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Searched refs:first_read_file (Results 1 – 6 of 6) sorted by relevance

/dports/biology/subread/subread-2.0.2-source/src/
H A DSUBindel.c55 …read_length<0 ||geinput_open_sam(context->config.first_read_file, &context->input_reads.first_read… in load_global_context_forindel()
57 …ission to read it, and it is in the FASTQ/FASTA/PLAIN format.\n", context->config.first_read_file); in load_global_context_forindel()
63 stat(context->config.first_read_file , &ginp1_stat); in load_global_context_forindel()
148 if(feof((FILE *)global_context -> input_reads.first_read_file.input_fp))break; in transfer_SAM_to_assembly()
152 geinput_readline(&global_context -> input_reads.first_read_file, linebuf,0); in transfer_SAM_to_assembly()
217 geinput_readline_back(&global_context -> input_reads.first_read_file, linebuf); in transfer_SAM_to_assembly()
273 print_in_box(80,0,0," Input file : %s", global_context -> config.first_read_file ); in print_configuration_forindel()
347 strncpy(global_context->config.first_read_file, optarg, MAX_FILE_NAME_LENGTH-1); in main()
393 …warning_file_type(global_context->config.first_read_file,global_context->config.is_BAM_input?FILE_… in main()
H A Dcore.c521 gene_input_t * ginp1 = &global_context->input_reads.first_read_file; in show_progress()
1091 fname = global_context ->config.first_read_file;
2221 *ginp1 = &global_context->input_reads.first_read_file;
3561 if(global_context -> input_reads.first_read_file.file_type == GENE_INPUT_BCL)
3569 if(global_context -> input_reads.first_read_file.file_type == GENE_INPUT_BCL)
3767 const char *strmm_tmp = context->config.first_read_file;
3832 if(!context->config.first_read_file[0])
4064 if(core_geinput_open(context, &context->input_reads.first_read_file, 1)) {
4115 stat(context->config.first_read_file , &ginp1_stat);
4315 geinput_close(&context -> input_reads.first_read_file);
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H A Dcore.h97 gene_input_t first_read_file; member
141 char first_read_file[MAX_FILE_NAME_LENGTH * MAX_SCRNA_FASTQ_FILES * 3]; member
H A Dcore-interface-aligner.c408 …strncpy(global_context->config.first_read_file, optarg, MAX_FILE_NAME_LENGTH * 3 * MAX_SCRNA_FASTQ… in parse_opts_aligner()
H A Dcore-interface-subjunc.c338 strncpy(global_context->config.first_read_file, optarg, MAX_FILE_NAME_LENGTH-1); in parse_opts_subjunc()
H A Dcore-indel.c4508 context->config.first_read_file[0] = 0; in init_global_context()