Make tview (and bits of pileup) work with 64 bit positions

bam_lpileup.c

@@ -100,7 +100,7 @@ void bam_lplbuf_reset(bam_lplbuf_t *buf)
     buf->n_nodes = 0;
 }
 
-static int tview_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data)
+static int tview_func(uint32_t tid, hts_pos_t pos, int n, const bam_pileup1_t *pl, void *data)
 {
     bam_lplbuf_t *tv = (bam_lplbuf_t*)data;
     freenode_t *p;

bam_lpileup.h

@@ -33,7 +33,7 @@ typedef struct __bam_lplbuf_t bam_lplbuf_t;
 
 #ifndef BAM_PILEUP_F_DEFINED
 #define BAM_PILEUP_F_DEFINED
-typedef int (*bam_pileup_f)(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data);
+typedef int (*bam_pileup_f)(uint32_t tid, hts_pos_t pos, int n, const bam_pileup1_t *pl, void *data);
 #endif //BAM_PILEUP_F_DEFINED
 
 

bam_plbuf.c

@@ -58,11 +58,12 @@ void bam_plbuf_destroy(bam_plbuf_t *buf)
 
 int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf)
 {
-    int ret, n_plp, tid, pos;
+    int ret, n_plp, tid;
+    hts_pos_t pos;
     const bam_pileup1_t *plp;
     ret = bam_plp_push(buf->iter, b);
     if (ret < 0) return ret;
-    while ((plp = bam_plp_next(buf->iter, &tid, &pos, &n_plp)) != 0)
+    while ((plp = bam_plp64_next(buf->iter, &tid, &pos, &n_plp)) != 0)
         buf->func(tid, pos, n_plp, plp, buf->data);
     return 0;
 }

bam_plbuf.h

@@ -29,7 +29,7 @@ DEALINGS IN THE SOFTWARE.  */
 
 #ifndef BAM_PILEUP_F_DEFINED
 #define BAM_PILEUP_F_DEFINED
-typedef int (*bam_pileup_f)(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data);
+typedef int (*bam_pileup_f)(uint32_t tid, hts_pos_t pos, int n, const bam_pileup1_t *pl, void *data);
 #endif //BAM_PILEUP_F_DEFINED
 
 typedef struct {

bam_tview.c

@@ -166,21 +166,24 @@ void base_tv_destroy(tview_t* tv)
 }
 
 
-int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data)
+int tv_pl_func(uint32_t tid, hts_pos_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;
+    hts_pos_t cp;
+    int i, j, c, rb, attr, max_ins = 0, interval;
     uint32_t call = 0;
     kstring_t ks = KS_INITIALIZE;
     if (pos < tv->left_pos || tv->ccol > tv->mcol) return 0; // out of screen
     // print reference
     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';
+    for (cp = tv->last_pos + 1; cp < pos; ++cp) {
+        interval = cp < 1000000000 ? 10 : 20;
+        if (cp%interval == 0 && tv->mcol - tv->ccol >= 10) tv->my_mvprintw(tv,0, tv->ccol, "%-"PRIhts_pos, cp+1);
+        c = tv->ref? tv->ref[cp - 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);
+    interval = pos < 1000000000 ? 10 : 20;
+    if (pos%interval == 0 && tv->mcol - tv->ccol >= 10) tv->my_mvprintw(tv,0, tv->ccol, "%-"PRIhts_pos, pos+1);
     { // call consensus
         bcf_callret1_t bcr;
         memset(&bcr, 0, sizeof bcr);
@@ -342,7 +345,7 @@ static int tv_push_aln(const bam1_t *b, tview_t *tv)
     return 0;
 }
 
-int base_draw_aln(tview_t *tv, int tid, int pos)
+int base_draw_aln(tview_t *tv, int tid, hts_pos_t pos)
 {
     assert(tv!=NULL);
     // reset
@@ -359,8 +362,8 @@ int base_draw_aln(tview_t *tv, int tid, int pos)
         const char *ref_name = sam_hdr_tid2name(tv->header, tv->curr_tid);
         str = (char*)calloc(strlen(ref_name) + 30, 1);
         assert(str!=NULL);
-        sprintf(str, "%s:%d-%d", ref_name, tv->left_pos + 1, tv->left_pos + tv->mcol);
-        tv->ref = fai_fetch(tv->fai, str, &tv->l_ref);
+        sprintf(str, "%s:%"PRIhts_pos"-%"PRIhts_pos, ref_name, tv->left_pos + 1, tv->left_pos + tv->mcol);
+        tv->ref = fai_fetch64(tv->fai, str, &tv->l_ref);
         free(str);
         if ( !tv->ref )
         {
@@ -378,8 +381,9 @@ int base_draw_aln(tview_t *tv, int tid, int pos)
     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);
+        hts_pos_t pos = tv->last_pos + 1;
+        int interval = pos < 1000000000 ? 10 : 20;
+        if (pos%interval == 0 && tv->mcol - tv->ccol >= 10) tv->my_mvprintw(tv,0, tv->ccol, "%-"PRIhts_pos, 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;
     }
@@ -493,8 +497,9 @@ int bam_tview_main(int argc, char *argv[])
 
     if ( position )
     {
-        int tid, beg, end;
-        char *name_lim = (char *) hts_parse_reg(position, &beg, &end);
+        int tid;
+        hts_pos_t beg, end;
+        char *name_lim = (char *) hts_parse_reg64(position, &beg, &end);
         if (name_lim) *name_lim = '\0';
         else beg = 0; // region parsing failed, but possibly a seq named "foo:a"
         tid = bam_name2id(tv->header, position);

bam_tview.h

@@ -49,11 +49,11 @@ typedef struct AbstractTview {
     bam_lplbuf_t* lplbuf;
     sam_hdr_t* header;
     samFile* 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;
+    hts_pos_t left_pos, last_pos, l_ref;
+    int curr_tid, ccol, row_shift, base_for, color_for, is_dot, ins;
     int no_skip, show_name, inverse;
     char *ref;
     /* maps @RG ID => SM (sample), in practice only used to determine whether a particular RG is in the list of allowed ones */
@@ -66,7 +66,7 @@ typedef struct AbstractTview {
     void (*my_attroff)(struct AbstractTview*,int);
     void (*my_clear)(struct AbstractTview*);
     int (*my_colorpair)(struct AbstractTview*,int);
-    int (*my_drawaln)(struct AbstractTview*,int,int);
+    int (*my_drawaln)(struct AbstractTview*,int,hts_pos_t);
     int (*my_loop)(struct AbstractTview*);
     int (*my_underline)(struct AbstractTview*);
 } tview_t;
@@ -89,12 +89,12 @@ char bam_aux_getCQi(bam1_t *b, int i);
 #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 tv_pl_func(uint32_t tid, hts_pos_t pos, int n, const bam_pileup1_t *pl, void *data);
 // Added fn_idx to arguments as index file
 int base_tv_init(tview_t*,const char *fn, const char *fn_fa, const char *fn_idx,
                  const char *samples, const htsFormat *fmt);
 void base_tv_destroy(tview_t*);
-int base_draw_aln(tview_t *tv, int tid, int pos);
+int base_draw_aln(tview_t *tv, int tid, hts_pos_t pos);
 
 typedef struct Tixel
     {

bam_tview_curses.c

@@ -136,11 +136,11 @@ static int curses_colorpair(struct AbstractTview* tv,int flag) {
     return COLOR_PAIR(flag);
 }
 
-static int curses_drawaln(struct AbstractTview* tv, int tid, int pos) {
+static int curses_drawaln(struct AbstractTview* tv, int tid, hts_pos_t pos) {
     return base_draw_aln(tv,  tid, pos);
 }
 
-static void tv_win_goto(curses_tview_t *tv, int *tid, int *pos) {
+static void tv_win_goto(curses_tview_t *tv, int *tid, hts_pos_t *pos) {
     char str[256], *p;
     int i, l = 0;
     tview_t *base=(tview_t*)tv;
@@ -153,15 +153,16 @@ static void tv_win_goto(curses_tview_t *tv, int *tid, int *pos) {
         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;
+            int _tid = -1;
+            hts_pos_t _beg, _end;
             if (str[0] == '=') {
-                _beg = strtol(str+1, &p, 10) - 1;
+                _beg = strtoll(str+1, &p, 10) - 1;
                 if (_beg > 0) {
                     *pos = _beg;
                     return;
                 }
             } else {
-                char *name_lim = (char *) hts_parse_reg(str, &_beg, &_end);
+                char *name_lim = (char *) hts_parse_reg64(str, &_beg, &_end);
                 if (name_lim) {
                     char name_terminator = *name_lim;
                     *name_lim = '\0';
@@ -234,7 +235,8 @@ static int curses_underline(tview_t* tv) {
 }
 
 static int curses_loop(tview_t* tv) {
-    int tid, pos;
+    int tid;
+    hts_pos_t pos;
     curses_tview_t *CTV=(curses_tview_t *)tv;
     tid = tv->curr_tid; pos = tv->left_pos;
     while (1) {

bam_tview_html.c

@@ -131,14 +131,14 @@ static int html_colorpair(struct AbstractTview* tv,int flag)
     return (1 << (flag));
     }
 
-static int html_drawaln(struct AbstractTview* tv, int tid, int pos)
+static int html_drawaln(struct AbstractTview* tv, int tid, hts_pos_t pos)
     {
     int y,x;
     html_tview_t* ptr=FROM_TV(tv);
     html_clear(tv);
     base_draw_aln(tv,  tid, pos);
     fputs("<html><head>",ptr->out);
-    fprintf(ptr->out,"<title>%s:%d</title>",
+    fprintf(ptr->out,"<title>%s:%"PRIhts_pos"</title>",
         sam_hdr_tid2name(tv->header, tid),
         pos+1
         );
@@ -164,7 +164,7 @@ static int html_drawaln(struct AbstractTview* tv, int tid, int pos)
 
     fputs("</head><body>",ptr->out);
 
-      fprintf(ptr->out,"<div class='tviewbody'><div class='tviewtitle'>%s:%d</div>",
+      fprintf(ptr->out,"<div class='tviewbody'><div class='tviewtitle'>%s:%"PRIhts_pos"</div>",
         sam_hdr_tid2name(tv->header, tid),
         pos+1
         );
@@ -233,7 +233,7 @@ static int html_drawaln(struct AbstractTview* tv, int tid, int pos)
 #define ANSI_UNDERLINE_SET "\033[4m"
 #define ANSI_UNDERLINE_UNSET "\033[0m"
 
-static int text_drawaln(struct AbstractTview* tv, int tid, int pos)
+static int text_drawaln(struct AbstractTview* tv, int tid, hts_pos_t pos)
     {
     int y,x;
     html_tview_t* ptr=FROM_TV(tv);