Add filtering on MAPQ to smoother

Parsoa · Nov 27, 2023 · 7894b19 · 7894b19
1 parent ef12b20
commit 7894b19
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Showing 2 changed files with 5 additions and 0 deletions.
diff --git a/config.hpp b/config.hpp
@@ -24,6 +24,8 @@ static const char INDEX_USAGE_MESSAGE[] =
 
 static const char SMOOTH_USAGE_MESSAGE[] =
   "SVDSS smooth --reference <reference> --bam <bam>\n"
+  "      --acc <INT>                      maximum percentage of errors in alignment (default: 0.02)\n"
+  "      --min-mapq                       minimum mapping quality (default: 20)\n"
   "      --threads <INT>                  number of threads to use (default: 4)\n"
   "      --help                           print help message\n";
 

diff --git a/smoother.cpp b/smoother.cpp
@@ -390,6 +390,9 @@ bool Smoother::load_batch_bam(int p) {
         alignment->core.flag & BAM_FSUPPLEMENTARY ||
         alignment->core.flag & BAM_FSECONDARY)
       continue;
+    if (alignment->core.qual < config->min_mapq) {
+      continue;
+    }
     if (alignment->core.l_qseq < 2) {
       // FIXME: why do we need this?
       spdlog::warn(