add patch to use Debian paths for resources

--- a/src/gth/bssm_param.c

+++ b/src/gth/bssm_param.c

@@ -29,6 +29,7 @@

 #include "gth/gthprobdef.h"

 #include "gth/gthspeciestab.h"

 #include "gth/showbool.h"

+#include "libgenomethreader/findfile.h"

 /*

   This is a collection of functions associated with

@@ -451,42 +452,7 @@

   if (gt_file_exists(filename))

     gt_str_append_cstr(path, filename);

   else {

-    if (strchr(filename, GT_PATH_SEPARATOR)) {

-      gt_error_set(err, "filename \"%s\" contains illegal symbol '%c': the "

-                        "path list specified by environment variable \"%s\" "

-                        "cannot be searched for it", filename,

-                        GT_PATH_SEPARATOR, BSSMENVNAME);

-      had_err = -1;

-    }

-    /* check for file path in environment variable */

-    if (!had_err)

-      had_err = gt_file_find_in_env(path, filename, BSSMENVNAME, err);

-    if (!had_err && !gt_str_length(path)) {

-      gt_error_set(err, "file \"%s\" not found in directory list specified "

-                        "by environment variable %s", filename, BSSMENVNAME);

-      had_err = -1;

-    }

-    if (!had_err) {

-      /* path found -> append filename */

-      gt_str_append_char(path, GT_PATH_SEPARATOR);

-      gt_str_append_cstr(path, filename);

-    }

-    else {

-      /* check for file path relative to binary */

-      int new_err = gt_file_find_exec_in_path(path, gt_error_get_progname(err),

-                                              NULL);

-      if (!new_err) {

-        gt_assert(gt_str_length(path));

-        gt_str_append_char(path, GT_PATH_SEPARATOR);

-        gt_str_append_cstr(path, "bssm");

-        gt_str_append_char(path, GT_PATH_SEPARATOR);

-        gt_str_append_cstr(path, filename);

-        if (gt_file_exists(gt_str_get(path))) {

-          gt_error_unset(err);

-          had_err = 0;

-        }

-      }

-    }

+    had_err = gth_find_file(filename, BSSMENVNAME, "bssm", path, err);

   }

   if (!had_err) {

--- a/src/gth/input.c

+++ b/src/gth/input.c

@@ -30,6 +30,7 @@

 #include "gth/input.h"

 #include "gth/md5_cache.h"

 #include "gth/parse_options.h"

+#include "libgenomethreader/findfile.h"

 #define GTHFORWARD  1        /* run program to match forward */

 #define GTHREVERSE  (1 << 1) /* run program to match reverse */

@@ -653,45 +654,14 @@

 {

   GtStr *path = gt_str_new();

   int had_err = 0;

+

   if (gt_file_exists(scorematrixfile)) {

     gt_str_set(path, scorematrixfile);

     return path;

   }

-  if (strchr(scorematrixfile, GT_PATH_SEPARATOR)) {

-    gt_error_set(err, "filename \"%s\" contains illegal symbol '%c': the path "

-                      "list specified by environment variable \"%s\" cannot be "

-                      "searched for it", scorematrixfile, GT_PATH_SEPARATOR,

-                      GTHDATAENVNAME);

-    had_err = -1;

-  }

-  if (!had_err)

-    had_err = gt_file_find_in_env(path, scorematrixfile, GTHDATAENVNAME, err);

-  if (!had_err && !gt_str_length(path)) {

-    gt_error_set(err, "file \"%s\" not found in directory list specified by "

-                 "environment variable %s", scorematrixfile, GTHDATAENVNAME);

-    had_err = -1;

-  }

-  if (!had_err) {

-    gt_assert(gt_str_length(path));

-    /* path found -> append score matrix file name */

-    gt_str_append_char(path, GT_PATH_SEPARATOR);

-    gt_str_append_cstr(path, scorematrixfile);

-  }

-  else {

-    /* check for file relative to binary */

-    int new_err = gt_file_find_exec_in_path(path, gt_error_get_progname(err),

-                                            NULL);

-    if (!new_err) {

-      gt_str_append_char(path, GT_PATH_SEPARATOR);

-      gt_str_append_cstr(path, GTHDATADIRNAME);

-      gt_str_append_char(path, GT_PATH_SEPARATOR);

-      gt_str_append_cstr(path, scorematrixfile);

-      if (gt_file_exists(gt_str_get(path))) {

-        gt_error_unset(err);

-        had_err = 0;

-      }

-    }

-  }

+

+  had_err = gth_find_file(scorematrixfile, GTHDATAENVNAME, GTHDATADIRNAME, path,

+                          err);

   if (had_err) {

     gt_str_delete(path);

     return NULL;

--- /dev/null

+++ b/src/libgenomethreader/findfile.c

@@ -0,0 +1,74 @@

+/*

+  Copyright (c) 2020 Sascha Steinbiss <sascha@steinbiss.name>

+

+  Permission to use, copy, modify, and distribute this software for any

+  purpose with or without fee is hereby granted, provided that the above

+  copyright notice and this permission notice appear in all copies.

+

+  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES

+  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF

+  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR

+  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES

+  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN

+  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF

+  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.

+*/

+

+#include "findfile.h"

+#include "core/fileutils_api.h"

+#include "core/compat_api.h"

+

+int gth_find_file(const char *filename, const char *envname,

+                  const char *dirname, GtStr *out, GtError *err)

+{

+  int had_err = 0;

+  const char **defaultpath;

+  static const char *defaultpaths[] = {

+    "/usr/share/genomethreader",

+    "/usr/local/share/genomethreader",

+    "/usr/lib/genomethreader",

+    "/usr/local/lib/genomethreader",

+    NULL

+  };

+

+  gt_str_reset(out);

+  /* check in directory given by envname */

+  if (getenv(envname)) {

+    gt_str_append_cstr(out, getenv(envname));

+    gt_str_append_char(out, GT_PATH_SEPARATOR);

+    gt_str_append_cstr(out, filename);

+    if (gt_file_exists(gt_str_get(out))) {

+      return 0;

+    }

+  }

+

+  /* check for file relative to binary */

+  gt_str_reset(out);

+  had_err = gt_file_find_exec_in_path(out, gt_error_get_progname(err), NULL);

+  if (!had_err) {

+    gt_str_append_char(out, GT_PATH_SEPARATOR);

+    gt_str_append_cstr(out, dirname);

+    gt_str_append_char(out, GT_PATH_SEPARATOR);

+    gt_str_append_cstr(out, filename);

+    if (gt_file_exists(gt_str_get(out))) {

+      return 0;

+    }

+  }

+  

+  /* check for file in set of default paths */

+  for (defaultpath = defaultpaths; *defaultpath; defaultpath++) {

+    gt_str_reset(out);

+    gt_str_append_cstr(out, *defaultpath);

+    gt_str_append_char(out, GT_PATH_SEPARATOR);

+    gt_str_append_cstr(out, dirname);

+    gt_str_append_char(out, GT_PATH_SEPARATOR);

+    gt_str_append_cstr(out, filename);

+    if (gt_file_exists(gt_str_get(out))) {

+      return 0;

+    }

+  }

+  

+  gt_error_set(err, "could not find file '%s' in any of the search paths",

+               filename);

+  return -1;

+}

--- /dev/null

+++ b/src/libgenomethreader/findfile.h

@@ -0,0 +1,26 @@

+/*

+  Copyright (c) 2020 Sascha Steinbiss <sascha@steinbiss.name>

+

+  Permission to use, copy, modify, and distribute this software for any

+  purpose with or without fee is hereby granted, provided that the above

+  copyright notice and this permission notice appear in all copies.

+

+  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES

+  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF

+  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR

+  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES

+  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN

+  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF

+  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.

+*/

+

+#ifndef GTH_FINDFILE_H

+#define GTH_FINDFILE_H

+

+#include "core/str_api.h"

+#include "core/error_api.h"

+

+int gth_find_file(const char *filename, const char *envname,

+                  const char *dirname, GtStr *out, GtError *err);

+                  

+#endif

--- a/src/libgenomethreader/gthmkvtree.c

+++ b/src/libgenomethreader/gthmkvtree.c

@@ -6,6 +6,7 @@

 #include "core/ma_api.h"

 #include "gth/gthdef.h"

 #include "gth/gthoutput.h"

+#include "libgenomethreader/findfile.h"

 #include "libgenomethreader/gthmkvtree.h"

 #include "types.h"

 #include "virtualdef.h"

@@ -52,39 +53,14 @@

 {

   int rval, had_err = 0;

   gt_error_check(err);

-  if (!getenv(GTHDATAENVNAME)) {

-    gt_error_set(err, "$%s not defined. Please set correctly", GTHDATAENVNAME);

-    had_err = -1;

-  }

+

+  GtStr *path = gt_str_new();

+  had_err = gth_find_file(mapping, GTHDATAENVNAME, GTHDATADIRNAME, path, err);

   if (!had_err) {

-    rval = snprintf(smapfile, PATH_MAX+1, "%s%c%s", getenv(GTHDATAENVNAME),

-                    GT_PATH_SEPARATOR, mapping);

-    gt_assert(rval < PATH_MAX + 1);

-    if (!gt_file_exists(smapfile)) {

-      gt_error_set(err, "cannot open smap file '%s'", smapfile);

-      had_err = -1;

-    }

-  }

-  if (had_err) {

-    /* check for file relative to binary */

-    GtStr *path;

-    int new_err;

-    path = gt_str_new();

-    new_err = gt_file_find_exec_in_path(path, gt_error_get_progname(err), NULL);

-    if (!new_err) {

-      gt_str_append_char(path, GT_PATH_SEPARATOR);

-      gt_str_append_cstr(path, GTHDATADIRNAME);

-      gt_str_append_char(path, GT_PATH_SEPARATOR);

-      gt_str_append_cstr(path, mapping);

-      if (gt_file_exists(gt_str_get(path))) {

-        rval = snprintf(smapfile, PATH_MAX+1, "%s", gt_str_get(path));

-        gt_assert(rval < PATH_MAX + 1);

-        gt_error_unset(err);

-        had_err = 0;

-      }

-    }

-    gt_str_delete(path);

+   rval = snprintf(smapfile, PATH_MAX+1, "%s", gt_str_get(path));

+   gt_assert(rval < PATH_MAX + 1);

   }

+  gt_str_delete(path);

   return had_err;

 }

--- a/src/libgenomethreader/gthpre.c

+++ b/src/libgenomethreader/gthpre.c

@@ -11,6 +11,7 @@

 #include "gth/gthdef.h"

 #include "gth/gthoutput.h"

 #include "gth/input.h"

+#include "libgenomethreader/findfile.h"

 #include "libgenomethreader/gthmkvtree.h"

 #include "libgenomethreader/gthpolyafunc.h"

 #include "libgenomethreader/gthpre.h"

@@ -301,49 +302,22 @@

   /* create masked file if necessary */

   if (createmaskedfile) {

-    sprintf(dnafilename, "%s.%s", POLYA_FASTAFILENAME, DNASUFFIX);

-    /* check if polyatail.dna exists */

-    fp = scanpathsforfile(GTHDATAENVNAME, dnafilename); /* XXX */

-    if (!fp) {

-      gt_error_set(err, "file \"%s\" not found in $%s. Set correctly?",

-                   dnafilename, GTHDATAENVNAME);

-      had_err = -1;

-    }

-    if (!had_err /* XXX */ && DELETEFILEHANDLE(fp)) {

-      fprintf(stderr,"%s\n", messagespace());

-      exit(EXIT_FAILURE);

-    }

-

-    /* call vmatch and save masked file */

-    if (!had_err && !getenv(GTHDATAENVNAME)) {

-      gt_error_set(err, "$%s not defined. Please set correctly",

-                   GTHDATAENVNAME);

-      had_err = -1;

-    }

+    int rval = 0;

+    GtStr *path = gt_str_new();

+    sprintf(dnafilename, "%s.%s", POLYA_FASTAFILENAME, DNASUFFIX);

+    had_err = gth_find_file(dnafilename, GTHDATAENVNAME, GTHDATADIRNAME, path,

+                            err);

     if (!had_err) {

-      sprintf(dnafilename, "%s%c%s", getenv(GTHDATAENVNAME), GT_PATH_SEPARATOR,

-              POLYA_FASTAFILENAME);

-    }

-    else {

-      /* check for file relative to binary */

-      GtStr *path;

-      int new_err;

-      path = gt_str_new();

-      new_err = gt_file_find_exec_in_path(path, gt_error_get_progname(err),

-                                          NULL);

-      if (!new_err) {

-        gt_str_append_char(path, GT_PATH_SEPARATOR);

-        gt_str_append_cstr(path, GTHDATADIRNAME);

-        if (gt_file_exists_and_is_dir(gt_str_get(path))) {

-          sprintf(dnafilename, "%s%c%s", gt_str_get(path), GT_PATH_SEPARATOR,

-                  POLYA_FASTAFILENAME);

-          gt_error_unset(err);

-          had_err = 0;

-        }

-      }

+       rval = snprintf(dnafilename, PATH_MAX+1, "%s", gt_str_get(path));

+       gt_assert(rval < PATH_MAX + 1);

+       /* clip off DNASUFFIX */

+       gt_assert(strlen(dnafilename) > 5);

+       dnafilename[strlen(dnafilename)-4] = '\0';

     }

+    gt_str_delete(path);

+    /* call vmatch and save masked file */

     if (!had_err) {

       /* open file pointer for masked reference file */

       fp = gt_fa_xfopen(maskedfilename, "w");

debian-gt-libs.patch

gt-path-fix.patch

hardening.patch

search-paths.patch