* samtools-0.1.5-9 (r405)

[samtools.git] / bam_tview.c

diff --git a/bam_tview.c b/bam_tview.c
index 5858e3b40c5999aed6ac09d91e681de4cb55a8c1..c6a31cd7fc73d20797d3c1d7e1d0fd4545cf8942 100644 (file)
--- a/bam_tview.c
+++ b/bam_tview.c
@@ -1,5 +1,21 @@
-#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>
@@ -7,6 +23,10 @@
 #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
@@ -45,11 +65,11 @@ 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) 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;
@@ -156,7 +176,9 @@ 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);
@@ -170,11 +192,8 @@ tview_t *tv_init(const char *fn, const char *fn_fa)
        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;
@@ -233,6 +252,13 @@ 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) 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;
 }
 
@@ -303,7 +329,6 @@ void tv_loop(tview_t *tv)
        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':
@@ -335,9 +360,7 @@ void tv_loop(tview_t *tv)
                        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;
@@ -361,4 +384,11 @@ int bam_tview_main(int argc, char *argv[])
        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