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/hts_internal.h src/htslib/hts_internal.h
new file mode 100644
index 0000000..bb23a6d
--- /dev/null
+++ src/htslib/hts_internal.h
@@ -0,0 +1,69 @@
+/*  hts_internal.h -- internal functions; not part of the public API.
+
+    Copyright (C) 2015 Genome Research Ltd.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#ifndef HTSLIB_HTS_INTERNAL_H
+#define HTSLIB_HTS_INTERNAL_H
+
+#include <stddef.h>
+
+#include "htslib/hts.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+struct cram_fd;
+
+char *hts_idx_getfn(const char *fn, const char *ext);
+
+// The CRAM implementation stores the loaded index within the cram_fd rather
+// than separately as is done elsewhere in htslib.  So if p is a pointer to
+// an hts_idx_t with p->fmt == HTS_FMT_CRAI, then it actually points to an
+// hts_cram_idx_t and should be cast accordingly.
+typedef struct hts_cram_idx_t {
+    int fmt;
+    struct cram_fd *cram;
+} hts_cram_idx_t;
+
+
+struct hts_path_itr {
+    kstring_t path, entry;
+    void *dirv;  // DIR * privately
+    const char *pathdir, *prefix, *suffix;
+    size_t prefix_len, suffix_len, entry_dir_l;
+};
+
+void hts_path_itr_setup(struct hts_path_itr *itr, const char *path,
+    const char *builtin_path, const char *prefix, size_t prefix_len,
+    const char *suffix, size_t suffix_len);
+
+const char *hts_path_itr_next(struct hts_path_itr *itr);
+
+void *load_plugin(void **pluginp, const char *filename, const char *symbol);
+void *plugin_sym(void *plugin, const char *name, const char **errmsg);
+void close_plugin(void *plugin);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif