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/vlen.h src/htslib/cram/vlen.h
new file mode 100644
index 0000000..6b9b07c
--- /dev/null
+++ src/htslib/cram/vlen.h
@@ -0,0 +1,48 @@
+/*
+Author: James Bonfield (jkb@sanger.ac.uk)
+
+Copyright (c) 1995-1996 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.
+*/
+
+#ifndef _VLEN_H_
+#define _VLEN_H_
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+extern int vflen(char *fmt, va_list ap);
+extern int flen(char *fmt, ...);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _VLEN_H_ */