7df6e18265341f87a69fba808aa1f92f8ebca841 markd Wed Apr 15 13:39:42 2026 -0700 move copy of htslib diff --git src/htslib/cram/open_trace_file.c src/htslib/cram/open_trace_file.c deleted file mode 100644 index 7c7e4854f0a..00000000000 --- src/htslib/cram/open_trace_file.c +++ /dev/null @@ -1,414 +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: - - 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 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, 2014 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 <config.h> - -#include <stdlib.h> -#include <stdio.h> -#include <string.h> -#include <unistd.h> -#include <ctype.h> -#include <limits.h> -#include <sys/types.h> -#include <sys/stat.h> -#include "cram/os.h" -#ifndef PATH_MAX -# define PATH_MAX 1024 -#endif - -#include "cram/open_trace_file.h" -#include "cram/misc.h" -#include "htslib/hfile.h" - -/* - * 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) { - char *newsearch; - unsigned int i, j; - size_t len; -#ifdef _WIN32 - char path_sep = ';'; -#else - char path_sep = ':'; -#endif - - if (!searchpath) - searchpath=""; - - newsearch = (char *)malloc((len = strlen(searchpath))+5); - if (!newsearch) - return NULL; - - for (i = 0, j = 0; i < len; i++) { - /* "::" => ":". Used for escaping colons in http://foo */ - if (i < len-1 && searchpath[i] == ':' && searchpath[i+1] == ':') { - newsearch[j++] = ':'; - i++; - continue; - } - - /* Handle http:// and ftp:// too without :: */ - if (path_sep == ':') { - if ((i == 0 || (i > 0 && searchpath[i-1] == ':')) && - (!strncmp(&searchpath[i], "http:", 5) || - !strncmp(&searchpath[i], "ftp:", 4) || - !strncmp(&searchpath[i], "|http:", 6) || - !strncmp(&searchpath[i], "|ftp:", 5) || - !strncmp(&searchpath[i], "URL=http:", 9) || - !strncmp(&searchpath[i], "URL=ftp:", 8))) { - do { - newsearch[j++] = searchpath[i]; - } while (i<len && searchpath[i++] != ':'); - if (searchpath[i] == ':') - i++; - if (searchpath[i]=='/') - newsearch[j++] = searchpath[i++]; - if (searchpath[i]=='/') - newsearch[j++] = searchpath[i++]; - // Look for host:port - do { - newsearch[j++] = searchpath[i++]; - } while (i<len && searchpath[i] != ':' && searchpath[i] != '/'); - newsearch[j++] = searchpath[i++]; - if (searchpath[i] == ':') - i++; - } - } - - if (searchpath[i] == path_sep) { - /* Skip blank path components */ - if (j && newsearch[j-1] != 0) - newsearch[j++] = 0; - } else { - newsearch[j++] = searchpath[i]; - } - } - - if (j) - newsearch[j++] = 0; - newsearch[j++] = '.'; - newsearch[j++] = '/'; - newsearch[j++] = 0; - newsearch[j++] = 0; - - return newsearch; -} - -mFILE *find_file_url(char *file, char *url) { - char buf[8192], *cp; - mFILE *mf = NULL; - int maxlen = 8190 - strlen(file), len; - hFILE *hf; - - /* Expand %s for the trace name */ - for (cp = buf; *url && cp - buf < maxlen; url++) { - if (*url == '%' && *(url+1) == 's') { - url++; - cp += strlen(strcpy(cp, file)); - } else { - *cp++ = *url; - } - } - *cp++ = 0; - - if (!(hf = hopen(buf, "r"))) - return NULL; - - if (NULL == (mf = mfcreate(NULL, 0))) - return NULL; - while ((len = hread(hf, buf, 8192)) > 0) { - if (mfwrite(buf, len, 1, mf) <= 0) { - hclose_abruptly(hf); - mfdestroy(mf); - return NULL; - } - } - if (hclose(hf) < 0) { - mfdestroy(mf); - return NULL; - } - - mrewind(mf); - return mf; -} - -/* - * Takes a dirname possibly including % rules and appends the filename - * to it. - * - * Returns expanded pathname or NULL for malloc failure. - */ -static char *expand_path(char *file, char *dirname) { - size_t len = strlen(dirname); - size_t lenf = strlen(file); - char *cp, *path; - - path = malloc(len+lenf+2); // worst expansion DIR/FILE - if (!path) - return NULL; - - if (dirname[len-1] == '/') - len--; - - /* Special case for "./" or absolute filenames */ - if (*file == '/' || (len==1 && *dirname == '.')) { - sprintf(path, "%s", file); - } else { - /* Handle %[0-9]*s expansions, if required */ - char *path_end = path; - *path = 0; - while ((cp = strchr(dirname, '%'))) { - char *endp; - long l = strtol(cp+1, &endp, 10); - if (*endp != 's') { - strncpy(path_end, dirname, (endp+1)-dirname); - path_end += (endp+1)-dirname; - dirname = endp+1; - continue; - } - - strncpy(path_end, dirname, cp-dirname); - path_end += cp-dirname; - if (l) { - strncpy(path_end, file, l); - path_end += MIN(strlen(file), l); - file += MIN(strlen(file), l); - } else { - strcpy(path_end, file); - path_end += strlen(file); - file += strlen(file); - } - len -= (endp+1) - dirname; - dirname = endp+1; - } - strncpy(path_end, dirname, len); - path_end += MIN(strlen(dirname), len); - *path_end = 0; - if (*file) { - *path_end++ = '/'; - strcpy(path_end, file); - } - } - - //fprintf(stderr, "*PATH=\"%s\"\n", path); - return path; -} - -/* - * Searches for file in the directory 'dirname'. If it finds it, it opens - * it. This also searches for compressed versions of the file in dirname - * too. - * - * Returns mFILE pointer if found - * NULL if not - */ -static mFILE *find_file_dir(char *file, char *dirname) { - char *path; - mFILE *mf = NULL; - - path = expand_path(file, dirname); - - if (is_file(path)) - mf = mfopen(path, "rbm"); - - free(path); - return mf; -} - -/* - * ------------------------------------------------------------------------ - * Public functions below. - */ - -/* - * 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) { - char *newsearch; - char *ele; - mFILE *fp; - - /* Use path first */ - if (!path) - path = getenv("RAWDATA"); - if (NULL == (newsearch = tokenise_search_path(path))) - return NULL; - - /* - * Step through the search path testing out each component. - * We now look through each path element treating some prefixes as - * special, otherwise we treat the element as a directory. - */ - for (ele = newsearch; *ele; ele += strlen(ele)+1) { - char *ele2; - - /* - * '|' prefixing a path component indicates that we do not - * wish to perform the compression extension searching in that - * location. - * - * NB: this has been removed from the htslib implementation. - */ - if (*ele == '|') { - ele2 = ele+1; - } else { - ele2 = ele; - } - - if (0 == strncmp(ele2, "URL=", 4)) { - if ((fp = find_file_url(file, ele2+4))) { - free(newsearch); - return fp; - } - } else if (!strncmp(ele2, "http:", 5) || - !strncmp(ele2, "ftp:", 4)) { - if ((fp = find_file_url(file, ele2))) { - free(newsearch); - return fp; - } - } else if ((fp = find_file_dir(file, ele2))) { - free(newsearch); - return fp; - } - } - - free(newsearch); - - /* Look in the same location as the incoming 'relative_to' filename */ - if (relative_to) { - char *cp; - char relative_path[PATH_MAX+1]; - strcpy(relative_path, relative_to); - if ((cp = strrchr(relative_path, '/'))) - *cp = 0; - if ((fp = find_file_dir(file, relative_path))) - return fp; - } - - return NULL; -} - - -/* - * 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) { - char *newsearch; - char *ele; - char *outpath = NULL; - - /* Use path first */ - if (!path) - path = getenv("RAWDATA"); - if (NULL == (newsearch = tokenise_search_path(path))) - return NULL; - - for (ele = newsearch; *ele; ele += strlen(ele)+1) { - char *ele2 = (*ele == '|') ? ele+1 : ele; - - if (!strncmp(ele2, "URL=", 4) || - !strncmp(ele2, "http:", 5) || - !strncmp(ele2, "ftp:", 4)) { - continue; - } else { - outpath = expand_path(file, ele2); - if (is_file(outpath)) { - free(newsearch); - return outpath; - } else { - free(outpath); - } - } - } - - free(newsearch); - - return NULL; -}