/*
* POST: Closes the gt_input_file
* RETURN VALUE: Returns zero on success and error code
*/
gt_status gt_input_file_close(gt_input_file* const input_file) {
GT_INPUT_FILE_CHECK(input_file);
gt_status status = GT_INPUT_FILE_OK;
#ifdef HAVE_BZLIB
int bzerr;
#endif
switch (input_file->file_type) {
case REGULAR_FILE:
gt_free(input_file->file_buffer);
if (fclose(input_file->file)) status = GT_INPUT_FILE_CLOSE_ERR;
break;
case GZIPPED_FILE:
gt_free(input_file->file_buffer);
#ifdef HAVE_ZLIB
if (gzclose((gzFile)input_file->file)) status = GT_INPUT_FILE_CLOSE_ERR;
#endif
break;
case BZIPPED_FILE:
gt_free(input_file->file_buffer);
#ifdef HAVE_BZLIB
BZ2_bzReadClose(&bzerr,input_file->file);
if (bzerr!=BZ_OK) status = GT_INPUT_FILE_CLOSE_ERR;
#endif
break;
case MAPPED_FILE:
gt_cond_error(munmap(input_file->file,input_file->file_size)==-1,SYS_UNMAP);
if (close(input_file->fildes)) status = GT_INPUT_FILE_CLOSE_ERR;
break;
case STREAM:
gt_free(input_file->file_buffer);
break;
}
gt_free(input_file);
return status;
}
GT_INLINE void gt_sam_header_add_sequence_record(gt_sam_headers* const sam_headers,gt_sam_header_record* const header_record) {
GT_SAM_HEADERS_CHECK(sam_headers);
gt_string *sn_tag=gt_sam_header_record_get_tag(header_record,"SN");
gt_cond_error(!sn_tag,PARSE_SAM_HEADER_MISSING_TAG,"SQ","SN");
gt_cond_error(!gt_sam_header_record_get_tag(header_record,"LN"),PARSE_SAM_HEADER_MISSING_TAG,"SQ","LN");
if(sn_tag) {
if(!sam_headers->sequence_dictionary_sn_hash) sam_headers->sequence_dictionary_sn_hash=gt_shash_new();
char *sn_str=gt_string_get_string(sn_tag);
size_t* ix=gt_shash_get_element(sam_headers->sequence_dictionary_sn_hash,sn_str);
// If SN Tag already exists, overwrite.
if(ix) {
gt_sam_header_record_delete(*(gt_sam_header_record **)gt_vector_get_elm(sam_headers->sequence_dictionary,*ix,gt_sam_header_record*));
gt_vector_set_elm(sam_headers->sequence_dictionary,*ix,gt_sam_header_record*,header_record);
gt_error(PARSE_SAM_HEADER_DUPLICATE_TAG,"SQ","SN",sn_str);
} else {
ix=gt_alloc(size_t);
*ix=gt_vector_get_used(sam_headers->sequence_dictionary);
gt_shash_insert(sam_headers->sequence_dictionary_sn_hash,sn_str,ix,size_t*);
gt_vector_insert(sam_headers->sequence_dictionary,header_record,gt_sam_header_record*);
}
}
