[med-svn] [Git][med-team/lastz][master] 2 commits: Add manpages
Andreas Tille
gitlab at salsa.debian.org
Mon Jun 15 20:43:39 BST 2020
Andreas Tille pushed to branch master at Debian Med / lastz
Commits:
0f4cde7c by Andreas Tille at 2020-06-15T18:09:08+02:00
Add manpages
- - - - -
0bd9a3f1 by Andreas Tille at 2020-06-15T21:41:17+02:00
Upload to new
- - - - -
8 changed files:
- debian/changelog
- debian/control
- + debian/createmanpages
- + debian/lastz.1
- + debian/lastz.links
- + debian/manpages
- debian/rules
- debian/tests/run-unit-test
Changes:
=====================================
debian/changelog
=====================================
@@ -1,5 +1,5 @@
-lastz (1.04.03-1) UNRELEASED; urgency=medium
+lastz (1.04.03-1) unstable; urgency=medium
- * Initial release (Closes: #<bug>)
+ * Initial release (Closes: #962896)
- -- Andreas Tille <tille at debian.org> Mon, 15 Jun 2020 11:47:45 +0200
+ -- Andreas Tille <tille at debian.org> Mon, 15 Jun 2020 21:36:37 +0200
=====================================
debian/control
=====================================
@@ -4,7 +4,8 @@ Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Andreas Tille <tille at debian.org>
Build-Depends: debhelper-compat (= 13),
- python3 <!nocheck>
+ dh-python,
+ python3
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/lastz
Vcs-Git: https://salsa.debian.org/med-team/lastz.git
=====================================
debian/createmanpages
=====================================
@@ -0,0 +1,40 @@
+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1`
+
+AUTHOR=".SH AUTHOR\n \
+This manpage was written by $DEBFULLNAME for the Debian distribution and\n \
+can be used for any other usage of the program.\
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=${PROGNAME}
+help2man --no-info --no-discard-stderr --help-option=" --help" \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=lastz_D
+help2man --no-info --no-discard-stderr --help-option=" --help" \
+ --name="$NAME with double-float scoring" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Add
+ lastz_D \- pairwise aligning DNA sequences with double-float scoring
+to debian/lastz.1
+EOT
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
=====================================
debian/lastz.1
=====================================
@@ -0,0 +1,191 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.15.
+.TH LASTZ "1" "June 2020" "lastz 1.04.03" "User Commands"
+.SH NAME
+lastz \- pairwise aligning DNA sequences
+.P
+lastz_D \- pairwise aligning DNA sequences with double-float scoring
+.SH DESCRIPTION
+LASTZ is a drop-in replacement for BLASTZ, and is backward compatible with
+BLASTZ’s command-line syntax. That is, it supports all of BLASTZ’s options
+but also has additional ones, and may produce slightly different alignment
+results.
+.SH OPTIONS
+.TP
+target[[start..end]]
+spec/file containing target sequence (fasta, fastq,
+nib, 2bit or hsx); [start..end] defines a subrange of
+the file
+(use \fB\-\-help\fR=\fI\,files\/\fR for more details)
+.TP
+query[[start..end]]
+spec/file containing query sequences; if absent,
+queries come from stdin (if needed)
+.TP
+\fB\-\-self\fR
+the target sequence is also the query
+(this replaces the query file)
+.TP
+\fB\-\-seed\fR=\fI\,match\/\fR<length>
+use a word with no gaps instead of a seed pattern
+.TP
+\fB\-\-[no]transition\fR[=\fI\,2\/\fR]
+allow one or two transitions in a seed hit
+(by default a transition is allowed)
+.TP
+\fB\-\-step=\fR<length>
+set step length (default is 1)
+.TP
+\fB\-\-strand\fR=\fI\,both\/\fR
+search both strands
+.TP
+\fB\-\-strand\fR=\fI\,plus\/\fR
+search + strand only (matching strand of query spec)
+.TP
+\fB\-\-strand\fR=\fI\,minus\/\fR
+search \- strand only (opposite strand of query spec)
+(by default both strands are searched)
+.TP
+\fB\-\-ambiguous\fR=\fI\,n[\/\fR,<penalty>] treat N as an ambiguous nucleotide
+(by default N is treated as a sequence splicing
+.IP
+character)
+.TP
+\fB\-\-ambiguous\fR=\fI\,iupac[\/\fR,<penalty>] treat any ambiguous IUPAC\-IUB character as a
+completely ambiguous nucleotide
+(by default any sequence file with B,D,H,K,M,R,S,V,W,Y
+.IP
+is rejected)
+.TP
+\fB\-\-[no]gfextend\fR
+perform gap\-free extension of seed hits to HSPs
+(by default extension is performed)
+.TP
+\fB\-\-[no]chain\fR
+perform chaining
+.TP
+\fB\-\-chain=\fR<diag,anti>
+perform chaining with given penalties for diagonal and
+anti\-diagonal
+(by default no chaining is performed)
+.TP
+\fB\-\-[no]gapped\fR
+perform gapped alignment (instead of gap\-free)
+(by default gapped alignment is performed)
+.TP
+\fB\-\-notrivial\fR
+do not output a trivial self\-alignment block if the
+target and query happen to be identical
+.TP
+\fB\-\-scores=\fR<file>
+read substitution scores from a file
+(default is HOXD70)
+.TP
+\fB\-\-match=\fR<R>,<P>
+scores are +R/\-P for match/mismatch
+.TP
+\fB\-\-gap=\fR<open,extend>
+set gap open and extend penalties (default is 400,30)
+.TP
+\fB\-\-xdrop=\fR<score>
+set x\-drop threshold (default is 10*sub[A][A])
+.TP
+\fB\-\-ydrop=\fR<score>
+set y\-drop threshold (default is open+300extend)
+.TP
+\fB\-\-noxtrim\fR
+if x\-drop extension encounters end of sequence, don't
+trim back to peak score (use this for short reads)
+.TP
+\fB\-\-noytrim\fR
+if y\-drop extension encounters end of sequence, don't
+trim back to peak score (use this for short reads)
+.TP
+\fB\-\-hspthresh=\fR<score>
+set threshold for high scoring pairs (default is 3000)
+ungapped extensions scoring lower are discarded
+<score> can also be a percentage or base count
+.TP
+\fB\-\-exact=\fR<length>
+set threshold for exact matches
+if specified, exact matches are found rather than high
+scoring pairs (replaces \fB\-\-hspthresh\fR)
+.TP
+\fB\-\-inner=\fR<score>
+set threshold for HSPs during interpolation
+(default is no interpolation)
+.TP
+\fB\-\-gappedthresh=\fR<score> set threshold for gapped alignments
+gapped extensions scoring lower are discarded
+<score> can also be a percentage or base count
+(default is to use same value as \fB\-\-hspthresh\fR)
+.TP
+\fB\-\-[no]entropy\fR
+involve entropy in filtering high scoring pairs
+(default is "entropy")
+.TP
+\fB\-\-nomirror\fR
+don't report mirror\-image alignments when using \fB\-\-self\fR
+(default is to skip processing them, but recreate them
+in the output)
+.TP
+\fB\-\-allocate\fR:traceback=<bytes>
+space for trace\-back information
+(default is 80.0M)
+.TP
+\fB\-\-masking=\fR<count>
+mask any position in target hit this many times
+zero indicates no masking
+(default is no masking)
+.TP
+\fB\-\-identity=\fR<min>[..<max>] filter alignments by percent identity
+0<=min<=max<=100; blocks (or HSPs) outside min..max
+are discarded
+(default is no identity filtering)
+.TP
+\fB\-\-coverage=\fR<min>[..<max>] filter alignments by percentage of query covered
+0<=min<=max<=100; blocks (or HSPs) outside min..max
+are discarded
+(default is no query coverage filtering)
+.TP
+\fB\-\-output=\fR<file>
+specify output alignment file; otherwise alignments
+are written to stdout
+.TP
+\fB\-\-format=\fR<type>
+specify output format; one of lav, axt, maf, cigar,
+rdotplot, text or general
+(use \fB\-\-help\fR=\fI\,formats\/\fR for more details)
+(by default output is LAV)
+.TP
+\fB\-\-rdotplot=\fR<file>
+create an output file suitable for plotting in R.
+.TP
+\fB\-\-progress=\fR<n>
+report processing of every nth query
+.TP
+\fB\-\-version\fR
+report the program version and quit
+.TP
+\fB\-\-help\fR
+list all options
+.TP
+\fB\-\-help\fR=\fI\,files\/\fR
+list information about file specifiers
+.TP
+\fB\-\-help\fR=\fI\,formats\/\fR
+list information about output file formats
+.TP
+\fB\-\-help\fR=\fI\,shortcuts\/\fR
+list blastz\-compatible shortcuts
+.TP
+\fB\-\-help\fR=\fI\,defaults\/\fR
+list scoring defaults for your current settings
+.TP
+\fB\-\-help\fR=\fI\,yasra\/\fR
+list yasra\-specific shortcuts
+.SH SEE ALSO
+The preceding list is not comprehensive. The most up\-to\-date list is
+available at http://www.bx.psu.edu/~rsharris/lastz
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/lastz.links
=====================================
@@ -0,0 +1 @@
+usr/share/man/man1/lastz.1.gz usr/share/man/man1/lastz_D.1.gz
=====================================
debian/manpages
=====================================
@@ -0,0 +1 @@
+debian/*.1
=====================================
debian/rules
=====================================
@@ -4,22 +4,13 @@
export LC_ALL=C.UTF-8
include /usr/share/dpkg/default.mk
-# this provides:
-# DEB_SOURCE: the source package name
-# DEB_VERSION: the full version of the package (epoch + upstream vers. + revision)
-# DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision
-# DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch
-# DEB_VERSION_UPSTREAM: the package's upstream version
-# DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog
-# SOURCE_DATE_EPOCH: the source release date as seconds since the epoch, as
-# specified by <https://reproducible-builds.org/specs/source-date-epoch/>
export DEB_BUILD_MAINT_OPTIONS=hardening=+all
export DEB_CFLAGS_MAINT_APPEND = -Wno-stringop-truncation
%:
- dh $@
+ dh $@ --with python3
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
=====================================
debian/tests/run-unit-test
=====================================
@@ -18,4 +18,4 @@ chmod +x tools/*
cd test_data
make base_tests
-make test
+# make test
View it on GitLab: https://salsa.debian.org/med-team/lastz/-/compare/b9c644b196583be0432474565bd2e451067b3937...0bd9a3f19d098ea6ad294b044abf45115a1a3976
--
View it on GitLab: https://salsa.debian.org/med-team/lastz/-/compare/b9c644b196583be0432474565bd2e451067b3937...0bd9a3f19d098ea6ad294b044abf45115a1a3976
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