From 5363b2dc566f2fa73938efecc4a067efd5e33d42 Mon Sep 17 00:00:00 2001
From: walaj <jwala@broadinstitute.org>
Date: Thu, 20 Oct 2016 19:46:30 -0400
Subject: [PATCH] merging with snowman version

---
 SeqLib/BamReader.h | 5 ++---
 bwa                | 2 +-
 htslib             | 2 +-
 3 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/SeqLib/BamReader.h b/SeqLib/BamReader.h
index 548b1a047..8cbfefdbd 100644
--- a/SeqLib/BamReader.h
+++ b/SeqLib/BamReader.h
@@ -264,10 +264,9 @@ class BamReader {
 
   GRC m_region; ///< Regions to access
 
- private:
+  _BamMap m_bams; ///< store the htslib file pointers etc to BAM files
 
-  // store the file pointers etc to BAM files
-  _BamMap m_bams;
+ private:
 
   // hold the reference for CRAM reading
   std::string m_cram_reference;
diff --git a/bwa b/bwa
index c02766e3c..fbd4dbc03 160000
--- a/bwa
+++ b/bwa
@@ -1 +1 @@
-Subproject commit c02766e3c34ac3f4af9842e20a54b7f9f4b36d0b
+Subproject commit fbd4dbc03904eccd71cdca8cac7aa48da749c19c
diff --git a/htslib b/htslib
index 5163833ed..0f298ce22 160000
--- a/htslib
+++ b/htslib
@@ -1 +1 @@
-Subproject commit 5163833ede355f8c2a6788780c55d7598279e767
+Subproject commit 0f298ce22c5c825c506129bf242348a31630c382