From 292b79f701c7501dbfd8f3d6ba0ec7e34f907276 Mon Sep 17 00:00:00 2001
From: Jeremiah Wala <jwala@broadinstitute.org>
Date: Thu, 18 Jun 2015 12:44:49 -0400
Subject: [PATCH] updates to walker

---
 .gitignore             | 26 ++++++++++++++++++++++++++
 src/VariantBamWalker.h |  2 +-
 src/variant.cpp        |  2 +-
 3 files changed, 28 insertions(+), 2 deletions(-)
 create mode 100644 .gitignore

diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..41db960
--- /dev/null
+++ 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
index 8273080..8d71ee0 100644
--- 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
index 6dbdbdf..9b3524a 100644
--- 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);