diff --git a/Makefile.am b/Makefile.am
index 1926745b2..ad2ebdd90 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -1,8 +1,8 @@
 AUTOMAKE_OPTIONS = foreign
-SUBDIRS = bwa htslib fermi-lite src
+SUBDIRS = bwa fermi-lite src
 
 install:  
-	mkdir -p lib && cp src/libseqlib.a fermi-lite/libfml.a bwa/libbwa.a htslib/libhts.a lib
+	mkdir -p lib && cp src/libseqlib.a fermi-lite/libfml.a bwa/libbwa.a lib
 
 seqtools:
 	mkdir -p bin && cd src/seqtools && make && mv seqtools ../../bin
diff --git a/Makefile.in b/Makefile.in
index bfb586701..09de47ae6 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -296,7 +296,7 @@ top_build_prefix = @top_build_prefix@
 top_builddir = @top_builddir@
 top_srcdir = @top_srcdir@
 AUTOMAKE_OPTIONS = foreign
-SUBDIRS = bwa htslib fermi-lite src
+SUBDIRS = bwa fermi-lite src
 all: config.h
 	$(MAKE) $(AM_MAKEFLAGS) all-recursive
 
@@ -778,7 +778,7 @@ uninstall-am:
 
 
 install:  
-	mkdir -p lib && cp src/libseqlib.a fermi-lite/libfml.a bwa/libbwa.a htslib/libhts.a lib
+	mkdir -p lib && cp src/libseqlib.a fermi-lite/libfml.a bwa/libbwa.a lib
 
 seqtools:
 	mkdir -p bin && cd src/seqtools && make && mv seqtools ../../bin
diff --git a/SeqLib/BamHeader.h b/SeqLib/BamHeader.h
index 12a2281b0..1d3ea3949 100644
--- a/SeqLib/BamHeader.h
+++ b/SeqLib/BamHeader.h
@@ -1,10 +1,10 @@
 #ifndef SEQLIB_BAM_HEADER_H__
 #define SEQLIB_BAM_HEADER_H__
 
-#include "htslib/htslib/hts.h"
-#include "htslib/htslib/sam.h"
-#include "htslib/htslib/bgzf.h"
-#include "htslib/htslib/kstring.h"
+#include <htslib/hts.h>
+#include <htslib/sam.h>
+#include <htslib/bgzf.h>
+#include <htslib/kstring.h>
 
 #include "SeqLib/SeqLibUtils.h"
 #include <string>
diff --git a/SeqLib/BamReader.h b/SeqLib/BamReader.h
index 9113ce8c2..50b602cd9 100644
--- a/SeqLib/BamReader.h
+++ b/SeqLib/BamReader.h
@@ -174,6 +174,11 @@ class BamReader {
    */
   bool SetMultipleRegions(const GRC& grc);
 
+  /** Return the current region index
+   * @return current region index
+   */
+  size_t GetRegionIdx();
+
   /** Return if the reader has opened the first file */
   bool IsOpen() const { if (m_bams.size()) return m_bams.begin()->second.fp.get() != NULL; return false; }
 
diff --git a/SeqLib/BamRecord.h b/SeqLib/BamRecord.h
index 3ad3b4e22..65f73a8b3 100644
--- a/SeqLib/BamRecord.h
+++ b/SeqLib/BamRecord.h
@@ -10,11 +10,11 @@
 #include <algorithm>
 
 extern "C" {
-#include "htslib/htslib/hts.h"
-#include "htslib/htslib/sam.h"
-#include "htslib/htslib/bgzf.h"
-#include "htslib/htslib/kstring.h"
-#include "htslib/htslib/faidx.h"
+#include <htslib/hts.h>
+#include <htslib/sam.h>
+#include <htslib/bgzf.h>
+#include <htslib/kstring.h>
+#include <htslib/faidx.h>
 
 }
 
@@ -665,31 +665,29 @@ class BamRecord {
   inline int32_t NumSoftClip() const {
       int32_t p = 0;
       uint32_t* c = bam_get_cigar(b);
-      for (size_t i = 0; i < b->core.n_cigar; ++i)
-	if (bam_cigar_opchr(c[i]) == 'S')
-	  p += bam_cigar_oplen(c[i]);
+
+      p = (((*c) & 0xF) == BAM_CSOFT_CLIP ? ((*c) >> 4) : 0);
+      c += b->core.n_cigar - 1;
+      p += (((*c) & 0xF) == BAM_CSOFT_CLIP ? ((*c) >> 4) : 0);
+
       return p;
-    }
+  }
 
   /** Get the number of hard clipped bases */
   inline int32_t NumHardClip() const {
       int32_t p = 0;
       uint32_t* c = bam_get_cigar(b);
-      for (size_t i = 0; i < b->core.n_cigar; ++i) 
-	if (bam_cigar_opchr(c[i]) == 'H')
-	  p += bam_cigar_oplen(c[i]);
-      return p;
-    }
 
+      p = (((*c) & 0xF) == BAM_CHARD_CLIP ? ((*c) >> 4) : 0);
+      c += b->core.n_cigar - 1;
+      p += (((*c) & 0xF) == BAM_CHARD_CLIP ? ((*c) >> 4) : 0);
+
+      return p;
+  }
 
   /** Get the number of clipped bases (hard clipped and soft clipped) */
   inline int32_t NumClip() const {
-    int32_t p = 0;
-    uint32_t* c = bam_get_cigar(b);
-    for (size_t i = 0; i < b->core.n_cigar; ++i)
-      if ( (bam_cigar_opchr(c[i]) == 'S') || (bam_cigar_opchr(c[i]) == 'H') )
-	p += bam_cigar_oplen(c[i]);
-    return p;
+      return NumSoftClip() + NumHardClip();
   }
   
   /** Get a string (Z) tag 
diff --git a/SeqLib/RefGenome.h b/SeqLib/RefGenome.h
index d76065a29..297157f8f 100644
--- a/SeqLib/RefGenome.h
+++ b/SeqLib/RefGenome.h
@@ -5,7 +5,7 @@
 #include <cstdlib>
 #include <iostream>
 
-#include "htslib/htslib/faidx.h"
+#include <htslib/faidx.h>
 
 namespace SeqLib {
   
diff --git a/bwa b/bwa
index c02766e3c..609311b88 160000
--- a/bwa
+++ b/bwa
@@ -1 +1 @@
-Subproject commit c02766e3c34ac3f4af9842e20a54b7f9f4b36d0b
+Subproject commit 609311b8842244c5c15405b3ea553455f542f786
diff --git a/htslib b/htslib
deleted file mode 160000
index 49fdfbda2..000000000
--- a/htslib
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 49fdfbda20acbd73303df3c7fef84f2d972c5f8d
diff --git a/src/BamReader.cpp b/src/BamReader.cpp
index b4aea4490..409c71b5a 100644
--- a/src/BamReader.cpp
+++ b/src/BamReader.cpp
@@ -141,6 +141,11 @@ void BamReader::Reset() {
   return false;
 }
 
+  size_t BamReader::GetRegionIdx() {
+    // this ought to be in sync across all open BAMs
+    return m_bams.begin()->second.m_region_idx;
+  }
+
   bool BamReader::Open(const std::string& bam) {
 
     // dont open same bam twice
diff --git a/src/ReadFilter.cpp b/src/ReadFilter.cpp
index 8c7de4781..3c148305c 100644
--- a/src/ReadFilter.cpp
+++ b/src/ReadFilter.cpp
@@ -1,7 +1,7 @@
 #include "SeqLib/ReadFilter.h"
 
 #include <cassert>
-#include "htslib/htslib/khash.h"
+#include <htslib/khash.h>
 
 //#define QNAME "D0EN0ACXX111207:7:2306:6903:136511"
 //#define QFLAG -1