diff ezBAMQC/src/htslib/cram/cram_stats.h @ 0:dfa3745e5fd8

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ezBAMQC/src/htslib/cram/cram_stats.h	Thu Mar 24 17:12:52 2016 -0400
@@ -0,0 +1,59 @@
+/*
+Copyright (c) 2012-2013 Genome Research Ltd.
+Author: James Bonfield <[e-mail]>
+
+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_STATS_H_
+#define _CRAM_STATS_H_
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+cram_stats *cram_stats_create(void);
+void cram_stats_add(cram_stats *st, int32_t val);
+void cram_stats_del(cram_stats *st, int32_t val);
+void cram_stats_dump(cram_stats *st);
+void cram_stats_free(cram_stats *st);
+
+/*
+ * Computes entropy from integer frequencies for various encoding methods and
+ * picks the best encoding.
+ *
+ * FIXME: we could reuse some of the code here for the actual encoding
+ * parameters too. Eg the best 'k' for SUBEXP or the code lengths for huffman.
+ *
+ * Returns the best codec to use.
+ */
+enum cram_encoding cram_stats_encoding(cram_fd *fd, cram_stats *st);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif