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comparison ideas.R @ 167:c5b77e9b36f1 draft

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Uploaded
author greg
date Fri, 19 Jan 2018 11:11:12 -0500
parents 7d33a8157c6b
children 59ed3d424524
comparison
equal deleted inserted replaced
166:7d33a8157c6b 167:c5b77e9b36f1
351 rc = system(cmd); 351 rc = system(cmd);
352 if (rc != 0) { 352 if (rc != 0) {
353 if (is.null(save_ideas_log)) { 353 if (is.null(save_ideas_log)) {
354 file.rename(default_log_name, output_log); 354 file.rename(default_log_name, output_log);
355 } 355 }
356 quit(rc); 356 quit(save="no", status=rc);
357 } 357 }
358 } 358 }
359 359
360 default_log_name = "ideas_log.txt"; 360 default_log_name = "ideas_log.txt";
361 windows_by_chrom = get_windows_by_chrom(opt$windows_config); 361 windows_by_chrom = get_windows_by_chrom(opt$windows_config);
379 line = windows_by_chrom[i]; 379 line = windows_by_chrom[i];
380 items = strsplit(line, " ")[[1]]; 380 items = strsplit(line, " ")[[1]];
381 chrom = items[1]; 381 chrom = items[1];
382 window_start = items[2]; 382 window_start = items[2];
383 window_end = items[3]; 383 window_end = items[3];
384 output_name = paste(output_base_name,, chrom, sep="."); 384 output_name = paste(output_base_name, chrom, sep=".");
385 cmd = paste(base_cmd, "-inv", window_start, window_end, sep=" "); 385 cmd = paste(base_cmd, "-inv", window_start, window_end, sep=" ");
386 cmd = paste(cmd, "-o", output_name, sep=" "); 386 cmd = paste(cmd, "-o", output_name, sep=" ");
387 cmd = add_output_redirect(cmd, opt$save_ideas_log, opt$output_log, default_log_name); 387 cmd = add_output_redirect(cmd, opt$save_ideas_log, opt$output_log, default_log_name);
388 run_cmd(cmd, opt$save_ideas_log, opt$output_log, default_log_name); 388 run_cmd(cmd, opt$save_ideas_log, opt$output_log, default_log_name);
389 } 389 }