#include <ctype.h>
#include <assert.h>
#include <string.h>
+#include <math.h>
#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);
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, no_skip, show_name;
char *ref;
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;
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);
+ { // 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<<a1)<<16 | (int)((p[1]<p[2]?p[1]:p[2]) - p[0] + .499);
+ else if (p[2] < p[1] && p[2] < p[0]) call = (1<<a2)<<16 | (int)((p[0]<p[1]?p[0]:p[1]) - p[2] + .499);
+ else call = (1<<a1|1<<a2)<<16 | (int)((p[0]<p[2]?p[0]:p[2]) - p[1] + .499);
+ }
attr = A_UNDERLINE;
- c = ",ACMGRSVTWYHKDBN"[call>>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 = '.';
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 {
{
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);
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);
int c = wgetch(tv->wgoto);
wrefresh(tv->wgoto);
if (c == KEY_BACKSPACE || c == '\010' || c == '\177') {
- --l;
+ if(l > 0) --l;
} else if (c == KEY_ENTER || c == '\012' || c == '\015') {
int _tid = -1, _beg, _end;
if (str[0] == '=') {