From f5064dc66fcf507370e7cfac2a8a8a2c018f0862 Mon Sep 17 00:00:00 2001 From: dnephi Date: Fri, 20 May 2016 13:13:55 -0600 Subject: [PATCH] Handle unused variable warning. --- src/bmf_depth.cpp | 2 ++ src/bmf_mark.cpp | 1 + src/bmf_rsq.cpp | 5 +++-- src/bmf_vetter.cpp | 1 - 4 files changed, 6 insertions(+), 3 deletions(-) diff --git a/src/bmf_depth.cpp b/src/bmf_depth.cpp index 24690556..67799926 100644 --- a/src/bmf_depth.cpp +++ b/src/bmf_depth.cpp @@ -271,7 +271,9 @@ namespace BMF { std::vector 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 index c9f4afeb..5d0ad66f 100644 --- a/src/bmf_mark.cpp +++ b/src/bmf_mark.cpp @@ -1,3 +1,4 @@ +#include #include #include "dlib/bam_util.h" #include "dlib/cstr_util.h" diff --git a/src/bmf_rsq.cpp b/src/bmf_rsq.cpp index e0f86951..18741597 100644 --- 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 index 50f10546..9b4d179a 100644 --- 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 } /*