Handle unused variable warning.

ARUP-NGS · May 20, 2016 · f5064dc · f5064dc
1 parent 9a2038e
commit f5064dc
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Showing 4 changed files with 6 additions and 3 deletions.
diff --git a/src/bmf_depth.cpp b/src/bmf_depth.cpp
@@ -271,7 +271,9 @@ namespace BMF {
         std::vector<uint64_t> singleton_capture_counts(n);
         kstring_t cov_str{0, 0, nullptr};
         kstring_t str{0};
+#if !NDEBUG
         const int n_lines = dlib::count_bed_lines(bedpath);
+#endif
         while (ks_getuntil(ks, KS_SEP_LINE, &str, &dret) >= 0) {
             char *p, *q;
             int tid, start, stop, pos, region_len, arr_ind;

diff --git a/src/bmf_mark.cpp b/src/bmf_mark.cpp
@@ -1,3 +1,4 @@
+#include <assert.h>
 #include <getopt.h>
 #include "dlib/bam_util.h"
 #include "dlib/cstr_util.h"

diff --git a/src/bmf_rsq.cpp b/src/bmf_rsq.cpp
@@ -283,8 +283,9 @@ namespace BMF {
                 } else {
                     LOG_DEBUG("About to output bam\n");
                     uint8_t *data;
-                    if((data = bam_aux_get(stack->a[i], "MU")) != nullptr)
-                        bam_aux_del(stack->a[i], data);
+                    for(const char *tag: {"MU", "ms", "LM"})
+                        if((data = bam_aux_get(stack->a[i], tag)) != nullptr)
+                            bam_aux_del(stack->a[i], data);
                     sam_write1(settings->out, settings->hdr, stack->a[i]);
                 }
                 bam_destroy1(stack->a[i]), stack->a[i] = nullptr;

diff --git a/src/bmf_vetter.cpp b/src/bmf_vetter.cpp
@@ -276,7 +276,6 @@ namespace BMF {
                         continue; // Only handle simple SNVs
                     }
                     if(!dlib::vcf_bed_test(vrec, aux->bed) && !aux->vet_all) {
-                        if(aux->write_outside_bed) bcf_write(aux->vcf_ofp, aux->vcf_header, vrec);
                         continue; // Only handle simple SNVs
                     }
                     /*