diff --git a/Makefile b/Makefile index 84ca553..a0c3705 100644 --- a/Makefile +++ b/Makefile @@ -39,7 +39,7 @@ readme: f=$$(mktemp);\ echo $$f;\ sed '/USAGE-BEGIN/q' README.md >> $$f; \ - printf -- '-->\n```' >> $$f; \ + printf -- '-->\n```\n' >> $$f; \ man ./ococo.1 | col -b | grep -A999999 SYNO | grep -B99999999 AUTH | ghead -n -1 >> $$f; \ printf '```\n - -```NAME +``` SYNOPSIS ococo -i [other options] DESCRIPTION - Ococo is a program to call genomic consensus directly from an unsorted - SAM/BAM stream. + Ococo is a program to call variants and a genomic consensus directly + from an unsorted SAM/BAM stream. Input options: -i, --input FILE - Input SAM/BAM file (- for standard input). + Input SAM/BAM file (- for standard input). -f, --fasta-ref FILE - Initial FASTA reference (otherwise seq of N's is used). + Initial FASTA reference (otherwise a seq of N's is used). -s, --stats-in FILE - Input statistics. + Input statistics. Output options: - -F, --fasta-cons FILE FASTA file with consensus + -F, --fasta-cons FILE Print consensus in FASTA. -S, --stats-out FILE - Output statistics. + Export statistics to a file. -V, --vcf-cons FILE - VCF file with updates of consensus (- for standard output) + Print inferred variants in VCF (- for standard output). -P, --pileup FILE - Truncated pileup (- for standard output). + Print SAMtools pileup (- for standard output). --verbose - Verbose mode (report every update of a counter). + Use the verbose mode (report every update of a counter). Parameters for consensus calling: -x, --counters STR - Counter configuration [ococo16]. + Counter configuration [ococo32]. - configuration bits/counter bits/position - ococo16 3 16 - ococo32 7 32 - ococo64 15 64 + configuration bits/counter bits/position + ococo16 3 16 + ococo32 7 32 + ococo64 15 64 -m, --mode STR - Mode [batch]. + Mode [batch]. - mode description - real-time updates reported immediately - batch updates reported after end of algn stream + mode description + real-time updates reported immediately + batch updates reported after end of algn stream -q, --min-MQ INT - Skip alignments with mapping quality smaller than INT [1]. + Skip alignments with mapping quality smaller than INT [1]. -Q, --min-BQ INT - Skip bases with base quality smaller than INT [13]. + Skip bases with base quality smaller than INT [13]. -w, --ref-weight INT - Initial counter value for nucleotides from ref [0]. + Initial counter value for nucleotides from ref [0]. -c, --min-cov INT - Minimum coverage required for update [2]. + Minimum coverage required for update [2]. -M, --maj-thres FLOAT - Majority threshold [0.51]. + Majority threshold [0.51]. + ```