[med-svn] [Git][med-team/mash][master] 4 commits: Team upload
Andreas Tille (@tille)
gitlab at salsa.debian.org
Tue Oct 12 08:38:40 BST 2021
Andreas Tille pushed to branch master at Debian Med / mash
Commits:
fcf4705e by Andreas Tille at 2021-10-12T09:31:20+02:00
Team upload
- - - - -
4a937b31 by Andreas Tille at 2021-10-12T09:33:35+02:00
Patch forwarded
- - - - -
616f151e by Andreas Tille at 2021-10-12T09:36:14+02:00
Install manpages provided by upstream
- - - - -
74b6d7eb by Andreas Tille at 2021-10-12T09:37:56+02:00
Upload to unstable
- - - - -
11 changed files:
- debian/changelog
- debian/control
- − debian/man_src/mash-dist.1.adoc
- − debian/man_src/mash-info.1.adoc
- − debian/man_src/mash-paste.1.adoc
- − debian/man_src/mash-screen.1.adoc
- − debian/man_src/mash-sketch.1.adoc
- − debian/man_src/mash.1.adoc
- debian/mash.manpages
- debian/patches/gcc-11.patch
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,12 +1,13 @@
-mash (2.3+dfsg-1.1) UNRELEASED; urgency=medium
+mash (2.3+dfsg-2) unstable; urgency=medium
- * Non-maintainer upload.
+ * Team upload.
* Standards-Version: 4.6.0 (routine-update)
* Add salsa-ci file (routine-update)
* d/watch: add filemangle
* Fix Build error with gcc-11
+ * Install manpages provided by upstream
- -- Andreas Tille <tille at debian.org> Tue, 12 Oct 2021 09:01:12 +0200
+ -- Andreas Tille <tille at debian.org> Tue, 12 Oct 2021 09:36:25 +0200
mash (2.3+dfsg-1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -9,7 +9,6 @@ Build-Depends: debhelper (>= 13),
libcapnp-dev,
libgsl-dev,
zlib1g-dev,
- asciidoctor,
libmurmurhash-dev,
pkg-config
Build-Depends-Indep: python3-sphinx,
=====================================
debian/man_src/mash-dist.1.adoc deleted
=====================================
@@ -1,107 +0,0 @@
-# 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)
=====================================
debian/man_src/mash-info.1.adoc deleted
=====================================
@@ -1,37 +0,0 @@
-# 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*.
-
-*-d*::
- Dump sketches in JSON format. Incompatible with *-H*, *-t*, and *-c*.
-
-## SEE ALSO
-
-mash(1)
=====================================
debian/man_src/mash-paste.1.adoc deleted
=====================================
@@ -1,25 +0,0 @@
-# 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)
=====================================
debian/man_src/mash-screen.1.adoc deleted
=====================================
@@ -1,50 +0,0 @@
-# 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)
=====================================
debian/man_src/mash-sketch.1.adoc deleted
=====================================
@@ -1,103 +0,0 @@
-# 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)
=====================================
debian/man_src/mash.1.adoc deleted
=====================================
@@ -1,38 +0,0 @@
-= 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.
-
-*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-screen(1), mash-sketch(1)
=====================================
debian/mash.manpages
=====================================
@@ -1 +1 @@
-debian/man/*.1
+usr/share/man/man1/*
=====================================
debian/patches/gcc-11.patch
=====================================
@@ -1,6 +1,7 @@
Author: Andreas Tille <tille at debian.org>
Last-Update: Tue, 12 Oct 2021 09:01:12 +0200
Description: Fix "error: ‘numeric_limits’ is not a member of ‘std’"
+Forwarded: https://github.com/marbl/Mash/issues/167
--- a/src/mash/robin_hood.h
+++ b/src/mash/robin_hood.h
=====================================
debian/rules
=====================================
@@ -23,12 +23,6 @@ override_dh_auto_configure:
execute_after_dh_auto_build-indep:
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/*.? $(CURDIR)/debian/man
- dh_installman --
-
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
ifeq ($(DEB_HOST_ARCH_BITS),32)
View it on GitLab: https://salsa.debian.org/med-team/mash/-/compare/f2aea6c8030bfb5df0218004bbfd95d2d0c0d603...74b6d7eb49362f1fc416f838286174c339528f6e
--
View it on GitLab: https://salsa.debian.org/med-team/mash/-/compare/f2aea6c8030bfb5df0218004bbfd95d2d0c0d603...74b6d7eb49362f1fc416f838286174c339528f6e
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20211012/65fcd2d0/attachment-0001.htm>
More information about the debian-med-commit
mailing list