--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PsiCLASS-1.0.2/samtools-0.1.19/bam_tview.c	Fri Mar 26 16:52:45 2021 +0000
@@ -0,0 +1,368 @@
+#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;
+	}