[med-svn] [reapr] 01/02: switch manpage building to asciidoctor
Sascha Steinbiss
sascha at steinbiss.name
Sat Mar 12 21:50:48 UTC 2016
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository reapr.
commit 27a1959f0fe8bf3bf9131b03edad0d722ec15b91
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date: Sat Mar 12 21:41:27 2016 +0000
switch manpage building to asciidoctor
---
debian/control | 2 +-
.../{reapr-break.1.ronn => reapr-break.1.adoc} | 33 +++++++++--------
.../{reapr-facheck.1.ronn => reapr-facheck.1.adoc} | 13 ++++---
debian/man_src/reapr-gapresize.1.adoc | 18 ++++++++++
debian/man_src/reapr-gapresize.1.ronn | 15 --------
...tfrombam.1.ronn => reapr-perfectfrombam.1.adoc} | 19 +++++-----
...r-perfectmap.1.ronn => reapr-perfectmap.1.adoc} | 11 +++---
...reapr-pipeline.1.ronn => reapr-pipeline.1.adoc} | 29 ++++++++-------
debian/man_src/reapr-plots.1.adoc | 18 ++++++++++
debian/man_src/reapr-plots.1.ronn | 15 --------
debian/man_src/reapr-preprocess.1.adoc | 13 +++++++
debian/man_src/reapr-preprocess.1.ronn | 10 ------
.../{reapr-score.1.ronn => reapr-score.1.adoc} | 35 +++++++++---------
debian/man_src/reapr-seqrename.1.adoc | 17 +++++++++
debian/man_src/reapr-seqrename.1.ronn | 14 --------
...reapr-smaltmap.1.ronn => reapr-smaltmap.1.adoc} | 27 +++++++-------
.../{reapr-stats.1.ronn => reapr-stats.1.adoc} | 29 ++++++++-------
debian/man_src/reapr-summary.1.adoc | 23 ++++++++++++
debian/man_src/reapr-summary.1.ronn | 20 -----------
debian/man_src/{reapr.1.ronn => reapr.1.adoc} | 41 ++++++++++++----------
debian/rules | 4 +--
21 files changed, 224 insertions(+), 182 deletions(-)
diff --git a/debian/control b/debian/control
index 2d252f3..e7bde57 100644
--- a/debian/control
+++ b/debian/control
@@ -8,7 +8,7 @@ Build-Depends: debhelper (>= 9),
libtabixpp-dev,
libhts-dev (>= 1.3),
zlib1g-dev,
- ruby-ronn,
+ asciidoctor,
samtools (>= 1.3),
bamtools,
smalt,
diff --git a/debian/man_src/reapr-break.1.ronn b/debian/man_src/reapr-break.1.adoc
similarity index 58%
rename from debian/man_src/reapr-break.1.ronn
rename to debian/man_src/reapr-break.1.adoc
index 6f7dbc1..31a8602 100644
--- a/debian/man_src/reapr-break.1.ronn
+++ b/debian/man_src/reapr-break.1.adoc
@@ -1,43 +1,46 @@
-reapr-break(1) -- make broken assembly via REAPR
-================================================
+= reapr-break(1)
+
+## NAME
+
+reapr-break - make broken assembly via REAPR
## SYNOPSIS
-`reapr break` [options] <assembly.fa> <errors.gff.gz> <outfileprefix>
+*reapr break* [options] <assembly.fa> <errors.gff.gz> <outfileprefix>
## DESCRIPTION
-<errors.gff.gz> is the errors GFF file made when running `score`.
+<errors.gff.gz> is the errors GFF file made when running *score*.
## OPTIONS
-* `-a`:
+*-a*::
Aggressive breaking: break contigs at any FCD or low_frag error, as
opposed to the default of replacing with Ns. Contigs are broken at the
- midpoint of each error. Also see option `-t`. Incompatible with `-b`.
+ midpoint of each error. Also see option *-t*. Incompatible with *-b*.
-* `-b`:
+*-b*::
Ignore FCD and low fragment coverage errors that do not contain
- a gap (the default is to replace these with Ns). Incompatible with `-a`.
+ a gap (the default is to replace these with Ns). Incompatible with *-a*.
-* `-e` <float>:
+*-e* <float>::
Minimum FCD error [0]
-* `-l` <int>:
+*-l* <int>::
Minimum sequence length to output [100]
-* `-m` <int>:
+*-m* <int>::
Max sequence length to write to the bin. Sequences longer
than this are written to the main assembly output. This is to stop
long stretches of sequence being lost [999]
-* `-t` <int>:
- When `-a` is used, use this option to specify how many bases
+*-t* <int>::
+ When *-a* is used, use this option to specify how many bases
are trimmed off the end of each new contig around a break.
- `-t` N means that, at an FCD error, a contig is broken at the middle
+ *-t* N means that, at an FCD error, a contig is broken at the middle
coordinate of the error, then N bases are
trimmed off each new contig end [0]
## SEE ALSO
-reapr(1)
\ No newline at end of file
+reapr(1)
diff --git a/debian/man_src/reapr-facheck.1.ronn b/debian/man_src/reapr-facheck.1.adoc
similarity index 64%
rename from debian/man_src/reapr-facheck.1.ronn
rename to debian/man_src/reapr-facheck.1.adoc
index 3d8fb11..e794bdb 100644
--- a/debian/man_src/reapr-facheck.1.ronn
+++ b/debian/man_src/reapr-facheck.1.adoc
@@ -1,14 +1,17 @@
-reapr-facheck(1) -- checks IDs in fasta file
-============================================
+# reapr-facheck(1)
+
+## NAME
+
+reapr-facheck - checks IDs in fasta file
## SYNOPSIS
-`reapr facheck` <in.fa> [out_prefix]
+*reapr facheck* <in.fa> [out_prefix]
## DESCRIPTION
Checks that the names in the fasta file are ok. Things like
-trailing whitespace or characters |':- could break the pipeline.
+trailing whitespace or characters (|':-) could break the pipeline.
If out_prefix is not given, it will die when a bad ID is found.
No output means everything is OK.
@@ -18,4 +21,4 @@ names, and out_prefix.info which has the mapping from old name to new name.
## SEE ALSO
-reapr(1)
\ No newline at end of file
+reapr(1)
diff --git a/debian/man_src/reapr-gapresize.1.adoc b/debian/man_src/reapr-gapresize.1.adoc
new file mode 100644
index 0000000..ca24e11
--- /dev/null
+++ b/debian/man_src/reapr-gapresize.1.adoc
@@ -0,0 +1,18 @@
+# reapr-gapresize(1)
+
+## NAME
+
+reapr-gapresize - calculates gap sizes based on read mapping
+
+## SYNOPSIS
+
+*reapr gapresize* [options] <assembly.fasta> <in.bam> <avg-fragment-length> <max-fragment-length> <outfileprefix>
+
+## OPTIONS
+
+*-g* <int>::
+ Only consider gaps of at least this length [1]
+
+## SEE ALSO
+
+reapr(1)
diff --git a/debian/man_src/reapr-gapresize.1.ronn b/debian/man_src/reapr-gapresize.1.ronn
deleted file mode 100644
index cdef108..0000000
--- a/debian/man_src/reapr-gapresize.1.ronn
+++ /dev/null
@@ -1,15 +0,0 @@
-reapr-gapresize(1) -- calculates gap sizes based on read mapping
-================================================================
-
-## SYNOPSIS
-
-`reapr gapresize` [options] <assembly.fasta> <in.bam> <avg-fragment-length> <max-fragment-length> <outfileprefix>
-
-## OPTIONS
-
-* `-g` <int>:
- Only consider gaps of at least this length [1]
-
-## SEE ALSO
-
-reapr(1)
\ No newline at end of file
diff --git a/debian/man_src/reapr-perfectfrombam.1.ronn b/debian/man_src/reapr-perfectfrombam.1.adoc
similarity index 67%
rename from debian/man_src/reapr-perfectfrombam.1.ronn
rename to debian/man_src/reapr-perfectfrombam.1.adoc
index b2413c5..f89cadd 100644
--- a/debian/man_src/reapr-perfectfrombam.1.ronn
+++ b/debian/man_src/reapr-perfectfrombam.1.adoc
@@ -1,20 +1,23 @@
-reapr-perfectfrombam(1) -- generate perfect mapping plots from a bam file
-=========================================================================
+# reapr-perfectfrombam(1)
+
+## NAME
+
+reapr-perfectfrombam - generate perfect mapping plots from a bam file
## SYNOPSIS
-`reapr perfectfrombam` [options] <in.bam> <outfileprefix> <mininsert> <maxinsert> <repetitive-max-qual> <perfect-min-qual> <perfect-min-alignment-score>
+*reapr perfectfrombam* [options] <in.bam> <outfileprefix> <mininsert> <maxinsert> <repetitive-max-qual> <perfect-min-qual> <perfect-min-alignment-score>
## DESCRIPTION
-Alternative to using `perfectmap`, for large genomes.
+Alternative to using *perfectmap*, for large genomes.
Takes a BAM, which must have AS:... tags in each line. Makes file
of perfect mapping depth, for use with the REAPR pipeline. Recommended to
-use `perfectmap` instead, unless your genome is large (more than ~300MB),
+use *perfectmap* instead, unless your genome is large (more than ~300MB),
since although very fast to run, 'reapr perfectmap' uses a lot of memory.
-A BAM file made by `smaltmap` is suitable input.
+A BAM file made by *smaltmap* is suitable input.
Reads in pair pointing towards each other, with the given minimum
alignment score and mapping quality and within the given insert size range
@@ -26,9 +29,9 @@ quality less than or equal to <repetitive max qual>.
## OPTIONS
-* `-noclean`:
+*-noclean*::
Use this to not delete the temporary bam file
## SEE ALSO
-reapr(1)
\ No newline at end of file
+reapr(1)
diff --git a/debian/man_src/reapr-perfectmap.1.ronn b/debian/man_src/reapr-perfectmap.1.adoc
similarity index 60%
rename from debian/man_src/reapr-perfectmap.1.ronn
rename to debian/man_src/reapr-perfectmap.1.adoc
index 1f2d610..a9be418 100644
--- a/debian/man_src/reapr-perfectmap.1.ronn
+++ b/debian/man_src/reapr-perfectmap.1.adoc
@@ -1,9 +1,12 @@
-reapr-perfectmap(1) -- make perfect uniquely mapping plot files
-===============================================================
+# reapr-perfectmap(1)
+
+## NAME
+
+reapr-perfectmap - make perfect uniquely mapping plot files
## SYNOPSIS
-`reapr perfectmap` <assembly.fa> <reads_1.fastq> <reads_2.fastq> <avginsertsize> <outprefix>
+*reapr perfectmap* <assembly.fa> <reads_1.fastq> <reads_2.fastq> <avginsertsize> <outprefix>
## DESCRIPTION
@@ -15,4 +18,4 @@ IMPORTANT: all reads must be the same length.
## SEE ALSO
-reapr(1)
\ No newline at end of file
+reapr(1)
diff --git a/debian/man_src/reapr-pipeline.1.ronn b/debian/man_src/reapr-pipeline.1.adoc
similarity index 56%
rename from debian/man_src/reapr-pipeline.1.ronn
rename to debian/man_src/reapr-pipeline.1.adoc
index cbe5f4f..8dfea6f 100644
--- a/debian/man_src/reapr-pipeline.1.ronn
+++ b/debian/man_src/reapr-pipeline.1.adoc
@@ -1,38 +1,41 @@
-reapr-pipeline(1) -- run the REAPR pipeline
-===========================================
+# reapr-pipeline(1)
+
+## NAME
+
+reapr-pipeline - run the REAPR pipeline
## SYNOPSIS
-`reapr pipeline` [options] <assembly.fa> <in.bam> <outdirectory> [perfectmapprefix]
+*reapr pipeline* [options] <assembly.fa> <in.bam> <outdirectory> [perfectmapprefix]
## DESCRIPTION
-where [perfectmapprefix] is optional and should be the prefix used when task
-`perfectmap` was run.
+[perfectmapprefix] is optional and should be the prefix used when task
+*perfectmap* was run.
It is assumed that reads in <in.bam> are 'innies', i.e. the correct orientation
is reads in a pair pointing towards each other (---> <---).
## OPTIONS
-* `-stats|fcdrate|score|break option=value`:
- You can pass options to `stats`, `fcdrate`, `score` or `break`
+*-stats|fcdrate|score|break option=value*::
+ You can pass options to *stats*, *fcdrate*, *score* or *break*
if you want to change the default settings. These
can be used multiple times to use more than one option. e.g.:
- `-stats i=100 -stats j=1000`
- If an option has no value, use `1`. e.g.
- `-break b=1`
+ *-stats i=100 -stats j=1000*
+ If an option has no value, use *1*. e.g.
+ *-break b=1*
-* `-fcdcut` <float>:
+*-fcdcut* <float>::
Set the fcdcutoff used when running score. Default is to
run fcdrate to determine the cutoff. Using this option will
skip fcdrate and use the given value.
-* `-x`:
+*-x*::
By default, a bash script is written to run all
the pipeline stages. Using this option stops the
script from being run.
## SEE ALSO
-reapr(1)
\ No newline at end of file
+reapr(1)
diff --git a/debian/man_src/reapr-plots.1.adoc b/debian/man_src/reapr-plots.1.adoc
new file mode 100644
index 0000000..3cb142c
--- /dev/null
+++ b/debian/man_src/reapr-plots.1.adoc
@@ -0,0 +1,18 @@
+# reapr-plots(1)
+
+## NAME
+
+reapr-plots - makes Artemis plot files for a given contig
+
+## SYNOPSIS
+
+*reapr plots* [options] <in.stats.gz> <outprefix> <assembly.fa> <contigid>
+
+## OPTIONS
+
+*-s* <prefix>::
+ This should be the outfiles prefix used when *score* task was run
+
+## SEE ALSO
+
+reapr(1)
diff --git a/debian/man_src/reapr-plots.1.ronn b/debian/man_src/reapr-plots.1.ronn
deleted file mode 100644
index 9bc71e0..0000000
--- a/debian/man_src/reapr-plots.1.ronn
+++ /dev/null
@@ -1,15 +0,0 @@
-reapr-plots(1) -- makes Artemis plot files for a given contig
-=============================================================
-
-## SYNOPSIS
-
-`reapr plots` [options] <in.stats.gz> <outprefix> <assembly.fa> <contigid>
-
-## OPTIONS
-
-* `-s` <prefix>:
- This should be the outfiles prefix used when `score` task was run
-
-## SEE ALSO
-
-reapr(1)
\ No newline at end of file
diff --git a/debian/man_src/reapr-preprocess.1.adoc b/debian/man_src/reapr-preprocess.1.adoc
new file mode 100644
index 0000000..d2d8e9a
--- /dev/null
+++ b/debian/man_src/reapr-preprocess.1.adoc
@@ -0,0 +1,13 @@
+# reapr-preprocess(1)
+
+## NAME
+
+reapr-preprocess - preprocess files for REAPR run
+
+## SYNOPSIS
+
+*reapr preprocess* <assembly.fa> <in.bam> <outputdir>
+
+## SEE ALSO
+
+reapr(1)
diff --git a/debian/man_src/reapr-preprocess.1.ronn b/debian/man_src/reapr-preprocess.1.ronn
deleted file mode 100644
index 5dbc843..0000000
--- a/debian/man_src/reapr-preprocess.1.ronn
+++ /dev/null
@@ -1,10 +0,0 @@
-reapr-preprocess(1) -- preprocess files for REAPR run
-===============================================================
-
-## SYNOPSIS
-
-`reapr preprocess` <assembly.fa> <in.bam> <outputdir>
-
-## SEE ALSO
-
-reapr(1)
\ No newline at end of file
diff --git a/debian/man_src/reapr-score.1.ronn b/debian/man_src/reapr-score.1.adoc
similarity index 70%
rename from debian/man_src/reapr-score.1.ronn
rename to debian/man_src/reapr-score.1.adoc
index ac07fcf..42fc831 100644
--- a/debian/man_src/reapr-score.1.ronn
+++ b/debian/man_src/reapr-score.1.adoc
@@ -1,52 +1,55 @@
-reapr-score(1) -- calculate scores and assembly errors
-======================================================
+# reapr-score(1)
+
+## NAME
+
+reapr-score - calculate scores and assembly errors
## SYNOPSIS
-`reapr score` [options] <assembly.fa.gaps.gz> <in.bam> <statsprefix> <FCDcutoff> <outprefix>
+*reapr score* [options] <assembly.fa.gaps.gz> <in.bam> <statsprefix> <FCDcutoff> <outprefix>
## OPTIONS
-* `-f` <int>:
+*-f* <int>::
Minimum inner fragment coverage [1]
-* `-g` <int>:
+*-g* <int>::
Max gap length to call over [0.5 * outer_mean_insert_size]
-* `-l` <int>:
+*-l* <int>::
Length of window [100]
-* `-p` <int>:
+*-p* <int>::
Use perfect mapping reads score with given min coverage.
Incompatible with -P.
-* `-P` <int>:
+*-P* <int>::
Same as -p, but force the score to be zero at any position with
at least the given coverage of perfect mapping reads and which has an
OK insert plot, , i.e. perfect mapping reads + insert distribution
override all other tests when calculating the score.
Incompatible with -p.
-* `-q` <float>:
+*-q* <float>::
Max bad read ratio [0.33]
-* `-r` <int>:
+*-r* <int>::
Min read coverage [max(1, mean_read_cov - 4 * read_cov_stddev)]
-* `-R` <int>:
+*-R* <int>::
Repeat calling cutoff. -R N means call a repeat if fragment
- coverage is >= N * (expected coverage).
+ coverage is >= N times (expected coverage).
Use -R 0 to not call repeats [2]
-* `-s` <int>:
+*-s* <int>::
Min score to report in errors file [0.4]
-* `-u` <int>:
+*-u* <int>::
FCD error window length for error calling [insert_size / 2]
-* `-w` <float>:
+*-w* <float>::
Min percentage of bases in window needed to call as bad [0.8]
## SEE ALSO
-reapr(1)
\ No newline at end of file
+reapr(1)
diff --git a/debian/man_src/reapr-seqrename.1.adoc b/debian/man_src/reapr-seqrename.1.adoc
new file mode 100644
index 0000000..a0ace16
--- /dev/null
+++ b/debian/man_src/reapr-seqrename.1.adoc
@@ -0,0 +1,17 @@
+# reapr-seqrename(1)
+
+## NAME
+
+reapr-seqrename - renames all sequences in a BAM file
+
+## SYNOPSIS
+
+*reapr seqrename* <renamefile> <in.bam> <out.bam>
+
+## DESCRIPTION
+
+<renamefile> is the file .info made by *facheck*, which contains the mapping of old name to new name.
+
+## SEE ALSO
+
+reapr(1)
diff --git a/debian/man_src/reapr-seqrename.1.ronn b/debian/man_src/reapr-seqrename.1.ronn
deleted file mode 100644
index cb315d2..0000000
--- a/debian/man_src/reapr-seqrename.1.ronn
+++ /dev/null
@@ -1,14 +0,0 @@
-reapr-seqrename(1) -- renames all sequences in a BAM file
-=====================================================
-
-## SYNOPSIS
-
-`reapr seqrename` <renamefile> <in.bam> <out.bam>
-
-## DESCRIPTION
-
-<renamefile> is the file `*.info` made by `facheck`, which contains the mapping of old name to new name.
-
-## SEE ALSO
-
-reapr(1)
\ No newline at end of file
diff --git a/debian/man_src/reapr-smaltmap.1.ronn b/debian/man_src/reapr-smaltmap.1.adoc
similarity index 76%
rename from debian/man_src/reapr-smaltmap.1.ronn
rename to debian/man_src/reapr-smaltmap.1.adoc
index 4f14772..fc43ea1 100644
--- a/debian/man_src/reapr-smaltmap.1.ronn
+++ b/debian/man_src/reapr-smaltmap.1.adoc
@@ -1,13 +1,16 @@
-reapr-smaltmap(1) -- map read pairs using SMALT
-===============================================
+# reapr-smaltmap(1)
+
+## NAME
+
+reapr-smaltmap - map read pairs using SMALT
## SYNOPSIS
-`reapr smaltmap` [options] <assembly.fa> <reads_1.fastq> <reads_2.fastq> <out.bam>
+*reapr smaltmap* [options] <assembly.fa> <reads_1.fastq> <reads_2.fastq> <out.bam>
## DESCRIPTION
-Maps read pairs to an asembly with SMALT, making a final BAM file that
+Maps read pairs to an assembly with SMALT, making a final BAM file that
is sorted, indexed and has duplicates removed.
The n-th read in <reads_1.fastq> should be the mate of the n-th read in
@@ -18,35 +21,35 @@ is reads in a pair pointing towards each other (---> <---).
## OPTIONS
- * `-k` <int>:
+ *-k* <int>::
The -k option (kmer hash length) when indexing the genome
with 'smalt index' [13]
- * `-s` <int>:
+ *-s* <int>::
The -s option (step length) when indexing the genome
with 'smalt index' [2]
- * `-m` <int>:
+ *-m* <int>::
The -m option when mapping reads with 'smalt map' [not used by default]
- * `-n` <int>:
+ *-n* <int>::
The number of threads used when running 'smalt map' [1]
- * `-y` <float>:
+ *-y* <float>::
The -y option when mapping reads with 'smalt map'.
The default of 0.5 means that at least 50% of each read must map
perfectly. Depending on the quality of your reads, you may want to
increase this to be more stringent (or consider using -m) [0.5]
- * `-x`:
+ *-x*::
Use this to just print the commands that will be run, instead of
actually running them
- * `-u` <int>:
+ *-u* <int>::
The -u option of 'smalt sample'. This is used to estimate the insert
size from a sample of the reads, by mapping every n^th read pair [1000]
## SEE ALSO
-reapr(1)
\ No newline at end of file
+reapr(1)
diff --git a/debian/man_src/reapr-stats.1.ronn b/debian/man_src/reapr-stats.1.adoc
similarity index 58%
rename from debian/man_src/reapr-stats.1.ronn
rename to debian/man_src/reapr-stats.1.adoc
index e98b665..6fadb99 100644
--- a/debian/man_src/reapr-stats.1.ronn
+++ b/debian/man_src/reapr-stats.1.adoc
@@ -1,39 +1,42 @@
-reapr-stats(1) -- generate REAPR stats from a BAM file
-======================================================
+# reapr-stats(1)
+
+## NAME
+
+reapr-stats - generate REAPR stats from a BAM file
## SYNOPSIS
-`reapr stats` [options] <preprocess-output-directory> <outprefix>
+*reapr stats* [options] <preprocess-output-directory> <outprefix>
## OPTIONS
-* `-f` <int>:
+*-f* <int>::
Insert size [ave from stats.txt]
-* `-i` <int>:
+*-i* <int>::
Minimum insert size [pc1 from stats.txt]
-* `-j` <int>:
+*-j* <int>::
Maximum insert size [pc99 from stats.txt]
-* `-m` <int>:
+*-m* <int>::
Maximum read length (this doesn't need to be exact, it just
determines memory allocation, so must be >= max read length) [2000]
-* `-p` <string>:
- Name of .gz perfect mapping file made by `perfectmap`
+*-p* <string>::
+ Name of .gz perfect mapping file made by *perfectmap*
-* `-q` <int>:
+*-q* <int>::
Ignore reads with mapping quality less than this [0]
-* `-s` <int>:
+*-s* <int>::
Calculate FCD error every n-th base
[ceil((fragment size) / 1000)]
-* `-u` <string>:
+*-u* <string>::
File containing list of chromosomes to look at
(one per line)
## SEE ALSO
-reapr(1)
\ No newline at end of file
+reapr(1)
diff --git a/debian/man_src/reapr-summary.1.adoc b/debian/man_src/reapr-summary.1.adoc
new file mode 100644
index 0000000..8d2a385
--- /dev/null
+++ b/debian/man_src/reapr-summary.1.adoc
@@ -0,0 +1,23 @@
+# reapr-summary(1)
+
+## NAME
+
+reapr-summary - make REAPR summary stats file
+
+## SYNOPSIS
+
+*reapr summary* [options] <assembly.fa> <scoreprefix> <breakprefix> <outfileprefix>
+
+## DESCRIPTION
+
+<scoreprefix> is the outfiles prefix used when *score* was run, and
+<breakprefix> is the outfiles prefix used when *break* was run.
+
+## OPTIONS
+
+*-e* <float>::
+ Minimum FCD error [0]
+
+## SEE ALSO
+
+reapr(1)
diff --git a/debian/man_src/reapr-summary.1.ronn b/debian/man_src/reapr-summary.1.ronn
deleted file mode 100644
index b83c920..0000000
--- a/debian/man_src/reapr-summary.1.ronn
+++ /dev/null
@@ -1,20 +0,0 @@
-reapr-summary(1) -- make REAPR summary stats file
-=================================================
-
-## SYNOPSIS
-
-`reapr summary` [options] <assembly.fa> <scoreprefix> <breakprefix> <outfileprefix>
-
-## DESCRIPTION
-
-<scoreprefix> is the outfiles prefix used when `score` was run, and
-<breakprefix> is the outfiles prefix used when `break` was run.
-
-## OPTIONS
-
-* `-e` <float>:
- Minimum FCD error [0]
-
-## SEE ALSO
-
-reapr(1)
\ No newline at end of file
diff --git a/debian/man_src/reapr.1.ronn b/debian/man_src/reapr.1.adoc
similarity index 65%
rename from debian/man_src/reapr.1.ronn
rename to debian/man_src/reapr.1.adoc
index d8e13fe..8889e9d 100644
--- a/debian/man_src/reapr.1.ronn
+++ b/debian/man_src/reapr.1.adoc
@@ -1,61 +1,64 @@
-reapr(1) -- universal tool for genome assembly evaluation
-=========================================================
+= reapr(1)
+
+== NAME
+
+reapr - universal tool for genome assembly evaluation
## SYNOPSIS
-`reapr` <task> [options]
+*reapr* <task> [options]
## DESCRIPTION
reapr is the main executable for the **REAPR** software. The actual
-functionality is provided by the subtools (`tasks'):
+functionality is provided by the subtools (*tasks'):
### Common tasks
-* `facheck`:
+*facheck*::
checks IDs in fasta file
-* `smaltmap`:
+*smaltmap*::
map read pairs using SMALT: makes a BAM file to be used as input to the pipeline
-* `perfectmap`:
+*perfectmap*::
make perfect uniquely mapping plot files
-* `pipeline`:
+*pipeline*::
runs the REAPR pipeline, using an assembly and mapped reads as input, and optionally results of perfectmap. (It runs facheck, preprocess, stats, fcdrate, score, summary and break)
-* `plots`:
+*plots*::
makes Artemis plot files for a given contig, using results from stats (and optionally results from score)
-* `seqrename`:
+*seqrename*::
renames all sequences in a BAM file: use this if you already mapped your reads but then found facheck failed - saves remapping the reads so that pipeline can be run
### Advanced tasks
-* `preprocess`:
+*preprocess*::
preprocess files: necessary for running stats
-* `stats`:
+*stats*::
generates stats from a BAM file
-* `fcdrate`:
+*fcdrate*::
estimates FCD cutoff for score, using results from stats
-* `score`:
+*score*::
calculates scores and assembly errors, using results from stats
-* `summary`:
+*summary*::
make summary stats file, using results from score
-* `break`:
+*break*::
makes broken assembly, using results from score
-* `gapresize`:
+*gapresize*::
experimental, calculates gap sizes based on read mapping
-* `perfectfrombam`:
+*perfectfrombam*::
generate perfect mapping plots from a bam file (alternative to using perfectmap for large genomes)
## SEE ALSO
-reapr-facheck(1), reapr-smaltmap(1), reapr-perfectmap(1) , reapr-pipeline(1), reapr-plots(1), reapr-seqrename(1), reapr-preprocess(1), reapr-stats(1), reapr-fcdrate(1), reapr-score(1), reapr-summary(1), reapr-break(1), reapr-gapresize(1), reapr-perfectfrombam(1)
\ No newline at end of file
+reapr-facheck(1), reapr-smaltmap(1), reapr-perfectmap(1), reapr-pipeline(1), reapr-plots(1), reapr-seqrename(1), reapr-preprocess(1), reapr-stats(1), reapr-fcdrate(1), reapr-score(1), reapr-summary(1), reapr-break(1), reapr-gapresize(1), reapr-perfectfrombam(1)
diff --git a/debian/rules b/debian/rules
index 0a5be53..cba7438 100755
--- a/debian/rules
+++ b/debian/rules
@@ -18,8 +18,8 @@ override_dh_auto_install:
override_dh_installman:
mkdir -p $(mandir)
- ronn $(debfolder)/man_src/*.ronn
- install $(debfolder)/man_src/*.? $(mandir)
+ asciidoctor -a docdate='' -b manpage $(debfolder)/man_src/*.adoc
+ cp $(debfolder)/man_src/*.? $(mandir)
dh_installman --
override_dh_auto_clean:
--
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