--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ezBAMQC/src/htslib/cram/cram_samtools.c	Thu Mar 24 17:12:52 2016 -0400
@@ -0,0 +1,147 @@
+/*
+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.
+*/
+
+#include <assert.h>
+#include <string.h>
+#include <stdlib.h>
+
+#include "cram/cram.h"
+#include "htslib/sam.h"
+
+/*---------------------------------------------------------------------------
+ * Samtools compatibility portion
+ */
+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) {
+    static const char L[256] = {
+	15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
+	15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
+	15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
+	15,15,15,15,15,15,15,15,15,15,15,15,15, 0,15,15,
+	15, 1,14, 2,13,15,15, 4,11,15,15,12,15, 3,15,15,
+	15,15, 5, 6, 8,15, 7, 9,15,10,15,15,15,15,15,15,
+	15, 1,14, 2,13,15,15, 4,11,15,15,12,15, 3,15,15,
+	15,15, 5, 6, 8,15, 7, 9,15,10,15,15,15,15,15,15,
+	15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
+	15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
+	15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
+	15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
+	15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
+	15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
+	15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
+	15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15
+    };
+    bam1_t *b = (bam1_t *)*bp;
+    uint8_t *cp;
+    int i, bam_len;
+
+    //b->l_aux = extra_len; // we fill this out later
+
+    bam_len = qname_len + 1 + ncigar*4 + (len+1)/2 + len + extra_len;
+    if (b->m_data < bam_len) {
+	b->m_data = bam_len;
+	kroundup32(b->m_data);
+	b->data = (uint8_t*)realloc(b->data, b->m_data);
+	if (!b->data)
+	    return -1;
+    }
+    b->l_data = bam_len;
+
+    b->core.tid     = rname;
+    b->core.pos     = pos-1;
+    b->core.bin     = bam_reg2bin(pos, end);
+    b->core.qual    = mapq;
+    b->core.l_qname = qname_len+1;
+    b->core.flag    = flag;
+    b->core.n_cigar = ncigar;
+    b->core.l_qseq  = len;
+    b->core.mtid    = mrnm;
+    b->core.mpos    = mpos-1;
+    b->core.isize   = isize;
+
+    cp = b->data;
+
+    strncpy((char *)cp, qname, qname_len);
+    cp[qname_len] = 0;
+    cp += qname_len+1;
+    memcpy(cp, cigar, ncigar*4);
+    cp += ncigar*4;
+
+    for (i = 0; i+1 < len; i+=2) {
+	*cp++ = (L[(uc)seq[i]]<<4) + L[(uc)seq[i+1]];
+    }
+    if (i < len)
+	*cp++ = L[(uc)seq[i]]<<4;
+
+    if (qual)
+	memcpy(cp, qual, len);
+    else
+	memset(cp, '\xff', len);
+
+    return 0;
+}
+
+bam_hdr_t *cram_header_to_bam(SAM_hdr *h) {
+    int i;
+    bam_hdr_t *header = bam_hdr_init();
+
+    header->l_text = ks_len(&h->text);
+    header->text = malloc(header->l_text+1);
+    memcpy(header->text, ks_str(&h->text), header->l_text);
+    header->text[header->l_text] = 0;
+
+    header->n_targets = h->nref;
+    header->target_name = (char **)calloc(header->n_targets,
+					  sizeof(char *));
+    header->target_len = (uint32_t *)calloc(header->n_targets, 4);
+
+    for (i = 0; i < h->nref; i++) {
+	header->target_name[i] = strdup(h->ref[i].name);
+	header->target_len[i] = h->ref[i].len;
+    }
+
+    return header;
+}
+
+SAM_hdr *bam_header_to_cram(bam_hdr_t *h) {
+    return sam_hdr_parse_(h->text, h->l_text);
+}