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/misc.h src/htslib/cram/misc.h
new file mode 100644
index 0000000..681b28c
--- /dev/null
+++ src/htslib/cram/misc.h
@@ -0,0 +1,110 @@
+/*
+Copyright (c) 1994-1997, 2001-2002 MEDICAL RESEARCH COUNCIL
+All rights reserved
+
+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 name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF 
+MOLECULAR BIOLOGY 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 THE COPYRIGHT HOLDERS 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 THE COPYRIGHT OWNER 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.
+ */
+
+/*
+Copyright (c) 2003-2013 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.
+*/
+
+#ifndef _misc_h
+#define _misc_h
+
+#include "cram/os.h"
+
+#include <stdio.h>
+#include <stdarg.h>  /* varargs needed for v*printf() prototypes */
+#include <sys/types.h>
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*
+ * This informs gcc that crash() doesn't return, so it doesn't need to
+ * concern itself that code paths going via crash could mean some variables
+ * being undefined and then issuing uninitialised variable warnings.
+ * This particularly affected convert.
+ */
+#ifdef __GNUC__
+#    define __NORETURN__ __attribute__ ((__noreturn__))
+#else
+#    define __NORETURN__
+#endif
+
+/*
+ * Used for printf style argument checking. We can request a function such
+ * as vTcl_SetResult does argument checking, avoiding bugs with using
+ * %d and passing in a 64-bit record.
+ */
+#ifdef __GNUC__
+#    define __PRINTF_FORMAT__(a,b) __attribute__ ((format (printf, a, b)))
+#else
+#    define __PRINTF_FORMAT__(a,b)
+#endif
+
+extern int is_directory(char * fn);
+extern int is_file(char * fn);
+extern int file_size(char * fn);
+
+#define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) )
+#define MAX(A,B) ( ( (A) > (B) ) ? (A) : (B) )
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /*_misc_h*/