[med-svn] [mash] 03/03: add manpages
Sascha Steinbiss
satta at debian.org
Tue Jul 19 20:08:34 UTC 2016
This is an automated email from the git hooks/post-receive script.
satta pushed a commit to branch master
in repository mash.
commit 8fed007261be5ef5a0b6f778ee10e144932aeffd
Author: Sascha Steinbiss <satta at debian.org>
Date: Tue Jul 19 20:08:25 2016 +0000
add manpages
---
debian/man_src/mash-dist.1.adoc | 107 ++++++++++++++++++++++++++++++++++++++
debian/man_src/mash-info.1.adoc | 34 ++++++++++++
debian/man_src/mash-paste.1.adoc | 25 +++++++++
debian/man_src/mash-sketch.1.adoc | 103 ++++++++++++++++++++++++++++++++++++
debian/man_src/mash.1.adoc | 35 +++++++++++++
debian/mash.manpages | 1 +
debian/rules | 8 ++-
7 files changed, 312 insertions(+), 1 deletion(-)
diff --git a/debian/man_src/mash-dist.1.adoc b/debian/man_src/mash-dist.1.adoc
new file mode 100644
index 0000000..74174fd
--- /dev/null
+++ b/debian/man_src/mash-dist.1.adoc
@@ -0,0 +1,107 @@
+# mash-dist(1)
+
+## NAME
+
+mash-dist - estimate the distance of query sequences to references
+
+## SYNOPSIS
+
+*mash dist* [options] <reference> <query> [<query>] ...
+
+## DESCRIPTION
+
+Estimate the distance of each query sequence to the reference. Both the
+reference and queries can be fasta or fastq, gzipped or not, or Mash sketch
+files (.msh) with matching k-mer sizes. Query files can also be files of file
+names (see *-l*). Whole files are compared by default (see *-i*). The output
+fields are [reference-ID, query-ID, distance, p-value, shared-hashes].
+
+## OPTIONS
+
+*-h*::
+ Help
+
+*-p* <int>::
+ Parallelism. This many threads will be spawned for processing. [1]
+
+### Input
+
+*-l*::
+ List input. Each query file contains a list of sequence files, one
+ per line. The reference file is not affected.
+
+### Output
+
+*-t*::
+ Table output (will not report p-values, but fields will be blank if
+ they do not meet the p-value threshold).
+
+*-v* <num>::
+ Maximum p-value to report. (0-1) [1.0]
+
+*-d* <num>::
+ Maximum distance to report. (0-1) [1.0]
+
+### Sketching
+
+*-k* <int>::
+ K-mer size. Hashes will be based on strings of this many
+ nucleotides. Canonical nucleotides are used by default (see
+ Alphabet options below). (1-32) [21]
+
+*-s* <int>::
+ Sketch size. Each sketch will have at most this many non-redundant
+ min-hashes. [1000]
+
+*-i*::
+ Sketch individual sequences, rather than whole files.
+
+*-w* <num>::
+ Probability threshold for warning about low k-mer size. (0-1) [0.01]
+
+*-r*::
+ Input is a read set. See Reads options below. Incompatible with *-i*.
+
+### Sketching (reads)
+
+*-b* <size>::
+ Use a Bloom filter of this size (raw bytes or with K/M/G/T) to
+ filter out unique k-mers. This is useful if exact filtering with *-m*
+ uses too much memory. However, some unique k-mers may pass
+ erroneously, and copies cannot be counted beyond 2. Implies *-r*.
+
+*-m* <int>::
+ Minimum copies of each k-mer required to pass noise filter for
+ reads. Implies *-r*. [1]
+
+*-c* <num>::
+ Target coverage. Sketching will conclude if this coverage is
+ reached before the end of the input file (estimated by average
+ k-mer multiplicity). Implies *-r*.
+
+*-g* <size>::
+ Genome size. If specified, will be used for p-value calculation
+ instead of an estimated size from k-mer content. Implies *-r*.
+
+### Sketching (alphabet)
+
+*-n*::
+ Preserve strand (by default, strand is ignored by using canonical
+ DNA k-mers, which are alphabetical minima of forward-reverse
+ pairs). Implied if an alphabet is specified with *-a* or *-z*.
+
+*-a*::
+ Use amino acid alphabet (A-Z, except BJOUXZ). Implies *-n*, *-k* 9.
+
+*-z* <text>::
+ Alphabet to base hashes on (case ignored by default; see *-Z*).
+ K-mers with other characters will be ignored. Implies *-n*.
+
+*-Z*::
+ Preserve case in k-mers and alphabet (case is ignored by default).
+ Sequence letters whose case is not in the current alphabet will be
+ skipped when sketching.
+
+## SEE ALSO
+
+mash(1)
diff --git a/debian/man_src/mash-info.1.adoc b/debian/man_src/mash-info.1.adoc
new file mode 100644
index 0000000..48aa8c1
--- /dev/null
+++ b/debian/man_src/mash-info.1.adoc
@@ -0,0 +1,34 @@
+# mash-info(1)
+
+## NAME
+
+mash-info - display information about sketch files
+
+## SYNOPSIS
+
+*mash info* [options] <sketch>
+
+## DESCRIPTION
+
+Displays information about sketch files.
+
+## OPTIONS
+
+*-h*::
+ Help
+
+*-H*::
+ Only show header info. Do not list each sketch. Incompatible with *-t*
+ and *-c*.
+
+*-t*::
+ Tabular output (rather than padded), with no header. Incompatible with
+ *-H* and *-c*.
+
+*-c*::
+ Show hash count histograms for each sketch. Incompatible with *-H* and
+ *-t*.
+
+## SEE ALSO
+
+mash(1)
diff --git a/debian/man_src/mash-paste.1.adoc b/debian/man_src/mash-paste.1.adoc
new file mode 100644
index 0000000..291f010
--- /dev/null
+++ b/debian/man_src/mash-paste.1.adoc
@@ -0,0 +1,25 @@
+# mash-paste(1)
+
+## NAME
+
+mash-paste - create a single sketch file from multiple sketch files
+
+## SYNOPSIS
+
+*mash paste* [options] <out_prefix> <sketch> [<sketch>] ...
+
+## DESCRIPTION
+
+Create a single sketch file from multiple sketch files.
+
+## OPTIONS
+
+*-h*::
+ Help
+
+*-l*::
+ Input files are lists of file names.
+
+## SEE ALSO
+
+mash(1)
diff --git a/debian/man_src/mash-sketch.1.adoc b/debian/man_src/mash-sketch.1.adoc
new file mode 100644
index 0000000..bd6b538
--- /dev/null
+++ b/debian/man_src/mash-sketch.1.adoc
@@ -0,0 +1,103 @@
+# mash-sketch(1)
+
+## NAME
+
+mash-sketch - create sketches (reduced representations for fast operations)
+
+## SYNOPSIS
+
+*mash sketch* [options] fast(a|q)[.gz] ...
+
+## DESCRIPTION
+
+Create a sketch file, which is a reduced representation of a sequence or set
+of sequences (based on min-hashes) that can be used for fast distance
+estimations. Input can be fasta or fastq files (gzipped or not), and "-" can
+be given to read from standard input. Input files can also be files of file
+names (see *-l*). For output, one sketch file will be generated, but it can have
+multiple sketches within it, divided by sequences or files (see *-i*). By
+default, the output file name will be the first input file with a '.msh'
+extension, or 'stdin.msh' if standard input is used (see *-o*).
+
+## OPTIONS
+
+*-h*::
+ Help
+
+*-p* <int>::
+ Parallelism. This many threads will be spawned for processing. [1]
+
+### Input
+
+*-l*::
+ List input. Each file contains a list of sequence files, one per line.
+
+### Output
+
+*-o* <path>::
+ Output prefix (first input file used if unspecified). The suffix
+ '.msh' will be appended.
+
+### Sketching
+
+*-k* <int>::
+ K-mer size. Hashes will be based on strings of this many
+ nucleotides. Canonical nucleotides are used by default (see
+ Alphabet options below). (1-32) [21]
+
+*-s* <int>::
+ Sketch size. Each sketch will have at most this many non-redundant
+ min-hashes. [1000]
+
+*-i*::
+ Sketch individual sequences, rather than whole files.
+
+*-w* <num>::
+ Probability threshold for warning about low k-mer size. (0-1) [0.01]
+
+*-r*::
+ Input is a read set. See Reads options below. Incompatible with *-i*.
+
+### Sketching (reads)
+
+*-b* <size>::
+ Use a Bloom filter of this size (raw bytes or with K/M/G/T) to
+ filter out unique k-mers. This is useful if exact filtering with *-m*
+ uses too much memory. However, some unique k-mers may pass
+ erroneously, and copies cannot be counted beyond 2. Implies *-r*.
+
+*-m* <int>::
+ Minimum copies of each k-mer required to pass noise filter for
+ reads. Implies *-r*. [1]
+
+*-c* <num>::
+ Target coverage. Sketching will conclude if this coverage is
+ reached before the end of the input file (estimated by average
+ k-mer multiplicity). Implies *-r*.
+
+*-g* <size>::
+ Genome size. If specified, will be used for p-value calculation
+ instead of an estimated size from k-mer content. Implies *-r*.
+
+### Sketching (alphabet)
+
+*-n*::
+ Preserve strand (by default, strand is ignored by using canonical
+ DNA k-mers, which are alphabetical minima of forward-reverse
+ pairs). Implied if an alphabet is specified with *-a* or *-z*.
+
+*-a*::
+ Use amino acid alphabet (A-Z, except BJOUXZ). Implies *-n*, *-k* 9.
+
+*-z* <text>::
+ Alphabet to base hashes on (case ignored by default; see *-Z*).
+ K-mers with other characters will be ignored. Implies *-n*.
+
+*-Z*::
+ Preserve case in k-mers and alphabet (case is ignored by default).
+ Sequence letters whose case is not in the current alphabet will be
+ skipped when sketching.
+
+## SEE ALSO
+
+mash(1)
diff --git a/debian/man_src/mash.1.adoc b/debian/man_src/mash.1.adoc
new file mode 100644
index 0000000..e8c24ab
--- /dev/null
+++ b/debian/man_src/mash.1.adoc
@@ -0,0 +1,35 @@
+= mash(1)
+
+== NAME
+
+mash - fast genome and metagenome distance estimation using MinHash
+
+## SYNOPSIS
+
+*mash* <command> [options] [arguments ...]
+
+## DESCRIPTION
+
+*mash* is the main executable for the **Mash** software. The actual
+functionality is provided by the subtools (*commands'):
+
+### Commands
+
+*bounds*::
+ Print a table of Mash error bounds.
+
+*dist*::
+ Estimate the distance of query sequences to references.
+
+*info*::
+ Display information about sketch files.
+
+*paste*::
+ Create a single sketch file from multiple sketch files.
+
+*sketch*::
+ Create sketches (reduced representations for fast operations).
+
+## SEE ALSO
+
+mash-dist(1), mash-info(1), mash-paste(1), mash-sketch(1)
diff --git a/debian/mash.manpages b/debian/mash.manpages
new file mode 100644
index 0000000..13cdaf4
--- /dev/null
+++ b/debian/mash.manpages
@@ -0,0 +1 @@
+debian/man/*.1
diff --git a/debian/rules b/debian/rules
index e260693..a086425 100755
--- a/debian/rules
+++ b/debian/rules
@@ -24,7 +24,7 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all
override_dh_auto_clean:
dh_auto_clean
- rm -rf $(CURDIR)/debian/sphinxdoc
+ rm -rf $(CURDIR)/debian/sphinxdoc $(CURDIR)/debian/man
override_dh_auto_configure:
dh_auto_configure -- --with-capnp=/usr --with-gsl=/usr --prefix=$(CURDIR)/debian/tmp/usr
@@ -32,3 +32,9 @@ override_dh_auto_configure:
override_dh_auto_build:
dh_auto_build
sphinx-build doc/sphinx $(CURDIR)/debian/sphinxdoc
+
+override_dh_installman:
+ mkdir -p $(CURDIR)/debian/man
+ asciidoctor -a docdate='' -b manpage $(CURDIR)/debian/man_src/*.adoc
+ cp $(CURDIR)/debian/man_src/*.? $(CURDIR)/debian/man
+ dh_installman --
--
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