X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam_tview.c;h=4eea955ce05574051c60591dac6a44b5a1ad5edc;hp=be2579ca0ee28f59792e863bd102b2f7937566d0;hb=e582623cf8c4778c7dc792318635821d3c494b0d;hpb=b27e00385f41769d03a8cca4dbd71275fc9fa906 diff --git a/bam_tview.c b/bam_tview.c index be2579c..4eea955 100644 --- a/bam_tview.c +++ b/bam_tview.c @@ -1,12 +1,28 @@ -#ifndef _NO_CURSES +#undef _HAVE_CURSES + +#if _CURSES_LIB == 0 +#elif _CURSES_LIB == 1 #include -#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 +#define _HAVE_CURSES +#else +#warning "_CURSES_LIB is not 0, 1 or 2; tview is NOT compiled" +#endif + +#ifdef _HAVE_CURSES #include #include #include +#include #include "bam.h" #include "faidx.h" -#include "bam_maqcns.h" +#include "bam2bcf.h" char bam_aux_getCEi(bam1_t *b, int i); char bam_aux_getCSi(bam1_t *b, int i); @@ -35,14 +51,15 @@ typedef struct { bamFile fp; int curr_tid, left_pos; faidx_t *fai; - bam_maqcns_t *bmc; + bcf_callaux_t *bca; - 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; 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; @@ -50,16 +67,31 @@ 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); - // print consensus - call = bam_maqcns_call(n, pl, tv->bmc); + if (pos%10 == 0 && tv->mcol - tv->ccol >= 10) mvprintw(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<>28&0xf]; - i = (call>>8&0xff)/10+1; + c = ",ACMGRSVTWYHKDBN"[call>>16&0xf]; + i = (call&0xffff)/10+1; if (i > 4) i = 4; attr |= COLOR_PAIR(i); if (c == toupper(rb)) c = '.'; @@ -85,20 +117,28 @@ 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)? ',' : '.'; + } 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 = 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 c = p->is_refskip? (bam1_strand(p->b)? '<' : '>') : '*'; } 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)? ',' : '.'; } @@ -160,30 +200,26 @@ 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->idx = bam_index_load(fn); + if (tv->idx == 0) exit(1); tv->lplbuf = bam_lplbuf_init(tv_pl_func, tv); if (fn_fa) tv->fai = fai_load(fn_fa); - tv->bmc = bam_maqcns_init(); + tv->bca = bcf_call_init(0.83, 13); tv->ins = 1; - bam_maqcns_prepare(tv->bmc); initscr(); keypad(stdscr, TRUE); 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->whelp = newwin(29, 40, 5, 5); tv->color_for = TV_COLOR_MAPQ; start_color(); init_pair(1, COLOR_BLUE, COLOR_BLACK); @@ -204,7 +240,7 @@ void tv_destroy(tview_t *tv) endwin(); bam_lplbuf_destroy(tv->lplbuf); - bam_maqcns_destroy(tv->bmc); + bcf_call_destroy(tv->bca); bam_index_destroy(tv->idx); if (tv->fai) fai_destroy(tv->fai); free(tv->ref); @@ -216,6 +252,14 @@ void tv_destroy(tview_t *tv) 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 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; } @@ -240,12 +284,19 @@ 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; } static void tv_win_goto(tview_t *tv, int *tid, int *pos) { - char str[256]; + char str[256], *p; int i, l = 0; wborder(tv->wgoto, '|', '|', '-', '-', '+', '+', '+', '+'); mvwprintw(tv->wgoto, 1, 2, "Goto: "); @@ -256,10 +307,18 @@ static void tv_win_goto(tview_t *tv, int *tid, int *pos) --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; + if (str[0] == '=') { + _beg = strtol(str+1, &p, 10) - 1; + if (_beg > 0) { + *pos = _beg; + return; + } + } else { + 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; @@ -292,6 +351,8 @@ 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, "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"); @@ -310,17 +371,19 @@ 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': case 'q': goto end_loop; + case '/': case 'g': tv_win_goto(tv, &tid, &pos); break; case 'm': tv->color_for = TV_COLOR_MAPQ; break; case 'b': tv->color_for = TV_COLOR_BASEQ; 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: @@ -342,9 +405,7 @@ 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; @@ -368,12 +429,12 @@ int bam_tview_main(int argc, char *argv[]) tv_destroy(tv); return 0; } -#else // #ifdef NCURSES_VERSION -#warning "The ncurses library is unavailable; tview is disabled." +#else // #ifdef _HAVE_CURSES +#include +#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; } -#endif -#endif // #ifndef _NO_CURSES +#endif // #ifdef _HAVE_CURSES