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[samtools.git] / bam_md.c

diff --git a/bam_md.c b/bam_md.c
index d2c84dcccd084c3399bf94ac6085af8902eb8532..746b2c03e6f471593721ce55f69c43ef04845923 100644 (file)
--- a/bam_md.c
+++ b/bam_md.c
@@ -200,7 +200,7 @@ int bam_realn(bam1_t *b, const char *ref)
                } else if (op == BAM_CSOFT_CLIP) y += ol;
                else if (op == BAM_CREF_SKIP) x += ol;
        }
-       if (score < 0) return -1; // no high scoring segments
+       if (q[1] < 0) return -1; // no high scoring segments
        endx = x - 1;
        // find the left boundary
        for (k = c->n_cigar - 1, score = max = 0, x = x-1, y = y-1; k >= 0; --k) {
@@ -229,7 +229,7 @@ int bam_realn(bam1_t *b, const char *ref)
                } else if (op == BAM_CSOFT_CLIP) y -= ol;
                else if (op == BAM_CREF_SKIP) x -= ol;
        }
-       if (q[1] - q[0] < 15) return -1; // the high-scoring segment is too short
+       if (q[0] < 0 || q[1] - q[0] < 15) return -1; // the high-scoring segment is too short
        // modify CIGAR
        n_cigar = 0;
        cigar = calloc(c->n_cigar + 4, 4);
@@ -263,16 +263,16 @@ int bam_realn(bam1_t *b, const char *ref)
 
 int bam_fillmd(int argc, char *argv[])
 {
-       int c, is_equal = 0, tid = -2, ret, len, is_bam_out, is_sam_in, is_uncompressed, max_nm = 0, is_realn, is_capQ;
+       int c, is_equal = 0, tid = -2, ret, len, is_bam_out, is_sam_in, is_uncompressed, max_nm = 0, is_realn, capQ = 0;
        samfile_t *fp, *fpout = 0;
        faidx_t *fai;
        char *ref = 0, mode_w[8], mode_r[8];
        bam1_t *b;
 
-       is_bam_out = is_sam_in = is_uncompressed = is_realn = is_capQ = 0;
+       is_bam_out = is_sam_in = is_uncompressed = is_realn = 0;
        mode_w[0] = mode_r[0] = 0;
        strcpy(mode_r, "r"); strcpy(mode_w, "w");
-       while ((c = getopt(argc, argv, "reubSCn:")) >= 0) {
+       while ((c = getopt(argc, argv, "reubSC:n:")) >= 0) {
                switch (c) {
                case 'r': is_realn = 1; break;
                case 'e': is_equal = 1; break;
@@ -280,7 +280,7 @@ int bam_fillmd(int argc, char *argv[])
                case 'u': is_uncompressed = is_bam_out = 1; break;
                case 'S': is_sam_in = 1; break;
                case 'n': max_nm = atoi(optarg); break;
-               case 'C': is_capQ = 1; break;
+               case 'C': capQ = atoi(optarg); break;
                default: fprintf(stderr, "[bam_fillmd] unrecognized option '-%c'\n", c); return 1;
                }
        }
@@ -319,8 +319,8 @@ int bam_fillmd(int argc, char *argv[])
                                                        fp->header->target_name[tid]);
                        }
                        if (is_realn) bam_realn(b, ref);
-                       if (is_capQ) {
-                               int q = bam_cap_mapQ(b, ref, 40);
+                       if (capQ > 10) {
+                               int q = bam_cap_mapQ(b, ref, capQ);
                                if (b->core.qual > q) b->core.qual = q;
                        }
                        if (ref) bam_fillmd1_core(b, ref, is_equal, max_nm);