X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_tview.c;h=61842139ebce1dcd60e99f76308f8da75445c254;hb=307c147168f7154e3755712797078c513e0b242a;hp=3dfb20108ee4cef7ba4d03f5294138240090883b;hpb=f93dae0d03856955f9424e8b2aaf261304ca647e;p=samtools.git

diff --git a/bam_tview.c b/bam_tview.c
index 3dfb201..6184213 100644
--- a/bam_tview.c
+++ b/bam_tview.c
@@ -1,40 +1,85 @@
-#ifndef _NO_CURSES
-#include <curses.h>
-#include <ctype.h>
 #include <assert.h>
-#include <string.h>
-#include "bam.h"
-#include "faidx.h"
-#include "bam_maqcns.h"
+#include "bam_tview.h"
 
-#define TV_MIN_ALNROW 2
-#define TV_MAX_GOTO  40
-#define TV_LOW_MAPQ  10
+int base_tv_init(tview_t* tv,const char *fn, const char *fn_fa, const char *samples)
+	{
+	assert(tv!=NULL);
+	assert(fn!=NULL);
+	tv->mrow = 24; tv->mcol = 80;
+	tv->color_for = TV_COLOR_MAPQ;
+	tv->is_dot = 1;
+	
+	tv->fp = bam_open(fn, "r");
+	if(tv->fp==0)
+		{
+		fprintf(stderr,"bam_open %s. %s\n", fn,fn_fa);
+            	exit(EXIT_FAILURE);
+		}
+	bgzf_set_cache_size(tv->fp, 8 * 1024 *1024);
+	assert(tv->fp);
+	
+	tv->header = bam_header_read(tv->fp);
+	if(tv->header==0)
+		{
+		fprintf(stderr,"Cannot read '%s'.\n", fn);
+            	exit(EXIT_FAILURE);
+		}
+	tv->idx = bam_index_load(fn);
+	if (tv->idx == 0)
+		{
+		fprintf(stderr,"Cannot read index for '%s'.\n", fn);
+		exit(EXIT_FAILURE);
+		}
+	tv->lplbuf = bam_lplbuf_init(tv_pl_func, tv);
+	if (fn_fa) tv->fai = fai_load(fn_fa);
+	tv->bca = bcf_call_init(0.83, 13);
+	tv->ins = 1;
 
-#define TV_COLOR_MAPQ  0
-#define TV_COLOR_BASEQ 1
-#define TV_COLOR_NUCL  2
+    if ( samples ) 
+    {
+        if ( !tv->header->dict ) tv->header->dict = sam_header_parse2(tv->header->text);
+        void *iter = tv->header->dict;
+        const char *key, *val;
+        int n = 0;
+        tv->rg_hash = kh_init(kh_rg);
+        while ( (iter = sam_header2key_val(iter, "RG","ID","SM", &key, &val)) )
+        {
+            if ( !strcmp(samples,key) || (val && !strcmp(samples,val)) )
+            {
+                khiter_t k = kh_get(kh_rg, tv->rg_hash, key);
+                if ( k != kh_end(tv->rg_hash) ) continue;
+                int ret;
+                k = kh_put(kh_rg, tv->rg_hash, key, &ret);
+                kh_value(tv->rg_hash, k) = val;
+                n++;
+            }
+        }
+        if ( !n )
+        {
+            fprintf(stderr,"The sample or read group \"%s\" not present.\n", samples);
+            exit(EXIT_FAILURE);
+        }
+    }
 
-typedef struct {
-	int mrow, mcol;
-	WINDOW *wgoto, *whelp;
+	return 0;
+	}
 
-	bam_index_t *idx;
-	bam_lplbuf_t *lplbuf;
-	bam_header_t *header;
-	bamFile fp;
-	int curr_tid, left_pos;
-	faidx_t *fai;
-	bam_maqcns_t *bmc;
 
-	int ccol, last_pos, row_shift, color_for, is_nucl, l_ref;
-	char *ref;
-} tview_t;
+void base_tv_destroy(tview_t* tv)
+	{
+	bam_lplbuf_destroy(tv->lplbuf);
+	bcf_call_destroy(tv->bca);
+	bam_index_destroy(tv->idx);
+	if (tv->fai) fai_destroy(tv->fai);
+	free(tv->ref);
+	bam_header_destroy(tv->header);
+	bam_close(tv->fp);
+	}
 
-char bam_nt16_nt4_table[] = { 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4 };
 
 int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data)
 {
+	extern unsigned char bam_nt16_table[256];
 	tview_t *tv = (tview_t*)data;
 	int i, j, c, rb, attr, max_ins = 0;
 	uint32_t call = 0;
@@ -42,26 +87,43 @@ int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void
 	// print referece
 	rb = (tv->ref && pos - tv->left_pos < tv->l_ref)? tv->ref[pos - tv->left_pos] : 'N';
 	for (i = tv->last_pos + 1; i < pos; ++i) {
-		if (i%10 == 0) mvprintw(0, tv->ccol, "%-d", i+1);
+		if (i%10 == 0 && tv->mcol - tv->ccol >= 10) tv->my_mvprintw(tv,0, tv->ccol, "%-d", i+1);
 		c = tv->ref? tv->ref[i - tv->left_pos] : 'N';
-		mvaddch(1, tv->ccol++, c);
+		tv->my_mvaddch(tv,1, tv->ccol++, c);
+	}
+	if (pos%10 == 0 && tv->mcol - tv->ccol >= 10) tv->my_mvprintw(tv,0, tv->ccol, "%-d", pos+1);
+	{ // call consensus
+		bcf_callret1_t bcr;
+		int qsum[4], a1, a2, tmp;
+		double p[3], prior = 30;
+		bcf_call_glfgen(n, pl, bam_nt16_table[rb], tv->bca, &bcr);
+		for (i = 0; i < 4; ++i) qsum[i] = bcr.qsum[i]<<2 | i;
+		for (i = 1; i < 4; ++i) // insertion sort
+			for (j = i; j > 0 && qsum[j] > qsum[j-1]; --j)
+				tmp = qsum[j], qsum[j] = qsum[j-1], qsum[j-1] = tmp;
+		a1 = qsum[0]&3; a2 = qsum[1]&3;
+		p[0] = bcr.p[a1*5+a1]; p[1] = bcr.p[a1*5+a2] + prior; p[2] = bcr.p[a2*5+a2];
+		if ("ACGT"[a1] != toupper(rb)) p[0] += prior + 3;
+		if ("ACGT"[a2] != toupper(rb)) p[2] += prior + 3;
+		if (p[0] < p[1] && p[0] < p[2]) call = (1<<a1)<<16 | (int)((p[1]<p[2]?p[1]:p[2]) - p[0] + .499);
+		else if (p[2] < p[1] && p[2] < p[0]) call = (1<<a2)<<16 | (int)((p[0]<p[1]?p[0]:p[1]) - p[2] + .499);
+		else call = (1<<a1|1<<a2)<<16 | (int)((p[0]<p[2]?p[0]:p[2]) - p[1] + .499);
 	}
-	if (pos%10 == 0) mvprintw(0, tv->ccol, "%-d", pos+1);
-	// print consensus
-	call = bam_maqcns_call(n, pl, tv->bmc);
-	attr = A_UNDERLINE;
-	c = ",ACMGRSVTWYHKDBN"[call>>28&0xf];
-	i = (call>>8&0xff)/10+1;
+	attr = tv->my_underline(tv);
+	c = ",ACMGRSVTWYHKDBN"[call>>16&0xf];
+	i = (call&0xffff)/10+1;
 	if (i > 4) i = 4;
-	attr |= COLOR_PAIR(i);
+	attr |= tv->my_colorpair(tv,i);
 	if (c == toupper(rb)) c = '.';
-	attron(attr);
-	mvaddch(2, tv->ccol, c);
-	attroff(attr);
-	// calculate maximum insert
-	for (i = 0; i < n; ++i) {
-		const bam_pileup1_t *p = pl + i;
-		if (p->indel > 0 && max_ins < p->indel) max_ins = p->indel;
+	tv->my_attron(tv,attr);
+	tv->my_mvaddch(tv,2, tv->ccol, c);
+	tv->my_attroff(tv,attr);
+	if(tv->ins) {
+		// calculate maximum insert
+		for (i = 0; i < n; ++i) {
+			const bam_pileup1_t *p = pl + i;
+			if (p->indel > 0 && max_ins < p->indel) max_ins = p->indel;
+		}
 	}
 	// core loop
 	for (j = 0; j <= max_ins; ++j) {
@@ -70,115 +132,119 @@ int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void
 			int row = TV_MIN_ALNROW + p->level - tv->row_shift;
 			if (j == 0) {
 				if (!p->is_del) {
-					c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos)];
-					if (!tv->is_nucl && toupper(c) == toupper(rb)) c = bam1_strand(p->b)? ',' : '.';
-				} else c = '*';
+					if (tv->base_for == TV_BASE_COLOR_SPACE && 
+							(c = bam_aux_getCSi(p->b, p->qpos))) {
+						// assume that if we found one color, we will be able to get the color error
+						if (tv->is_dot && '-' == bam_aux_getCEi(p->b, p->qpos)) c = bam1_strand(p->b)? ',' : '.';
+					} else {
+						if (tv->show_name) {
+							char *name = bam1_qname(p->b);
+							c = (p->qpos + 1 >= p->b->core.l_qname)? ' ' : name[p->qpos];
+						} else {
+							c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos)];
+							if (tv->is_dot && toupper(c) == toupper(rb)) c = bam1_strand(p->b)? ',' : '.';
+						}
+					}
+				} else c = p->is_refskip? (bam1_strand(p->b)? '<' : '>') : '*';
 			} else { // padding
 				if (j > p->indel) c = '*';
 				else { // insertion
-					c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos + j)];
-					if (j == 0 && !tv->is_nucl && toupper(c) == toupper(rb)) c = bam1_strand(p->b)? ',' : '.';
+					if (tv->base_for ==  TV_BASE_NUCL) {
+						if (tv->show_name) {
+							char *name = bam1_qname(p->b);
+							c = (p->qpos + j + 1 >= p->b->core.l_qname)? ' ' : name[p->qpos + j];
+						} else {
+							c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos + j)];
+							if (j == 0 && tv->is_dot && toupper(c) == toupper(rb)) c = bam1_strand(p->b)? ',' : '.';
+						}
+					} else {
+						c = bam_aux_getCSi(p->b, p->qpos + j);
+						if (tv->is_dot && '-' == bam_aux_getCEi(p->b, p->qpos + j)) c = bam1_strand(p->b)? ',' : '.';
+					}
 				}
 			}
 			if (row > TV_MIN_ALNROW && row < tv->mrow) {
 				int x;
 				attr = 0;
 				if (((p->b->core.flag&BAM_FPAIRED) && !(p->b->core.flag&BAM_FPROPER_PAIR))
-					|| (p->b->core.flag & BAM_FSECONDARY)) attr |= A_UNDERLINE;
+						|| (p->b->core.flag & BAM_FSECONDARY)) attr |= tv->my_underline(tv);
 				if (tv->color_for == TV_COLOR_BASEQ) {
 					x = bam1_qual(p->b)[p->qpos]/10 + 1;
 					if (x > 4) x = 4;
-					attr |= COLOR_PAIR(x);
+					attr |= tv->my_colorpair(tv,x);
 				} else if (tv->color_for == TV_COLOR_MAPQ) {
 					x = p->b->core.qual/10 + 1;
 					if (x > 4) x = 4;
-					attr |= COLOR_PAIR(x);
+					attr |= tv->my_colorpair(tv,x);
 				} else if (tv->color_for == TV_COLOR_NUCL) {
 					x = bam_nt16_nt4_table[bam1_seqi(bam1_seq(p->b), p->qpos)] + 5;
-					attr |= COLOR_PAIR(x);
+					attr |= tv->my_colorpair(tv,x);
+				} else if(tv->color_for == TV_COLOR_COL) {
+					x = 0;
+					switch(bam_aux_getCSi(p->b, p->qpos)) {
+						case '0': x = 0; break;
+						case '1': x = 1; break;
+						case '2': x = 2; break;
+						case '3': x = 3; break;
+						case '4': x = 4; break;
+						default: x = bam_nt16_nt4_table[bam1_seqi(bam1_seq(p->b), p->qpos)]; break;
+					}
+					x+=5;
+					attr |= tv->my_colorpair(tv,x);
+				} else if(tv->color_for == TV_COLOR_COLQ) {
+					x = bam_aux_getCQi(p->b, p->qpos);
+					if(0 == x) x = bam1_qual(p->b)[p->qpos];
+					x = x/10 + 1;
+					if (x > 4) x = 4;
+					attr |= tv->my_colorpair(tv,x);
 				}
-				attron(attr);
-				mvaddch(row, tv->ccol, bam1_strand(p->b)? tolower(c) : toupper(c));
-				attroff(attr);
+				tv->my_attron(tv,attr);
+				tv->my_mvaddch(tv,row, tv->ccol, bam1_strand(p->b)? tolower(c) : toupper(c));
+				tv->my_attroff(tv,attr);
 			}
 		}
 		c = j? '*' : rb;
 		if (c == '*') {
-			attr = COLOR_PAIR(8);
-			attron(attr);
-			mvaddch(1, tv->ccol++, c);
-			attroff(attr);
-		} else mvaddch(1, tv->ccol++, c);
+			attr = tv->my_colorpair(tv,8);
+			tv->my_attron(tv,attr);
+			tv->my_mvaddch(tv,1, tv->ccol++, c);
+			tv->my_attroff(tv,attr);
+		} else tv->my_mvaddch(tv,1, tv->ccol++, c);
 	}
 	tv->last_pos = pos;
 	return 0;
 }
 
-tview_t *tv_init(const char *fn, const char *fn_fa)
-{
-	tview_t *tv = (tview_t*)calloc(1, sizeof(tview_t));
-	tv->idx = bam_index_load(fn);
-	tv->fp = bam_open(fn, "r");
-	assert(tv->fp);
-	tv->header = bam_header_read(tv->fp);
-	tv->lplbuf = bam_lplbuf_init(tv_pl_func, tv);
-	if (fn_fa) tv->fai = fai_load(fn_fa);
-	tv->bmc = bam_maqcns_init();
-	bam_maqcns_prepare(tv->bmc);
 
-	initscr();
-	keypad(stdscr, TRUE);
-    clear();
-    noecho();
-    cbreak();
-#ifdef NCURSES_VERSION
-	getmaxyx(stdscr, tv->mrow, tv->mcol);
-#else
-	tv->mrow = 80; tv->mcol = 40;
-#endif
-	tv->wgoto = newwin(3, TV_MAX_GOTO + 10, 10, 5);
-	tv->whelp = newwin(22,40, 5, 5);
-	tv->color_for = TV_COLOR_MAPQ;
-	start_color();
-	init_pair(1, COLOR_BLUE, COLOR_BLACK);
-	init_pair(2, COLOR_GREEN, COLOR_BLACK);
-	init_pair(3, COLOR_YELLOW, COLOR_BLACK);
-	init_pair(4, COLOR_WHITE, COLOR_BLACK);
-	init_pair(5, COLOR_GREEN, COLOR_BLACK);
-	init_pair(6, COLOR_CYAN, COLOR_BLACK);
-	init_pair(7, COLOR_YELLOW, COLOR_BLACK);
-	init_pair(8, COLOR_RED, COLOR_BLACK);
-	init_pair(9, COLOR_BLUE, COLOR_BLACK);
-	return tv;
-}
 
-void tv_destroy(tview_t *tv)
-{
-	delwin(tv->wgoto); delwin(tv->whelp);
-	endwin();
-
-	bam_lplbuf_destroy(tv->lplbuf);
-	bam_maqcns_destroy(tv->bmc);
-	bam_index_destroy(tv->idx);
-	if (tv->fai) fai_destroy(tv->fai);
-	free(tv->ref);
-	bam_header_destroy(tv->header);
-	bam_close(tv->fp);
-	free(tv);
-}
 
 int tv_fetch_func(const bam1_t *b, void *data)
 {
 	tview_t *tv = (tview_t*)data;
+    if ( tv->rg_hash )
+    {
+        const uint8_t *rg = bam_aux_get(b, "RG");
+        if ( !rg ) return 0; 
+        khiter_t k = kh_get(kh_rg, tv->rg_hash, (const char*)(rg + 1));
+        if ( k == kh_end(tv->rg_hash) ) return 0;
+    }
+	if (tv->no_skip) {
+		uint32_t *cigar = bam1_cigar(b); // this is cheating...
+		int i;
+		for (i = 0; i <b->core.n_cigar; ++i) {
+			if ((cigar[i]&0xf) == BAM_CREF_SKIP)
+				cigar[i] = cigar[i]>>4<<4 | BAM_CDEL;
+		}
+	}
 	bam_lplbuf_push(b, tv->lplbuf);
 	return 0;
 }
 
-int tv_draw_aln(tview_t *tv, int tid, int pos)
-{
-	int end;
+int base_draw_aln(tview_t *tv, int tid, int pos)
+	{
+	assert(tv!=NULL);
 	// reset
-	clear();
+	tv->my_clear(tv);
 	tv->curr_tid = tid; tv->left_pos = pos;
 	tv->last_pos = tv->left_pos - 1;
 	tv->ccol = 0;
@@ -186,7 +252,10 @@ int tv_draw_aln(tview_t *tv, int tid, int pos)
 	if (tv->fai) {
 		char *str;
 		if (tv->ref) free(tv->ref);
+		assert(tv->curr_tid>=0);
+		
 		str = (char*)calloc(strlen(tv->header->target_name[tv->curr_tid]) + 30, 1);
+		assert(str!=NULL);
 		sprintf(str, "%s:%d-%d", tv->header->target_name[tv->curr_tid], tv->left_pos + 1, tv->left_pos + tv->mcol);
 		tv->ref = fai_fetch(tv->fai, str, &tv->l_ref);
 		free(str);
@@ -195,121 +264,104 @@ int tv_draw_aln(tview_t *tv, int tid, int pos)
 	bam_lplbuf_reset(tv->lplbuf);
 	bam_fetch(tv->fp, tv->idx, tv->curr_tid, tv->left_pos, tv->left_pos + tv->mcol, tv, tv_fetch_func);
 	bam_lplbuf_push(0, tv->lplbuf);
+
+	while (tv->ccol < tv->mcol) {
+		int pos = tv->last_pos + 1;
+		if (pos%10 == 0 && tv->mcol - tv->ccol >= 10) tv->my_mvprintw(tv,0, tv->ccol, "%-d", pos+1);
+		tv->my_mvaddch(tv,1, tv->ccol++, (tv->ref && pos < tv->l_ref)? tv->ref[pos - tv->left_pos] : 'N');
+		++tv->last_pos;
+	}
 	return 0;
 }
 
-static void tv_win_goto(tview_t *tv, int *tid, int *pos)
-{
-	char str[256];
-	int i, l = 0;
-	wborder(tv->wgoto, '|', '|', '-', '-', '+', '+', '+', '+');
-    mvwprintw(tv->wgoto, 1, 2, "Goto: ");
-    for (;;) {
-		int c = wgetch(tv->wgoto);
-		wrefresh(tv->wgoto);
-		if (c == KEY_BACKSPACE || c == '\010' || c == '\177') {
-			--l;
-		} else if (c == KEY_ENTER || c == '\012' || c == '\015') {
-			int _tid = -1, _beg, _end;
-			bam_parse_region(tv->header, str, &_tid, &_beg, &_end);
-			if (_tid >= 0) {
-				*tid = _tid; *pos = _beg;
-				return;
-			}
-		} else if (isgraph(c)) {
-			if (l < TV_MAX_GOTO) str[l++] = c;
-		} else if (c == '\027') l = 0;
-		else if (c == '\033') return;
-		str[l] = '\0';
-		for (i = 0; i < TV_MAX_GOTO; ++i) mvwaddch(tv->wgoto, 1, 8 + i, ' ');
-		mvwprintw(tv->wgoto, 1, 8, "%s", str);
-    }
-}
 
-static void tv_win_help(tview_t *tv) {
-    int r = 1;
-	WINDOW *win = tv->whelp;
-    wborder(win, '|', '|', '-', '-', '+', '+', '+', '+');
-    mvwprintw(win, r++, 2, "        -=-    Help    -=- ");
-    r++;
-    mvwprintw(win, r++, 2, "?          This window");
-    mvwprintw(win, r++, 2, "Arrows     Small scroll movement");
-    mvwprintw(win, r++, 2, "h,j,k,l    Small scroll movement");
-    mvwprintw(win, r++, 2, "H,J,K,L    Large scroll movement");
-    mvwprintw(win, r++, 2, "ctrl-H     Scroll 1k left");
-    mvwprintw(win, r++, 2, "ctrl-L     Scroll 1k right");
-    mvwprintw(win, r++, 2, "space      Scroll one screen");
-    mvwprintw(win, r++, 2, "backspace  Scroll back one screen");
-    mvwprintw(win, r++, 2, "g          Go to specific location");
-    mvwprintw(win, r++, 2, "b          Color for base quality");
-    mvwprintw(win, r++, 2, "m          Color for mapping qual");
-    mvwprintw(win, r++, 2, "n          Color for nucleotide");
-    mvwprintw(win, r++, 2, ".          Toggle on/off dot view");
-    mvwprintw(win, r++, 2, "q          Exit");
-	r++;
-	mvwprintw(win, r++, 2, "Underline:      Secondary or orphan");
-	mvwprintw(win, r++, 2, "Blue:    0-9    Green: 10-19");
-	mvwprintw(win, r++, 2, "Yellow: 20-29   White: >=30");
-    wrefresh(win);
-    wgetch(win);
-}
 
-void tv_loop(tview_t *tv)
+
+static void error(const char *format, ...)
 {
-	int tid, pos;
-	tid = tv->curr_tid; pos = tv->left_pos;
-	while (1) {
-		int c = getch();
-		switch (c) {
-		case '?': tv_win_help(tv); break;
-		case '\033':
-		case 'q': goto end_loop;
-		case 'g': tv_win_goto(tv, &tid, &pos); break;
-		case 'b': tv->color_for = TV_COLOR_BASEQ; break;
-		case 'm': tv->color_for = TV_COLOR_MAPQ; break;
-		case 'n': tv->color_for = TV_COLOR_NUCL; break;
-		case KEY_LEFT:
-		case 'h': --pos; break;
-		case KEY_RIGHT:
-		case 'l': ++pos; break;
-		case KEY_SLEFT:
-		case 'H': pos -= 20; break;
-		case KEY_SRIGHT:
-		case 'L': pos += 20; break;
-		case '.': tv->is_nucl = !tv->is_nucl; break;
-		case '\010': pos -= 1000; break;
-		case '\014': pos += 1000; break;
-		case ' ': pos += tv->mcol; break;
-		case KEY_UP:
-		case 'j': --tv->row_shift; break;
-		case KEY_DOWN:
-		case 'k': ++tv->row_shift; break;
-		case KEY_BACKSPACE:
-		case '\177': pos -= tv->mcol; break;
-#ifdef KEY_RESIZE
-		case KEY_RESIZE: getmaxyx(stdscr, tv->mrow, tv->mcol); break;
-#endif
-		default: continue;
-		}
-		if (pos < 0) pos = 0;
-		if (tv->row_shift < 0) tv->row_shift = 0;
-		tv_draw_aln(tv, tid, pos);
-	}
-end_loop:
-	return;
+    if ( !format )
+    {
+        fprintf(stderr, "\n");
+        fprintf(stderr, "Usage: bamtk tview [options] <aln.bam> [ref.fasta]\n");
+        fprintf(stderr, "Options:\n");
+        fprintf(stderr, "   -p chr:pos      go directly to this position\n");
+        fprintf(stderr, "   -s STR          display only reads from this sample or group\n");
+        fprintf(stderr, "   -d display      (H)tml or (C)urses or (T)ext \n");
+        fprintf(stderr, "\n\n");
+    }
+    else
+    {
+        va_list ap;
+        va_start(ap, format);
+        vfprintf(stderr, format, ap);
+        va_end(ap);
+    }
+    exit(-1);
 }
 
+enum dipsay_mode {display_ncurses,display_html,display_text};
+extern tview_t* curses_tv_init(const char *fn, const char *fn_fa, const char *samples);
+extern tview_t* html_tv_init(const char *fn, const char *fn_fa, const char *samples);
+extern tview_t* text_tv_init(const char *fn, const char *fn_fa, const char *samples);
 int bam_tview_main(int argc, char *argv[])
-{
-	tview_t *tv;
-	if (argc == 1) {
-		fprintf(stderr, "Usage: bamtk tview <aln.bam> [ref.fasta]\n");
-		return 1;
+	{
+	int view_mode=display_ncurses;
+	tview_t* tv=NULL;
+    char *samples=NULL, *position=NULL;
+    int c;
+    while ((c = getopt(argc, argv, "s:p:d:")) >= 0) {
+        switch (c) {
+            case 's': samples=optarg; break;
+            case 'p': position=optarg; break;
+            case 'd':
+            	{
+            	switch(optarg[0])
+            		{
+            		case 'H': case 'h': view_mode=display_html;break;
+            		case 'T': case 't': view_mode=display_text;break;
+            		case 'C': case 'c': view_mode=display_ncurses;break;
+			default: view_mode=display_ncurses;break;
+			}
+            	break;
+            	}
+            default: error(NULL);
+        }
+    }
+	if (argc==optind) error(NULL);
+	
+	switch(view_mode)
+		{
+		case display_ncurses:
+			{
+			tv = curses_tv_init(argv[optind], (optind+1>=argc)? 0 : argv[optind+1], samples);
+			break;
+			}
+		case display_text:
+			{
+			tv = text_tv_init(argv[optind], (optind+1>=argc)? 0 : argv[optind+1], samples);
+			break;
+			}
+		case display_html:
+			{
+			tv = html_tv_init(argv[optind], (optind+1>=argc)? 0 : argv[optind+1], samples);
+			break;
+			}
+		}
+	if(tv==NULL)
+		{
+		error("cannot create view");
+		return EXIT_FAILURE;
+		}
+	
+	if ( position )
+	   	 {
+		int _tid = -1, _beg, _end;
+		bam_parse_region(tv->header, position, &_tid, &_beg, &_end);
+		if (_tid >= 0) { tv->curr_tid = _tid; tv->left_pos = _beg; }
+	    	}
+	tv->my_drawaln(tv, tv->curr_tid, tv->left_pos);
+	tv->my_loop(tv);
+	tv->my_destroy(tv);
+	
+	return EXIT_SUCCESS;
 	}
-	tv = tv_init(argv[1], (argc == 2)? 0 : argv[2]);
-	tv_draw_aln(tv, 0, 0);
-	tv_loop(tv);
-	tv_destroy(tv);
-	return 0;
-}
-#endif