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/config.h.in src/htslib/config.h.in
new file mode 100644
index 0000000..09b23ff
--- /dev/null
+++ src/htslib/config.h.in
@@ -0,0 +1,27 @@
+/* config.h.in -- template for config.h.  If you use configure, this file
+   provides #defines reflecting your configuration choices.  If you don't
+   run configure, suitable conservative defaults will be used.
+
+   This template file can be updated with autoheader, but do so carefully
+   as autoheader adds #defines such as PACKAGE_* that we don't want.  */
+
+/* Define if HTSlib should enable plugins. */
+#undef ENABLE_PLUGINS
+
+/* Define if you have the Common Crypto library. */
+#undef HAVE_COMMONCRYPTO
+
+/* Define to 1 if you have the `gmtime_r' function. */
+#undef HAVE_GMTIME_R
+
+/* Define if you have libcrypto-style HMAC(). */
+#undef HAVE_HMAC
+
+/* Define to 1 if iRODS file access is enabled. */
+#undef HAVE_IRODS
+
+/* Define if libcurl file access is enabled. */
+#undef HAVE_LIBCURL
+
+/* Define to 1 if you have a working `mmap' system call. */
+#undef HAVE_MMAP