const std::vector<int>& City::get_requests() const
{
refresh_intermediates();
#if 0
for (auto it = request_indices.begin(); it != request_indices.end(); ++it)
{
int to = *it;
if (get_stop(to)->get_operation() == Store
|| get_stop(to)->get_operation() == UnStore
|| get_stop(to)->get_operation() == Dump)
{
std::cout << "Error" << get_stop(to)->get_operation() << std::endl;
die();
}
}
#endif
return request_indices;
}
static void menu_draw_row_callback(GContext* ctx, const Layer *cell_layer, MenuIndex *cell_index, void *callback_context) {
stop_t *stop;
switch (cell_index->section) {
case MENU_SECTION_MAIN:
stop = get_stop(cell_index->row);
if (stop == NULL) {
return;
}
menu_cell_basic_draw(ctx, cell_layer, stop->name, NULL, NULL);
break;
}
}
static void menu_select_click_callback(MenuLayer* menu_layer, MenuIndex* cell_index, void* callback_context) {
realtime_transport_type_t *ttype = (realtime_transport_type_t *) callback_context;
if (!layer_get_hidden(transport_type_to_loadinglayer_map[*ttype])) {
APP_LOG(APP_LOG_LEVEL_DEBUG, "No clicks allowed while loading layer is visible");
return;
}
stop_t *stop;
switch (cell_index->section) {
case MENU_SECTION_MAIN:
stop = get_stop(cell_index->row);
if (stop == NULL) {
return;
}
show_departures_window(stop->id, *ttype, true);
break;
}
}
static int /* O - 0 = success, 1 = fail */
make_subpackage(const char *prodname,
/* I - Product short name */
const char *directory,
/* I - Directory for distribution files */
const char *platname,
/* I - Platform name */
dist_t *dist, /* I - Distribution information */
struct utsname *platform,
/* I - Platform information */
const char *subpackage)
/* I - Subpackage */
{
int i, j; /* Looping vars */
const char *header; /* Dependency header string */
FILE *fp; /* Control file */
char prodfull[255], /* Full name of product */
name[1024], /* Full product name */
filename[1024]; /* Destination filename */
command_t *c; /* Current command */
depend_t *d; /* Current dependency */
file_t *file; /* Current distribution file */
struct passwd *pwd; /* Pointer to user record */
struct group *grp; /* Pointer to group record */
const char *runlevels, /* Run levels */
*rlptr; /* Pointer into runlevels */
static const char *depends[] = /* Dependency names */
{
"Depends:",
"Conflicts:",
"Replaces:",
"Provides:"
};
/*
* Figure out the full name of the distribution...
*/
if (subpackage)
snprintf(prodfull, sizeof(prodfull), "%s-%s", prodname, subpackage);
else
strlcpy(prodfull, prodname, sizeof(prodfull));
/*
* Then the subdirectory name...
*/
if (dist->release[0])
snprintf(name, sizeof(name), "%s-%s-%s", prodfull, dist->version,
dist->release);
else
snprintf(name, sizeof(name), "%s-%s", prodfull, dist->version);
if (platname[0])
{
strlcat(name, "-", sizeof(name));
strlcat(name, platname, sizeof(name));
}
if (Verbosity)
printf("Creating Debian %s distribution...\n", name);
/*
* Write the control file for DPKG...
*/
if (Verbosity)
puts("Creating control file...");
snprintf(filename, sizeof(filename), "%s/%s", directory, name);
mkdir(filename, 0777);
strlcat(filename, "/DEBIAN", sizeof(filename));
mkdir(filename, 0777);
chmod(filename, 0755);
strlcat(filename, "/control", sizeof(filename));
if ((fp = fopen(filename, "w")) == NULL)
{
fprintf(stderr, "epm: Unable to create control file \"%s\" - %s\n", filename,
strerror(errno));
return (1);
}
fprintf(fp, "Package: %s\n", prodfull);
if (dist->release[0])
fprintf(fp, "Version: %s-%s\n", dist->version, dist->release);
else
fprintf(fp, "Version: %s\n", dist->version);
fprintf(fp, "Maintainer: %s\n", dist->vendor);
/*
* The Architecture attribute needs to match the uname info
* (which we change in get_platform to a common name)
*/
if (!strcmp(platform->machine, "intel"))
fputs("Architecture: i386\n", fp);
else if (!strcmp(platform->machine, "ppc"))
fputs("Architecture: powerpc\n", fp);
else
fprintf(fp, "Architecture: %s\n", platform->machine);
fprintf(fp, "Description: %s\n", dist->product);
fprintf(fp, " Copyright: %s\n", dist->copyright);
for (i = 0; i < dist->num_descriptions; i ++)
if (dist->descriptions[i].subpackage == subpackage)
fprintf(fp, " %s\n", dist->descriptions[i].description);
for (j = DEPEND_REQUIRES; j <= DEPEND_PROVIDES; j ++)
{
for (i = dist->num_depends, d = dist->depends; i > 0; i --, d ++)
if (d->type == j && d->subpackage == subpackage)
break;
if (i)
{
for (header = depends[j]; i > 0; i --, d ++, header = ",")
if (d->type == j && d->subpackage == subpackage)
{
if (!strcmp(d->product, "_self"))
fprintf(fp, "%s %s", header, prodname);
else
fprintf(fp, "%s %s", header, d->product);
if (d->vernumber[0] == 0)
{
if (d->vernumber[1] < INT_MAX)
fprintf(fp, " (<= %s)", d->version[1]);
}
else
{
if (d->vernumber[1] < INT_MAX)
fprintf(fp, " (>= %s, <= %s)", d->version[0], d->version[1]);
else
fprintf(fp, " (>= %s)", d->version[0]);
}
}
putc('\n', fp);
}
}
fclose(fp);
/*
* Write the preinst file for DPKG...
*/
for (i = dist->num_commands, c = dist->commands; i > 0; i --, c ++)
if (c->type == COMMAND_PRE_INSTALL && c->subpackage == subpackage)
break;
if (i)
{
if (Verbosity)
puts("Creating preinst script...");
snprintf(filename, sizeof(filename), "%s/%s/DEBIAN/preinst", directory, name);
if ((fp = fopen(filename, "w")) == NULL)
{
fprintf(stderr, "epm: Unable to create script file \"%s\" - %s\n", filename,
strerror(errno));
return (1);
}
fchmod(fileno(fp), 0755);
fputs("#!/bin/sh\n", fp);
fputs("# " EPM_VERSION "\n", fp);
for (; i > 0; i --, c ++)
if (c->type == COMMAND_PRE_INSTALL && c->subpackage == subpackage)
fprintf(fp, "%s\n", c->command);
fclose(fp);
}
/*
* Write the postinst file for DPKG...
*/
for (i = dist->num_commands, c = dist->commands; i > 0; i --, c ++)
if (c->type == COMMAND_POST_INSTALL && c->subpackage == subpackage)
break;
if (!i)
for (i = dist->num_files, file = dist->files; i > 0; i --, file ++)
if (tolower(file->type) == 'i' && file->subpackage == subpackage)
break;
if (i)
{
if (Verbosity)
puts("Creating postinst script...");
snprintf(filename, sizeof(filename), "%s/%s/DEBIAN/postinst", directory, name);
if ((fp = fopen(filename, "w")) == NULL)
{
fprintf(stderr, "epm: Unable to create script file \"%s\" - %s\n", filename,
strerror(errno));
return (1);
}
fchmod(fileno(fp), 0755);
fputs("#!/bin/sh\n", fp);
fputs("# " EPM_VERSION "\n", fp);
for (i = dist->num_commands, c = dist->commands; i > 0; i --, c ++)
if (c->type == COMMAND_POST_INSTALL && c->subpackage == subpackage)
fprintf(fp, "%s\n", c->command);
for (i = dist->num_files, file = dist->files; i > 0; i --, file ++)
if (tolower(file->type) == 'i' && file->subpackage == subpackage)
{
runlevels = get_runlevels(file, "02345");
fprintf(fp, "update-rc.d %s start %02d", file->dst,
get_start(file, 99));
for (rlptr = runlevels; isdigit(*rlptr & 255); rlptr ++)
if (*rlptr != '0')
fprintf(fp, " %c", *rlptr);
if (strchr(runlevels, '0') != NULL)
fprintf(fp, " . stop %02d 0", get_stop(file, 0));
fputs(" . >/dev/null\n", fp);
fprintf(fp, "/etc/init.d/%s start\n", file->dst);
}
fclose(fp);
}
/*
* Write the prerm file for DPKG...
*/
for (i = dist->num_commands, c = dist->commands; i > 0; i --, c ++)
if (c->type == COMMAND_PRE_REMOVE && c->subpackage == subpackage)
break;
if (!i)
for (i = dist->num_files, file = dist->files; i > 0; i --, file ++)
if (tolower(file->type) == 'i' && file->subpackage == subpackage)
break;
if (i)
{
if (Verbosity)
puts("Creating prerm script...");
snprintf(filename, sizeof(filename), "%s/%s/DEBIAN/prerm", directory, name);
if ((fp = fopen(filename, "w")) == NULL)
{
fprintf(stderr, "epm: Unable to create script file \"%s\" - %s\n", filename,
strerror(errno));
return (1);
}
fchmod(fileno(fp), 0755);
fputs("#!/bin/sh\n", fp);
fputs("# " EPM_VERSION "\n", fp);
for (i = dist->num_commands, c = dist->commands; i > 0; i --, c ++)
if (c->type == COMMAND_PRE_REMOVE && c->subpackage == subpackage)
fprintf(fp, "%s\n", c->command);
for (i = dist->num_files, file = dist->files; i > 0; i --, file ++)
if (tolower(file->type) == 'i' && file->subpackage == subpackage)
fprintf(fp, "/etc/init.d/%s stop\n", file->dst);
fclose(fp);
}
/*
* Write the postrm file for DPKG...
*/
for (i = dist->num_commands, c = dist->commands; i > 0; i --, c ++)
if (c->type == COMMAND_POST_REMOVE && c->subpackage == subpackage)
break;
if (!i)
for (i = dist->num_files, file = dist->files; i > 0; i --, file ++)
if (tolower(file->type) == 'i' && file->subpackage == subpackage)
break;
if (i)
{
if (Verbosity)
puts("Creating postrm script...");
snprintf(filename, sizeof(filename), "%s/%s/DEBIAN/postrm", directory, name);
if ((fp = fopen(filename, "w")) == NULL)
{
fprintf(stderr, "epm: Unable to create script file \"%s\" - %s\n", filename,
strerror(errno));
return (1);
}
fchmod(fileno(fp), 0755);
fputs("#!/bin/sh\n", fp);
fputs("# " EPM_VERSION "\n", fp);
for (i = dist->num_commands, c = dist->commands; i > 0; i --, c ++)
if (c->type == COMMAND_POST_REMOVE && c->subpackage == subpackage)
fprintf(fp, "%s\n", c->command);
for (i = dist->num_files, file = dist->files; i > 0; i --, file ++)
if (tolower(file->type) == 'i' && file->subpackage == subpackage)
{
fputs("if [ purge = \"$1\" ]; then\n", fp);
fprintf(fp, " update-rc.d %s remove >/dev/null\n", file->dst);
fputs("fi\n", fp);
}
fclose(fp);
}
/*
* Write the conffiles file for DPKG...
*/
if (Verbosity)
puts("Creating conffiles...");
snprintf(filename, sizeof(filename), "%s/%s/DEBIAN/conffiles", directory, name);
if ((fp = fopen(filename, "w")) == NULL)
{
fprintf(stderr, "epm: Unable to create script file \"%s\" - %s\n", filename,
strerror(errno));
return (1);
}
for (i = dist->num_files, file = dist->files; i > 0; i --, file ++)
if (tolower(file->type) == 'c' && file->subpackage == subpackage)
fprintf(fp, "%s\n", file->dst);
else if (tolower(file->type) == 'i' && file->subpackage == subpackage)
fprintf(fp, "/etc/init.d/%s\n", file->dst);
fclose(fp);
/*
* Copy the files over...
*/
if (Verbosity)
puts("Copying temporary distribution files...");
for (i = dist->num_files, file = dist->files; i > 0; i --, file ++)
{
if (file->subpackage != subpackage)
continue;
/*
* Find the username and groupname IDs...
*/
pwd = getpwnam(file->user);
grp = getgrnam(file->group);
endpwent();
endgrent();
/*
* Copy the file or make the directory or make the symlink as needed...
*/
switch (tolower(file->type))
{
case 'c' :
case 'f' :
snprintf(filename, sizeof(filename), "%s/%s%s", directory, name,
file->dst);
if (Verbosity > 1)
printf("%s -> %s...\n", file->src, filename);
if (copy_file(filename, file->src, file->mode, pwd ? pwd->pw_uid : 0,
grp ? grp->gr_gid : 0))
return (1);
break;
case 'i' :
snprintf(filename, sizeof(filename), "%s/%s/etc/init.d/%s",
directory, name, file->dst);
if (Verbosity > 1)
printf("%s -> %s...\n", file->src, filename);
if (copy_file(filename, file->src, file->mode, pwd ? pwd->pw_uid : 0,
grp ? grp->gr_gid : 0))
return (1);
break;
case 'd' :
snprintf(filename, sizeof(filename), "%s/%s%s", directory, name,
file->dst);
if (Verbosity > 1)
printf("Directory %s...\n", filename);
make_directory(filename, file->mode, pwd ? pwd->pw_uid : 0,
grp ? grp->gr_gid : 0);
break;
case 'l' :
snprintf(filename, sizeof(filename), "%s/%s%s", directory, name,
file->dst);
if (Verbosity > 1)
printf("%s -> %s...\n", file->src, filename);
make_link(filename, file->src);
break;
}
}
/*
* Build the distribution from the spec file...
*/
if (Verbosity)
printf("Building Debian %s binary distribution...\n", name);
if (run_command(directory, "dpkg --build %s", name))
return (1);
/*
* Remove temporary files...
*/
if (!KeepFiles)
{
if (Verbosity)
printf("Removing temporary %s distribution files...\n", name);
snprintf(filename, sizeof(filename), "%s/%s", directory, name);
unlink_directory(filename);
}
return (0);
}
static int /* O - 0 on success, -1 on error */
write_spec(int format, /* I - Subformat */
const char *prodname, /* I - Product name */
dist_t *dist, /* I - Distribution */
FILE *fp, /* I - Spec file */
const char *subpackage) /* I - Subpackage name */
{
int i; /* Looping var */
char name[1024]; /* Full product name */
const char *product; /* Product to depend on */
file_t *file; /* Current distribution file */
command_t *c; /* Current command */
depend_t *d; /* Current dependency */
const char *runlevels; /* Run levels */
int number; /* Start/stop number */
int have_commands; /* Have commands in current section? */
/*
* Get the name we'll use for the subpackage...
*/
if (subpackage)
snprintf(name, sizeof(name), " %s", subpackage);
else
name[0] = '\0';
/*
* Common stuff...
*/
if (subpackage)
{
fprintf(fp, "%%package%s\n", name);
fprintf(fp, "Summary: %s", dist->product);
for (i = 0; i < dist->num_descriptions; i ++)
if (dist->descriptions[i].subpackage == subpackage)
break;
if (i < dist->num_descriptions)
{
char line[1024], /* First line of description... */
*ptr; /* Pointer into line */
strlcpy(line, dist->descriptions[i].description, sizeof(line));
if ((ptr = strchr(line, '\n')) != NULL)
*ptr = '\0';
fprintf(fp, " - %s", line);
}
fputs("\n", fp);
}
else
fprintf(fp, "Summary: %s\n", dist->product);
fputs("Group: Applications\n", fp);
/*
* List all of the dependencies...
*/
for (i = dist->num_depends, d = dist->depends; i > 0; i --, d ++)
{
if (d->subpackage != subpackage)
continue;
if (!strcmp(d->product, "_self"))
product = prodname;
else
product = d->product;
if (d->type == DEPEND_REQUIRES)
fprintf(fp, "Requires: %s", product);
else if (d->type == DEPEND_PROVIDES)
fprintf(fp, "Provides: %s", product);
else if (d->type == DEPEND_REPLACES)
fprintf(fp, "Obsoletes: %s", product);
else
fprintf(fp, "Conflicts: %s", product);
if (d->vernumber[0] == 0)
{
if (d->vernumber[1] < INT_MAX)
fprintf(fp, " <= %s\n", d->version[1]);
else
putc('\n', fp);
}
else if (d->vernumber[0] && d->vernumber[1] < INT_MAX)
{
if (d->vernumber[0] < INT_MAX && d->vernumber[1] < INT_MAX)
fprintf(fp, " >= %s, %s <= %s\n", d->version[0], product,
d->version[1]);
}
else if (d->vernumber[0] != d->vernumber[1])
fprintf(fp, " >= %s\n", d->version[0]);
else
fprintf(fp, " = %s\n", d->version[0]);
}
/*
* Pre/post install commands...
*/
for (i = dist->num_commands, c = dist->commands; i > 0; i --, c ++)
if (c->type == COMMAND_PRE_INSTALL && c->subpackage == subpackage)
break;
if (i > 0)
{
fprintf(fp, "%%pre%s\n", name);
for (; i > 0; i --, c ++)
if (c->type == COMMAND_PRE_INSTALL && c->subpackage == subpackage)
fprintf(fp, "%s\n", c->command);
}
for (i = dist->num_commands, c = dist->commands; i > 0; i --, c ++)
if (c->type == COMMAND_POST_INSTALL && c->subpackage == subpackage)
break;
if (i > 0)
{
have_commands = 1;
fprintf(fp, "%%post%s\n", name);
for (; i > 0; i --, c ++)
if (c->type == COMMAND_POST_INSTALL && c->subpackage == subpackage)
fprintf(fp, "%s\n", c->command);
}
else
have_commands = 0;
for (i = dist->num_commands, c = dist->commands; i > 0; i --, c ++)
if (c->type == COMMAND_LITERAL && c->subpackage == subpackage &&
!strcmp(c->section, "spec"))
break;
if (i > 0)
{
for (; i > 0; i --, c ++)
if (c->type == COMMAND_LITERAL && c->subpackage == subpackage &&
!strcmp(c->section, "spec"))
fprintf(fp, "%s\n", c->command);
}
for (i = dist->num_files, file = dist->files; i > 0; i --, file ++)
if (tolower(file->type) == 'i' && file->subpackage == subpackage)
break;
if (i)
{
if (!have_commands)
fprintf(fp, "%%post%s\n", name);
fputs("if test \"x$1\" = x1; then\n", fp);
fputs(" echo Setting up init scripts...\n", fp);
if (format == PACKAGE_LSB)
{
/*
* Use LSB commands to install the init scripts...
*/
for (; i > 0; i --, file ++)
if (tolower(file->type) == 'i' && file->subpackage == subpackage)
{
fprintf(fp, " /usr/lib/lsb/install_initd /etc/init.d/%s\n", file->dst);
fprintf(fp, " /etc/init.d/%s start\n", file->dst);
}
}
else
{
/*
* Find where the frigging init scripts go...
*/
fputs(" rcdir=\"\"\n", fp);
fputs(" for dir in /sbin/rc.d /sbin /etc/rc.d /etc ; do\n", fp);
fputs(" if test -d $dir/rc3.d -o -h $dir/rc3.d; then\n", fp);
fputs(" rcdir=\"$dir\"\n", fp);
fputs(" fi\n", fp);
fputs(" done\n", fp);
fputs(" if test \"$rcdir\" = \"\" ; then\n", fp);
fputs(" echo Unable to determine location of startup scripts!\n", fp);
fputs(" else\n", fp);
for (; i > 0; i --, file ++)
if (tolower(file->type) == 'i' && file->subpackage == subpackage)
{
fputs(" if test -d $rcdir/init.d; then\n", fp);
qprintf(fp, " /bin/rm -f $rcdir/init.d/%s\n", file->dst);
qprintf(fp, " /bin/ln -s %s/init.d/%s "
"$rcdir/init.d/%s\n", SoftwareDir, file->dst, file->dst);
fputs(" else\n", fp);
fputs(" if test -d /etc/init.d; then\n", fp);
qprintf(fp, " /bin/rm -f /etc/init.d/%s\n", file->dst);
qprintf(fp, " /bin/ln -s %s/init.d/%s "
"/etc/init.d/%s\n", SoftwareDir, file->dst, file->dst);
fputs(" fi\n", fp);
fputs(" fi\n", fp);
for (runlevels = get_runlevels(dist->files + i, "0123456");
isdigit(*runlevels & 255);
runlevels ++)
{
if (*runlevels == '0')
number = get_stop(file, 0);
else
number = get_start(file, 99);
qprintf(fp, " /bin/rm -f $rcdir/rc%c.d/%c%02d%s\n", *runlevels,
(*runlevels == '0' || *runlevels == '1' ||
*runlevels == '6') ? 'K' : 'S', number, file->dst);
qprintf(fp, " /bin/ln -s %s/init.d/%s "
"$rcdir/rc%c.d/%c%02d%s\n", SoftwareDir, file->dst,
*runlevels,
(*runlevels == '0' || *runlevels == '1' ||
*runlevels == '6') ? 'K' : 'S', number, file->dst);
}
qprintf(fp, " %s/init.d/%s start\n", SoftwareDir, file->dst);
}
fputs(" fi\n", fp);
}
fputs("fi\n", fp);
}
for (i = dist->num_files, file = dist->files; i > 0; i --, file ++)
if (tolower(file->type) == 'i' && file->subpackage == subpackage)
break;
if (i)
{
have_commands = 1;
fprintf(fp, "%%preun%s\n", name);
fputs("if test \"x$1\" = x0; then\n", fp);
fputs(" echo Cleaning up init scripts...\n", fp);
if (format == PACKAGE_LSB)
{
/*
* Use LSB commands to remove the init scripts...
*/
for (; i > 0; i --, file ++)
if (tolower(file->type) == 'i' && file->subpackage == subpackage)
{
fprintf(fp, " /etc/init.d/%s stop\n", file->dst);
fprintf(fp, " /usr/lib/lsb/remove_initd /etc/init.d/%s\n", file->dst);
}
}
else
{
/*
* Find where the frigging init scripts go...
*/
fputs(" rcdir=\"\"\n", fp);
fputs(" for dir in /sbin/rc.d /sbin /etc/rc.d /etc ; do\n", fp);
fputs(" if test -d $dir/rc3.d -o -h $dir/rc3.d; then\n", fp);
fputs(" rcdir=\"$dir\"\n", fp);
fputs(" fi\n", fp);
fputs(" done\n", fp);
fputs(" if test \"$rcdir\" = \"\" ; then\n", fp);
fputs(" echo Unable to determine location of startup scripts!\n", fp);
fputs(" else\n", fp);
for (; i > 0; i --, file ++)
if (tolower(file->type) == 'i' && file->subpackage == subpackage)
{
qprintf(fp, " %s/init.d/%s stop\n", SoftwareDir, file->dst);
fputs(" if test -d $rcdir/init.d; then\n", fp);
qprintf(fp, " /bin/rm -f $rcdir/init.d/%s\n", file->dst);
fputs(" else\n", fp);
fputs(" if test -d /etc/init.d; then\n", fp);
qprintf(fp, " /bin/rm -f /etc/init.d/%s\n", file->dst);
fputs(" fi\n", fp);
fputs(" fi\n", fp);
for (runlevels = get_runlevels(dist->files + i, "0123456");
isdigit(*runlevels & 255);
runlevels ++)
{
if (*runlevels == '0')
number = get_stop(file, 0);
else
number = get_start(file, 99);
qprintf(fp, " /bin/rm -f $rcdir/rc%c.d/%c%02d%s\n", *runlevels,
(*runlevels == '0' || *runlevels == '1' ||
*runlevels == '6') ? 'K' : 'S', number, file->dst);
}
}
fputs(" fi\n", fp);
}
fputs("fi\n", fp);
}
else
have_commands = 0;
for (i = dist->num_commands, c = dist->commands; i > 0; i --, c ++)
if (c->type == COMMAND_PRE_REMOVE && c->subpackage == subpackage)
break;
if (i > 0)
{
if (!have_commands)
fprintf(fp, "%%preun%s\n", name);
for (; i > 0; i --, c ++)
if (c->type == COMMAND_PRE_REMOVE && c->subpackage == subpackage)
fprintf(fp, "%s\n", c->command);
}
for (i = dist->num_commands, c = dist->commands; i > 0; i --, c ++)
if (c->type == COMMAND_POST_REMOVE && c->subpackage == subpackage)
break;
if (i > 0)
{
fprintf(fp, "%%postun%s\n", name);
for (; i > 0; i --, c ++)
if (c->type == COMMAND_POST_REMOVE && c->subpackage == subpackage)
fprintf(fp, "%s\n", c->command);
}
/*
* Description...
*/
for (i = 0; i < dist->num_descriptions; i ++)
if (dist->descriptions[i].subpackage == subpackage)
break;
if (i < dist->num_descriptions)
{
fprintf(fp, "%%description %s\n", name);
for (; i < dist->num_descriptions; i ++)
if (dist->descriptions[i].subpackage == subpackage)
fprintf(fp, "%s\n", dist->descriptions[i].description);
}
/*
* Files...
*/
fprintf(fp, "%%files%s\n", name);
for (i = dist->num_files, file = dist->files; i > 0; i --, file ++)
if (file->subpackage == subpackage)
switch (tolower(file->type))
{
case 'c' :
fprintf(fp, "%%attr(%04o,%s,%s) %%config(noreplace) \"%s\"\n",
file->mode, file->user, file->group, file->dst);
break;
case 'd' :
fprintf(fp, "%%attr(%04o,%s,%s) %%dir \"%s\"\n", file->mode,
file->user, file->group, file->dst);
break;
case 'f' :
case 'l' :
fprintf(fp, "%%attr(%04o,%s,%s) \"%s\"\n", file->mode, file->user,
file->group, file->dst);
break;
case 'i' :
if (format == PACKAGE_LSB)
fprintf(fp, "%%attr(0555,root,root) \"/etc/init.d/%s\"\n",
file->dst);
else
fprintf(fp, "%%attr(0555,root,root) \"%s/init.d/%s\"\n",
SoftwareDir, file->dst);
break;
}
return (0);
}
Haplotype* generate_haplotype(Region& str_region, int32_t max_ref_flank_len, std::string& chrom_seq,
std::vector< std::vector<Alignment> >& alignments, std::vector<std::string>& vcf_alleles,
StutterModel* stutter_model, bool search_bams_for_alleles,
std::vector<HapBlock*>& blocks, std::vector<bool>& call_sample, std::ostream& logger){
assert(blocks.size() == 0);
assert(call_sample.size() == 0);
std::map<std::string, int> seqs;
// Determine the minimum and maximum alignment boundaries
int32_t min_start = INT_MAX, max_stop = INT_MIN;
for (auto vec_iter = alignments.begin(); vec_iter != alignments.end(); vec_iter++){
for (auto aln_iter = vec_iter->begin(); aln_iter != vec_iter->end(); aln_iter++){
min_start = std::min(min_start, aln_iter->get_start());
max_stop = std::max(max_stop, aln_iter->get_stop());
seqs[aln_iter->get_sequence()]++;
}
}
logger << "# Seqs = " << seqs.size() << std::endl;
// Extract candidate STR sequences (use some padding to ensure indels near STR ends are included)
std::vector<std::string> str_seqs;
int32_t left_padding = 5, right_padding = 5;
int32_t rep_region_start = str_region.start() < left_padding ? 0 : str_region.start()-left_padding;
int32_t rep_region_end = str_region.stop() + right_padding;
std::string ref_seq = uppercase(chrom_seq.substr(rep_region_start, rep_region_end-rep_region_start));
int ideal_min_length = 3*str_region.period(); // Would ideally have at least 3 repeat units in each allele after trimming
// TO DO: Use frequency of deletions not contained within window to
// i) Identify problematic regions
// ii) Retry with increased window padding?
int32_t min_del_start, max_del_stop, flank_del_start, flank_del_stop, min_ins_pos, max_ins_pos;
std::vector<bool> flank_del_call_sample, flank_ins_call_sample;
int num_ext_del = check_deletion_bounds(alignments, rep_region_start, rep_region_end, min_del_start, max_del_stop, call_sample);
int num_flank_del = check_flanking_deletions(alignments, rep_region_start, rep_region_end, flank_del_start, flank_del_stop, flank_del_call_sample);
int num_flank_ins = check_flanking_insertions(alignments, rep_region_start, rep_region_end, min_ins_pos, max_ins_pos, flank_ins_call_sample);
int nfail = std::max(num_ext_del, std::max(num_flank_del, num_flank_ins));
// Recheck deletions after expanding the STR window
if(1.0*nfail/alignments.size() <= MAX_FRAC_SAMPLE_DEL_FAIL){
logger << "PASS SAMPLE DEL STATS: " << rep_region_start << "\t" << rep_region_end << "\t" << num_ext_del
<< "\t" << min_del_start << "\t" << max_del_stop << "\t" << std::endl;
}
else {
logger << "FAIL SAMPLE DEL STATS: " << rep_region_start << "\t" << rep_region_end << "\t" << num_ext_del
<< "\t" << min_del_start << "\t" << max_del_stop << "\t" << std::endl;
int32_t min_s = std::min(min_del_start, std::min(flank_del_start, min_ins_pos));
int32_t max_e = std::max(max_del_stop, std::max(flank_del_stop, max_ins_pos));
call_sample.clear();
flank_del_call_sample.clear();
flank_ins_call_sample.clear();
rep_region_start = std::min(rep_region_start, std::max(rep_region_start-10, min_s-5));
rep_region_end = std::max(rep_region_end, std::min(rep_region_end+10, max_e+5));
left_padding = str_region.start() - rep_region_start;
right_padding = rep_region_end - str_region.stop();
ref_seq = uppercase(chrom_seq.substr(rep_region_start, rep_region_end-rep_region_start));
num_ext_del = check_deletion_bounds(alignments, rep_region_start, rep_region_end, min_del_start, max_del_stop, call_sample);
num_flank_del = check_flanking_deletions(alignments, rep_region_start, rep_region_end, flank_del_start, flank_del_stop, flank_del_call_sample);
num_flank_ins = check_flanking_insertions(alignments, rep_region_start, rep_region_end, min_ins_pos, max_ins_pos, flank_ins_call_sample);
/*
if(1.0*sample_fail_count/alignments.size() <= MAX_FRAC_SAMPLE_DEL_FAIL){
logger << "REDONE_PASS SAMPLE DEL STATS: " << rep_region_start << "\t" << rep_region_end << "\t" << sample_fail_count
<< "\t" << min_del_start << "\t" << max_del_stop << "\t" << std::endl;
}
else {
logger << "REDONE_FAIL SAMPLE DEL STATS: " << rep_region_start << "\t" << rep_region_end << "\t" << sample_fail_count
<< "\t" << min_del_start << "\t" << max_del_stop << "\t" << std::endl;
}
*/
}
/*
logger << "# Flank deletions = " << num_flank_del << ", # Flank insertions = " << num_flank_ins << std::endl;
for (unsigned int i = 0; i < call_sample.size(); i++)
call_sample[i] = call_sample[i] && flank_del_call_sample[i] && flank_ins_call_sample[i];
*/
// Trim boundaries so that the reference flanks aren't too long
if (rep_region_start > max_ref_flank_len)
min_start = std::max(rep_region_start-max_ref_flank_len, min_start);
max_stop = std::min(rep_region_end+max_ref_flank_len, max_stop);
// Extend each VCF allele by padding size
std::vector<std::string> ext_vcf_alleles;
if (vcf_alleles.size() != 0){
std::string lflank = uppercase(chrom_seq.substr(rep_region_start, str_region.start()-rep_region_start));
std::string rflank = uppercase(chrom_seq.substr(str_region.stop(), rep_region_end-str_region.stop()));
for (unsigned int i = 0; i < vcf_alleles.size(); i++){
ext_vcf_alleles.push_back(lflank + vcf_alleles[i] + rflank);
logger << ext_vcf_alleles.back() << std::endl;
}
logger << ext_vcf_alleles[0] << std::endl << ref_seq << std::endl;
assert(ext_vcf_alleles[0].compare(ref_seq) == 0);
}
generate_candidate_str_seqs(ref_seq, chrom_seq, left_padding, right_padding, ideal_min_length, alignments,
ext_vcf_alleles, search_bams_for_alleles, rep_region_start, rep_region_end, str_seqs, logger);
// Create a set of haplotype regions, consisting of STR sequence block flanked by two reference sequence stretches
assert(rep_region_start > min_start && rep_region_end < max_stop);
assert(str_seqs[0].compare(uppercase(chrom_seq.substr(rep_region_start, rep_region_end-rep_region_start))) == 0);
blocks.clear();
blocks.push_back(new HapBlock(min_start, rep_region_start, uppercase(chrom_seq.substr(min_start, rep_region_start-min_start)))); // Ref sequence preceding STRS
blocks.push_back(new RepeatBlock(rep_region_start, rep_region_end,
uppercase(chrom_seq.substr(rep_region_start, rep_region_end-rep_region_start)), str_region.period(), stutter_model));
blocks.push_back(new HapBlock(rep_region_end, max_stop, uppercase(chrom_seq.substr(rep_region_end, max_stop-rep_region_end)))); // Ref sequence following STRs
for (unsigned int j = 1; j < str_seqs.size(); j++)
blocks[1]->add_alternate(str_seqs[j]);
// Initialize each block's data structures, namely the homopolymer length information
for (unsigned int i = 0; i < blocks.size(); i++)
blocks[i]->initialize();
logger << "Constructing haplotype" << std::endl;
Haplotype* haplotype = new Haplotype(blocks);
haplotype->print_block_structure(30, 100, logger);
return haplotype;
}
