Separate kaln and kprobaln as I am preparing further changes. At

[samtools.git] / bam_md.c

diff --git a/bam_md.c b/bam_md.c
index f65b845b5d594980d4b4dba36122672c71b19cc9..0377226773262dadca7185a12fa9aec755810e4f 100644 (file)
--- a/bam_md.c
+++ b/bam_md.c
@@ -7,6 +7,7 @@
 #include "sam.h"
 #include "kstring.h"
 #include "kaln.h"
+#include "kprobaln.h"
 
 void bam_fillmd1_core(bam1_t *b, char *ref, int is_equal, int max_nm)
 {
@@ -166,7 +167,7 @@ int bam_prob_realn(bam1_t *b, const char *ref)
        int k, i, bw, x, y, yb, ye, xb, xe;
        uint32_t *cigar = bam1_cigar(b);
        bam1_core_t *c = &b->core;
-       ka_probpar_t conf = ka_probpar_def;
+       kpa_par_t conf = kpa_par_def;
        // find the start and end of the alignment
        if (c->flag & BAM_FUNMAP) return -1;
        x = c->pos, y = 0, yb = ye = xb = xe = -1;
@@ -201,7 +202,7 @@ int bam_prob_realn(bam1_t *b, const char *ref)
                        r[i-xb] = bam_nt16_nt4_table[bam_nt16_table[(int)ref[i]]];
                state = calloc(c->l_qseq, sizeof(int));
                q = calloc(c->l_qseq, 1);
-               ka_prob_glocal(r, xe-xb, s, c->l_qseq, qual, &conf, state, q);
+               kpa_glocal(r, xe-xb, s, c->l_qseq, qual, &conf, state, q);
                for (k = 0, x = c->pos, y = 0; k < c->n_cigar; ++k) {
                        int op = cigar[k]&0xf, l = cigar[k]>>4;
                        if (op == BAM_CMATCH) {
@@ -275,7 +276,6 @@ int bam_fillmd(int argc, char *argv[])
                                        fprintf(stderr, "[bam_fillmd] fail to find sequence '%s' in the reference.\n",
                                                        fp->header->target_name[tid]);
                        }
-//                     if (is_realn) bam_realn(b, ref);
                        if (is_realn) bam_prob_realn(b, ref);
                        if (capQ > 10) {
                                int q = bam_cap_mapQ(b, ref, capQ);