void help_augment(char** argv, ConfigurableParser& parser) {
cerr << "usage: " << argv[0] << " augment [options] <graph.vg> [alignment.gam] > augmented_graph.vg" << endl
<< "Embed GAM alignments into a graph to facilitate variant calling" << endl
<< endl
<< "general options:" << endl
<< " -a, --augmentation-mode M augmentation mode. M = {pileup, direct} [direct]" << endl
<< " -i, --include-paths merge the paths implied by alignments into the graph" << endl
<< " -B, --label-paths don't augment with alignments, just use them for labeling the graph" << endl
<< " -Z, --translation FILE save translations from augmented back to base graph to FILE" << endl
<< " -A, --alignment-out FILE save augmented GAM reads to FILE" << endl
<< " -h, --help print this help message" << endl
<< " -p, --progress show progress" << endl
<< " -v, --verbose print information and warnings about vcf generation" << endl
<< " -t, --threads N number of threads to use" << endl
<< "loci file options:" << endl
<< " -l, --include-loci FILE merge all alleles in loci into the graph" << endl
<< " -L, --include-gt FILE merge only the alleles in called genotypes into the graph" << endl
<< "pileup options:" << endl
<< " -P, --pileup FILE save pileups to FILE" << endl
<< " -S, --support FILE save supports to FILE" << endl
<< " -g, --min-aug-support N minimum support to augment graph ["
<< PileupAugmenter::Default_min_aug_support << "]" << endl
<< " -U, --subgraph expect a subgraph and ignore extra pileup entries outside it" << endl
<< " -q, --min-quality N ignore bases with PHRED quality < N (default=10)" << endl
<< " -m, --max-mismatches N ignore bases with > N mismatches within window centered on read (default=1)" << endl
<< " -w, --window-size N size of window to apply -m option (default=0)" << endl
<< " -M, --ignore-mapq do not combine mapping qualities with base qualities in pileup" << endl;
// Then report more options
parser.print_help(cerr);
}
void help_call(char** argv, ConfigurableParser& parser) {
cerr << "usage: " << argv[0] << " call [options] <augmented-graph.vg> > output.vcf" << endl
<< "Output variant calls in VCF or Loci format given a graph and pileup" << endl
<< endl
<< "genotyper options:" << endl
<< "general options:" << endl
<< " -z, --translation FILE input translation table" << endl
<< " -b, --base-graph FILE base graph. currently needed for XREF tag" << endl
<< " -h, --help print this help message" << endl
<< " -p, --progress show progress" << endl
<< " -v, --verbose print information and warnings about vcf generation" << endl
<< " -t, --threads N number of threads to use" << endl;
// Then report more options
parser.print_help(cerr);
}