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@@ -167,35 +167,35 @@ static int index_build_usage() | |
| } | ||
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| static int load_input_usage() | ||
| { | ||
| { | ||
| fprintf(stderr, "\n"); | ||
| fprintf(stderr, "Program: De Brijn Graph mapping system seed reduction and alignment\n"); | ||
| fprintf(stderr, "Version: %s\n", PACKAGE_VERSION); | ||
| fprintf(stderr, "Contact: Hongzhe Guo <[email protected]>\n\n"); | ||
| fprintf(stderr, "Usage: deBGA aln [options] <index_route> <read pair-end1.fq> [read pair-end2.fq] <result_file.sam>\n\n"); | ||
| fprintf(stderr, "Options: -k INT length of kmer [21-28]\n"); | ||
| fprintf(stderr, " -u INT upper limit of library insert-size [%u] (only for pair-end)\n", upper_ins); | ||
| fprintf(stderr, " -f INT floor limit of library insert-size [%u] (only for pair-end)\n", floor_ins); | ||
| fprintf(stderr, " -o INT the maximum output number (only for pair-end)[%u]\n", cus_ali_n); | ||
| fprintf(stderr, " -v NUM the max editing distance rate for LandauVishkin [%.2f] (only for pair-end)\n", lv_rate); | ||
| fprintf(stderr, " -p INT number of threads [%u]\n", thread_n); | ||
| fprintf(stderr, " -l INT the maximum read length [%u]\n", readlen_max); | ||
| fprintf(stderr, " -r INT seed coverage length filter [%u]\n", length_reduce); | ||
| fprintf(stderr, " -i INT minimum seeds interval on read [%u]\n", seed_step); | ||
| fprintf(stderr, " -s INT number of seed circulation [%u]\n", cir_fix_n); | ||
| fprintf(stderr, " -n INT seed positions filter [%u]\n", pos_n_max); | ||
| fprintf(stderr, " -x INT the maximum output number of anchor [%u]\n", cus_max_output_ali); | ||
| fprintf(stderr, " -c NUM the max rate of alignment score [%.2f]\n", max_pair_score_r); | ||
| fprintf(stderr, " -e INT the filter number of seed positions [%u]\n", seed_filter_pos_numn); | ||
| //fprintf(stderr, " --aanchor NUM the max rate of mismatch alignment on anchor [%.2f]\n", mis_match_r_single); | ||
| //fprintf(stderr, " --vanchor NUM the max editing distance rate for LandauVishkin on anchor [%.2f]\n", lv_rate_anchor); | ||
| fprintf(stderr, " --cl NUM the max rate of alignment score on the last circle [%.2f]\n", last_circle_rate); | ||
| fprintf(stderr, " --local use the ksw local alignment\n"); | ||
| fprintf(stderr, " --mg use the mode of multi-genomes\n"); | ||
| fprintf(stderr, " --local-match NUM local alignment score match [%d]\n", mat_score); | ||
| fprintf(stderr, " --local-mismatch NUM local alignment score match [%d]\n", mis_score); | ||
| fprintf(stderr, " --local-gap-open NUM local alignment score match [%d]\n", gapo_score); | ||
| fprintf(stderr, " --local-gap-extension NUM local alignment score match [%d]\n", gape_score); | ||
| fprintf(stderr, "Usage: deBGA aln [options] <index_route> <read pair-end1.fq> [read pair-end2.fq] <result_file.sam>\n\nOptions:\n"); | ||
| fprintf(stderr, " -k INT the minimum length of a valid Uni-MEM seed [21-28]\n"); | ||
| fprintf(stderr, " -u INT the upper limit of insert size (only for pair-end reads) [%u] \n", upper_ins); | ||
| fprintf(stderr, " -f INT the lower limit of insert size (only for pair-end reads) [%u] \n", floor_ins); | ||
| fprintf(stderr, " -o INT the maximum number of alignment output [%u]\n", cus_ali_n); | ||
| //fprintf(stderr, " -v NUM the max editing distance rate for LandauVishkin [%.2f] (only for pair-end)\n", lv_rate); | ||
| fprintf(stderr, " -p INT the number of threads [%u]\n", thread_n); | ||
| fprintf(stderr, " -l INT the maximum allowed read length [%u]\n", readlen_max); | ||
| //fprintf(stderr, " -r INT seed coverage length filter [%u]\n", length_reduce); | ||
| fprintf(stderr, " -i INT the minimum interval of seeding [%u]\n", seed_step); | ||
| fprintf(stderr, " -s INT the number of rounds of re-seeding [%u]\n", cir_fix_n); | ||
| fprintf(stderr, " -n INT the maximum allowed number of hits per seed [%u]\n", pos_n_max); | ||
| fprintf(stderr, " -x INT the maximum number of alignment output for anchoring alignment [%u]\n", cus_max_output_ali); | ||
| fprintf(stderr, " -c NUM the threshold of confident alignment [%.2f]\n", max_pair_score_r); | ||
| fprintf(stderr, " -e INT the budget for single-end alignment [%u]\n", seed_filter_pos_numn); | ||
| //fprintf(stderr, " --aanchor NUM the max rate of mismatch alignment on anchor [%.2f]\n", mis_match_r_single); | ||
| //fprintf(stderr, " --vanchor NUM the max editing distance rate for LandauVishkin on anchor [%.2f]\n", lv_rate_anchor); | ||
| fprintf(stderr, " --cl NUM the adjusted threshold of confident alignment [%.2f]\n", last_circle_rate); | ||
| fprintf(stderr, " --local the local alignment option for confident alignment\n"); | ||
| //fprintf(stderr, " --mg use the mode of multi-genomes\n"); | ||
| fprintf(stderr, " --local-match NUM the score for a matched base in the local alignment [%d]\n", mat_score); | ||
| fprintf(stderr, " --local-mismatch NUM the penalty for a mismatched base in the local alignment [%d]\n", mis_score); | ||
| fprintf(stderr, " --local-gap-open NUM the penalty for a gap open in the local alignment [%d]\n", gapo_score); | ||
| fprintf(stderr, " --local-gap-extension NUM the penalty for gap extension in the local alignment [%d]\n", gape_score); | ||
| fprintf(stderr, "\n"); | ||
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| return 1; | ||
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| Original file line number | Diff line number | Diff line change |
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@@ -25,8 +25,8 @@ static int usage() | |
| fprintf(stderr, "Version: %s\n", COMMAND_VERSION); | ||
| fprintf(stderr, "Contact: Hongzhe Guo <[email protected]>\n\n"); | ||
| fprintf(stderr, "Usage: deBGA <command> [options]\n\n"); | ||
| fprintf(stderr, "Command: index index sequences in the FASTA format\n"); | ||
| fprintf(stderr, " aln pair-end and single-end reads seed reduction and alignment based on De bruijn graph\n"); | ||
| fprintf(stderr, "Command: index index sequences in the FASTA format\n"); | ||
| fprintf(stderr, " aln pair-end and single-end reads seed reduction and alignment based on De bruijn graph\n"); | ||
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| return 1; | ||
| } | ||
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