[med-svn] [mash] 04/05: add new man page

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository mash.

commit a9786201baa89ca92130e616f42f61a76eac544b
Author: Sascha Steinbiss <satta at debian.org>
Date:   Sun Oct 1 11:01:35 2017 +0100

    add new man page
---
 debian/changelog                  |  1 +
 debian/man_src/mash-screen.1.adoc | 50 +++++++++++++++++++++++++++++++++++++++
 debian/man_src/mash.1.adoc        |  5 +++-
 3 files changed, 55 insertions(+), 1 deletion(-)

diff --git a/debian/changelog b/debian/changelog
index e5cb782..b36e49e 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -2,6 +2,7 @@ mash (2.0-1) UNRELEASED; urgency=medium
 
   * New upstream release.
   * Refresh patches.
+  * Add new manpage for 'mash screen' subcommand.
 
  -- Sascha Steinbiss <satta at debian.org>  Sun, 01 Oct 2017 10:26:28 +0100
 
diff --git a/debian/man_src/mash-screen.1.adoc b/debian/man_src/mash-screen.1.adoc
new file mode 100644
index 0000000..99285b3
--- /dev/null
+++ b/debian/man_src/mash-screen.1.adoc
@@ -0,0 +1,50 @@
+# mash-screen(1)
+
+## NAME
+
+mash-screen - determine whether query sequences are within a larger pool of sequences
+
+## SYNOPSIS
+
+*mash screen* [options] <queries>.msh <pool> [<pool>] ...
+
+## DESCRIPTION
+
+Determine how well query sequences are contained within a pool of sequences.
+The queries must be formatted as a single Mash sketch file (.msh), created
+with the `mash sketch` command. The <pool> files can be contigs or reads, in
+fasta or fastq, gzipped or not, and "-" can be given for <pool> to read from
+standard input. The <pool> sequences are assumed to be nucleotides, and will
+be 6-frame translated if the <queries> are amino acids. The output fields are
+[identity, shared-hashes, median-multiplicity, p-value, query-ID, query-comment],
+where median-multiplicity is computed for shared hashes, based on the number of
+observations of those hashes within the pool.
+
+## OPTIONS
+
+*-h*::
+  Help
+
+*-p* <int>::
+  Parallelism. This many threads will be spawned for processing.
+
+*-w*::
+  Winner-takes-all strategy for identity estimates. After counting
+  hashes for each query, hashes that appear in multiple queries will
+  be removed from all except the one with the best identity (ties
+  broken by larger query), and other identities will be reduced. This
+  removes output redundancy, providing a rough compositional outline.
+
+### Output
+
+*-i* <num>::
+  Minimum identity to report. Inclusive unless set to zero, in which
+  case only identities greater than zero (i.e. with at least one
+  shared hash) will be reported. Set to -1 to output everything.
+
+*-v* <num>::
+  Maximum p-value to report.
+
+## SEE ALSO
+
+mash(1)
diff --git a/debian/man_src/mash.1.adoc b/debian/man_src/mash.1.adoc
index 277ab77..a6cf6be 100644
--- a/debian/man_src/mash.1.adoc
+++ b/debian/man_src/mash.1.adoc
@@ -27,9 +27,12 @@ functionality is provided by the subtools ('commands'):
 *paste*::
   Create a single sketch file from multiple sketch files.
 
+*screen*::
+  Determine whether query sequences are within a larger pool of sequences.
+
 *sketch*::
   Create sketches (reduced representations for fast operations).
 
 ## SEE ALSO
 
-mash-dist(1), mash-info(1), mash-paste(1), mash-sketch(1)
+mash-dist(1), mash-info(1), mash-paste(1), mash-screen(1), mash-sketch(1)

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