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commit a9786201baa89ca92130e616f42f61a76eac544b Author: Sascha Steinbiss <[email protected]> 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 <[email protected]> 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) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/mash.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
