--- /dev/null
+#include "pysam.h"
+
+#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 "bam.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
+
+#define TV_COLOR_MAPQ 0
+#define TV_COLOR_BASEQ 1
+#define TV_COLOR_NUCL 2
+#define TV_COLOR_COL 3
+#define TV_COLOR_COLQ 4
+
+#define TV_BASE_NUCL 0
+#define TV_BASE_COLOR_SPACE 1
+
+typedef struct {
+ int mrow, mcol;
+ WINDOW *wgoto, *whelp;
+
+ 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, 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)
+{
+ tview_t *tv = (tview_t*)data;
+ int i, j, c, rb, attr, max_ins = 0;
+ uint32_t call = 0;
+ if (pos < tv->left_pos || tv->ccol > tv->mcol) return 0; // out of screen
+ // 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 && 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 && 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;
+ c = ",ACMGRSVTWYHKDBN"[call>>28&0xf];
+ i = (call>>8&0xff)/10+1;
+ if (i > 4) i = 4;
+ attr |= COLOR_PAIR(i);
+ if (c == toupper(rb)) c = '.';
+ attron(attr);
+ mvaddch(2, tv->ccol, c);
+ attroff(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) {
+ for (i = 0; i < n; ++i) {
+ const bam_pileup1_t *p = pl + i;
+ int row = TV_MIN_ALNROW + p->level - tv->row_shift;
+ if (j == 0) {
+ if (!p->is_del) {
+ if (tv->base_for == TV_BASE_COLOR_SPACE &&
+ (c = bam_aux_getCSi(p->b, p->qpos))) {
+ 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
+ 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;
+ 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);
+ } else if (tv->color_for == TV_COLOR_MAPQ) {
+ x = p->b->core.qual/10 + 1;
+ if (x > 4) x = 4;
+ attr |= COLOR_PAIR(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);
+ } 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 |= COLOR_PAIR(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 |= COLOR_PAIR(x);
+ }
+ attron(attr);
+ mvaddch(row, tv->ccol, bam1_strand(p->b)? tolower(c) : toupper(c));
+ attroff(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);
+ }
+ 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->is_dot = 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->ins = 1;
+ bam_maqcns_prepare(tv->bmc);
+
+ initscr();
+ keypad(stdscr, TRUE);
+ clear();
+ noecho();
+ cbreak();
+ tv->mrow = 24; tv->mcol = 80;
+ getmaxyx(stdscr, tv->mrow, tv->mcol);
+ tv->wgoto = newwin(3, TV_MAX_GOTO + 10, 10, 5);
+ tv->whelp = newwin(29, 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->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)
+{
+ // reset
+ clear();
+ tv->curr_tid = tid; tv->left_pos = pos;
+ tv->last_pos = tv->left_pos - 1;
+ tv->ccol = 0;
+ // print ref and consensus
+ if (tv->fai) {
+ char *str;
+ if (tv->ref) free(tv->ref);
+ str = (char*)calloc(strlen(tv->header->target_name[tv->curr_tid]) + 30, 1);
+ 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);
+ }
+ // draw aln
+ 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], *p;
+ 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;
+ 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;
+ } 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, "m Color for mapping qual");
+ mvwprintw(win, r++, 2, "n Color for nucleotide");
+ mvwprintw(win, r++, 2, "b Color for base quality");
+ 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, "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)
+{
+ 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 '/':
+ 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:
+ case 'l': ++pos; break;
+ case KEY_SLEFT:
+ case 'H': pos -= 20; break;
+ case KEY_SRIGHT:
+ case 'L': pos += 20; break;
+ case '.': tv->is_dot = !tv->is_dot; break;
+ case 'N': tv->base_for = TV_BASE_NUCL; break;
+ case 'C': tv->base_for = TV_BASE_COLOR_SPACE; break;
+ case 'i': tv->ins = !tv->ins; 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;
+ case KEY_RESIZE: getmaxyx(stdscr, tv->mrow, tv->mcol); break;
+ 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;
+}
+
+int bam_tview_main(int argc, char *argv[])
+{
+ tview_t *tv;
+ if (argc == 1) {
+ fprintf(pysamerr, "Usage: bamtk tview <aln.bam> [ref.fasta]\n");
+ return 1;
+ }
+ tv = tv_init(argv[1], (argc == 2)? 0 : argv[2]);
+ tv_draw_aln(tv, 0, 0);
+ tv_loop(tv);
+ tv_destroy(tv);
+ return 0;
+}
+#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(pysamerr, "[bam_tview_main] The ncurses library is unavailable; tview is not compiled.\n");
+ return 1;
+}
+#endif // #ifdef _HAVE_CURSES
projects / pysam.git / blobdiff