[med-svn] [kmc] 01/02: switch to asciidoctor
Sascha Steinbiss
sascha at steinbiss.name
Thu Mar 10 22:21:22 UTC 2016
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository kmc.
commit 1c9d1b926a50f792acb0dc0819fdc0d9b1fefbb9
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date: Thu Mar 10 17:01:15 2016 +0000
switch to asciidoctor
---
debian/control | 2 +-
...ols-compact.1.ronn => kmc_tools-compact.1.adoc} | 27 +++++-----
...ols-complex.1.ronn => kmc_tools-complex.1.adoc} | 44 ++++++++-------
...t.1.ronn => kmc_tools-counters_subtract.1.adoc} | 33 ++++++------
...kmc_tools-dump.1.ronn => kmc_tools-dump.1.adoc} | 29 +++++-----
...tools-filter.1.ronn => kmc_tools-filter.1.adoc} | 37 +++++++------
...histogram.1.ronn => kmc_tools-histogram.1.adoc} | 27 +++++-----
...intersect.1.ronn => kmc_tools-intersect.1.adoc} | 33 ++++++------
...ract.1.ronn => kmc_tools-kmers_subtract.1.adoc} | 33 ++++++------
...kmc_tools-sort.1.ronn => kmc_tools-sort.1.adoc} | 29 +++++-----
...c_tools-union.1.ronn => kmc_tools-union.1.adoc} | 35 ++++++------
.../man_src/{kmc_tools.1.ronn => kmc_tools.1.adoc} | 63 +++++++++++-----------
debian/rules | 3 +-
13 files changed, 214 insertions(+), 181 deletions(-)
diff --git a/debian/control b/debian/control
index 4b498f2..33fe129 100644
--- a/debian/control
+++ b/debian/control
@@ -11,7 +11,7 @@ Build-Depends: debhelper (>= 9),
zlib1g-dev,
libbz2-dev,
help2man,
- ruby-ronn,
+ asciidoctor,
d-shlibs
Standards-Version: 3.9.7
Testsuite: autopkgtest
diff --git a/debian/man_src/kmc_tools-compact.1.ronn b/debian/man_src/kmc_tools-compact.1.adoc
similarity index 64%
rename from debian/man_src/kmc_tools-compact.1.ronn
rename to debian/man_src/kmc_tools-compact.1.adoc
index 7861f3f..6e0f09b 100644
--- a/debian/man_src/kmc_tools-compact.1.ronn
+++ b/debian/man_src/kmc_tools-compact.1.adoc
@@ -1,28 +1,31 @@
-kmc_tools-compact(1) - remove counters of k-mers
-================================================
+= kmc_tools-compact(1)
-## SYNOPSIS
+== NAME
-kmc_tools compact <inputdb> [input_params] <output>
+kmc_tools-compact - remove counters of k-mers
-## DESCRIPTION
+== SYNOPSIS
+
+*kmc_tools* compact <inputdb> [input_params] <output>
+
+== DESCRIPTION
This command removes counters from the database and stores only k-mers.
-## OPTIONS
+== OPTIONS
For each input there are additional parameters:
- * `-ci<value>`:
+ *-ci<value>*::
exclude k-mers occurring less than <value> times
- * `-cx<value>`:
+ *-cx<value>*::
exclude k-mers occurring more of than <value> times
-## EXAMPLE
+== EXAMPLE
kmc_tools compact wy_kmc2 -ci3 -cx1000 wy_kmc1
-## AUTHOR
+== AUTHOR
KMC was originally written by:
@@ -34,7 +37,7 @@ KMC was originally written by:
- Agnieszka Debudaj-Grabysz
-## COPYING
+== COPYING
KMC is a free software distributed under GNU GPL3 licence for academic,
-research, and commercial use.
\ No newline at end of file
+research, and commercial use.
diff --git a/debian/man_src/kmc_tools-complex.1.ronn b/debian/man_src/kmc_tools-complex.1.adoc
similarity index 81%
rename from debian/man_src/kmc_tools-complex.1.ronn
rename to debian/man_src/kmc_tools-complex.1.adoc
index f86668c..3e62f76 100644
--- a/debian/man_src/kmc_tools-complex.1.ronn
+++ b/debian/man_src/kmc_tools-complex.1.adoc
@@ -1,11 +1,14 @@
-kmc_tools-complex(1) - complex operations with a number of input databases
-==========================================================================
+= kmc_tools-complex(1)
-## SYNOPSIS
+== NAME
+
+kmc_tools-complex - complex operations with a number of input databases
+
+== SYNOPSIS
kmc_tools complex <operations_definition_file>
-## DESCRIPTION
+== DESCRIPTION
This command executes a combination of operations as defined by <operations_definition_file>. It is text file with following syntax:
@@ -22,39 +25,40 @@ This command executes a combination of operations as defined by <operations_defi
| | /
|_______________________________________________________________|/
-where
- * `input1, input2, ..., inputN`:
+== PARAMETERS
+
+ *input1, input2, ..., inputN*::
names of inputs used to define equation
- * `input1_db_path, input2_db_path, ..., inputN_db_path`:
+ *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>`:
+ *-ci<value>*::
exclude k-mers occurring less than <value> times
- * `cx<value>`:
+ *cx<value>*::
exclude k-mers occurring more of than <value> times
- * `out_db_path`:
+ *out_db_path*::
path to output database
- * `ref_input`:
+ *ref_input*::
one of input1, input2, ..., inputN
- * `oper`:
+ *oper*::
one of {*,-,~,+}, which refers to {intersect, kmers_subtract, counters_subtract, union}
-Operator * has the highest priority. Other operators have equal priorities.
+Operator '*' has the highest priority. Other operators have equal priorities.
The order of operations can be changed with parentheses.
Output parameters:
- * `-ci<value>`:
+ *-ci<value>*::
exclude k-mers occurring less than <value> times
- * `-cx<value>`:
+ *-cx<value>*::
exclude k-mers occurring more of than <value> times
- * `-cs<value>`:
+ *-cs<value>*::
maximal value of a counter
-## EXAMPLE
+== EXAMPLE
__________________________________________________________________
|INPUT: |
@@ -65,7 +69,7 @@ Output parameters:
|result = (set3+set1)*set2 | /
|_______________________________________________________________|/
-## AUTHOR
+== AUTHOR
KMC was originally written by:
@@ -77,7 +81,7 @@ KMC was originally written by:
- Agnieszka Debudaj-Grabysz
-## COPYING
+== COPYING
KMC is a free software distributed under GNU GPL3 licence for academic,
-research, and commercial use.
\ No newline at end of file
+research, and commercial use.
diff --git a/debian/man_src/kmc_tools-counters_subtract.1.ronn b/debian/man_src/kmc_tools-counters_subtract.1.adoc
similarity index 68%
rename from debian/man_src/kmc_tools-counters_subtract.1.ronn
rename to debian/man_src/kmc_tools-counters_subtract.1.adoc
index f9c3da4..da1801e 100644
--- a/debian/man_src/kmc_tools-counters_subtract.1.ronn
+++ b/debian/man_src/kmc_tools-counters_subtract.1.adoc
@@ -1,39 +1,42 @@
-kmc_tools-counters_subtract(1) - calculate counters subtraction of two KMC databases
-====================================================================================
+= kmc_tools-counters_subtract(1)
-## SYNOPSIS
+== NAME
-kmc_tools counters_subtract <input1 [input1_params]> <input2 [input2_params]> <output [output_params]>
+kmc_tools-counters_subtract - calculate counters subtraction of two KMC databases
-## DESCRIPTION
+== 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
+== OPTIONS
For each input there are additional parameters:
- * `-ci<value>`:
+ *-ci<value>*::
exclude k-mers occurring less than <value> times
- * `-cx<value>`:
+ *-cx<value>*::
exclude k-mers occurring more of than <value> times
For output there are additional parameters:
- * `-ci<value>`:
+ *-ci<value>*::
exclude k-mers occurring less than <value> times
- * `-cx<value>`:
+ *-cx<value>*::
exclude k-mers occurring more of than <value> times
- * `-cs<value>`:
+ *-cs<value>*::
maximal value of a counter
-## EXAMPLE
+== EXAMPLE
kmc - k28 file1.fastq kmers1 tmp
kmc - k28 file2.fastq kmers2 tmp
kmc_tools counters_subtract kmers1 kmers2 kmers1_kmers2_counters_subtract
-## AUTHOR
+== AUTHOR
KMC was originally written by:
@@ -45,7 +48,7 @@ KMC was originally written by:
- Agnieszka Debudaj-Grabysz
-## COPYING
+== COPYING
KMC is a free software distributed under GNU GPL3 licence for academic,
-research, and commercial use.
\ No newline at end of file
+research, and commercial use.
diff --git a/debian/man_src/kmc_tools-dump.1.ronn b/debian/man_src/kmc_tools-dump.1.adoc
similarity index 62%
rename from debian/man_src/kmc_tools-dump.1.ronn
rename to debian/man_src/kmc_tools-dump.1.adoc
index a72457a..62018a1 100644
--- a/debian/man_src/kmc_tools-dump.1.ronn
+++ b/debian/man_src/kmc_tools-dump.1.adoc
@@ -1,33 +1,36 @@
-kmc_tools-dump(1) - dump k-mers and counters to text file
-=========================================================
+= kmc_tools-dump(1)
-## SYNOPSIS
+== NAME
-kmc_tools dump [dump_params] <inputdb> [input_params] <output>
+kmc_tools-dump - dump k-mers and counters to text file
-## DESCRIPTION
+== SYNOPSIS
+
+*kmc_tools dump* [dump_params] <inputdb> [input_params] <output>
+
+== DESCRIPTION
This command produces a text dump of the KMC database.
-## OPTIONS
+== OPTIONS
For each input there are additional parameters:
- * `-ci<value>`:
+ *-ci<value>*::
exclude k-mers occurring less than <value> times
- * `-cx<value>`:
+ *-cx<value>*::
exclude k-mers occurring more of than <value> times
Dump operation parameters:
- * `-s`:
+ *-s*::
sorted output
-## EXAMPLE
+== EXAMPLE
kmc_tools dump wy_kmc2 -ci3 -cx1000 dump.txt
-## AUTHOR
+== AUTHOR
KMC was originally written by:
@@ -39,7 +42,7 @@ KMC was originally written by:
- Agnieszka Debudaj-Grabysz
-## COPYING
+== COPYING
KMC is a free software distributed under GNU GPL3 licence for academic,
-research, and commercial use.
\ No newline at end of file
+research, and commercial use.
diff --git a/debian/man_src/kmc_tools-filter.1.ronn b/debian/man_src/kmc_tools-filter.1.adoc
similarity index 65%
rename from debian/man_src/kmc_tools-filter.1.ronn
rename to debian/man_src/kmc_tools-filter.1.adoc
index 71b4597..98ef538 100644
--- a/debian/man_src/kmc_tools-filter.1.ronn
+++ b/debian/man_src/kmc_tools-filter.1.adoc
@@ -1,44 +1,47 @@
-kmc_tools-filter(1) - filter out reads with too small number of k-mers
-======================================================================
+= kmc_tools-filter(1)
-## SYNOPSIS
+== NAME
- kmc_tools filter <kmc_input_db> [kmc_input_db_params] <input_read_set> [input_read_set_params] <output_read_set> [output_read_set_params]
+kmc_tools-filter - filter out reads with too small number of k-mers
-## DESCRIPTION
+== 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
+== OPTIONS
- For k-mers' database there are additional parameters:
+ For k-mers database there are additional parameters:
- * `-ci<value>`:
+ *-ci<value>*::
exclude k-mers occurring less than <value> times
- * `-cx<value>`:
+ *-cx<value>*::
exclude k-mers occurring more of than <value> times
For the input set of reads there are additional parameters:
- * `-ci<value>`:
+ *-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>`:
+ *-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>`:
+ *-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>`:
+ *-f<a/q>*::
output in FASTA format (-fa), FASTQ format (-fq); default: same as input
-## EXAMPLE
+== 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
+== AUTHOR
KMC was originally written by:
@@ -50,7 +53,7 @@ KMC was originally written by:
- Agnieszka Debudaj-Grabysz
-## COPYING
+== COPYING
KMC is a free software distributed under GNU GPL3 licence for academic,
-research, and commercial use.
\ No newline at end of file
+research, and commercial use.
diff --git a/debian/man_src/kmc_tools-histogram.1.ronn b/debian/man_src/kmc_tools-histogram.1.adoc
similarity index 61%
rename from debian/man_src/kmc_tools-histogram.1.ronn
rename to debian/man_src/kmc_tools-histogram.1.adoc
index 0b92672..7db500a 100644
--- a/debian/man_src/kmc_tools-histogram.1.ronn
+++ b/debian/man_src/kmc_tools-histogram.1.adoc
@@ -1,28 +1,31 @@
-kmc_tools-histogram(1) - produce histogram of k-mer occurrences
-===============================================================
+= kmc_tools-histogram(1)
-## SYNOPSIS
+== NAME
-kmc_tools histogram <inputdb> [input_params] <output>
+kmc_tools-histogram - produce histogram of k-mer occurrences
-## DESCRIPTION
+== SYNOPSIS
+
+*kmc_tools histogram* <inputdb> [input_params] <output>
+
+== DESCRIPTION
This command produces a histogram of k-mer occurrences.
-## OPTIONS
+== OPTIONS
For each input there are additional parameters:
- * `-ci<value>`:
+ *-ci<value>*::
exclude k-mers occurring less than <value> times
- * `-cx<value>`:
+ *-cx<value>*::
exclude k-mers occurring more of than <value> times
-## EXAMPLE
+== EXAMPLE
kmc_tools histogram wy_kmc2 -ci3 -cx1000 histo.txt
-## AUTHOR
+== AUTHOR
KMC was originally written by:
@@ -34,7 +37,7 @@ KMC was originally written by:
- Agnieszka Debudaj-Grabysz
-## COPYING
+== COPYING
KMC is a free software distributed under GNU GPL3 licence for academic,
-research, and commercial use.
\ No newline at end of file
+research, and commercial use.
diff --git a/debian/man_src/kmc_tools-intersect.1.ronn b/debian/man_src/kmc_tools-intersect.1.adoc
similarity index 68%
rename from debian/man_src/kmc_tools-intersect.1.ronn
rename to debian/man_src/kmc_tools-intersect.1.adoc
index fa248d4..a531370 100644
--- a/debian/man_src/kmc_tools-intersect.1.ronn
+++ b/debian/man_src/kmc_tools-intersect.1.adoc
@@ -1,39 +1,42 @@
-kmc_tools-intersect(1) - calculate intersection of two KMC databases
-====================================================================
+= kmc_tools-intersect(1)
-## SYNOPSIS
+== NAME
-kmc_tools intersect <input1 [input1_params]> <input2 [input2_params]> <output [output_params]>
+kmc_tools-intersect - calculate intersection of two KMC databases
-## DESCRIPTION
+== 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
+== OPTIONS
For each input there are additional parameters:
- * `-ci<value>`:
+ *-ci<value>*::
exclude k-mers occurring less than <value> times
- * `-cx<value>`:
+ *-cx<value>*::
exclude k-mers occurring more of than <value> times
For output there are additional parameters:
- * `-ci<value>`:
+ *-ci<value>*::
exclude k-mers occurring less than <value> times
- * `-cx<value>`:
+ *-cx<value>*::
exclude k-mers occurring more of than <value> times
- * `-cs<value>`:
+ *-cs<value>*::
maximal value of a counter
-## EXAMPLE
+== 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
+== AUTHOR
KMC was originally written by:
@@ -45,7 +48,7 @@ KMC was originally written by:
- Agnieszka Debudaj-Grabysz
-## COPYING
+== COPYING
KMC is a free software distributed under GNU GPL3 licence for academic,
-research, and commercial use.
\ No newline at end of file
+research, and commercial use.
diff --git a/debian/man_src/kmc_tools-kmers_subtract.1.ronn b/debian/man_src/kmc_tools-kmers_subtract.1.adoc
similarity index 67%
rename from debian/man_src/kmc_tools-kmers_subtract.1.ronn
rename to debian/man_src/kmc_tools-kmers_subtract.1.adoc
index 26fb934..32f6f6f 100644
--- a/debian/man_src/kmc_tools-kmers_subtract.1.ronn
+++ b/debian/man_src/kmc_tools-kmers_subtract.1.adoc
@@ -1,39 +1,42 @@
-kmc_tools-kmers_subtract(1) - calculate subtraction of two KMC databases
-========================================================================
+= kmc_tools-kmers_subtract(1)
-## SYNOPSIS
+== NAME
-kmc_tools kmers_subtract <input1 [input1_params]> <input2 [input2_params]> <output [output_params]>
+kmc_tools-kmers_subtract - calculate subtraction of two KMC databases
-## DESCRIPTION
+== 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
+== OPTIONS
For each input there are additional parameters:
- * `-ci<value>`:
+ *-ci<value>*::
exclude k-mers occurring less than <value> times
- * `-cx<value>`:
+ *-cx<value>*::
exclude k-mers occurring more of than <value> times
For output there are additional parameters:
- * `-ci<value>`:
+ *-ci<value>*::
exclude k-mers occurring less than <value> times
- * `-cx<value>`:
+ *-cx<value>*::
exclude k-mers occurring more of than <value> times
- * `-cs<value>`:
+ *-cs<value>*::
maximal value of a counter
-## EXAMPLE
+== EXAMPLE
kmc -k28 file1.fastq kmers1 tmp
kmc -k28 file2.fastq kmers2 tmp
kmc_tools kmers_subtract kmers1 kmers2 kmers1_kmers2_subtract -cs200
-## AUTHOR
+== AUTHOR
KMC was originally written by:
@@ -45,7 +48,7 @@ KMC was originally written by:
- Agnieszka Debudaj-Grabysz
-## COPYING
+== COPYING
KMC is a free software distributed under GNU GPL3 licence for academic,
-research, and commercial use.
\ No newline at end of file
+research, and commercial use.
diff --git a/debian/man_src/kmc_tools-sort.1.ronn b/debian/man_src/kmc_tools-sort.1.adoc
similarity index 68%
rename from debian/man_src/kmc_tools-sort.1.ronn
rename to debian/man_src/kmc_tools-sort.1.adoc
index 16f6250..fe49f5c 100644
--- a/debian/man_src/kmc_tools-sort.1.ronn
+++ b/debian/man_src/kmc_tools-sort.1.adoc
@@ -1,33 +1,36 @@
-kmc_tools-sort(1) - sort KMC databases
-======================================
+= kmc_tools-sort(1)
-## SYNOPSIS
+== NAME
-kmc_tools sort <inputdb> [input_params] <output> [output_params]
+kmc_tools-sort - sort KMC databases
-## DESCRIPTION
+== 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
+== OPTIONS
For each input there are additional parameters:
- * `-ci<value>`:
+ *-ci<value>*::
exclude k-mers occurring less than <value> times
- * `-cx<value>`:
+ *-cx<value>*::
exclude k-mers occurring more of than <value> times
For output there are additional parameters:
- * `-cs<value>`:
+ *-cs<value>*::
maximal value of a counter
-## EXAMPLE
+== EXAMPLE
kmc_tools sort wy_kmc2 -ci3 -cx1000 wy_kmc1 -cs255
-## AUTHOR
+== AUTHOR
KMC was originally written by:
@@ -39,7 +42,7 @@ KMC was originally written by:
- Agnieszka Debudaj-Grabysz
-## COPYING
+== COPYING
KMC is a free software distributed under GNU GPL3 licence for academic,
-research, and commercial use.
\ No newline at end of file
+research, and commercial use.
diff --git a/debian/man_src/kmc_tools-union.1.ronn b/debian/man_src/kmc_tools-union.1.adoc
similarity index 55%
rename from debian/man_src/kmc_tools-union.1.ronn
rename to debian/man_src/kmc_tools-union.1.adoc
index b86e420..cd420dc 100644
--- a/debian/man_src/kmc_tools-union.1.ronn
+++ b/debian/man_src/kmc_tools-union.1.adoc
@@ -1,39 +1,42 @@
-kmc_tools-union(1) - calculate union of two KMC databases
-=========================================================
+= kmc_tools-union(1)
-## SYNOPSIS
+== NAME
-kmc_tools union <input1 [input1_params]> <input2 [input2_params]> <output [output_params]>
+kmc_tools-union - calculate union of two KMC databases
-## DESCRIPTION
+== SYNOPSIS
-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.
+*kmc_tools union* <input1 [input1_params]> <input2 [input2_params]> <output [output_params]>
-## OPTIONS
+== DESCRIPTION
+
+The 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>`:
+ *-ci<value>*::
exclude k-mers occurring less than <value> times
- * `-cx<value>`:
+ *-cx<value>*::
exclude k-mers occurring more of than <value> times
For output there are additional parameters:
- * `-ci<value>`:
+ *-ci<value>*::
exclude k-mers occurring less than <value> times
- * `-cx<value>`:
+ *-cx<value>*::
exclude k-mers occurring more of than <value> times
- * `-cs<value>`:
+ *-cs<value>*::
maximal value of a counter
-## EXAMPLE
+== 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
+== AUTHOR
KMC was originally written by:
@@ -45,7 +48,7 @@ KMC was originally written by:
- Agnieszka Debudaj-Grabysz
-## COPYING
+== COPYING
KMC is a free software distributed under GNU GPL3 licence for academic,
-research, and commercial use.
\ No newline at end of file
+research, and commercial use.
diff --git a/debian/man_src/kmc_tools.1.ronn b/debian/man_src/kmc_tools.1.adoc
similarity index 65%
rename from debian/man_src/kmc_tools.1.ronn
rename to debian/man_src/kmc_tools.1.adoc
index 02742d4..ea7ea47 100644
--- a/debian/man_src/kmc_tools.1.ronn
+++ b/debian/man_src/kmc_tools.1.adoc
@@ -1,80 +1,83 @@
-kmc_tools(1) - additional operations on k-mer databases
-=======================================================
+= kmc_tools(1)
-## SYNOPSIS
+== NAME
- kmc_tools [global parameters] <operation> [operation parameters]
+kmc_tools - additional operations on k-mer databases
-## DESCRIPTION
+== 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 databases
+=== k-mers sets operations for 2 KMC databases
- * `intersect`:
+ *intersect*::
intersection of 2 k-mers sets
- * `kmers_subtract`:
+ *kmers_subtract*::
subtraction of 2 k-mers sets
- * `counters_subtract`:
+ *counters_subtract*::
counters subtraction of 2 k-mer sets
- * `union`:
+ *union*::
union of 2 k-mers sets
-### operations for single kmc database
+=== operations for single kmc database
- * `sort`:
+ *sort*::
sorts k-mers from database generated by KMC2.x
- * `reduce`:
+ *reduce*::
exclude too rare and too frequent k-mers
- * `compact`:
+ *compact*::
remove counters (store only k-mers)
- * `histogram`:
+ *histogram*::
histogram of k-mers occurr ences
- * `dump`:
+ *dump*::
dump k-mers and counters to text file
-### more complex operations:
+=== more complex operations:
- * `complex`:
+ *complex*::
complex operations with a number of input databases
-### other operations:
+=== other operations:
- * `filter`:
+ *filter*::
filter out reads with too small number of k-mers
-## OPTIONS
+== OPTIONS
-### global parameters:
+=== global parameters:
- * `-t<value>`:
+ *-t<value>*::
total number of threads (default: no. of CPU cores)
- * `-v`:
+ *-v*::
enable verbose mode (shows some information) (default: false)
- * `-hp`:
+ *-hp*::
hide percentage progress (default: false)
-## EXAMPLE
+== EXAMPLE
kmc_tools union db1 -ci3 db2 -ci5 -cx300 db1_union_db2 -ci10
-## SEE ALSO
+== SEE ALSO
kmc(1), kmc_tools-histogram(1), kmc_tools-compact(1), kmc_tools-intersect(1),
kmc_tools-complex(1), kmc_tools-kmers_subtract(1), kmc_tools-counters_subtract(1),
kmc_tools-sort(1), kmc_tools-dump(1), kmc_tools-union(1), kmc_tools-filter(1)
-## AUTHOR
+== AUTHOR
KMC was originally written by:
@@ -86,7 +89,7 @@ KMC was originally written by:
- Agnieszka Debudaj-Grabysz
-## COPYING
+== COPYING
KMC is free software distributed under GNU GPL3 licence for academic,
-research, and commercial use.
\ No newline at end of file
+research, and commercial use.
diff --git a/debian/rules b/debian/rules
index d082d9e..ae7f73b 100755
--- a/debian/rules
+++ b/debian/rules
@@ -2,7 +2,6 @@
export DH_VERBOSE := 1
DATE := $(shell dpkg-parsechangelog -S Date)
-SHORTDATE := $(shell date -d '$(DATE)' +%Y-%m-%d)
mandir := $(CURDIR)/debian/man
debfolder := $(CURDIR)/debian
@@ -21,7 +20,7 @@ override_dh_auto_clean:
override_dh_installman:
mkdir -p $(mandir)
$(debfolder)/usage_to_man
- ronn --date=$(SHORTDATE) $(debfolder)/man_src/*.ronn
+ asciidoctor -a docdate='' -b manpage $(debfolder)/man_src/*.adoc
cp $(debfolder)/man_src/*.? $(mandir)
dh_installman --
--
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