7df6e18265341f87a69fba808aa1f92f8ebca841 markd Wed Apr 15 13:39:42 2026 -0700 move copy of htslib diff --git src/htslib/cram/open_trace_file.h src/htslib/cram/open_trace_file.h deleted file mode 100644 index a067dc62295..00000000000 --- src/htslib/cram/open_trace_file.h +++ /dev/null @@ -1,125 +0,0 @@ -/* -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 <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 _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); - - -/* - * As per open_path_mfile, but searching only for local filenames. - * This is useful as we may avoid doing a full mfopen and loading - * the entire file into memory. - * - * Returns the expanded pathname if found. - * NULL if not - */ -char *find_path(char *file, char *path); - -#ifdef __cplusplus -} -#endif - -#endif /* _OPEN_TRACE_FILE_H_ */