From 3880f184334b2b5afe27de5c5a0f344cdcff1ef9 Mon Sep 17 00:00:00 2001 From: Pierre Lindenbaum Date: Thu, 24 Jan 2013 21:40:40 +0100 Subject: [PATCH 1/1] ... --- Makefile | 10 +- bam_tview.c | 422 ++++++++++----------------------------------- bam_tview.h | 71 ++++++++ bam_tview_curses.c | 234 +++++++++++++++++++++++++ bam_tview_curses.h | 16 ++ 5 files changed, 418 insertions(+), 335 deletions(-) create mode 100644 bam_tview.h create mode 100644 bam_tview_curses.c create mode 100644 bam_tview_curses.h diff --git a/Makefile b/Makefile index dbd90af..c7ac7fd 100644 --- a/Makefile +++ b/Makefile @@ -9,7 +9,8 @@ LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \ AOBJS= bam_tview.o bam_plcmd.o sam_view.o \ bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o \ bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o \ - cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o + cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o \ + bam_tview_curses.o PROG= samtools INCLUDES= -I. SUBDIRS= . bcftools misc @@ -46,10 +47,10 @@ samtools:lib-recur $(AOBJS) $(CC) $(CFLAGS) -o $@ $(AOBJS) $(LDFLAGS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread razip:razip.o razf.o $(KNETFILE_O) - $(CC) $(CFLAGS) -o $@ razf.o razip.o $(KNETFILE_O) -lz + $(CC) $(CFLAGS) -o $@ $^ -lz bgzip:bgzip.o bgzf.o $(KNETFILE_O) - $(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o $(KNETFILE_O) -lz -lpthread + $(CC) $(CFLAGS) -o $@ $^ -lz -lpthread bgzf.o:bgzf.c bgzf.h $(CC) -c $(CFLAGS) $(DFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@ @@ -62,7 +63,8 @@ bam_pileup.o:bam.h razf.h ksort.h bam_plcmd.o:bam.h faidx.h bcftools/bcf.h bam2bcf.h bam_index.o:bam.h khash.h ksort.h razf.h bam_endian.h bam_lpileup.o:bam.h ksort.h -bam_tview.o:bam.h faidx.h +bam_tview.o:bam.h faidx.h bam_tview.h +bam_tview_curses.o:bam.h faidx.h bam_tview.h bam_tview_curses.h bam_sort.o:bam.h ksort.h razf.h bam_md.o:bam.h faidx.h sam_header.o:sam_header.h khash.h diff --git a/bam_tview.c b/bam_tview.c index f8a1f2c..165eadd 100644 --- a/bam_tview.c +++ b/bam_tview.c @@ -1,67 +1,77 @@ -#undef _HAVE_CURSES - -#if _CURSES_LIB == 0 -#elif _CURSES_LIB == 1 -#include -#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 -#include "bam.h" -#include "faidx.h" -#include "bam2bcf.h" -#include "sam_header.h" -#include "khash.h" - -KHASH_MAP_INIT_STR(kh_rg, const char *) +#include "bam_tview.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 +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; + fprintf(stderr,"Opening '%s'\n",fn); + 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); + fprintf(stderr,"Opening header '%s'\n",fn); + 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) exit(1); + 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; -#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 + 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); + } + } -#define TV_BASE_NUCL 0 -#define TV_BASE_COLOR_SPACE 1 + return 0; + } -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; - bcf_callaux_t *bca; +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 ccol, last_pos, row_shift, base_for, color_for, is_dot, l_ref, ins, no_skip, show_name; - char *ref; - khash_t(kh_rg) *rg_hash; -} tview_t; int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data) { @@ -73,11 +83,11 @@ 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) { - if (i%10 == 0 && tv->mcol - tv->ccol >= 10) mvprintw(0, tv->ccol, "%-d", i+1); + 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'; - mvaddch(1, tv->ccol++, c); + tv->my_mvaddch(tv,1, tv->ccol++, c); } - if (pos%10 == 0 && tv->mcol - tv->ccol >= 10) mvprintw(0, tv->ccol, "%-d", pos+1); + 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; @@ -95,15 +105,15 @@ int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void else if (p[2] < p[1] && p[2] < p[0]) call = (1<>16&0xf]; i = (call&0xffff)/10+1; if (i > 4) i = 4; - attr |= COLOR_PAIR(i); + attr |= tv->my_colorpair(tv,i); if (c == toupper(rb)) c = '.'; - attron(attr); - mvaddch(2, tv->ccol, c); - attroff(attr); + 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) { @@ -153,7 +163,7 @@ int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void 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; + || (p->b->core.flag & BAM_FSECONDARY)) attr |= BAM_TVIEW_UNDERLINE; if (tv->color_for == TV_COLOR_BASEQ) { x = bam1_qual(p->b)[p->qpos]/10 + 1; if (x > 4) x = 4; @@ -184,101 +194,25 @@ int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void 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); + 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 = COLOR_PAIR(8); - attron(attr); - mvaddch(1, tv->ccol++, c); - attroff(attr); - } else mvaddch(1, tv->ccol++, c); + 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; } -tview_t *tv_init(const char *fn, const char *fn_fa, char *samples) -{ - 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->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(-1); - } - } - 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); - 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); - free(tv); -} int tv_fetch_func(const bam1_t *b, void *data) { @@ -303,9 +237,10 @@ int tv_fetch_func(const bam1_t *b, void *data) } int tv_draw_aln(tview_t *tv, int tid, int pos) -{ + { + assert(tv!=NULL); // reset - clear(); + tv->my_clear(tv); tv->curr_tid = tid; tv->left_pos = pos; tv->last_pos = tv->left_pos - 1; tv->ccol = 0; @@ -313,7 +248,10 @@ int tv_draw_aln(tview_t *tv, int tid, int pos) 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); @@ -325,188 +263,10 @@ int tv_draw_aln(tview_t *tv, int tid, int pos) 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'); + 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 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') { - if(l > 0) --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; -} - -void error(const char *format, ...) -{ - if ( !format ) - { - fprintf(stderr, "\n"); - fprintf(stderr, "Usage: bamtk tview [options] [ref.fasta]\n"); - fprintf(stderr, "Options:\n"); - fprintf(stderr, " -p chr:pos go directly to this position\n"); - fprintf(stderr, " -s STR display only reads from this sample or grou\n"); - fprintf(stderr, "\n\n"); - } - else - { - va_list ap; - va_start(ap, format); - vfprintf(stderr, format, ap); - va_end(ap); - } - exit(-1); -} - - -int bam_tview_main(int argc, char *argv[]) -{ - tview_t *tv; - char *samples=NULL, *position=NULL; - int c; - while ((c = getopt(argc, argv, "s:p:")) >= 0) { - switch (c) { - case 's': samples=optarg; break; - case 'p': position=optarg; break; - default: error(NULL); - } - } - if (argc==optind) error(NULL); - tv = tv_init(argv[optind], (optind+1>=argc)? 0 : argv[optind+1], samples); - 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_draw_aln(tv, tv->curr_tid, tv->left_pos); - tv_loop(tv); - tv_destroy(tv); - return 0; -} -#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 // #ifdef _HAVE_CURSES diff --git a/bam_tview.h b/bam_tview.h new file mode 100644 index 0000000..2f395ff --- /dev/null +++ b/bam_tview.h @@ -0,0 +1,71 @@ +#ifndef BAM_TVIEW_H +#define BAM_TVIEW_H + +#include +#include +#include +#include +#include +#include "bam.h" +#include "faidx.h" +#include "bam2bcf.h" +#include "sam_header.h" +#include "khash.h" + +KHASH_MAP_INIT_STR(kh_rg, const char *) + +typedef struct AbstractTview { + int mrow, mcol; + + bam_index_t *idx; + bam_lplbuf_t *lplbuf; + bam_header_t *header; + bamFile fp; + int curr_tid, left_pos; + faidx_t *fai; + 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; + khash_t(kh_rg) *rg_hash; + /* callbacks */ + void (*destroy)(struct AbstractTview* ); + void (*my_mvprintw)(struct AbstractTview* ,int,int,const char*,...); + void (*my_mvaddch)(struct AbstractTview*,int,int,int); + void (*my_attron)(struct AbstractTview*,int); + void (*my_attroff)(struct AbstractTview*,int); + void (*my_clear)(struct AbstractTview*); + int (*my_colorpair)(struct AbstractTview*,int); +} tview_t; + + +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 + +int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data); +int base_tv_init(tview_t*,const char *fn, const char *fn_fa, const char *samples); +void base_tv_destroy(tview_t*); + +int tv_draw_aln(tview_t *tv, int tid, int pos); + + +enum { + BAM_TVIEW_UNDERLINE + }; + +#endif + diff --git a/bam_tview_curses.c b/bam_tview_curses.c new file mode 100644 index 0000000..571633c --- /dev/null +++ b/bam_tview_curses.c @@ -0,0 +1,234 @@ +#include "bam_tview_curses.h" + + + + +static void curses_tv_destroy(tview_t* base) + { + curses_tview_t* tv=(curses_tview_t*)base; + + + delwin(tv->wgoto); delwin(tv->whelp); + endwin(); + + base_tv_destroy(base); + + free(tv); + } + +curses_tview_t* curses_tv_init(const char *fn, const char *fn_fa, const char *samples) + { + curses_tview_t *tv = (curses_tview_t*)calloc(1, sizeof(curses_tview_t)); + tview_t* base=(tview_t*)tv; + if(tv==0) + { + fprintf(stderr,"Calloc failed\n"); + return 0; + } + + base_tv_init(base,fn,fn_fa,samples); + /* initialize callbacks */ + base->destroy=curses_tv_destroy; + + initscr(); + keypad(stdscr, TRUE); + clear(); + noecho(); + cbreak(); + + getmaxyx(stdscr, base->mrow, base->mcol); + tv->wgoto = newwin(3, TV_MAX_GOTO + 10, 10, 5); + tv->whelp = newwin(29, 40, 5, 5); + + 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; + } + + +static void tv_win_goto(curses_tview_t *tv, int *tid, int *pos) + { + char str[256], *p; + int i, l = 0; + tview_t *base=(tview_t*)tv; + 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') { + if(l > 0) --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(base->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(curses_tview_t *tv) { + int r = 1; + tview_t* base=(tview_t*)base; + 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(curses_tview_t *CTV) +{ + int tid, pos; + tview_t* tv=(tview_t*)CTV; + tid = tv->curr_tid; pos = tv->left_pos; + while (1) { + int c = getch(); + switch (c) { + case '?': tv_win_help(CTV); break; + case '\033': + case 'q': goto end_loop; + case '/': + case 'g': tv_win_goto(CTV, &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; +} + +void error(const char *format, ...) +{ + if ( !format ) + { + fprintf(stderr, "\n"); + fprintf(stderr, "Usage: bamtk tview [options] [ref.fasta]\n"); + fprintf(stderr, "Options:\n"); + fprintf(stderr, " -p chr:pos go directly to this position\n"); + fprintf(stderr, " -s STR display only reads from this sample or grou\n"); + fprintf(stderr, "\n\n"); + } + else + { + va_list ap; + va_start(ap, format); + vfprintf(stderr, format, ap); + va_end(ap); + } + exit(-1); +} + + +int bam_tview_main(int argc, char *argv[]) +{ + curses_tview_t *CTV; + tview_t* tv=NULL; + char *samples=NULL, *position=NULL; + int c; + while ((c = getopt(argc, argv, "s:p:")) >= 0) { + switch (c) { + case 's': samples=optarg; break; + case 'p': position=optarg; break; + default: error(NULL); + } + } + if (argc==optind) error(NULL); + CTV = curses_tv_init(argv[optind], (optind+1>=argc)? 0 : argv[optind+1], samples); + tv=(tview_t*)CTV; + 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_draw_aln(tv, tv->curr_tid, tv->left_pos); + tv_loop(CTV); + tv->destroy(tv); + free(tv); + return 0; +} diff --git a/bam_tview_curses.h b/bam_tview_curses.h new file mode 100644 index 0000000..1d616d6 --- /dev/null +++ b/bam_tview_curses.h @@ -0,0 +1,16 @@ +#ifndef BAM_TVIEW_CURSES_H +#define BAM_TVIEW_CURSES_H + +#include +#include "bam_tview.h" + +typedef struct CursesTview { + struct AbstractTview* view; + WINDOW *wgoto, *whelp; + } curses_tview_t; + + +curses_tview_t* curses_tv_init(const char *fn, const char *fn_fa,const char *samples); + +#endif + -- 2.39.2