[med-svn] [Git][med-team/genometester][master] Add manpages
Liubov Chuprikova
gitlab at salsa.debian.org
Fri Jun 1 09:47:34 BST 2018
Liubov Chuprikova pushed to branch master at Debian Med / genometester
Commits:
95a08b97 by Liubov Chuprikova at 2018-06-01T10:47:00+02:00
Add manpages
- - - - -
6 changed files:
- + debian/glistcompare.1
- + debian/glistmaker.1
- + debian/glistquery.1
- + debian/gmer_caller.1
- + debian/gmer_counter.1
- + debian/manpages
Changes:
=====================================
debian/glistcompare.1
=====================================
--- /dev/null
+++ b/debian/glistcompare.1
@@ -0,0 +1,44 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH GLISTCOMPARE "1" "31 May 2018" "GenomeTester" "GenomeTester User Manuals"
+.SH NAME
+glistcompare \- generate union, intersection or difference of k-mers from two list files
+.SH SYNOPSIS
+.B glistcompare
+\fI\,<INPUTLIST1> <INPUTLIST2> \/\fR[\fI\,OPTIONS\/\fR]
+.SH OPTIONS
+.HP
+\fB\-v\fR, \fB\-\-version\fR \- print version information and exit
+.HP
+\fB\-h\fR, \fB\-\-help\fR \- print this usage screen and exit
+.HP
+\fB\-u\fR, \fB\-\-union\fR \- union of input lists
+.HP
+\fB\-i\fR, \fB\-\-intersection\fR \- intersection of input lists
+.HP
+\fB\-d\fR, \fB\-\-difference\fR \- difference of input lists
+.HP
+\fB\-dd\fR, \fB\-\-double_difference\fR \- double difference of input lists
+.HP
+\fB\-du\fR, \fB\-\-diff_union\fR \- subtract first list from the second and finds difference
+.TP
+\fB\-mm\fR, \fB\-\-mismatch\fR
+NUMBER \- specify number of mismatches (default 0, can be used with \fB\-diff\fR and \fB\-ddiff\fR)
+.HP
+\fB\-c\fR, \fB\-\-cutoff\fR NUMBER \- specify frequency cut\-off (default 1)
+.HP
+\fB\-o\fR, \fB\-\-outputname\fR STRING \- specify output name (default "out")
+.TP
+\fB\-r\fR, \fB\-\-rule\fR STRING \- specify rule how final frequencies are calculated (default, add, subtract, min, max, first, second, 1, 2)
+NOTE: rules min, subtract, first and second can only be used with finding the intersection.
+.HP
+\fB\-ss\fR \fB\-\-subset\fR METHOD SIZE \- make subset with given method (rand_unique)
+.HP
+\fB\-\-count_only\fR \- output count of k\-mers instead of k\-mers themself
+.HP
+\fB\-\-disable_scouts\fR \- disable list read\-ahead in background thread
+.HP
+\fB\-D\fR \- increase debug level
+.SH EXAMPLES
+ You could find some usage examples in /usr/share/doc/genometester/README.GenomeTester4.md
+.SH "SEE ALSO"
+ \fBglistquery\fR(1), \fBglistmaker\fR(1), \fBgmer_caller\fR(1), \fBgmer_counter\fR(1)
=====================================
debian/glistmaker.1
=====================================
--- /dev/null
+++ b/debian/glistmaker.1
@@ -0,0 +1,30 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH GLISTMAKER "1" "31 May 2018" "GenomeTester" "GenomeTester User Manuals"
+.SH NAME
+glistmaker \- generate a list of all unique k-mers in input file with their frequencies
+.SH SYNOPSIS
+.B glistmaker
+\fI\,<INPUTFILES> \/\fR[\fI\,OPTIONS\/\fR]
+.SH OPTIONS
+.HP
+\fB\-v\fR, \fB\-\-version\fR \- print version information and exit
+.HP
+\fB\-h\fR, \fB\-\-help\fR \- print this usage screen and exit
+.HP
+\fB\-w\fR, \fB\-\-wordlength\fR NUMBER \- specify index wordsize (1\-32) (default 16)
+.HP
+\fB\-c\fR, \fB\-\-cutoff\fR NUMBER \- specify frequency cut\-off (default 1)
+.HP
+\fB\-o\fR, \fB\-\-outputname\fR STRING \- specify output name (default "out")
+.HP
+\fB\-\-num_threads\fR \- number of threads the program is run on (default MIN(8, num_input_files))
+.HP
+\fB\-\-max_tables\fR \- maximum number of temporary tables (default MAX(num_threads, 2))
+.HP
+\fB\-\-table_size\fR \- maximum size of the temporary table (default 500000000)
+.HP
+\fB\-D\fR \- increase debug level
+.SH EXAMPLES
+ You could find some usage examples in /usr/share/doc/genometester/README.GenomeTester4.md
+.SH "SEE ALSO"
+ \fBglistquery\fR(1), \fBglistcompare\fR(1), \fBgmer_caller\fR(1), \fBgmer_counter\fR(1)
=====================================
debian/glistquery.1
=====================================
--- /dev/null
+++ b/debian/glistquery.1
@@ -0,0 +1,40 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH GLISTQUERY "1" "31 May 2018" "GenomeTester" "GenomeTester User Manuals"
+.SH NAME
+glistquery \- print the frequencies of k-mers in a list file
+.SH SYNOPSIS
+.B glistquery
+\fI\,<INPUTLIST> \/\fR[\fI\,OPTIONS\/\fR]
+.SH OPTIONS
+.HP
+\fB\-v\fR, \fB\-\-version\fR \- print version information and exit
+.HP
+\fB\-h\fR, \fB\-\-help\fR \- print this usage screen and exit
+.HP
+\fB\-stat\fR \- print statistics of the list file and exit
+.HP
+\fB\-median\fR \- print min/max/median/average and exit
+.HP
+\fB\-q\fR, \fB\-\-query\fR \- single query word
+.HP
+\fB\-f\fR, \fB\-\-queryfile\fR \- list of query words in a file
+.HP
+\fB\-s\fR, \fB\-\-seqfile\fR \- FastA/FastQ file
+.HP
+\fB\-l\fR, \fB\-\-listfile\fR \- list file made by glistmaker
+.HP
+\fB\-mm\fR, \fB\-\-mismatch\fR NUMBER \- specify number of mismatches (default 0, can be used with \fB\-d\fR and \fB\-dd\fR)
+.HP
+\fB\-p\fR, \fB\-\-perfectmatch\fR NUMBER \- specify number of 3' perfect matches (default 0)
+.HP
+\fB\-min\fR, \fB\-\-minfreq\fR NUMBER \- minimum frequency of the printed words (default 0)
+.HP
+\fB\-max\fR, \fB\-\-maxfreq\fR NUMBER \- maximum frequency of the printed words (default MAX_UINT)
+.HP
+\fB\-all\fR \- in case of mismatches prints all found words
+.HP
+\fB\-D\fR \- increase debug level
+.SH EXAMPLES
+ You could find some usage examples in /usr/share/doc/genometester/README.GenomeTester4.md
+.SH "SEE ALSO"
+ \fBglistmaker\fR(1), \fBglistcompare\fR(1), \fBgmer_caller\fR(1), \fBgmer_counter\fR(1)
=====================================
debian/gmer_caller.1
=====================================
--- /dev/null
+++ b/debian/gmer_caller.1
@@ -0,0 +1,38 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH GMER_CALLER "1" "31 May 2018" "GenomeTester" "GenomeTester User Manuals"
+.SH NAME
+gmer_caller \- call the genotypes from a file with counted k-mers
+.SH SYNOPSIS
+.B gmer_caller
+[\fI\,OPTIONS\/\fR] \fI\,<COUNTS_FILE>\/\fR
+.SH OPTIONS
+.HP
+\fB\-\-training_size\fR NUM \- Use NUM markers for training (default 100000)
+.HP
+\fB\-\-runs\fR NUMBER \- Perform NUMBER runs of model training (use 0 for no training)
+.HP
+\fB\-\-num_threads\fR NUM \- Use NUM threads (min 1, max 32, default 16)
+.HP
+\fB\-\-header\fR \- Print table header
+.HP
+\fB\-\-non_canonical\fR \- Output non\-canonical genotypes
+.HP
+\fB\-\-prob_cutoff\fR \- probability cutoff for calling genotype (default 0)
+.HP
+\fB\-\-alternatives\fR \- Print probabilities of all alternative genotypes
+.HP
+\fB\-\-info\fR \- Print information about individual
+.HP
+\fB\-\-no_genotypes\fR \- Print only summary information, not actual genotypes
+.HP
+\fB\-\-model\fR TYPE \- Model type (full, diploid, haploid)
+.HP
+\fB\-\-params\fR PARAMS \- Model parameters (error, p0, p1, p2, coverage, size, size2)
+.HP
+\fB\-\-coverage\fR NUM \- Average coverage of reads
+.HP
+\fB\-D\fR \- increase debug level
+.SH EXAMPLES
+ You could find some usage examples in /usr/share/doc/genometester/README.FastGT.md
+.SH "SEE ALSO"
+ \fBglistquery\fR(1), \fBglistmaker\fR(1), \fBglistcompare\fR(1), \fBgmer_counter\fR(1)
=====================================
debian/gmer_counter.1
=====================================
--- /dev/null
+++ b/debian/gmer_counter.1
@@ -0,0 +1,40 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH GMER_COUNTER "1" "31 May 2018" "GenomeTester" "GenomeTester User Manuals"
+.SH NAME
+gmer_counter \- count k-mers from raw reads in FASTQ file
+.SH SYNOPSIS
+.B gmer_counter
+[\fI\,OPTIONS\/\fR] \fI\,<SEQUENCES...>\/\fR
+.SH OPTIONS
+.HP
+\fB\-db\fR DATABASE \- SNP/KMER database file
+.HP
+\fB\-dbb\fR DBBINARY \- binary database file
+.HP
+\fB\-w\fR FILENAME \- write binary database to file
+.HP
+\fB\-32\fR \- use 32\-bit integeres for counts (default 16\-bit)
+.HP
+\fB\-\-max_kmers\fR NUM \- maximum number of kmers per node
+.HP
+\fB\-\-header\fR \- print header row
+.HP
+\fB\-\-total\fR \- print the total number of kmers per node
+.HP
+\fB\-\-unique\fR \- print the number of nonzero kmers per node
+.HP
+\fB\-\-kmers\fR \- print individual kmer counts (default if no other output)
+.HP
+\fB\-\-compile_index\fR \- Add read index to database and write it to file
+.HP
+\fB\-\-distribution\fR NUM \- print kmer distribution (up to given number)
+.HP
+\fB\-\-num_threads\fR \- number of worker threads (default 24)
+.HP
+\fB\-\-low_memory\fR \- optimize for low memory usage
+.HP
+\fB\-D\fR \- increase debug level
+.SH EXAMPLES
+ You could find some usage examples in /usr/share/doc/genometester/README.FastGT.md
+.SH "SEE ALSO"
+ \fBglistquery\fR(1), \fBglistmaker\fR(1), \fBglistcompare\fR(1), \fBgmer_caller\fR(1)
=====================================
debian/manpages
=====================================
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/*.1
View it on GitLab: https://salsa.debian.org/med-team/genometester/commit/95a08b9757fa6897ee627b1e8a008ca0ac6602d0
--
View it on GitLab: https://salsa.debian.org/med-team/genometester/commit/95a08b9757fa6897ee627b1e8a008ca0ac6602d0
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