bam x11

tmp.c

#include <X11/Xlib.h>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include <string>
#include <vector>
#include <iostream>
#include <fstream>
#include <limits.h>
#include <unistd.h>
#include <getopt.h>

#include <htslib/sam.h>
#include <htslib/faidx.h>
#include <htslib/kstring.h>
#include <htslib/khash_str2int.h>

using namespace std;

class App;

class BamW
	{
	public:
		App* owner;
		string filename;
		hts_idx_t *idx = NULL;
		vector<double> depth;
		int y;
		BamW(App* owner,string fn,htsFormat* fmt,int y):owner(owner),filename(fn),idx(0),y(y)
			{
			sam_open_format(fn.c_str(), "r",fmt); // open BAM
			 idx = sam_index_load(data[i]->fp, argv[optind+i]);
			}
		~BamW() {
			::hts_idx_destroy(idx);
			::sam_close(data[i]->fp);
			}
	
		void rescan() {
		data[i]->iter = sam_itr_querys(idx, data[i]->hdr, reg); // set the iterator
		depth.clear();
		depth.resize(owner->window_width,0.0);
		}
		
	};

class App
	{
	public:
		vector<BamW*> bams;
		vector<string> regions;
		size_t region_idx;
		Display *display;
   		Screen *screen;
		Window window;
		unsigned int window_width;
		unsigned int window_height;
		
		App() {
		}
	
		int doWork(int argc,char** argv);

		~App();
		};

void App::resized() {
	int x,y;
	unsigned int w,h, bw, d;
	::XGetGeometry(display, window, &wr, &x, &y, &w, &h, &bw, &d);
	if(w!=this->window_width || h!=his->window_height) {
		this->window_width = w;
		this->window_height = h;
		repaint();
		}
	}
void App:repaint() {
	::XClearWindow(this->display, this->window);
	}

int App::doWork(int argc,char** argv) {
	int n;
	htsFormat format;
	 char *bam_list = NULL;

	 static const struct option lopts[] = {
		 {"bams",required_argument,NULL,'B'},
		{ NULL, 0, NULL, 0 }
	    };

	    // parse the command line
	    while ((n = getopt_long(argc, argv, "B:", lopts, NULL)) >= 0) {
	      	

		
		}

	if(bam_list == NULL) {
		cerr << "List of bams is undefined" << endl;
		return EXIT_FAILURE;		
		}
	ifstream bamin(bam_list);
	if(!bamin.is_open()) {
		cerr << "Cannot open " << bam_list << endl;
		return EXIT_FAILURE;				
		}
	string line;
	while(getline(bamin,line)) {
		if(line.empty() || line[0]=='#') continue;
		BamW* bamFile	 = new BamW(this,line,&format,this->bams.size());
		this->bams.push_back(bamFile);	
		}
	bamin.close();
	if(this->bams.empty()) {
		cerr << "List of bams is empty." << endl;
		return EXIT_FAILURE;		
		}

	return 0;
	}

App::~App() {
	size_t i;
	for(i=0;i< this->bams.size();i++) delete this->bams[i];
	this->bams.clear();
	}

int main(int argc,char** argv) {
   Display *display;
   Screen *screen;
   Window w;
   XEvent e;
   const char *msg = "Hello, World!";
   int s;
 
   display = XOpenDisplay(NULL);
   if (display == NULL) {
      fprintf(stderr, "Cannot open display\n");
      exit(EXIT_FAILURE);
   }
  s = DefaultScreen(display);
printf("%d.",s);
  screen = ScreenOfDisplay(display, 0);

  w = XCreateSimpleWindow(display, RootWindow(display, s), 150, 150, screen->width-300, screen->height-300, 1,
                           BlackPixel(display, s), WhitePixel(display, s));
XSelectInput(display, w, ExposureMask | KeyPressMask);
   XMapWindow(display, w);
 while (1) {
      XNextEvent(display, &e);
      if (e.type == Expose) {
	this->resized();
         XFillRectangle(display, w, DefaultGC(display, s), 20, 20, 10, 10);
         XDrawString(display, w, DefaultGC(display, s), 10, 50, msg, strlen(msg));
      	 }
      if (e.type == KeyPress)
         {
	 if (e.xkey.keycode == XKeysymToKeycode(video.screens[0].display, XK_Q))
		{
		break;
		}
	 if (e.xkey.keycode == XKeysymToKeycode(video.screens[0].display, XK_leftarrow))
		{
		region_idx = (region_idx==0UL?regions.size()-1:region_idx-1);
		repaint();
		}
	 if (e.xkey.keycode == XKeysymToKeycode(video.screens[0].display, XK_rightarrow))
		{
		region_idx = (region_idx+1>=regions.size():0:region_idx+1);
		repaint();
		}
	 }
   }
  XCloseDisplay(display);
 return EXIT_SUCCESS;
}