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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ezBAMQC/src/htslib/cram/open_trace_file.h	Thu Mar 24 17:12:52 2016 -0400
@@ -0,0 +1,115 @@
+/*
+Author: James Bonfield
+
+Copyright (c) 2000-2001 MEDICAL RESEARCH COUNCIL
+All rights reserved
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   . Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   . 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.
+
+   . Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF 
+MOLECULAR BIOLOGY 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 THE COPYRIGHT HOLDERS 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 THE COPYRIGHT OWNER 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.
+*/
+
+/*
+Copyright (c) 2008, 2009, 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 _OPEN_TRACE_FILE_H_
+#define _OPEN_TRACE_FILE_H_
+
+#include "cram/mFILE.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*
+ * Tokenises the search path splitting on colons (unix) or semicolons
+ * (windows).
+ * We also  explicitly add a "./" to the end of the search path
+ *
+ * Returns: A new search path with items separated by nul chars. Two nul
+ *          chars in a row represent the end of the tokenised path.
+ * Returns NULL for a failure.
+ *
+ * The returned data has been malloced. It is up to the caller to free this
+ * memory.
+ */
+char *tokenise_search_path(char *searchpath);
+
+/*
+ * Opens a trace file named 'file'. This is initially looked for as a
+ * pathname relative to a file named "relative_to". This may (for
+ * example) be the name of an experiment file referencing the trace
+ * file. In this case by passing relative_to as the experiment file
+ * filename the trace file will be picked up in the same directory as
+ * the experiment file. Relative_to may be supplied as NULL.
+ *
+ * 'file' is looked for at relative_to, then the current directory, and then
+ * all of the locations listed in 'path' (which is a colon separated list).
+ * If 'path' is NULL it uses the RAWDATA environment variable instead.
+ *
+ * Returns a mFILE pointer when found.
+ *           NULL otherwise.
+ */
+mFILE *open_path_mfile(char *file, char *path, char *relative_to);
+
+/*
+ * Returns a mFILE containing the entire contents of the url;
+ *         NULL on failure.
+ */
+mFILE *find_file_url(char *file, char *url);
+
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _OPEN_TRACE_FILE_H_ */