int load_global_context_forindel(global_context_t * context)
{
char tmp_fname [MAX_FILE_NAME_LENGTH];
warning_file_limit();
context -> input_reads.avg_read_length = guess_reads_density_format(context->config.first_read_file , 0, NULL, NULL);
if(context -> input_reads.avg_read_length<0 )context -> input_reads.avg_read_length = 250;
if(context -> input_reads.avg_read_length<0 ||geinput_open_sam(context->config.first_read_file, &context->input_reads.first_read_file, context -> input_reads.is_paired_end_reads))
{
SUBREADprintf("Unable to open '%s' as a read file. Please check if it exists, you have the permission to read it, and it is in the FASTQ/FASTA/PLAIN format.\n", context->config.first_read_file);
return -1;
}
struct stat ginp1_stat;
stat(context->config.first_read_file , &ginp1_stat);
context->input_reads.first_read_file_size = ginp1_stat.st_size;
sprintf(tmp_fname, "%s.reads", context->config.index_prefix);
if(!does_file_exist(tmp_fname))
{
SUBREADprintf("Unable top open index '%s'. Please make sure that the correct prefix is specified and you have the permission to read these files. For example, if there are files '/opt/my_index.reads', '/opt/my_index.files' and etc, the index prefix should be specified as '/opt/my_index' without any suffix. \n", context->config.index_prefix);
return -1;
}
if(context->config.space_type == GENE_SPACE_COLOR)
sprintf(tmp_fname, "%s.00.c.tab", context->config.index_prefix);
else
sprintf(tmp_fname, "%s.00.b.tab", context->config.index_prefix);
if(!does_file_exist(tmp_fname))
{
SUBREADprintf("Your reads are in the %s space but the index was not built in the same space. Unable to precess the reads.\n", context->config.space_type == GENE_SPACE_COLOR?"color":"base");
return -1;
}
context->index_block_number = 0;
while(1)
{
sprintf(tmp_fname, "%s.%02d.%c.tab", context->config.index_prefix, context->index_block_number, context->config.space_type == GENE_SPACE_COLOR?'c':'b');
if(!does_file_exist(tmp_fname))break;
context->index_block_number ++;
}
context->current_index_block_number = 0;
load_offsets(&context->chromosome_table, context->config.index_prefix);
context->all_processed_reads = 0;
context->all_mapped_reads = 0;
memset( context->all_value_indexes , 0 , 100 * sizeof(gene_value_index_t));
return 0;
}
/**
* The function creates and loads a new flux_cube structure
* The data is taken from the file specified in the input.
*
* @param fcube_file - the file name of the fluxcube
*
* @return ret - the new flux_cube structure
*/
flux_cube *
load_fluxcube(const char fcube_file[])
{
flux_cube *fcube;
gsl_matrix *test;
int nflux, n_ext=0;
int i;
// get the number of extensions
n_ext = FITSextnum(fcube_file);
if (n_ext <3)
aXe_message(aXe_M_FATAL, __FILE__, __LINE__,
"aXe_PETCONT: " "the fluxcube file %s has only %i extensions!\n",
fcube_file, n_ext);
// determine the number of flux images and allocate
// the space for the fluxcube structure
nflux = n_ext-2;
fcube = alloc_fluxcube(nflux);
// load XOFFS and YOFFS
load_offsets(fcube_file, fcube);
// load the segmentation image into the structure
fcube->segmentation = load_segmentation(fcube_file);
// gsl_to_FITSimage (fcube->segmentation, "gogo.fits", 1, "MOO");
// load the fluximages
for (i=0; i < nflux; i++)
{
fcube->fluxims[i] = load_fluximage(fcube_file, i+3);
}
// fill the number of fluximages
fcube->n_fimage = nflux;
// order the fluximages and store the
// vector with the ordered indices
fcube->fimage_order = order_fluxims(fcube);
return fcube;
}
int main_Fst2Txt(int argc,char* const argv[]) {
if (argc==1) {
usage();
return SUCCESS_RETURN_CODE;
}
struct fst2txt_parameters* p=new_fst2txt_parameters();
char in_offsets[FILENAME_MAX]="";
char out_offsets[FILENAME_MAX]="";
int val,index=-1;
bool only_verify_arguments = false;
UnitexGetOpt options;
while (EOF!=(val=options.parse_long(argc,argv,optstring_Fst2Txt,lopts_Fst2Txt,&index))) {
switch(val) {
case 't': if (options.vars()->optarg[0]=='\0') {
error("You must specify a non empty text file name\n");
free_fst2txt_parameters(p);
return USAGE_ERROR_CODE;
}
p->input_text_file=strdup(options.vars()->optarg);
if (p->input_text_file==NULL) {
alloc_error("main_Fst2Txt");
free_fst2txt_parameters(p);
return ALLOC_ERROR_CODE;
}
break;
case 'o': if (options.vars()->optarg[0]=='\0') {
error("You must specify a non empty text output file name\n");
free_fst2txt_parameters(p);
return USAGE_ERROR_CODE;
}
p->output_text_file=strdup(options.vars()->optarg);
p->output_text_file_is_temp=0;
if (p->output_text_file==NULL) {
alloc_error("main_Fst2Txt");
free_fst2txt_parameters(p);
return ALLOC_ERROR_CODE;
}
break;
case 'a': if (options.vars()->optarg[0]=='\0') {
error("You must specify a non empty alphabet file name\n");
free_fst2txt_parameters(p);
return USAGE_ERROR_CODE;
}
p->alphabet_file=strdup(options.vars()->optarg);
if (p->alphabet_file==NULL) {
alloc_error("main_Fst2Txt");
free_fst2txt_parameters(p);
return ALLOC_ERROR_CODE;
}
break;
case 'M': p->output_policy=MERGE_OUTPUTS; break;
case 'R': p->output_policy=REPLACE_OUTPUTS; break;
case 'c': p->tokenization_policy=CHAR_BY_CHAR_TOKENIZATION; break;
case 'w': p->tokenization_policy=WORD_BY_WORD_TOKENIZATION; break;
case 's': p->space_policy=START_WITH_SPACE; break;
case 'x': p->space_policy=DONT_START_WITH_SPACE; break;
case 'V': only_verify_arguments = true;
break;
case 'h': usage();
free_fst2txt_parameters(p);
return SUCCESS_RETURN_CODE;
case ':': index==-1 ? error("Missing argument for option -%c\n",options.vars()->optopt) :
error("Missing argument for option --%s\n",lopts_Fst2Txt[index].name);
free_fst2txt_parameters(p);
return USAGE_ERROR_CODE;
case 'k': if (options.vars()->optarg[0]=='\0') {
error("Empty input_encoding argument\n");
free_fst2txt_parameters(p);
return USAGE_ERROR_CODE;
}
decode_reading_encoding_parameter(&(p->vec.mask_encoding_compatibility_input),options.vars()->optarg);
break;
case 'q': if (options.vars()->optarg[0]=='\0') {
error("Empty output_encoding argument\n");
free_fst2txt_parameters(p);
return USAGE_ERROR_CODE;
}
decode_writing_encoding_parameter(&(p->vec.encoding_output),&(p->vec.bom_output),options.vars()->optarg);
break;
case '$': if (options.vars()->optarg[0]=='\0') {
error("Empty input_offsets argument\n");
free_fst2txt_parameters(p);
return USAGE_ERROR_CODE;
}
strcpy(in_offsets,options.vars()->optarg);
break;
case '@': if (options.vars()->optarg[0]=='\0') {
error("Empty output_offsets argument\n");
free_fst2txt_parameters(p);
return USAGE_ERROR_CODE;
}
strcpy(out_offsets,options.vars()->optarg);
break;
case 'l': p->convLFtoCRLF=0; break;
case 'r': p->keepCR = 1; break;
case '?': index==-1 ? error("Invalid option -%c\n",options.vars()->optopt) :
error("Invalid option --%s\n",options.vars()->optarg);
free_fst2txt_parameters(p);
return USAGE_ERROR_CODE;
}
index=-1;
}
if (options.vars()->optind!=argc-1) {
error("Invalid arguments: rerun with --help\n");
free_fst2txt_parameters(p);
return USAGE_ERROR_CODE;
}
if (p->input_text_file==NULL) {
error("You must specify the text file\n");
free_fst2txt_parameters(p);
return USAGE_ERROR_CODE;
}
if (only_verify_arguments) {
// freeing all allocated memory
free_fst2txt_parameters(p);
return SUCCESS_RETURN_CODE;
}
if (out_offsets[0]!='\0') {
/* We deal with offsets only if the program is expected to produce some */
if (in_offsets[0]!='\0') {
p->v_in_offsets=load_offsets(&(p->vec),in_offsets);
if (p->v_in_offsets==NULL) {
error("Cannot load offset file %s\n",in_offsets);
free_fst2txt_parameters(p);
return DEFAULT_ERROR_CODE;
}
} else {
/* If there is no input offset file, we create an empty offset vector
* in order to avoid testing whether the vector is NULL or not */
p->v_in_offsets=new_vector_offset(1);
}
p->f_out_offsets=u_fopen(&(p->vec),out_offsets,U_WRITE);
if (p->f_out_offsets==NULL) {
error("Cannot create file %s\n",out_offsets);
free_fst2txt_parameters(p);
return DEFAULT_ERROR_CODE;
}
}
if (p->output_text_file == NULL) {
char tmp[FILENAME_MAX];
remove_extension(p->input_text_file, tmp);
strcat(tmp, ".tmp");
p->output_text_file_is_temp=1;
p->output_text_file = strdup(tmp);
if (p->output_text_file == NULL) {
alloc_error("main_Fst2Txt");
free_fst2txt_parameters(p);
return ALLOC_ERROR_CODE;
}
}
p->fst_file=strdup(argv[options.vars()->optind]);
if (p->fst_file==NULL) {
alloc_error("main_Fst2Txt");
free_fst2txt_parameters(p);
return ALLOC_ERROR_CODE;
}
int result=main_fst2txt(p);
free_fst2txt_parameters(p);
return result;
}
int main_Normalize(int argc,char* const argv[]) {
if (argc==1) {
usage();
return SUCCESS_RETURN_CODE;
}
int mode=KEEP_CARRIAGE_RETURN;
int separator_normalization=1;
char rules[FILENAME_MAX]="";
char input_offsets[FILENAME_MAX]="";
char output_offsets[FILENAME_MAX]="";
VersatileEncodingConfig vec=VEC_DEFAULT;
int convLFtoCRLF=1;
int val,index=-1;
bool only_verify_arguments = false;
UnitexGetOpt options;
while (EOF!=(val=options.parse_long(argc,argv,optstring_Normalize,lopts_Normalize,&index))) {
switch(val) {
case 'l': convLFtoCRLF=0; break;
case 'n': mode=REMOVE_CARRIAGE_RETURN; break;
case 'r': if (options.vars()->optarg[0]=='\0') {
error("You must specify a non empty replacement rule file name\n");
return USAGE_ERROR_CODE;
}
strcpy(rules,options.vars()->optarg);
break;
case 1: separator_normalization=0; break;
case 'k': if (options.vars()->optarg[0]=='\0') {
error("Empty input_encoding argument\n");
return USAGE_ERROR_CODE;
}
decode_reading_encoding_parameter(&(vec.mask_encoding_compatibility_input),options.vars()->optarg);
break;
case 'q': if (options.vars()->optarg[0]=='\0') {
error("Empty output_encoding argument\n");
return USAGE_ERROR_CODE;
}
decode_writing_encoding_parameter(&(vec.encoding_output),&(vec.bom_output),options.vars()->optarg);
break;
case '$': if (options.vars()->optarg[0]=='\0') {
error("You must specify a non empty input offset file name\n");
return USAGE_ERROR_CODE;
}
strcpy(input_offsets,options.vars()->optarg);
break;
case '@': if (options.vars()->optarg[0]=='\0') {
error("You must specify a non empty output offset file name\n");
return USAGE_ERROR_CODE;
}
strcpy(output_offsets,options.vars()->optarg);
break;
case 'V': only_verify_arguments = true;
break;
case 'h': usage();
return SUCCESS_RETURN_CODE;
case ':': index==-1 ? error("Missing argument for option -%c\n",options.vars()->optopt) :
error("Missing argument for option --%s\n",lopts_Normalize[index].name);
return USAGE_ERROR_CODE;
break;
case '?': index==-1 ? error("Invalid option -%c\n",options.vars()->optopt) :
error("Invalid option --%s\n",options.vars()->optarg);
return USAGE_ERROR_CODE;
break;
}
index=-1;
}
if (options.vars()->optind!=argc-1) {
error("Invalid arguments: rerun with --help\n");
return USAGE_ERROR_CODE;
}
if (only_verify_arguments) {
// freeing all allocated memory
return SUCCESS_RETURN_CODE;
}
vector_offset* v_input_offsets=NULL;
vector_offset* v_output_offsets=NULL;
U_FILE* f_output_offsets=NULL;
if (output_offsets[0]!='\0') {
/* We deal with offsets only if we have to produce output offsets */
if (input_offsets[0]!='\0') {
v_input_offsets=load_offsets(&vec,input_offsets);
}
f_output_offsets=u_fopen(&vec, output_offsets, U_WRITE);
if (f_output_offsets==NULL) {
error("Cannot create offset file %s\n",output_offsets);
return DEFAULT_ERROR_CODE;
}
v_output_offsets=new_vector_offset();
}
char tmp_file[FILENAME_MAX];
get_extension(argv[options.vars()->optind],tmp_file);
if (!strcmp(tmp_file, ".snt")) {
/* If the file to process has already the .snt extension, we temporary rename it to
* .snt.normalizing */
strcpy(tmp_file,argv[options.vars()->optind]);
strcat(tmp_file,".normalizing");
af_rename(argv[options.vars()->optind],tmp_file);
} else {
strcpy(tmp_file,argv[options.vars()->optind]);
}
/* We set the destination file */
char dest_file[FILENAME_MAX];
remove_extension(argv[options.vars()->optind],dest_file);
strcat(dest_file,".snt");
u_printf("Normalizing %s...\n",argv[options.vars()->optind]);
int return_value = normalize(tmp_file,
dest_file,
&vec,
mode,
convLFtoCRLF,
rules,
v_output_offsets,
separator_normalization);
u_printf("\n");
/* If we have used a temporary file, we delete it */
if (strcmp(tmp_file,argv[options.vars()->optind])) {
af_remove(tmp_file);
}
process_offsets(v_input_offsets,v_output_offsets,f_output_offsets);
u_fclose(f_output_offsets);
free_vector_offset(v_input_offsets);
free_vector_offset(v_output_offsets);
u_printf((return_value==SUCCESS_RETURN_CODE) ? "Done.\n" : "Unsuccessfull.\n");
return return_value;
}
