11e45667d4e291b3038ccda729a1cdf5bcaf004a
braney
  Mon Jul 11 15:46:54 2016 -0700
incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
defines, modify a bunch of makefiles to include kentSrc variable
pointing to top of the tree.

diff --git src/htslib/cram/cram.h src/htslib/cram/cram.h
new file mode 100644
index 0000000..c4e8809
--- /dev/null
+++ src/htslib/cram/cram.h
@@ -0,0 +1,61 @@
+/*
+Copyright (c) 2012-2013 Genome Research Ltd.
+Author: James Bonfield <jkb@sanger.ac.uk>
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+Institute nor the names of its contributors may be used to endorse or promote
+products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+/*! \file
+ * CRAM interface.
+ *
+ * Consider using the higher level hts_*() API for programs that wish to
+ * be file format agnostic (see htslib/hts.h).
+ *
+ * This API should be used for CRAM specific code. The specifics of the
+ * public API are implemented in cram_io.h, cram_encode.h and cram_decode.h
+ * although these should not be included directly (use this file instead).
+ */
+
+#ifndef _CRAM_H_
+#define _CRAM_H_
+
+#include "cram/cram_samtools.h"
+#include "cram/sam_header.h"
+#include "cram_structs.h"
+#include "cram_io.h"
+#include "cram_encode.h"
+#include "cram_decode.h"
+#include "cram_stats.h"
+#include "cram_codecs.h"
+#include "cram_index.h"
+
+// Validate against the external cram.h,
+//
+// This contains duplicated portions from cram_io.h and cram_structs.h,
+// so we want to ensure that the prototypes match.
+#include "htslib/cram.h"
+
+#endif