Add manpages

.\" 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)

.\" 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)

.\" 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)

.\" 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)

.\" 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)