From 7586d7030c0634be6a2499cf966cc4124ceacefb Mon Sep 17 00:00:00 2001 From: agudys Date: Wed, 1 Jul 2020 19:47:14 +0200 Subject: [PATCH] Fixed inconsistencies in README and help messages. Fixed bug in command line arguments control (#10, #11, #12, #13). --- README.md | 2 +- src/common/defs.h | 2 +- src/mapper/whisper.cpp | 17 +++++++++-------- 3 files changed, 11 insertions(+), 10 deletions(-) diff --git a/README.md b/README.md index 200943f..b08223e 100644 --- a/README.md +++ b/README.md @@ -81,7 +81,7 @@ Options: * `-gap-del-extend ` - score for gap (del) extend (default: -0.4) * `-gap-ins-open ` - score for gap (ins) open (default: -5) * `-gap-ins-extend ` - score for gap (ins) extend (default: -0.4) - * `-gzipped-SAM-level ` - gzip compression level of SAM/BAM, 0 - no compression (default: 0) + * `-gzipped-SAM ` - gzip compression level of SAM/BAM, 0 - no compression (default: 0) * `-high-confidence-sigmas ` - (default: 4) * `-hit-merging-threshold ` - minimal distance between different mappings (default: 12) * `-hit-merging-wrt-first ` - calculate distance in marged group w.r.t. first (default: 1) diff --git a/src/common/defs.h b/src/common/defs.h index 177a46f..cfc9f64 100644 --- a/src/common/defs.h +++ b/src/common/defs.h @@ -34,7 +34,7 @@ #include using namespace std; -#define MAPPER_VERSION "2.0 (2019-12-15)" +#define MAPPER_VERSION "2.0.1 (2020-07-02)" #define MAPPER_ID "Whisper" #define MAPPER_NAME "Whisper" diff --git a/src/mapper/whisper.cpp b/src/mapper/whisper.cpp index 4ca3fd8..f8ba8ab 100644 --- a/src/mapper/whisper.cpp +++ b/src/mapper/whisper.cpp @@ -41,7 +41,7 @@ void usage() cerr << " whisper [options] file_se \n"; cerr << " whisper [options] file_pe1 file_pe2\n"; cerr << "Parameters:\n"; - cerr << " index_name - name of the index (as created by asm_pp)\n"; + cerr << " index_name - name of the index (as created by whisper-index)\n"; cerr << " files - name of the file containing list of FASTQ files with seq. reads\n"; cerr << " file_se - FASTQ file (single-end)\n"; cerr << " file_pe[1|2] - FASTQ files (paired-end)\n"; @@ -70,7 +70,7 @@ void usage() cerr << " -gap-del-extend - score for gap (del) extend (default: " << cmd_params.gap_del_extend << ")\n"; cerr << " -gap-ins-open - score for gap (ins) open (default: " << cmd_params.gap_ins_open << ")\n"; cerr << " -gap-ins-extend - score for gap (ins) extend (default: " << cmd_params.gap_ins_extend << ")\n"; - cerr << " -gzipped-SAM-level - gzip compression level of SAM/BAM, 0 - no compression (default: " << cmd_params.gzipped_SAM_level << ")\n"; + cerr << " -gzipped-SAM - gzip compression level of SAM/BAM, 0 - no compression (default: " << cmd_params.gzipped_SAM_level << ")\n"; cerr << " -high-confidence-sigmas - (default: " << cmd_params.high_confidence_sigmas << ")\n"; cerr << " -hit-merging-threshold - minimal distance between different mappings (default: " << cmd_params.hit_merging_threshold << ")\n"; cerr << " -hit-merging-wrt-first - calculate distance in marged group w.r.t. first (default: " << cmd_params.hit_merging_wrt_first << ")\n"; @@ -85,7 +85,7 @@ void usage() cerr << " -min-clipped-factor - mask bases of quality lower than value (default: " << cmd_params.min_clipped_factor << ")\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 << " -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 << " -score-discretization-threshold (default: " << cmd_params.score_discretization_threshold << ")\n"; cerr << " -score-clipping score for clipping (default: " << cmd_params.clipping_score << ")\n"; @@ -117,10 +117,11 @@ void usage() cerr << " -sr :-: - perform only stages from : to :\n"; cerr << " -v - verbosity level (default: " << cmd_params.verbosity_level << ")\n"; #endif - cerr << "Examples:\n"; - cerr << " whisper human @files\n"; - cerr << " whisper -temp temp/ human reads1.fq reads2.fq\n"; - cerr << " whisper -out result.sam -temp temp/ -t 12 human reads1.fq reads2.fq\n"; + cerr << "Example\n" + << "Map paired-end reads from reads_1.fq and reads_2.fq FASTQ files using hg38 index.\n" + << "Distribute computations over 12 threads, store results in result.sam file:\n" + << " whisper -out result.sam -rp -t 12 hg38 reads_1.fq reads_2.fq\n"; + } // ************************************************************************************ @@ -132,7 +133,7 @@ bool parse_parameters(int argc, char **argv) // uint64_t tmp; #endif - if(argc < 6) + if(argc < 3) return false; #ifndef _DEVELOPMENT_MODE