Imported Upstream version 0.5

[pysam.git] / samtools / bam_tview.c.pysam.c

diff --git a/samtools/bam_tview.c.pysam.c b/samtools/bam_tview.c.pysam.c
index 3709702b57d0bae19adf98a24f926be3ae910227..d4abf671f143fe803c9919ecf6dc7c85b1a7e01a 100644 (file)
--- a/samtools/bam_tview.c.pysam.c
+++ b/samtools/bam_tview.c.pysam.c
@@ -21,10 +21,9 @@
 #include <ctype.h>
 #include <assert.h>
 #include <string.h>
-#include <math.h>
 #include "bam.h"
 #include "faidx.h"
-#include "bam2bcf.h"
+#include "bam_maqcns.h"
 
 char bam_aux_getCEi(bam1_t *b, int i);
 char bam_aux_getCSi(bam1_t *b, int i);
@@ -53,7 +52,7 @@ typedef struct {
        bamFile fp;
        int curr_tid, left_pos;
        faidx_t *fai;
-       bcf_callaux_t *bca;
+       bam_maqcns_t *bmc;
 
        int ccol, last_pos, row_shift, base_for, color_for, is_dot, l_ref, ins, no_skip, show_name;
        char *ref;
@@ -61,7 +60,6 @@ typedef struct {
 
 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;
@@ -74,26 +72,11 @@ int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void
                mvaddch(1, tv->ccol++, c);
        }
        if (pos%10 == 0 && tv->mcol - tv->ccol >= 10) mvprintw(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);
-       }
+       // print consensus
+       call = bam_maqcns_call(n, pl, tv->bmc);
        attr = A_UNDERLINE;
-       c = ",ACMGRSVTWYHKDBN"[call>>16&0xf];
-       i = (call&0xffff)/10+1;
+       c = ",ACMGRSVTWYHKDBN"[call>>28&0xf];
+       i = (call>>8&0xff)/10+1;
        if (i > 4) i = 4;
        attr |= COLOR_PAIR(i);
        if (c == toupper(rb)) c = '.';
@@ -210,8 +193,9 @@ tview_t *tv_init(const char *fn, const char *fn_fa)
        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->bmc = bam_maqcns_init();
        tv->ins = 1;
+       bam_maqcns_prepare(tv->bmc);
 
        initscr();
        keypad(stdscr, TRUE);
@@ -242,7 +226,7 @@ void tv_destroy(tview_t *tv)
        endwin();
 
        bam_lplbuf_destroy(tv->lplbuf);
-       bcf_call_destroy(tv->bca);
+       bam_maqcns_destroy(tv->bmc);
        bam_index_destroy(tv->idx);
        if (tv->fai) fai_destroy(tv->fai);
        free(tv->ref);