updates to walker

walaj · Jun 18, 2015 · 292b79f · 292b79f
1 parent cc67161
commit 292b79f
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Showing 3 changed files with 28 additions and 2 deletions.
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,26 @@
+SVSim*
+[#]*[#]
+.\#*
+*~
+*.csv
+*.o
+*.gif
+.*
+Test
+autom4te.cache
+.Rhistory
+.in
+.deps*
+html
+latex
+config.log
+tmp*
+libhts.*
+libsnowtools.a
+libaho*
+libbwa.a
+example*
+tabix
+htsfile
+bgzip
+back*
diff --git a/src/VariantBamWalker.h b/src/VariantBamWalker.h
@@ -16,7 +16,7 @@ class VariantBamWalker: public SnowTools::BamWalker
 
   void TrackSeenRead(Read &r);
 
-  void printMessage(const SnowTools::ReadCount &rc_main, const Read &r) const;
+  void printMessage(const SnowTools::ReadCount &rc_main, const BamRead &r) const;
 
  private:
 

diff --git a/src/variant.cpp b/src/variant.cpp
@@ -162,7 +162,7 @@ int main(int argc, char** argv) {
   if (opt::counts_only || opt::counts_file.length())
     walk.setCountAllRules();
 
-  // open the output file
+  // open the output BAM/CRAM. If we already set SAM, this does nothing
   if (!opt::counts_only)
     walk.OpenWriteBam(opt::out);