'\" t
.\"     Title: kmc_tools-complex
.\"    Author: [see the "AUTHOR(S)" section]
.\" Generator: Asciidoctor 2.0.20
.\"      Date: 
.\"    Manual: \ \&
.\"    Source: \ \&
.\"  Language: English
.\"
.TH "KMC_TOOLS\-COMPLEX" "1" "" "\ \&" "\ \&"
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.SH "NAME"
kmc_tools-complex \- complex operations with a number of input databases
.SH "SYNOPSIS"
.sp
kmc_tools complex <operations_definition_file>
.SH "DESCRIPTION"
.sp
This command executes a combination of operations as defined by <operations_definition_file>. It is text file with following syntax:
.sp
.if n .RS 4
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.fam C
 __________________________________________________________________
|INPUT:                                                            |
|<input1>=<input1_db_path> [params]                                |
|<input2>=<input2_db_path> [params]                                |
|...                                                               |
|<inputN>=<inputN_db_path> [params]                                |
|OUTPUT:                                                           |
|<out_db_path>=<ref_input><oper><ref_input>[<oper><ref_input>[...] |
|[OUTPUT_PARAMS:                                                 __|
|<output_params>]                                               |  /
|                                                               | /
|_______________________________________________________________|/
.fam
.fi
.if n .RE
.SH "PARAMETERS"
.sp
\fBinput1, input2, ..., inputN\fP
.RS 4
names of inputs used to define equation
.RE
.sp
\fBinput1_db_path, input2_db_path, ..., inputN_db_path\fP
.RS 4
paths to k\-mers sets
.RE
.sp
For each input there are additional parameters which can be set:
.sp
\fB\-ci<value>\fP
.RS 4
exclude k\-mers occurring less than <value> times
.RE
.sp
\fBcx<value>\fP
.RS 4
exclude k\-mers occurring more of than <value> times
.RE
.sp
\fBout_db_path\fP
.RS 4
path to output database
.RE
.sp
\fBref_input\fP
.RS 4
one of input1, input2, ..., inputN
.RE
.sp
\fBoper\fP
.RS 4
one of {*,\-,~,+}, which refers to {intersect, kmers_subtract, counters_subtract, union}
.RE
.sp
Operator \*(Aq*\*(Aq has the highest priority. Other operators have equal priorities.
The order of operations can be changed with parentheses.
.sp
Output parameters:
.sp
\fB\-ci<value>\fP
.RS 4
exclude k\-mers occurring less than <value> times
.RE
.sp
\fB\-cx<value>\fP
.RS 4
exclude k\-mers occurring more of than <value> times
.RE
.sp
\fB\-cs<value>\fP
.RS 4
maximal value of a counter
.RE
.SH "EXAMPLE"
.sp
.if n .RS 4
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.fam C
 __________________________________________________________________
|INPUT:                                                            |
|set1 = kmc_o1 \-ci5                                                |
|set2 = kmc_o2                                                     |
|set3 = kmc_o3 \-ci10 \-cx100                                      __|
|OUTPUT:                                                        |  /
|result = (set3+set1)*set2                                      | /
|_______________________________________________________________|/
.fam
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.SH "AUTHOR"
.sp
KMC was originally written by:
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.RS 4
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Sebastian Deorowicz (\c
.MTO "sebastian.deorowicz\(atpolsl.pl" "" ")"
.RE
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.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
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Marek Kokot
.RE
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.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
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.el \{\
.  sp -1
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Szymon Grabowski
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
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.el \{\
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Agnieszka Debudaj\-Grabysz
.RE
.SH "COPYING"
.sp
KMC is a free software distributed under GNU GPL3 licence for academic,
research, and commercial use.