added the phase command

[samtools.git] / bam_md.c

diff --git a/bam_md.c b/bam_md.c
index a1a6d669885a278d6f330b8afb07e324cd92b310..20b1913efa09ce796392885b0f4b831c8c759f4a 100644 (file)
--- a/bam_md.c
+++ b/bam_md.c
@@ -223,8 +223,10 @@ int bam_prob_realn_core(bam1_t *b, const char *ref, int flag)
                s = calloc(c->l_qseq, 1);
                for (i = 0; i < c->l_qseq; ++i) s[i] = bam_nt16_nt4_table[bam1_seqi(seq, i)];
                r = calloc(xe - xb, 1);
-               for (i = xb; i < xe; ++i)
+               for (i = xb; i < xe; ++i) {
+                       if (ref[i] == 0) { xe = i; break; }
                        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);
                kpa_glocal(r, xe-xb, s, c->l_qseq, qual, &conf, state, q);
@@ -313,7 +315,8 @@ int bam_fillmd(int argc, char *argv[])
                fprintf(stderr, "         -b       compressed BAM output\n");
                fprintf(stderr, "         -S       the input is SAM with header\n");
                fprintf(stderr, "         -A       modify the quality string\n");
-               fprintf(stderr, "         -r       read-independent local realignment\n\n");
+               fprintf(stderr, "         -r       compute the BQ tag (without -A) or cap baseQ by BAQ (with -A)\n");
+               fprintf(stderr, "         -E       extended BAQ for better sensitivity but lower specificity\n\n");
                return 1;
        }
        fp = samopen(argv[optind], mode_r, 0);