[med-svn] [kmc] 01/03: add kmc_tools man page sources
Sascha Steinbiss
sascha at steinbiss.name
Tue Dec 22 22:19:42 UTC 2015
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository kmc.
commit 1cd8124d84e43b83ddb6536760e7ea7f26d873d8
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date: Tue Dec 22 17:13:16 2015 +0000
add kmc_tools man page sources
---
debian/man_src/kmc_tools-compact.1.ronn | 40 +++++++++++
debian/man_src/kmc_tools-complex.1.ronn | 83 ++++++++++++++++++++++
debian/man_src/kmc_tools-counters_subtract.1.ronn | 51 ++++++++++++++
debian/man_src/kmc_tools-dump.1.ronn | 45 ++++++++++++
debian/man_src/kmc_tools-filter.1.ronn | 56 +++++++++++++++
debian/man_src/kmc_tools-histogram.1.ronn | 40 +++++++++++
debian/man_src/kmc_tools-intersect.1.ronn | 51 ++++++++++++++
debian/man_src/kmc_tools-kmers_subtract.1.ronn | 51 ++++++++++++++
debian/man_src/kmc_tools-sort.1.ronn | 45 ++++++++++++
debian/man_src/kmc_tools-union.1.ronn | 51 ++++++++++++++
debian/man_src/kmc_tools.1.ronn | 84 +++++++++++++++++++++++
11 files changed, 597 insertions(+)
diff --git a/debian/man_src/kmc_tools-compact.1.ronn b/debian/man_src/kmc_tools-compact.1.ronn
new file mode 100644
index 0000000..7861f3f
--- /dev/null
+++ b/debian/man_src/kmc_tools-compact.1.ronn
@@ -0,0 +1,40 @@
+kmc_tools-compact(1) - remove counters of k-mers
+================================================
+
+## SYNOPSIS
+
+kmc_tools compact <inputdb> [input_params] <output>
+
+## DESCRIPTION
+
+This command removes counters from the database and stores only k-mers.
+
+## OPTIONS
+
+For each input there are additional parameters:
+
+ * `-ci<value>`:
+ exclude k-mers occurring less than <value> times
+ * `-cx<value>`:
+ exclude k-mers occurring more of than <value> times
+
+## EXAMPLE
+
+ kmc_tools compact wy_kmc2 -ci3 -cx1000 wy_kmc1
+
+## AUTHOR
+
+KMC was originally written by:
+
+ - Sebastian Deorowicz (sebastian.deorowicz at polsl.pl)
+
+ - Marek Kokot
+
+ - Szymon Grabowski
+
+ - Agnieszka Debudaj-Grabysz
+
+## COPYING
+
+KMC is a free software distributed under GNU GPL3 licence for academic,
+research, and commercial use.
\ No newline at end of file
diff --git a/debian/man_src/kmc_tools-complex.1.ronn b/debian/man_src/kmc_tools-complex.1.ronn
new file mode 100644
index 0000000..f86668c
--- /dev/null
+++ b/debian/man_src/kmc_tools-complex.1.ronn
@@ -0,0 +1,83 @@
+kmc_tools-complex(1) - complex operations with a number of input databases
+==========================================================================
+
+## SYNOPSIS
+
+kmc_tools complex <operations_definition_file>
+
+## DESCRIPTION
+
+This command executes a combination of operations as defined by <operations_definition_file>. It is text file with following syntax:
+
+ __________________________________________________________________
+ |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>] | /
+ | | /
+ |_______________________________________________________________|/
+
+where
+
+ * `input1, input2, ..., inputN`:
+ names of inputs used to define equation
+ * `input1_db_path, input2_db_path, ..., inputN_db_path`:
+ paths to k-mers sets
+
+For each input there are additional parameters which can be set:
+
+ * `-ci<value>`:
+ exclude k-mers occurring less than <value> times
+ * `cx<value>`:
+ exclude k-mers occurring more of than <value> times
+ * `out_db_path`:
+ path to output database
+ * `ref_input`:
+ one of input1, input2, ..., inputN
+ * `oper`:
+ one of {*,-,~,+}, which refers to {intersect, kmers_subtract, counters_subtract, union}
+
+Operator * has the highest priority. Other operators have equal priorities.
+The order of operations can be changed with parentheses.
+
+Output parameters:
+
+ * `-ci<value>`:
+ exclude k-mers occurring less than <value> times
+ * `-cx<value>`:
+ exclude k-mers occurring more of than <value> times
+ * `-cs<value>`:
+ maximal value of a counter
+
+## EXAMPLE
+
+ __________________________________________________________________
+ |INPUT: |
+ |set1 = kmc_o1 -ci5 |
+ |set2 = kmc_o2 |
+ |set3 = kmc_o3 -ci10 -cx100 __|
+ |OUTPUT: | /
+ |result = (set3+set1)*set2 | /
+ |_______________________________________________________________|/
+
+## AUTHOR
+
+KMC was originally written by:
+
+ - Sebastian Deorowicz (sebastian.deorowicz at polsl.pl)
+
+ - Marek Kokot
+
+ - Szymon Grabowski
+
+ - Agnieszka Debudaj-Grabysz
+
+## COPYING
+
+KMC is a free software distributed under GNU GPL3 licence for academic,
+research, and commercial use.
\ No newline at end of file
diff --git a/debian/man_src/kmc_tools-counters_subtract.1.ronn b/debian/man_src/kmc_tools-counters_subtract.1.ronn
new file mode 100644
index 0000000..f9c3da4
--- /dev/null
+++ b/debian/man_src/kmc_tools-counters_subtract.1.ronn
@@ -0,0 +1,51 @@
+kmc_tools-counters_subtract(1) - calculate counters subtraction of two KMC databases
+====================================================================================
+
+## SYNOPSIS
+
+kmc_tools counters_subtract <input1 [input1_params]> <input2 [input2_params]> <output [output_params]>
+
+## DESCRIPTION
+
+The output database will contain only k-mers that are present in the first input set and have counters higher than the appropriate k-mers in the second set. For each k-mer the counter is equal to the difference between the counter in the first set and the counter in the second set.
+
+## OPTIONS
+
+For each input there are additional parameters:
+
+ * `-ci<value>`:
+ exclude k-mers occurring less than <value> times
+ * `-cx<value>`:
+ exclude k-mers occurring more of than <value> times
+
+For output there are additional parameters:
+
+ * `-ci<value>`:
+ exclude k-mers occurring less than <value> times
+ * `-cx<value>`:
+ exclude k-mers occurring more of than <value> times
+ * `-cs<value>`:
+ maximal value of a counter
+
+## EXAMPLE
+
+ kmc - k28 file1.fastq kmers1 tmp
+ kmc - k28 file2.fastq kmers2 tmp
+ kmc_tools counters_subtract kmers1 kmers2 kmers1_kmers2_counters_subtract
+
+## AUTHOR
+
+KMC was originally written by:
+
+ - Sebastian Deorowicz (sebastian.deorowicz at polsl.pl)
+
+ - Marek Kokot
+
+ - Szymon Grabowski
+
+ - Agnieszka Debudaj-Grabysz
+
+## COPYING
+
+KMC is a free software distributed under GNU GPL3 licence for academic,
+research, and commercial use.
\ No newline at end of file
diff --git a/debian/man_src/kmc_tools-dump.1.ronn b/debian/man_src/kmc_tools-dump.1.ronn
new file mode 100644
index 0000000..a72457a
--- /dev/null
+++ b/debian/man_src/kmc_tools-dump.1.ronn
@@ -0,0 +1,45 @@
+kmc_tools-dump(1) - dump k-mers and counters to text file
+=========================================================
+
+## SYNOPSIS
+
+kmc_tools dump [dump_params] <inputdb> [input_params] <output>
+
+## DESCRIPTION
+
+This command produces a text dump of the KMC database.
+
+## OPTIONS
+
+For each input there are additional parameters:
+
+ * `-ci<value>`:
+ exclude k-mers occurring less than <value> times
+ * `-cx<value>`:
+ exclude k-mers occurring more of than <value> times
+
+Dump operation parameters:
+
+ * `-s`:
+ sorted output
+
+## EXAMPLE
+
+ kmc_tools dump wy_kmc2 -ci3 -cx1000 dump.txt
+
+## AUTHOR
+
+KMC was originally written by:
+
+ - Sebastian Deorowicz (sebastian.deorowicz at polsl.pl)
+
+ - Marek Kokot
+
+ - Szymon Grabowski
+
+ - Agnieszka Debudaj-Grabysz
+
+## COPYING
+
+KMC is a free software distributed under GNU GPL3 licence for academic,
+research, and commercial use.
\ No newline at end of file
diff --git a/debian/man_src/kmc_tools-filter.1.ronn b/debian/man_src/kmc_tools-filter.1.ronn
new file mode 100644
index 0000000..71b4597
--- /dev/null
+++ b/debian/man_src/kmc_tools-filter.1.ronn
@@ -0,0 +1,56 @@
+kmc_tools-filter(1) - filter out reads with too small number of k-mers
+======================================================================
+
+## SYNOPSIS
+
+ kmc_tools filter <kmc_input_db> [kmc_input_db_params] <input_read_set> [input_read_set_params] <output_read_set> [output_read_set_params]
+
+## DESCRIPTION
+
+This command filters out reads with too small number of k-mers.
+
+
+## OPTIONS
+
+ For k-mers' database there are additional parameters:
+
+ * `-ci<value>`:
+ exclude k-mers occurring less than <value> times
+ * `-cx<value>`:
+ exclude k-mers occurring more of than <value> times
+
+For the input set of reads there are additional parameters:
+
+ * `-ci<value>`:
+ remove reads containing less k-mers than value. It can be integer or floating number in range [0.0;1.0]
+ * `-ci<value>`:
+ remove reads containing more k-mers than value. It can be integer or floating number in range [0.0;1.0]
+ * `-f<a/q>`:
+ input in FASTA format (-fa), FASTQ format (-fq); default: FASTQ
+
+ For the output set of reads there are additional parameters:
+
+ * `-f<a/q>`:
+ output in FASTA format (-fa), FASTQ format (-fq); default: same as input
+
+## EXAMPLE
+
+ kmc_tools filter kmc_db -ci3 input.fastq -ci0.5 -cx1.0 filtered.fastq
+ kmc_tools filter kmc_db input.fastq -ci10 -cx100 filtered.fastq
+
+## AUTHOR
+
+KMC was originally written by:
+
+ - Sebastian Deorowicz (sebastian.deorowicz at polsl.pl)
+
+ - Marek Kokot
+
+ - Szymon Grabowski
+
+ - Agnieszka Debudaj-Grabysz
+
+## COPYING
+
+KMC is a free software distributed under GNU GPL3 licence for academic,
+research, and commercial use.
\ No newline at end of file
diff --git a/debian/man_src/kmc_tools-histogram.1.ronn b/debian/man_src/kmc_tools-histogram.1.ronn
new file mode 100644
index 0000000..0b92672
--- /dev/null
+++ b/debian/man_src/kmc_tools-histogram.1.ronn
@@ -0,0 +1,40 @@
+kmc_tools-histogram(1) - produce histogram of k-mer occurrences
+===============================================================
+
+## SYNOPSIS
+
+kmc_tools histogram <inputdb> [input_params] <output>
+
+## DESCRIPTION
+
+This command produces a histogram of k-mer occurrences.
+
+## OPTIONS
+
+For each input there are additional parameters:
+
+ * `-ci<value>`:
+ exclude k-mers occurring less than <value> times
+ * `-cx<value>`:
+ exclude k-mers occurring more of than <value> times
+
+## EXAMPLE
+
+ kmc_tools histogram wy_kmc2 -ci3 -cx1000 histo.txt
+
+## AUTHOR
+
+KMC was originally written by:
+
+ - Sebastian Deorowicz (sebastian.deorowicz at polsl.pl)
+
+ - Marek Kokot
+
+ - Szymon Grabowski
+
+ - Agnieszka Debudaj-Grabysz
+
+## COPYING
+
+KMC is a free software distributed under GNU GPL3 licence for academic,
+research, and commercial use.
\ No newline at end of file
diff --git a/debian/man_src/kmc_tools-intersect.1.ronn b/debian/man_src/kmc_tools-intersect.1.ronn
new file mode 100644
index 0000000..fa248d4
--- /dev/null
+++ b/debian/man_src/kmc_tools-intersect.1.ronn
@@ -0,0 +1,51 @@
+kmc_tools-intersect(1) - calculate intersection of two KMC databases
+====================================================================
+
+## SYNOPSIS
+
+kmc_tools intersect <input1 [input1_params]> <input2 [input2_params]> <output [output_params]>
+
+## DESCRIPTION
+
+The output database will contain only k-mers that are present in both input sets. The counter value in the output database is equal to the lower counter value in the input.
+
+## OPTIONS
+
+For each input there are additional parameters:
+
+ * `-ci<value>`:
+ exclude k-mers occurring less than <value> times
+ * `-cx<value>`:
+ exclude k-mers occurring more of than <value> times
+
+For output there are additional parameters:
+
+ * `-ci<value>`:
+ exclude k-mers occurring less than <value> times
+ * `-cx<value>`:
+ exclude k-mers occurring more of than <value> times
+ * `-cs<value>`:
+ maximal value of a counter
+
+## EXAMPLE
+
+ kmc -k28 file1.fastq kmers1 tmp
+ kmc -k28 file2.fastq kmers2 tmp
+ kmc_tools intersect kmers1 -ci10 -cx200 kmers2 -ci4 -cx100 kmers1_kmers2_intersect -ci20 -cx150
+
+## AUTHOR
+
+KMC was originally written by:
+
+ - Sebastian Deorowicz (sebastian.deorowicz at polsl.pl)
+
+ - Marek Kokot
+
+ - Szymon Grabowski
+
+ - Agnieszka Debudaj-Grabysz
+
+## COPYING
+
+KMC is a free software distributed under GNU GPL3 licence for academic,
+research, and commercial use.
\ No newline at end of file
diff --git a/debian/man_src/kmc_tools-kmers_subtract.1.ronn b/debian/man_src/kmc_tools-kmers_subtract.1.ronn
new file mode 100644
index 0000000..26fb934
--- /dev/null
+++ b/debian/man_src/kmc_tools-kmers_subtract.1.ronn
@@ -0,0 +1,51 @@
+kmc_tools-kmers_subtract(1) - calculate subtraction of two KMC databases
+========================================================================
+
+## SYNOPSIS
+
+kmc_tools kmers_subtract <input1 [input1_params]> <input2 [input2_params]> <output [output_params]>
+
+## DESCRIPTION
+
+The output database will contains only k-mers that are present in the first input set but absent in the second one. The counter value is equal to the value from the first input set.
+
+## OPTIONS
+
+For each input there are additional parameters:
+
+ * `-ci<value>`:
+ exclude k-mers occurring less than <value> times
+ * `-cx<value>`:
+ exclude k-mers occurring more of than <value> times
+
+For output there are additional parameters:
+
+ * `-ci<value>`:
+ exclude k-mers occurring less than <value> times
+ * `-cx<value>`:
+ exclude k-mers occurring more of than <value> times
+ * `-cs<value>`:
+ maximal value of a counter
+
+## EXAMPLE
+
+ kmc -k28 file1.fastq kmers1 tmp
+ kmc -k28 file2.fastq kmers2 tmp
+ kmc_tools kmers_subtract kmers1 kmers2 kmers1_kmers2_subtract -cs200
+
+## AUTHOR
+
+KMC was originally written by:
+
+ - Sebastian Deorowicz (sebastian.deorowicz at polsl.pl)
+
+ - Marek Kokot
+
+ - Szymon Grabowski
+
+ - Agnieszka Debudaj-Grabysz
+
+## COPYING
+
+KMC is a free software distributed under GNU GPL3 licence for academic,
+research, and commercial use.
\ No newline at end of file
diff --git a/debian/man_src/kmc_tools-sort.1.ronn b/debian/man_src/kmc_tools-sort.1.ronn
new file mode 100644
index 0000000..16f6250
--- /dev/null
+++ b/debian/man_src/kmc_tools-sort.1.ronn
@@ -0,0 +1,45 @@
+kmc_tools-sort(1) - sort KMC databases
+======================================
+
+## SYNOPSIS
+
+kmc_tools sort <inputdb> [input_params] <output> [output_params]
+
+## DESCRIPTION
+
+Converts database produced by KMC2.x to KMC1.x database format (which contains k-mers in sorted order)
+
+## OPTIONS
+
+For each input there are additional parameters:
+
+ * `-ci<value>`:
+ exclude k-mers occurring less than <value> times
+ * `-cx<value>`:
+ exclude k-mers occurring more of than <value> times
+
+For output there are additional parameters:
+
+ * `-cs<value>`:
+ maximal value of a counter
+
+## EXAMPLE
+
+ kmc_tools sort wy_kmc2 -ci3 -cx1000 wy_kmc1 -cs255
+
+## AUTHOR
+
+KMC was originally written by:
+
+ - Sebastian Deorowicz (sebastian.deorowicz at polsl.pl)
+
+ - Marek Kokot
+
+ - Szymon Grabowski
+
+ - Agnieszka Debudaj-Grabysz
+
+## COPYING
+
+KMC is a free software distributed under GNU GPL3 licence for academic,
+research, and commercial use.
\ No newline at end of file
diff --git a/debian/man_src/kmc_tools-union.1.ronn b/debian/man_src/kmc_tools-union.1.ronn
new file mode 100644
index 0000000..b86e420
--- /dev/null
+++ b/debian/man_src/kmc_tools-union.1.ronn
@@ -0,0 +1,51 @@
+kmc_tools-union(1) - calculate union of two KMC databases
+=========================================================
+
+## SYNOPSIS
+
+kmc_tools union <input1 [input1_params]> <input2 [input2_params]> <output [output_params]>
+
+## DESCRIPTION
+
+he output database will contain all k-mers present in both input sets. For the same k-mers in the first and the second input, the counter in the output is equal to the sum from both inputs.
+
+## OPTIONS
+
+For each input there are additional parameters:
+
+ * `-ci<value>`:
+ exclude k-mers occurring less than <value> times
+ * `-cx<value>`:
+ exclude k-mers occurring more of than <value> times
+
+For output there are additional parameters:
+
+ * `-ci<value>`:
+ exclude k-mers occurring less than <value> times
+ * `-cx<value>`:
+ exclude k-mers occurring more of than <value> times
+ * `-cs<value>`:
+ maximal value of a counter
+
+## EXAMPLE
+
+kmc -k28 file1.fastq kmers1 tmp
+kmc -k28 file2.fastq kmers2 tmp
+kmc_tools union kmers1 -ci3 -cx70000 kmers2 kmers1_kmers2_union -cs65536
+
+## AUTHOR
+
+KMC was originally written by:
+
+ - Sebastian Deorowicz (sebastian.deorowicz at polsl.pl)
+
+ - Marek Kokot
+
+ - Szymon Grabowski
+
+ - Agnieszka Debudaj-Grabysz
+
+## COPYING
+
+KMC is a free software distributed under GNU GPL3 licence for academic,
+research, and commercial use.
\ No newline at end of file
diff --git a/debian/man_src/kmc_tools.1.ronn b/debian/man_src/kmc_tools.1.ronn
new file mode 100644
index 0000000..dd52525
--- /dev/null
+++ b/debian/man_src/kmc_tools.1.ronn
@@ -0,0 +1,84 @@
+kmc_tools(1) - additional operations on KMC databases
+=====================================================
+
+## SYNOPSIS
+
+kmc_tools [global parameters] <operation> [operation parameters]
+
+## DESCRIPTION
+
+This command and its various subcomments implement a number of operations on
+KMC databases.
+
+### k-mers sets' operations for 2 KMC's databases:
+
+ * `intersect`:
+ intersection of 2 k-mers' sets
+
+ * `kmers_subtract`:
+ subtraction of 2 k-mers' sets
+
+ * `counters_subtract`:
+ counters' subtraction of 2 k-mers' sets
+
+ * `union`:
+ union of 2 k-mers' sets
+
+### operations for single kmc database:
+
+ * `sort`:
+ sorts k-mers from database generated by KMC2.x
+
+ * `reduce`:
+ exclude too rare and too frequent k-mers
+
+ * `compact`:
+ remove counters (store only k-mers)
+
+ * `histogram`:
+ histogram of k-mers occurr ences
+
+ * `dump`:
+ dump k-mers and counters to text file
+
+### more complex operations:
+
+ * `complex`:
+ complex operations with a number of input databases
+
+### other operatations:
+
+ * `filter`:
+ filter out reads with too small number of k-mers
+
+## OPTIONS
+
+### global parameters:
+
+ * `-t<value>`:
+ total number of threads (default: no. of CPU cores)
+ * `-v`:
+ enable verbose mode (shows some information) (default: false)
+ * `-hp`
+ hide percentage progress (default: false)
+
+## EXAMPLE
+
+kmc_tools union db1 -ci3 db2 -ci5 -cx300 db1_union_db2 -ci10
+
+## AUTHOR
+
+KMC was originally written by:
+
+ - Sebastian Deorowicz (sebastian.deorowicz at polsl.pl)
+
+ - Marek Kokot
+
+ - Szymon Grabowski
+
+ - Agnieszka Debudaj-Grabysz
+
+## COPYING
+
+KMC is free software distributed under GNU GPL3 licence for academic,
+research, and commercial use.
\ No newline at end of file
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