Imported Upstream version 0.1.6~dfsg

[samtools.git] / bam_tview.c

diff --git a/bam_tview.c b/bam_tview.c
index be2579ca0ee28f59792e863bd102b2f7937566d0..4c121e7cbfa012ac0c3fa61d574f03c893e6d271 100644 (file)
--- a/bam_tview.c
+++ b/bam_tview.c
@@ -1,6 +1,21 @@
-#ifndef _NO_CURSES
+#undef _HAVE_CURSES
+
+#if _CURSES_LIB == 0
+#elif _CURSES_LIB == 1

 #include <curses.h>
 #include <curses.h>

-#ifdef NCURSES_VERSION
+#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 <ctype.h>
 #include <assert.h>
 #include <string.h>


@@ -37,7 +52,7 @@ typedef struct {
        faidx_t *fai;
        bam_maqcns_t *bmc;
 
        faidx_t *fai;
        bam_maqcns_t *bmc;
 

-       int ccol, last_pos, row_shift, base_for, color_for, is_dot, l_ref, ins;
+       int ccol, last_pos, row_shift, base_for, color_for, is_dot, l_ref, ins, no_skip, show_name;

        char *ref;
 } tview_t;
 
        char *ref;
 } tview_t;
 


@@ -50,11 +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) {
        // 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);
        }
                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;
        // print consensus
        call = bam_maqcns_call(n, pl, tv->bmc);
        attr = A_UNDERLINE;


@@ -85,20 +100,28 @@ int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void
                                                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)? ',' : '.';
                                                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 {
-                                               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 {
+                                               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 = '*';
                        } else { // padding
                                if (j > p->indel) c = '*';
                                else { // insertion
                                        if (tv->base_for ==  TV_BASE_NUCL) {
                                        }
                                } else c = '*';
                        } else { // padding
                                if (j > p->indel) c = '*';
                                else { // insertion
                                        if (tv->base_for ==  TV_BASE_NUCL) {

-                                               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 {
+                                               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)? ',' : '.';
                                        }
                                                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)? ',' : '.';
                                        }


@@ -177,13 +200,10 @@ tview_t *tv_init(const char *fn, const char *fn_fa)
        clear();
        noecho();
        cbreak();
        clear();
        noecho();
        cbreak();

-#ifdef NCURSES_VERSION
+       tv->mrow = 24; tv->mcol = 80;

        getmaxyx(stdscr, tv->mrow, tv->mcol);
        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->wgoto = newwin(3, TV_MAX_GOTO + 10, 10, 5);

-       tv->whelp = newwin(27, 40, 5, 5);
+       tv->whelp = newwin(29, 40, 5, 5);

        tv->color_for = TV_COLOR_MAPQ;
        start_color();
        init_pair(1, COLOR_BLUE, COLOR_BLACK);
        tv->color_for = TV_COLOR_MAPQ;
        start_color();
        init_pair(1, COLOR_BLUE, COLOR_BLACK);


@@ -216,6 +236,14 @@ void tv_destroy(tview_t *tv)
 int tv_fetch_func(const bam1_t *b, void *data)
 {
        tview_t *tv = (tview_t*)data;
 int tv_fetch_func(const bam1_t *b, void *data)
 {
        tview_t *tv = (tview_t*)data;

+       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;
 }
        bam_lplbuf_push(b, tv->lplbuf);
        return 0;
 }


@@ -240,6 +268,13 @@ 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);
        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;
 }
 
        return 0;
 }
 


@@ -292,6 +327,8 @@ static void tv_win_help(tview_t *tv) {
        mvwprintw(win, r++, 2, "c          Color for cs color");
        mvwprintw(win, r++, 2, "z          Color for cs qual");
        mvwprintw(win, r++, 2, ".          Toggle on/off dot view");
        mvwprintw(win, r++, 2, "c          Color for cs color");
        mvwprintw(win, r++, 2, "z          Color for cs qual");
        mvwprintw(win, r++, 2, ".          Toggle on/off dot view");

+       mvwprintw(win, r++, 2, "s          Toggle on/off ref skip");
+       mvwprintw(win, r++, 2, "r          Toggle on/off rd name");

        mvwprintw(win, r++, 2, "N          Turn on nt view");
        mvwprintw(win, r++, 2, "C          Turn on cs view");
        mvwprintw(win, r++, 2, "i          Toggle on/off ins");
        mvwprintw(win, r++, 2, "N          Turn on nt view");
        mvwprintw(win, r++, 2, "C          Turn on cs view");
        mvwprintw(win, r++, 2, "i          Toggle on/off ins");


@@ -310,7 +347,6 @@ void tv_loop(tview_t *tv)
        tid = tv->curr_tid; pos = tv->left_pos;
        while (1) {
                int c = getch();
        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':
                switch (c) {
                        case '?': tv_win_help(tv); break;
                        case '\033':


@@ -321,6 +357,8 @@ void tv_loop(tview_t *tv)
                        case 'n': tv->color_for = TV_COLOR_NUCL; break;
                        case 'c': tv->color_for = TV_COLOR_COL; break;
                        case 'z': tv->color_for = TV_COLOR_COLQ; break;
                        case 'n': tv->color_for = TV_COLOR_NUCL; break;
                        case 'c': tv->color_for = TV_COLOR_COL; break;
                        case 'z': tv->color_for = TV_COLOR_COLQ; break;

+                       case 's': tv->no_skip = !tv->no_skip; break;
+                       case 'r': tv->show_name = !tv->show_name; break;

                        case KEY_LEFT:
                        case 'h': --pos; break;
                        case KEY_RIGHT:
                        case KEY_LEFT:
                        case 'h': --pos; break;
                        case KEY_RIGHT:


@@ -342,9 +380,7 @@ void tv_loop(tview_t *tv)
                        case 'k': ++tv->row_shift; break;
                        case KEY_BACKSPACE:
                        case '\177': pos -= tv->mcol; break;
                        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;
                        case KEY_RESIZE: getmaxyx(stdscr, tv->mrow, tv->mcol); break;

-#endif

                        default: continue;
                }
                if (pos < 0) pos = 0;
                        default: continue;
                }
                if (pos < 0) pos = 0;


@@ -368,12 +404,12 @@ int bam_tview_main(int argc, char *argv[])
        tv_destroy(tv);
        return 0;
 }
        tv_destroy(tv);
        return 0;
 }

-#else // #ifdef NCURSES_VERSION
-#warning "The ncurses library is unavailable; tview is disabled."
+#else // #ifdef _HAVE_CURSES
+#include <stdio.h>
+#warning "No curses library is available; 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;
 }
 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
-#endif // #ifndef _NO_CURSES
+#endif // #ifdef _HAVE_CURSES