.\" 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)