Added header command. Fixed sam command. Fixed few issues around scre…

…en updating for various commands. Consistent menu interactions with mouse.

.github/workflows/main.yml

@@ -5,7 +5,7 @@ on:
   pull_request:
 
 env:
-  version: 0.10.1
+  version: 1.0.0
 
 jobs:
   mingw:

.gw.ini

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

deps/gw.desktop

@@ -1,6 +1,6 @@
 [Desktop Entry]
 Encoding=UTF-8
-Version=0.10.1
+Version=1.0.0
 Type=Application
 Terminal=true
 Exec=bash -c "/usr/bin/gw"

docs/docs/guide/Commands.md

@@ -270,6 +270,12 @@ Set the grid size for viewing image tiles.
 
     grid 8x8   # this will display 64 image tiles
 
+- ## header
+
+Prints the header of the current selected bam to the terminal. Use `header names` to print only the @SQ lines.
+
+    header        # print the full header
+    header names  # prints only the @SQ lines (chromosome names)
 
 - ## indel-length
 
@@ -375,9 +381,16 @@ Add a region of interest. If no arguments are added, the visible region will be
 
 - ## sam
 
-Print the entire seclected read in sam format to the terminal.
+Print the selected read to the terminal, or save in a file.
+
+First select a read using the mouse then type `sam`. Alternatively, use the the `>` key to redirect to a file, or `>>`
+to append to a file. Note, the header will also be written, and the output file will be unsorted:
+
+    sam
+    sam > single_read.sam       # save in sam format
+    sam >> multiple_reads.bam   # Append read to a bam file
+    sam >> multiple_reads.cram  # Append in cram format
 
-First select a read using the mouse then type `sam`
 <br>
 
 - ## save

docs/docs/install/Linux.md

@@ -11,7 +11,7 @@ For best performance, install GW as a desktop application on (Intel debian syste
 Use the installer below, or head over to the GitHub [Releases page](https://github.com/kcleal/gw/releases).
 
 
-[GW Intel x86_64 debian installer](https://github.com/kcleal/gw/releases/download/v0.10.0/gw_0.10.0_amd64.deb)
+[GW Intel x86_64 debian installer](https://github.com/kcleal/gw/releases/download/v1.0.0/gw_1.0.0_amd64.deb)
 
 
 

docs/docs/install/MacOS.md

@@ -11,9 +11,9 @@ For best performance, install GW as a desktop application (Intel or Apple silico
 installers below, or head over to the GitHub [Releases page](https://github.com/kcleal/gw/releases).
 
 
-[GW Intel x86_64 mac dmg installer](https://github.com/kcleal/gw/releases/download/v0.10.0/gw_macos_intel.dmg)
+[GW Intel x86_64 mac dmg installer](https://github.com/kcleal/gw/releases/download/v1.0.0/gw_macos_intel.dmg)
 
-[GW Apple arm64 mac dmg installer](https://github.com/kcleal/gw/releases/download/v0.9.3/gw-macos-arm.dmg)
+[GW Apple arm64 mac dmg installer](https://github.com/kcleal/gw/releases/download/v1.0.0/gw_macos_m1.dmg)
 
 
 GW can be copied to your bin directory to make it available as a command-line tool:

docs/docs/install/Windows.md

@@ -25,7 +25,7 @@ Follow the installation instructions on the website to set up MSYS2 on your Wind
 Download the GW installer script below:
 
 
-[GW Intel x86_64 Windows installer](https://github.com/kcleal/gw/releases/download/v0.10.0/gw-windows-installer.vbs)
+[GW Intel x86_64 Windows installer](https://github.com/kcleal/gw/releases/download/v1.0.0/gw-windows-installer.vbs)
 
 
 Run the downloaded visual-basic script by double-clicking, or right-clicking and selecting Run as program.

src/main.cpp

@@ -10,7 +10,6 @@
 #include <string>
 #include "argparse.h"
 #include "BS_thread_pool.h"
-//#include "../include/natsort.hpp"
 #include "glob_cpp.hpp"
 #include "hts_funcs.h"
 #include "parser.h"
@@ -68,7 +67,7 @@ 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] = "0.10.1";
+const char GW_VERSION [7] = "1.0.0";
 
 
 bool str_is_number(const std::string &s) {

src/menu.cpp

@@ -114,7 +114,7 @@ namespace Menu {
         SkPaint menuBg;
         SkPaint tcMenu;
         if (opts.theme_str != "igv") {
-            bg.setARGB(255, 15, 15, 25);
+            bg.setARGB(255, 35, 35, 45);
             tcMenu.setARGB(255, 255, 255, 255);
             menuBg = opts.theme.fcDup;
         } else {
@@ -284,7 +284,7 @@ namespace Menu {
 
         if (opts.control_level.empty()) {
             if (opts.menu_table == Themes::MenuTable::MAIN) {
-                tip = opts.ini_path + "  v0.10.1";
+                tip = opts.ini_path + "  v1.0.0";
             }
             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"; }