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/zfio.h src/htslib/cram/zfio.h
new file mode 100644
index 0000000..ab9c9c9
--- /dev/null
+++ src/htslib/cram/zfio.h
@@ -0,0 +1,62 @@
+/*
+Copyright (c) 2009-2013 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 _ZFIO_H_
+#define _ZFIO_H_
+
+#include <stdio.h>
+#include <zlib.h>
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*
+ * Either a gzFile or a FILE.
+ */
+typedef struct {
+    FILE   *fp;
+    gzFile  gz;
+} zfp;
+
+off_t zftello(zfp *zf);
+int zfseeko(zfp *zf, off_t offset, int whence);
+char *zfgets(char *line, int size, zfp *zf);
+int zfputs(char *line, zfp *zf);
+zfp *zfopen(const char *path, const char *mode);
+int zfclose(zfp *zf);
+int zfpeek(zfp *zf);
+int zfeof(zfp *zf);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _ZFIO_H_ */