#include <assert.h>
#include "bam_tview.h"
int base_tv_init(tview_t* tv,const char *fn, const char *fn_fa, const char *samples)
{
assert(tv!=NULL);
assert(fn!=NULL);
tv->mrow = 24; tv->mcol = 80;
tv->color_for = TV_COLOR_MAPQ;
tv->is_dot = 1;
tv->fp = bam_open(fn, "r");
if(tv->fp==0)
{
fprintf(stderr,"bam_open %s. %s\n", fn,fn_fa);
exit(EXIT_FAILURE);
}
bgzf_set_cache_size(tv->fp, 8 * 1024 *1024);
assert(tv->fp);
tv->header = bam_header_read(tv->fp);
if(tv->header==0)
{
fprintf(stderr,"Cannot read '%s'.\n", fn);
exit(EXIT_FAILURE);
}
tv->idx = bam_index_load(fn);
if (tv->idx == 0)
{
fprintf(stderr,"Cannot read index for '%s'.\n", fn);
exit(EXIT_FAILURE);
}
tv->lplbuf = bam_lplbuf_init(tv_pl_func, tv);
if (fn_fa) tv->fai = fai_load(fn_fa);
tv->bca = bcf_call_init(0.83, 13);
tv->ins = 1;
if ( samples )
{
if ( !tv->header->dict ) tv->header->dict = sam_header_parse2(tv->header->text);
void *iter = tv->header->dict;
const char *key, *val;
int n = 0;
tv->rg_hash = kh_init(kh_rg);
while ( (iter = sam_header2key_val(iter, "RG","ID","SM", &key, &val)) )
{
if ( !strcmp(samples,key) || (val && !strcmp(samples,val)) )
{
khiter_t k = kh_get(kh_rg, tv->rg_hash, key);
if ( k != kh_end(tv->rg_hash) ) continue;
int ret;
k = kh_put(kh_rg, tv->rg_hash, key, &ret);
kh_value(tv->rg_hash, k) = val;
n++;
}
}
if ( !n )
{
fprintf(stderr,"The sample or read group \"%s\" not present.\n", samples);
exit(EXIT_FAILURE);
}
}
return 0;
}
void base_tv_destroy(tview_t* tv)
{
bam_lplbuf_destroy(tv->lplbuf);
bcf_call_destroy(tv->bca);
bam_index_destroy(tv->idx);
if (tv->fai) fai_destroy(tv->fai);
free(tv->ref);
bam_header_destroy(tv->header);
bam_close(tv->fp);
}
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;
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) tv->my_mvprintw(tv,0, tv->ccol, "%-d", i+1);
c = tv->ref? tv->ref[i - tv->left_pos] : 'N';
tv->my_mvaddch(tv,1, tv->ccol++, c);
}
if (pos%10 == 0 && tv->mcol - tv->ccol >= 10) tv->my_mvprintw(tv,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<<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 = tv->my_underline(tv);
c = ",ACMGRSVTWYHKDBN"[call>>16&0xf];
i = (call&0xffff)/10+1;
if (i > 4) i = 4;
attr |= tv->my_colorpair(tv,i);
if (c == toupper(rb)) c = '.';
tv->my_attron(tv,attr);
tv->my_mvaddch(tv,2, tv->ccol, c);
tv->my_attroff(tv,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))) {
// 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 |= tv->my_underline(tv);
if (tv->color_for == TV_COLOR_BASEQ) {
x = bam1_qual(p->b)[p->qpos]/10 + 1;
if (x > 4) x = 4;
attr |= tv->my_colorpair(tv,x);
} else if (tv->color_for == TV_COLOR_MAPQ) {
x = p->b->core.qual/10 + 1;
if (x > 4) x = 4;
attr |= tv->my_colorpair(tv,x);
} else if (tv->color_for == TV_COLOR_NUCL) {
x = bam_nt16_nt4_table[bam1_seqi(bam1_seq(p->b), p->qpos)] + 5;
attr |= tv->my_colorpair(tv,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 |= tv->my_colorpair(tv,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 |= tv->my_colorpair(tv,x);
}
tv->my_attron(tv,attr);
tv->my_mvaddch(tv,row, tv->ccol, bam1_strand(p->b)? tolower(c) : toupper(c));
tv->my_attroff(tv,attr);
}
}
c = j? '*' : rb;
if (c == '*') {
attr = tv->my_colorpair(tv,8);
tv->my_attron(tv,attr);
tv->my_mvaddch(tv,1, tv->ccol++, c);
tv->my_attroff(tv,attr);
} else tv->my_mvaddch(tv,1, tv->ccol++, c);
}
tv->last_pos = pos;
return 0;
}
int tv_fetch_func(const bam1_t *b, void *data)
{
tview_t *tv = (tview_t*)data;
if ( tv->rg_hash )
{
const uint8_t *rg = bam_aux_get(b, "RG");
if ( !rg ) return 0;
khiter_t k = kh_get(kh_rg, tv->rg_hash, (const char*)(rg + 1));
if ( k == kh_end(tv->rg_hash) ) return 0;
}
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 base_draw_aln(tview_t *tv, int tid, int pos)
{
assert(tv!=NULL);
// reset
tv->my_clear(tv);
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);
assert(tv->curr_tid>=0);
str = (char*)calloc(strlen(tv->header->target_name[tv->curr_tid]) + 30, 1);
assert(str!=NULL);
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) tv->my_mvprintw(tv,0, tv->ccol, "%-d", pos+1);
tv->my_mvaddch(tv,1, tv->ccol++, (tv->ref && pos < tv->l_ref)? tv->ref[pos - tv->left_pos] : 'N');
++tv->last_pos;
}
return 0;
}
static void error(const char *format, ...)
{
if ( !format )
{
fprintf(stderr, "\n");
fprintf(stderr, "Usage: bamtk tview [options] <aln.bam> [ref.fasta]\n");
fprintf(stderr, "Options:\n");
fprintf(stderr, " -d display output as (H)tml or (C)urses or (T)ext \n");
fprintf(stderr, " -p chr:pos go directly to this position\n");
fprintf(stderr, " -s STR display only reads from this sample or group\n");
fprintf(stderr, "\n\n");
}
else
{
va_list ap;
va_start(ap, format);
vfprintf(stderr, format, ap);
va_end(ap);
}
exit(-1);
}
enum dipsay_mode {display_ncurses,display_html,display_text};
extern tview_t* curses_tv_init(const char *fn, const char *fn_fa, const char *samples);
extern tview_t* html_tv_init(const char *fn, const char *fn_fa, const char *samples);
extern tview_t* text_tv_init(const char *fn, const char *fn_fa, const char *samples);
int bam_tview_main(int argc, char *argv[])
{
int view_mode=display_ncurses;
tview_t* tv=NULL;
char *samples=NULL, *position=NULL;
int c;
while ((c = getopt(argc, argv, "s:p:d:")) >= 0) {
switch (c) {
case 's': samples=optarg; break;
case 'p': position=optarg; break;
case 'd':
{
switch(optarg[0])
{
case 'H': case 'h': view_mode=display_html;break;
case 'T': case 't': view_mode=display_text;break;
case 'C': case 'c': view_mode=display_ncurses;break;
default: view_mode=display_ncurses;break;
}
break;
}
default: error(NULL);
}
}
if (argc==optind) error(NULL);
switch(view_mode)
{
case display_ncurses:
{
tv = curses_tv_init(argv[optind], (optind+1>=argc)? 0 : argv[optind+1], samples);
break;
}
case display_text:
{
tv = text_tv_init(argv[optind], (optind+1>=argc)? 0 : argv[optind+1], samples);
break;
}
case display_html:
{
tv = html_tv_init(argv[optind], (optind+1>=argc)? 0 : argv[optind+1], samples);
break;
}
}
if(tv==NULL)
{
error("cannot create view");
return EXIT_FAILURE;
}
if ( position )
{
int _tid = -1, _beg, _end;
bam_parse_region(tv->header, position, &_tid, &_beg, &_end);
if (_tid >= 0) { tv->curr_tid = _tid; tv->left_pos = _beg; }
}
tv->my_drawaln(tv, tv->curr_tid, tv->left_pos);
tv->my_loop(tv);
tv->my_destroy(tv);
return EXIT_SUCCESS;
}
