static int gt_csa_runner(GT_UNUSED int argc, const char **argv, int parsed_args,
void *tool_arguments, GtError *err)
{
GtNodeStream *gff3_in_stream, *csa_stream, *gff3_out_stream;
CSAArguments *arguments = tool_arguments;
int had_err;
gt_error_check(err);
gt_assert(arguments);
/* create the streams */
gff3_in_stream = gt_gff3_in_stream_new_sorted(argv[parsed_args]);
if (arguments->verbose && arguments->outfp)
gt_gff3_in_stream_show_progress_bar((GtGFF3InStream*) gff3_in_stream);
csa_stream = gt_csa_stream_new(gff3_in_stream, arguments->join_length);
gff3_out_stream = gt_gff3_out_stream_new(csa_stream, arguments->outfp);
/* pull the features through the stream and free them afterwards */
had_err = gt_node_stream_pull(gff3_out_stream, err);
/* free */
gt_node_stream_delete(gff3_out_stream);
gt_node_stream_delete(csa_stream);
gt_node_stream_delete(gff3_in_stream);
return had_err;
}
static int csa_stream_lua_new(lua_State *L)
{
GtNodeStream **csa_stream, **in_stream;
long join_length;
in_stream = check_genome_stream(L, 1);
if (lua_gettop(L) >= 2) {
join_length = luaL_checklong(L, 2);
luaL_argcheck(L, join_length >= 0, 2, "must be >= 0");
}
else
join_length = GT_DEFAULT_JOIN_LENGTH;
csa_stream = lua_newuserdata(L, sizeof (GtNodeStream*));
gt_assert(csa_stream);
*csa_stream = gt_csa_stream_new(*in_stream, join_length);
luaL_getmetatable(L, GENOME_STREAM_METATABLE);
lua_setmetatable(L, -2);
return 1;
}