--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ezBAMQC/src/htslib/cram/cram_decode.h	Thu Mar 24 17:12:52 2016 -0400
@@ -0,0 +1,112 @@
+/*
+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 decoding portion of CRAM I/O. Also see
+ * cram_codecs.[ch] for the actual encoding functions themselves.
+ */
+
+#ifndef _CRAM_READ_H_
+#define _CRAM_READ_H_
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/* ----------------------------------------------------------------------
+ * CRAM sequence iterators.
+ */
+
+/*! Read the next cram record and return it as a cram_record.
+ *
+ * Note that to decode cram_record the caller will need to look up some data
+ * in the current slice, pointed to by fd->ctr->slice. This is valid until
+ * the next call to cram_get_seq (which may invalidate it).
+ *
+ * @return
+ * Returns record pointer on success (do not free);
+ *        NULL on failure
+ */
+cram_record *cram_get_seq(cram_fd *fd);
+
+/*! Read the next cram record and convert it to a bam_seq_t struct.
+ *
+ * @return
+ * Returns 0 on success;
+ *        -1 on EOF or failure (check fd->err)
+ */
+int cram_get_bam_seq(cram_fd *fd, bam_seq_t **bam);
+
+
+/* ----------------------------------------------------------------------
+ * Internal functions
+ */
+
+/*! INTERNAL:
+ * Decodes a CRAM block compression header.
+ *
+ * @return
+ * Returns header ptr on success;
+ *         NULL on failure
+ */
+cram_block_compression_hdr *cram_decode_compression_header(cram_fd *fd,
+							   cram_block *b);
+
+/*! INTERNAL:
+ * Decodes a CRAM (un)mapped slice header block.
+ *
+ * @return
+ * Returns slice header ptr on success;
+ *         NULL on failure
+ */
+cram_block_slice_hdr *cram_decode_slice_header(cram_fd *fd, cram_block *b);
+
+
+/*! INTERNAL:
+ * Decode an entire slice from container blocks. Fills out s->crecs[] array.
+ *
+ * @return
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+int cram_decode_slice(cram_fd *fd, cram_container *c, cram_slice *s,
+		      SAM_hdr *hdr);
+
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif