--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ezBAMQC/src/htslib/cram/cram_encode.h	Thu Mar 24 17:12:52 2016 -0400
@@ -0,0 +1,105 @@
+/*
+Copyright (c) 2012-2013 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.
+*/
+
+/*! \file
+ * Include cram.h instead.
+ *
+ * This is an internal part of the CRAM system and is automatically included
+ * when you #include cram.h.
+ *
+ * Implements the encoding portion of CRAM I/O. Also see
+ * cram_codecs.[ch] for the actual encoding functions themselves.
+ */
+
+#ifndef _CRAM_WRITE_H_
+#define _CRAM_WRITE_H_
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/* ----------------------------------------------------------------------
+ * CRAM sequence iterators.
+ */
+
+/*! Write iterator: put BAM format sequences into a CRAM file.
+ *
+ * We buffer up a containers worth of data at a time.
+ *
+ * FIXME: break this into smaller pieces.
+ *
+ * @return
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+int cram_put_bam_seq(cram_fd *fd, bam_seq_t *b);
+
+
+/* ----------------------------------------------------------------------
+ * Internal functions
+ */
+
+/*! INTERNAL:
+ * Encodes a compression header block into a generic cram_block structure.
+ *
+ * @return
+ * Returns cram_block ptr on success;
+ *         NULL on failure
+ */
+cram_block *cram_encode_compression_header(cram_fd *fd, cram_container *c,
+					   cram_block_compression_hdr *h);
+
+/*! INTERNAL:
+ * Encodes a slice compression header. 
+ *
+ * @return
+ * Returns cram_block on success;
+ *         NULL on failure
+ */
+cram_block *cram_encode_slice_header(cram_fd *fd, cram_slice *s);
+
+/*! INTERNAL:
+ * Encodes all slices in a container into blocks.
+ *
+ * @return
+ * Returns 0 on success;
+ *        -1 on failure
+ *
+ * FIXME: separate into encode_container and write_container. Ideally
+ * we should be able to do read_container / write_container or
+ * decode_container / encode_container.
+ */
+int cram_encode_container(cram_fd *fd, cram_container *c);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif