Updated samtools to 0.1.19

[rsem.git] / sam / bam_tview.h

diff --git a/sam/bam_tview.h b/sam/bam_tview.h
new file mode 100644 (file)
index 0000000..80f0464
--- /dev/null
+++ b/sam/bam_tview.h
@@ -0,0 +1,75 @@
+#ifndef BAM_TVIEW_H
+#define BAM_TVIEW_H
+
+#include <ctype.h>
+#include <assert.h>
+#include <string.h>
+#include <math.h>
+#include <unistd.h>
+#include <stdarg.h>
+#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 (*my_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);
+    int (*my_drawaln)(struct AbstractTview*,int,int);
+    int (*my_loop)(struct AbstractTview*);
+    int (*my_underline)(struct AbstractTview*);
+} 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 base_draw_aln(tview_t *tv, int tid, int pos);
+
+typedef struct Tixel
+       {
+       int ch;
+       int attributes;
+       }tixel_t;
+
+#endif
+