--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ezBAMQC/src/htslib/cram/cram_samtools.h	Thu Mar 24 17:12:52 2016 -0400
@@ -0,0 +1,97 @@
+/*
+Copyright (c) 2010-2013 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_SAMTOOLS_H_
+#define _CRAM_SAMTOOLS_H_
+
+/* Samtools compatible API */
+#define bam_blk_size(b)  ((b)->l_data)
+#define bam_set_blk_size(b,v) ((b)->data_len = (v))
+
+#define bam_ref(b)       (b)->core.tid
+#define bam_pos(b)       (b)->core.pos
+#define bam_mate_pos(b)  (b)->core.mpos
+#define bam_mate_ref(b)  (b)->core.mtid
+#define bam_ins_size(b)  (b)->core.isize
+#define bam_seq_len(b)   (b)->core.l_qseq
+#define bam_cigar_len(b) (b)->core.n_cigar
+#define bam_flag(b)      (b)->core.flag
+#define bam_bin(b)       (b)->core.bin
+#define bam_map_qual(b)  (b)->core.qual
+#define bam_name_len(b)  (b)->core.l_qname
+#define bam_name(b)      bam_get_qname((b))
+#define bam_qual(b)      bam_get_qual((b))
+#define bam_seq(b)       bam_get_seq((b))
+#define bam_cigar(b)     bam_get_cigar((b))
+#define bam_aux(b)       bam_get_aux((b))
+
+#define bam_dup(b)       bam_copy1(bam_init1(), (b))
+
+#define bam_free(b)      bam_destroy1((b))
+
+#define bam_reg2bin(beg,end) hts_reg2bin((beg),(end),14,5)
+
+#include "htslib/sam.h"
+
+enum cigar_op {
+    BAM_CMATCH_=BAM_CMATCH,
+    BAM_CINS_=BAM_CINS,
+    BAM_CDEL_=BAM_CDEL,
+    BAM_CREF_SKIP_=BAM_CREF_SKIP,
+    BAM_CSOFT_CLIP_=BAM_CSOFT_CLIP,
+    BAM_CHARD_CLIP_=BAM_CHARD_CLIP,
+    BAM_CPAD_=BAM_CPAD,
+    BAM_CBASE_MATCH=BAM_CEQUAL,
+    BAM_CBASE_MISMATCH=BAM_CDIFF
+};
+
+typedef bam1_t bam_seq_t;
+
+#include "cram/sam_header.h"
+
+bam_hdr_t *cram_header_to_bam(SAM_hdr *h);
+SAM_hdr *bam_header_to_cram(bam_hdr_t *h);
+
+int bam_construct_seq(bam_seq_t **bp, size_t extra_len,
+		      const char *qname, size_t qname_len,
+		      int flag,
+		      int rname,      // Ref ID
+		      int pos,
+		      int end,        // aligned start/end coords
+		      int mapq,
+		      uint32_t ncigar, const uint32_t *cigar,
+		      int mrnm,       // Mate Ref ID
+		      int mpos,
+		      int isize,
+		      int len,
+		      const char *seq,
+		      const char *qual);
+
+#endif /* _CRAM_SAMTOOLS_H_ */