-#ifndef _NO_CURSES
+#undef _HAVE_CURSES
+
+#if _CURSES_LIB == 0
+#elif _CURSES_LIB == 1
#include <curses.h>
+#ifndef NCURSES_VERSION
+#warning "_CURSES_LIB=1 but NCURSES_VERSION not defined; tview is NOT compiled"
+#else
+#define _HAVE_CURSES
+#endif
+#elif _CURSES_LIB == 2
+#include <xcurses.h>
+#define _HAVE_CURSES
+#else
+#warning "_CURSES_LIB is not 0, 1 or 2; tview is NOT compiled"
+#endif
+
+#ifdef _HAVE_CURSES
#include <ctype.h>
#include <assert.h>
#include <string.h>
#include "faidx.h"
#include "bam_maqcns.h"
+char bam_aux_getCEi(bam1_t *b, int i);
+char bam_aux_getCSi(bam1_t *b, int i);
+char bam_aux_getCQi(bam1_t *b, int i);
+
#define TV_MIN_ALNROW 2
#define TV_MAX_GOTO 40
#define TV_LOW_MAPQ 10
// 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) mvprintw(0, tv->ccol, "%-d", i+1);
c = tv->ref? tv->ref[i - tv->left_pos] : 'N';
mvaddch(1, tv->ccol++, c);
}
- if (pos%10 == 0) mvprintw(0, tv->ccol, "%-d", pos+1);
+ if (pos%10 == 0 && tv->mcol - tv->ccol >= 10) mvprintw(0, tv->ccol, "%-d", pos+1);
// print consensus
call = bam_maqcns_call(n, pl, tv->bmc);
attr = A_UNDERLINE;
tview_t *tv_init(const char *fn, const char *fn_fa)
{
tview_t *tv = (tview_t*)calloc(1, sizeof(tview_t));
+ tv->is_dot = 1;
tv->idx = bam_index_load(fn);
+ if (tv->idx == 0) exit(1);
tv->fp = bam_open(fn, "r");
+ bgzf_set_cache_size(tv->fp, 8 * 1024 *1024);
assert(tv->fp);
tv->header = bam_header_read(tv->fp);
tv->lplbuf = bam_lplbuf_init(tv_pl_func, tv);
clear();
noecho();
cbreak();
-#ifdef NCURSES_VERSION
+ tv->mrow = 24; tv->mcol = 80;
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(27, 40, 5, 5);
tv->color_for = TV_COLOR_MAPQ;
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) mvprintw(0, tv->ccol, "%-d", pos+1);
+ mvaddch(1, tv->ccol++, (tv->ref && pos < tv->l_ref)? tv->ref[pos - tv->left_pos] : 'N');
+ ++tv->last_pos;
+ }
return 0;
}
tid = tv->curr_tid; pos = tv->left_pos;
while (1) {
int c = getch();
- if(256 < c) {c = 1 + (c%256);} // Terminal was displaying ctrl-H as 263 via ssh from Mac OS X 10.5 computer
switch (c) {
case '?': tv_win_help(tv); break;
case '\033':
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;
tv_destroy(tv);
return 0;
}
-#endif
+#else // #ifdef NCURSES_VERSION
+#warning "The ncurses library is unavailable; tview is disabled."
+int bam_tview_main(int argc, char *argv[])
+{
+ fprintf(stderr, "[bam_tview_main] The ncurses library is unavailable; tview is not compiled.\n");
+ return 1;
+}
+#endif // #ifdef _HAVE_CURSES