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 <[email protected]> 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 -- -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/kmc.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
