From 72ee103549d9e268ccd1b97f60228b575b84e07d Mon Sep 17 00:00:00 2001 From: agudys Date: Fri, 13 Jul 2018 13:45:20 +0200 Subject: [PATCH] Small changes in help screen. --- src/mapper/whisper.cpp | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/src/mapper/whisper.cpp b/src/mapper/whisper.cpp index 9b0069a..415020c 100644 --- a/src/mapper/whisper.cpp +++ b/src/mapper/whisper.cpp @@ -74,16 +74,18 @@ void usage() // cerr << " -o - approximate amount of RAM in GB (default: " << cmd_params.max_total_memory << "; must be at least equal no. threads, but not less than 8)\n"; cerr << " -out - name of the output file (default: " << cmd_params.project_name << ")\n"; cerr << " -penalty-saturation - no. of sigmas for max. penalty in matching pairs (default: " << cmd_params.penalty_saturation_sigmas << ")\n"; - cerr << " -rg - complete read group header line, ’\t’ character will be converted to a TAB in the output SAM while the read group ID will be attached to every read (example line: ’@RG\tID:foo\tSM:bar’)\n"; - cerr << " -r[s|p] - single or paired-end reads (default: " << (cmd_params.paired_reads ? "paired" : "single") << ")\n"; + cerr << " -rg - complete read group header line, (example: '@RG\\tID:foo\\tSM:bar')\n" + " '\\t' character will be converted to a TAB in the output SAM/BAM,\n" + " while the read group ID will be attached to every read \n"; + cerr << " -r[s|p] - single or paired-end reads (default: " << (cmd_params.paired_reads ? "paired" : "single") << ")\n"; cerr << " -score-discretization-threshold (default: " << cmd_params.score_discretization_threshold << ")\n"; cerr << " -score-match - score for matching symbol (default: " << cmd_params.match_score << ")\n"; cerr << " -score-clipping score for clipping (default: " << cmd_params.clipping_score << ")\n"; cerr << " -score-mismatch - score for mismatching symbol (default: " << cmd_params.mismatch_score << ")\n"; cerr << " -sens - turn on/off sensitive mode (default: " << (bool) cmd_params.sensitive_mode << ")\n"; cerr << " -sens-factor - sensitivity factor (default: " << cmd_params.sensitivity_factor << ")\n"; - cerr << " -stdout - use stdout to store the output (default: " << cmd_params.use_stdout << ")\n"; - cerr << " -store-BAM - turn on saving in BAM (default: " << (bool)cmd_params.store_BAM << ")\n"; + cerr << " -stdout - use stdout to store the output\n"; + cerr << " -store-BAM - turn on saving in BAM\n"; cerr << " -t - no. of threads (0-adjust to hardware) (default: " << cmd_params.no_threads << ")\n"; cerr << " -temp - prefix for temporary files (default: " << cmd_params.temp_prefix << ")\n"; cerr << " -x - load complete suffix arrays in main memory (default: " << cmd_params.sa_in_ram << ")\n";