config_handler::config_handler(argos::index::Index* the_index)
: the_index_(the_index)
, idx_name(get_index_name(the_index))
, logger(Logger::getInstance("main"))
, acc(Logger::getInstance(std::string("access.")+idx_name))
, err(Logger::getInstance(std::string("error.")+idx_name))
{}
void SRAssembler::merge_mapped_files(int round){
for (unsigned int lib_idx=0;lib_idx<this->libraries.size();lib_idx++){
Library lib = this->libraries[lib_idx];
logger->debug("Merge files...");
//copy reads we have so far, for debugging
string left_files = tmp_dir + "/output_matched_left_" + int2str(round) + "_" + int2str(lib_idx + 1) + "_*";
string cmd = "cat " + left_files + " >> " + lib.get_matched_left_read_name();
logger->debug(cmd);
run_shell_command(cmd);
cmd = "rm -f " + left_files;
logger->debug(cmd);
run_shell_command(cmd);
if (lib.get_paired_end()) {
string right_files = tmp_dir + "/output_matched_right_" + int2str(round) + "_" + int2str(lib_idx + 1) + "_*";
cmd = "cat " + right_files + " >> " + lib.get_matched_right_read_name();
logger->debug(cmd);
run_shell_command(cmd);
cmd = "rm -f " + right_files;
logger->debug(cmd);
run_shell_command(cmd);
}
//cmd = "cat " + tmp_dir + "/output_matched_joined_" + int2str(round) + "_" + int2str(lib_idx) + "* > " + tmp_dir + "/output_matched_joined_" + int2str(round) + "_" + int2str(lib_idx) + ".fasta";
if (round > 1)
run_shell_command("cp " + lib.get_matched_left_read_name() + " " + lib.get_matched_left_read_name(round));
if (lib.get_paired_end() && round > 1)
run_shell_command("cp " + lib.get_matched_right_read_name() + " " + lib.get_matched_right_read_name(round));
}
string cmd = "rm -f " + get_index_name(round) + ".*";;
logger->debug(cmd);
run_shell_command(cmd);
logger->debug("done.");
}
off_t bi_tree_search(FILE *bindexfile, FILE *indexfile, char *seqname){
char *tmp=NULL;
off_t maxposition, minposition=-1, target;
off_t fposition;
int sw;
size_t size;
/* int no_found_count=0; */
/* set position */
fseeko(bindexfile, (off_t)0, SEEK_SET);
/* measure data size */
/* tmp=(char *)malloc(MAXLETTER_FIRSTPIC_B);*/
uhmin_fgets(&tmp,MAXLETTER_FIRSTPIC_B-1,bindexfile);
size=strlen(tmp);
/* measure file length */
fseeko(bindexfile, (off_t)0, SEEK_END);
/* printf("Max File Position: %lld\n", ftello(bindexfile)); */ /* debug */
maxposition=ftello(bindexfile)/size;
/* seek sequence */
target=(minposition+maxposition)/2;
fseeko(bindexfile,target*(off_t)size,SEEK_SET);
while(1){
if(tmp!=NULL){free(tmp); tmp=NULL;}
fposition=get_index_name(bindexfile,indexfile,&tmp);
sw=compare(tmp,seqname);
/* fprintf(stderr,"comp: [%s], %d \n",tmp, sw); */ /* debug */
if (sw==0) break;
else if (sw<0) maxposition=target;
else minposition=target;
if (maxposition-minposition==1) break;
target=(maxposition+minposition)/2 ;
/*printf("current %ld, jump %ld\n",ftello(bindexfile),target*size-ftello(bindexfile));*/
if (fseeko(bindexfile,target*(off_t)size,SEEK_SET)!=0) break;
}
if(tmp!=NULL){free(tmp); tmp=NULL;}
if (sw==0) {
/*fprintf(stderr,"successfully find sequence \n%s\n",tmp);*/
}else {
fprintf(stderr,"could not find the sequence %s.\n",seqname);
return -1;
}
return fposition;
}
int SRAssembler::do_alignment(int round, int lib_idx, int idx) {
Library lib = this->libraries[lib_idx];
logger->info("Aligning: round = " + int2str(round) + " Lib (" + int2str(lib_idx+1) + "/" + int2str(this->libraries.size()) + "), Reads (" + int2str(idx) + "/" + int2str(lib.get_num_parts()) + ")");
Aligner* aligner = get_aligner(round);
string program_name = aligner->get_program_name();
if (round == 1)
program_name += "_init";
Params params = this->read_param_file(program_name);
aligner->do_alignment(get_index_name(round), get_type(round), get_match_length(round), get_mismatch_allowed(round), lib.get_split_file_name(idx, aligner->get_format()), params, get_output_file_name(round, lib_idx, idx));
int ret = aligner->parse_output(get_output_file_name(round, lib_idx, idx), mapped_reads, lib.get_split_file_name(idx, lib.get_format()), lib.get_matched_left_read_name(round, idx), lib.get_matched_right_read_name(round, idx), fastq_format, lib.get_format());
string cmd = "rm -f " + get_output_file_name(round, lib_idx, idx);
save_mapped_reads(round);
run_shell_command(cmd);
return ret;
}
void SRAssembler::create_index(int round) {
Aligner* aligner = get_aligner(round);
aligner->create_index(get_index_name(round), get_type(round), get_index_fasta_file_name(round));
}
