--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ezBAMQC/src/htslib/cram/cram_index.h	Thu Mar 24 17:12:52 2016 -0400
@@ -0,0 +1,98 @@
+/*
+Copyright (c) 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 _CRAM_INDEX_H_
+#define _CRAM_INDEX_H_
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*
+ * Loads a CRAM .crai index into memory.
+ * Returns 0 for success
+ *        -1 for failure
+ */
+int cram_index_load(cram_fd *fd, const char *fn);
+
+void cram_index_free(cram_fd *fd);
+
+/*
+ * Searches the index for the first slice overlapping a reference ID
+ * and position.
+ *
+ * Returns the cram_index pointer on sucess
+ *         NULL on failure
+ */
+cram_index *cram_index_query(cram_fd *fd, int refid, int pos, cram_index *frm);
+
+/*
+ * Skips to a container overlapping the start coordinate listed in
+ * cram_range.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int cram_seek_to_refpos(cram_fd *fd, cram_range *r);
+
+void cram_index_free(cram_fd *fd);
+
+/*
+ * Skips to a container overlapping the start coordinate listed in
+ * cram_range.
+ *
+ * In theory we call cram_index_query multiple times, once per slice
+ * overlapping the range. However slices may be absent from the index
+ * which makes this problematic. Instead we find the left-most slice
+ * and then read from then on, skipping decoding of slices and/or
+ * whole containers when they don't overlap the specified cram_range.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int cram_seek_to_refpos(cram_fd *fd, cram_range *r);
+
+/*
+ * Builds an index file.
+ *
+ * fd is a newly opened cram file that we wish to index.
+ * fn_base is the filename of the associated CRAM file. Internally we
+ * add ".crai" to this to get the index filename.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int cram_index_build(cram_fd *fd, const char *fn_base);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif