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modify options usage
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@HongzheGuo
HongzheGuo committed Sep 19, 2015
1 parent 5599c1a commit 35e4e7b
Showing 1 changed file with 20 additions and 19 deletions.
39 changes: 20 additions & 19 deletions load_input.c
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Original file line number Diff line number Diff line change
Expand Up @@ -156,11 +156,11 @@ int8_t mat_score = 1, mis_score = 4, gapo_score = 6, gape_score = 1;
static int index_build_usage()
{
fprintf(stderr, "\n");
fprintf(stderr, "Program: De Brijn Graph mapping system index building\n");
fprintf(stderr, "Program: de Brijn Graph-based mapping system index building\n");
fprintf(stderr, "Version: %s\n", PACKAGE_VERSION);
fprintf(stderr, "Contact: Hongzhe Guo <[email protected]>\n\n");
fprintf(stderr, "Usage: deBGA index [options] reference.fasta <index_route> \n\n");
fprintf(stderr, "Options: -k INT length of kmer [20-28]\n");
fprintf(stderr, "Options: -k INT the k-mer length of the vertices of RdBG [20-28]\n");

fprintf(stderr, "\n");
return 1;
Expand All @@ -169,34 +169,35 @@ static int index_build_usage()
static int load_input_usage()
{
fprintf(stderr, "\n");
fprintf(stderr, "Program: De Brijn Graph mapping system seed reduction and alignment\n");
fprintf(stderr, "Program: de Brijn Graph-based 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\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, " -s INT the number of iterations of re-seeding [%u]\n", cir_fix_n);
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, " -c NUM the threshold on the edit distance for early stop [%.2f]\n", max_pair_score_r);
fprintf(stderr, " --cl NUM the adjusted threshold on the edit distance for early stop [%.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, " For more details about the options, please see the README at https://github.com/HongzheGuo/deBGA\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, " -x INT the maximum number of alignment output for anchoring alignment [%u]\n", cus_max_output_ali);
fprintf(stderr, " -l INT the maximum allowed read length [%u]\n", readlen_max);
fprintf(stderr, " -e INT the budget for single-end alignment [%u]\n", seed_filter_pos_numn);
fprintf(stderr, " -p INT the number of threads [%u]\n", thread_n);
//fprintf(stderr, " --mg use the mode of multi-genomes\n");
//fprintf(stderr, " -v NUM the max editing distance rate for LandauVishkin [%.2f] (only for pair-end)\n", lv_rate);
//fprintf(stderr, " -r INT seed coverage length filter [%u]\n", length_reduce);
//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, " Please refer to the following link for more detailed information about the options: https://github.com/HIT-Bioinformatics/deBGA\n");
fprintf(stderr, "\n");

return 1;
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