 const wchar_t* outp = out_path.c_str();
@@ -769,12 +773,12 @@ int main(int argc, char *argv[]) {
 #endif
                 SkDynamicMemoryWStream buffer;
 
-                if (format_str == "pdf") {
+                if (format_str == ".pdf") {
                     auto pdfDocument = SkPDF::MakeDocument(&buffer);
                     SkCanvas *pageCanvas = pdfDocument->beginPage(iopts.dimensions.x, iopts.dimensions.y);
                     plotter.fb_width = iopts.dimensions.x;
                     plotter.fb_height = iopts.dimensions.y;
-                    plotter.setRasterSize(plotter.fb_width, plotter.fb_height);
+                    plotter.setImageSize(plotter.fb_width, plotter.fb_height);
                     if (!extra_commands.empty()) {
                         for (const auto& command: extra_commands) {
                             plotter.inputText = command;
@@ -787,7 +791,7 @@ int main(int argc, char *argv[]) {
                 } else {
                     plotter.fb_width = iopts.dimensions.x;
                     plotter.fb_height = iopts.dimensions.y;
-                    plotter.setRasterSize(plotter.fb_width, plotter.fb_height);
+                    plotter.setImageSize(plotter.fb_width, plotter.fb_height);
                     SkPictureRecorder recorder;
                     SkCanvas* canvas = recorder.beginRecording(SkRect::MakeWH(iopts.dimensions.x, iopts.dimensions.y));
                     if (!extra_commands.empty()) {
@@ -810,7 +814,7 @@ int main(int argc, char *argv[]) {
                 // Plot a png image, either of target region or whole chromosome
                 sk_sp<SkImage> img;
                 if (!regions.empty()) {  // plot target regions
-                    plotter.setRasterSize(iopts.dimensions.x, iopts.dimensions.y);
+                    plotter.setImageSize(iopts.dimensions.x, iopts.dimensions.y);
                     sk_sp<SkSurface> rasterSurface = SkSurface::MakeRasterN32Premul(iopts.dimensions.x,
                                                                                     iopts.dimensions.y);
                     SkCanvas *canvas = rasterSurface->getCanvas();
@@ -864,7 +868,7 @@ int main(int argc, char *argv[]) {
                     for (int i = 0; i < iopts.threads; ++i) {
                         auto *m = new Manager::GwPlot(genome, bam_paths, iopts, regions, tracks);
                         m->opts.theme.setAlphas();
-                        m->setRasterSize(iopts.dimensions.x, iopts.dimensions.y);
+                        m->setImageSize(iopts.dimensions.x, iopts.dimensions.y);
                         m->opts.threads = 1;
                         m->gap = 0;
                         m->drawLocation = false;
@@ -984,7 +988,7 @@ int main(int argc, char *argv[]) {
                 for (int i = 0; i < iopts.threads; ++i) {
                     auto *m = new Manager::GwPlot(genome, bam_paths, iopts, regions, tracks);
                     m->opts.theme.setAlphas();
-                    m->setRasterSize(iopts.dimensions.x, iopts.dimensions.y);
+                    m->setImageSize(iopts.dimensions.x, iopts.dimensions.y);
                     m->opts.threads = 1;
                     for (auto &s: filters) {
                         m->addFilter(s);

src/menu.cpp

@@ -284,7 +284,7 @@ namespace Menu {
 
         if (opts.control_level.empty()) {
             if (opts.menu_table == Themes::MenuTable::MAIN) {
-                tip = opts.ini_path + "  v1.1.0";
+                tip = opts.ini_path + "  v1.1.1";
             }
             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"; }

src/parser.h

@@ -87,6 +87,19 @@ namespace Parse {
         Parser(std::ostream& errOutput);
         ~Parser() = default;
 
+        // Copy assignment operator
+        Parser& operator=(const Parser& other) {
+            if (this != &other) {
+                orBlock = other.orBlock;
+                filter_str = other.filter_str;
+                opMap = other.opMap;
+                permit = other.permit;
+                evaluations_block = other.evaluations_block;
+                targetIndexes = other.targetIndexes;
+            }
+            return *this;
+        }
+
         bool orBlock;
         std::string filter_str;
         ankerl::unordered_dense::map< std::string, Property> opMap;

src/plot_commands.cpp

@@ -35,6 +35,16 @@
 #include "themes.h"
 
 
+#include "include/core/SkCanvas.h"
+#include "include/core/SkSurface.h"
+#include "include/core/SkDocument.h"
+#include "include/docs/SkPDFDocument.h"
+#include "include/core/SkStream.h"
+#include "include/core/SkPictureRecorder.h"
+#include "include/core/SkPicture.h"
+#include "include/svg/SkSVGCanvas.h"
+
+
 /* Notes for adding new commands:
  * 1. Make a new function, accepting a pointer to a GwPlot instance and any other args
  * 2. Add function to run_command_map below
@@ -785,7 +795,7 @@ namespace Commands {
         }
         std::string fname;
         p->currentVarTrack = &p->variantTracks[p->variantFileSelection];
-        if (parts.size() == 1) {
+        if (parts.size() == 1) {  // Choose filename automatically based on region
             if (p->mode == Manager::Show::SINGLE) {
                 std::filesystem::path fname_path = Utils::makeFilenameFromRegions(p->regions);
 #if defined(_WIN32) || defined(_WIN64)
@@ -802,6 +812,7 @@ namespace Commands {
             }
         } else {
             std::string nameFormat = parts[1];
+            // try and parse information from vcf record e.g. {pos}.png
             if (p->currentVarTrack != nullptr && p->currentVarTrack->type == HGW::TrackType::VCF && p->mode == Manager::Show::SINGLE) {
                 if (p->mouseOverTileIndex == -1 || p->currentVarTrack->blockStart + p->mouseOverTileIndex > (int) p->currentVarTrack->multiLabels.size()) {
                     return Err::SILENT;
@@ -831,10 +842,50 @@ namespace Commands {
             out << termcolor::red << "Error:" << termcolor::reset << " path not found " << out_path.parent_path() << std::endl;
             return Err::INVALID_PATH;
         } else {
-            if (!p->imageCacheQueue.empty()) {
-                Manager::imagePngToFile(p->imageCacheQueue.back().second, out_path.string());
-                Term::clearLine(out);
+            if (out_path.extension() == ".png") {
+                if (!p->imageCacheQueue.empty()) {
+                    Manager::imagePngToFile(p->imageCacheQueue.back().second, out_path.string());
+                    Term::clearLine(out);
+                    out << "\rSaved to " << out_path << std::endl;
+                }
+            } else if (out_path.extension() == ".pdf" || out_path.extension() == ".svg") {
+                std::string format_str = (out_path.extension() == ".pdf") ? "pdf" : "svg";
+
+#if defined(_WIN32) || defined(_WIN64)
+                const wchar_t* outp = out_path.c_str();
+                std::wstring pw(outp);
+                std::string outp_str(pw.begin(), pw.end());
+                SkFILEWStream out(outp_str.c_str());
+#else
+                SkFILEWStream out_stream(out_path.c_str());
+#endif
+                SkDynamicMemoryWStream buffer;
+
+                for (auto &cl: p->collections) {
+                    cl.skipDrawingCoverage = false;
+                    cl.skipDrawingReads = false;
+                }
+                if (format_str == "pdf") {
+                    auto pdfDocument = SkPDF::MakeDocument(&buffer);
+                    SkCanvas *pageCanvas = pdfDocument->beginPage(p->fb_width, p->fb_height);
+                    p->runDrawOnCanvas(pageCanvas);
+                    pdfDocument->close();
+                    buffer.writeToStream(&out_stream);
+                } else {
+                    SkPictureRecorder recorder;
+                    SkCanvas* canvas = recorder.beginRecording(SkRect::MakeWH(p->fb_width, p->fb_height));
+                    p->runDrawOnCanvas(canvas);
+                    sk_sp<SkPicture> picture = recorder.finishRecordingAsPicture();
+                    std::unique_ptr<SkCanvas> svgCanvas = SkSVGCanvas::Make(SkRect::MakeWH(p->fb_width, p->fb_height), &out_stream);
+                    if (svgCanvas) {
+                        picture->playback(svgCanvas.get());
+                        svgCanvas->flush();
+                    };
+                }
                 out << "\rSaved to " << out_path << std::endl;
+            } else {
+                out << termcolor::red << "Error:" << termcolor::reset << " extension not supported " << out_path.extension() << std::endl;
+                return Err::OPTION_NOT_SUPPORTED;
             }
         }
         return Err::NONE;
@@ -1049,16 +1100,12 @@ namespace Commands {
             } else {
                 return Err::OPTION_NOT_UNDERSTOOD;
             }
-        }
-        //  Err snapshot(Plot* p, std::vector<std::string> parts, std::ostream& out) {
-        else if (Utils::endsWith(command, ".png")) {
+        } else if (Utils::endsWith(command, ".png") || Utils::endsWith(command, ".pdf") || Utils::endsWith(command, ".svg")) {
             return snapshot(p, parts, out);
-        }
-        else if (Utils::endsWith(parts.back(), ".ini")) {
+        } else if (Utils::endsWith(parts.back(), ".ini")) {
             out << "Saved session: " << parts.back() << std::endl;
             p->saveSession(parts.back());
-        }
-        else if (Utils::endsWith(parts.back(), ".tsv") || (Utils::endsWith(parts.back(), ".txt"))) {
+        } else if (Utils::endsWith(parts.back(), ".tsv") || (Utils::endsWith(parts.back(), ".txt"))) {
             out << "Output label file set as: " << parts.back() << std::endl;
             p->setOutLabelFile(parts.back());
             p->saveLabels();

src/plot_manager.cpp

@@ -327,12 +327,14 @@ namespace Manager {
             if (!gladLoadGLLoader((GLADloadproc) glfwGetProcAddress)) {
                 std::cerr << "Error: failed to initialize GLAD GL\n";
             }
-            if (GLAD_GL_VERSION_4_1) {
-                std::cerr << "OpenGL 4.1 is supported\n";
-            } else {
-                std::cerr << "OpenGL 4.1 is not supported\n";
-                std::cerr << "OpenGL 3.3 is " << ((GLAD_GL_VERSION_3_3) ? "" : "not ") << "supported\n";
-                std::cerr << "OpenGL 2.1 is " << ((GLAD_GL_VERSION_2_1) ? "" : "not ") << "supported\n";
+            if (debug) {
+                if (GLAD_GL_VERSION_4_1) {
+                    std::cerr << "OpenGL 4.1 is supported\n";
+                } else {
+                    std::cerr << "OpenGL 4.1 is not supported\n";
+                    std::cerr << "OpenGL 3.3 is " << ((GLAD_GL_VERSION_3_3) ? "" : "not ") << "supported\n";
+                    std::cerr << "OpenGL 2.1 is " << ((GLAD_GL_VERSION_2_1) ? "" : "not ") << "supported\n";
+                }
             }
         }
         if (debug) {
@@ -986,7 +988,7 @@ namespace Manager {
 
     }
 
-    void GwPlot::setRasterSize(int width, int height) {
+    void GwPlot::setImageSize(int width, int height) {
 //        monitorScale = 1;
         fb_width = width;
         fb_height = height;
@@ -1669,21 +1671,30 @@ namespace Manager {
         }
         canvas->drawPaint(opts.theme.bgPaint);
         SkRect clip;
-        for (auto &cl: collections) {
-
-            canvas->save();
 
-            if (cl.bamIdx == 0) {  // cover the ref too
-                clip.setXYWH(cl.xOffset, 0, cl.regionPixels, cl.yOffset + trackY + covY + refSpace);
-            } else {
-                clip.setXYWH(cl.xOffset, cl.yOffset - covY, cl.regionPixels, cl.yOffset + trackY + covY);
+        for (auto &cl: collections) {
+            if (cl.skipDrawingCoverage && cl.skipDrawingReads) {  // keep read and coverage area
+                continue;
             }
-            canvas->clipRect(clip, false);
+            canvas->save();
+            // for now cl.skipDrawingCoverage and cl.skipDrawingReads are almost always the same
+            if ((!cl.skipDrawingCoverage && !cl.skipDrawingReads) || imageCacheQueue.empty()) {
+                clip.setXYWH(cl.xOffset, cl.yOffset - covY, cl.regionPixels, trackY + covY - gap);
+                canvas->clipRect(clip, false);
+            } else if (cl.skipDrawingCoverage) {
+                clip.setXYWH(cl.xOffset, cl.yOffset, cl.regionPixels, cl.yPixels);
+                canvas->clipRect(clip, false);
+            } else if (cl.skipDrawingReads){
+                clip.setXYWH(cl.xOffset, cl.yOffset - covY, cl.regionPixels, covY);
+                canvas->clipRect(clip, false);
+            }  // else no clip
             canvas->drawPaint(opts.theme.bgPaint);
 
-            if (!cl.skipDrawingReads) {
+            if (!cl.skipDrawingReads && !bams.empty()) {
 
-                if (cl.regionLen >= opts.low_memory && !bams.empty() && opts.link_op == 0) {  // low memory mode will be used
+                if (cl.regionLen >= opts.low_memory) {
+                    assert (opts.link_op == 0 && regions[cl.regionIdx].getSortOption() == SortType::NONE);
+                    // low memory mode will be used
                     cl.clear();
                     if (opts.threads == 1) {
                         HGW::iterDraw(cl, bams[cl.bamIdx], headers[cl.bamIdx], indexes[cl.bamIdx],
@@ -1702,9 +1713,8 @@ namespace Manager {
                 }
             }
             canvas->restore();
-
-//            Drawing::drawCollection(opts, cl, canvas, trackY, yScaling, fonts, opts.link_op, refSpace, pointSlop, textDrop, pH, monitorScale);
         }
+
         if (opts.max_coverage) {
             Drawing::drawCoverage(opts, collections, canvas, fonts, covY, refSpace, gap);
         }
@@ -1720,7 +1730,6 @@ namespace Manager {
 
     void GwPlot::runDrawNoBufferOnCanvas(SkCanvas* canvas) {
 //        std::chrono::high_resolution_clock::time_point initial = std::chrono::high_resolution_clock::now();
-
         if (bams.empty()) {
             return;
         }

src/plot_manager.h

@@ -163,7 +163,7 @@ namespace Manager {
 
         void setGlfwFrameBufferSize();
 
-        void setRasterSize(int width, int height);
+        void setImageSize(int width, int height);
 
         int makeRasterSurface();