* samtools-0.1.8-15 (r379)

 * allow to change capQ parameter in calmd

diff --git a/bam_md.c b/bam_md.c
index f3f7e228a62c18e5d1beba2686cb2095da385002..746b2c03e6f471593721ce55f69c43ef04845923 100644 (file)
--- a/bam_md.c
+++ b/bam_md.c
@@ -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);

diff --git a/bamtk.c b/bamtk.c
index 0ee62bc448b97661cd8a171fb089493aaeab8380..56ba7322b58d5d8e1ac3f85d019dadb82ec73496 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.8-14 (r727)"
+#define PACKAGE_VERSION "0.1.8-15 (r739)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);