[med-svn] [Git][med-team/tantan][master] 6 commits: New upstream version 52
Sascha Steinbiss (@satta)
gitlab at salsa.debian.org
Sun Aug 9 19:17:11 BST 2026
Sascha Steinbiss pushed to branch master at Debian Med / tantan
Commits:
36f1952f by Sascha Steinbiss at 2026-08-09T19:47:13+02:00
New upstream version 52
- - - - -
38283d26 by Sascha Steinbiss at 2026-08-09T19:47:13+02:00
Update upstream source from tag 'upstream/52'
Update to upstream version '52'
with Debian dir d40e33de858d24a2006922af418b24aa0b6e7fbf
- - - - -
65052109 by Sascha Steinbiss at 2026-08-09T20:16:12+02:00
new upstream version
- - - - -
4676ed87 by Sascha Steinbiss at 2026-08-09T20:16:26+02:00
bump Standards-Version
- - - - -
58ea2bf3 by Sascha Steinbiss at 2026-08-09T20:16:34+02:00
bump copyright date for debian/ directory
- - - - -
2de79d64 by Sascha Steinbiss at 2026-08-09T20:16:55+02:00
generate manpage at build time
- - - - -
8 changed files:
- debian/changelog
- debian/control
- debian/copyright
- debian/createmanpages
- debian/rules
- debian/tantan.1
- src/Makefile
- src/tantan.cc
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+tantan (52-1) unstable; urgency=medium
+
+ * New upstream version 52.
+ * Bump Standards-Version.
+ * Bump copyright date for debian/ directory.
+ * Generate manpage at build time instead of shipping a static copy.
+
+ -- Sascha Steinbiss <satta at debian.org> Sun, 09 Aug 2026 19:47:16 +0200
+
tantan (51-1) unstable; urgency=medium
* New upstream version 51.
=====================================
debian/control
=====================================
@@ -4,8 +4,9 @@ Uploaders: Sascha Steinbiss <satta at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
+ help2man,
zlib1g-dev
-Standards-Version: 4.7.0
+Standards-Version: 4.7.2
Vcs-Browser: https://salsa.debian.org/med-team/tantan
Vcs-Git: https://salsa.debian.org/med-team/tantan.git
Homepage: https://gitlab.com/mcfrith/tantan
=====================================
debian/copyright
=====================================
@@ -15,7 +15,7 @@ Copyright: 2008 Michiaki Hamada
License: GPL-3+
Files: debian/*
-Copyright: © 2015-2024 Sascha Steinbiss <satta at debian.org>
+Copyright: © 2015-2026 Sascha Steinbiss <satta at debian.org>
License: GPL-3+
License: GPL-3+
=====================================
debian/createmanpages
=====================================
@@ -8,9 +8,3 @@ help2man --no-info --no-discard-stderr --help-option="-h" \
--name='low complexity and tandem repeat masker for biosequences' \
--version-string="$VERSION" tantan > $MANDIR/tantan.1
-cat <<EOT
-Please enhance the help2man output.
-The following web page might be helpful in doing so:
- http://liw.fi/manpages/
-EOT
-
=====================================
debian/rules
=====================================
@@ -8,9 +8,14 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
%:
dh $@
+override_dh_auto_build:
+ dh_auto_build
+ PATH=$(CURDIR)/bin:$$PATH debian/createmanpages
+
override_dh_auto_install:
make prefix=$(DESTDIR) install
override_dh_auto_clean:
dh_auto_clean
rm -f src/version.hh
+ rm -f debian/tantan.1
=====================================
debian/tantan.1
=====================================
@@ -1,58 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
-.TH TANTAN "1" "July 2015" "tantan 13" "User Commands"
-.SH NAME
-tantan \- low complexity and tandem repeat masker for biosequences
-.SH SYNOPSIS
-.B tantan
-[\fI\,options\/\fR] \fI\,fasta-sequence-file(s)\/\fR
-.SH DESCRIPTION
-Find simple repeats in sequences
-.SS "Options (default settings):"
-.TP
-\fB\-p\fR
-interpret the sequences as proteins
-.TP
-\fB\-x\fR
-letter to use for masking, instead of lowercase
-.TP
-\fB\-c\fR
-preserve uppercase/lowercase in non\-masked regions
-.TP
-\fB\-m\fR
-file for letter pair scores (+1/\-1, but \fB\-p\fR selects BLOSUM62)
-.TP
-\fB\-r\fR
-probability of a repeat starting per position (0.005)
-.TP
-\fB\-e\fR
-probability of a repeat ending per position (0.05)
-.TP
-\fB\-w\fR
-maximum tandem repeat period to consider (100, but \fB\-p\fR selects 50)
-.TP
-\fB\-d\fR
-probability decay per period (0.9)
-.TP
-\fB\-a\fR
-gap existence cost (0)
-.TP
-\fB\-b\fR
-gap extension cost (infinite: no gaps)
-.TP
-\fB\-s\fR
-minimum repeat probability for masking (0.5)
-.TP
-\fB\-f\fR
-output type: 0=masked sequence, 1=repeat probabilities,
-.IP
-2=repeat counts, 3=BED (0)
-.TP
-\fB\-h\fR, \fB\-\-help\fR
-show help message, then exit
-.TP
-\fB\-\-version\fR
-show version information, then exit
-.SH "REPORTING BUGS"
-Report bugs to: tantan at cbrc.jp
-.br
-Home page: http://www.cbrc.jp/tantan/
=====================================
src/Makefile
=====================================
@@ -10,7 +10,7 @@ clean:
rm -f ../bin/tantan
VERSION1 = git describe --dirty
-VERSION2 = echo ' (HEAD -> main, tag: 51) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'
+VERSION2 = echo ' (HEAD -> main, tag: 52) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'
VERSION = \"`test -e ../.git && $(VERSION1) || $(VERSION2)`\"
=====================================
src/tantan.cc
=====================================
@@ -425,13 +425,14 @@ struct Tantan {
}
double z = forwardTotal();
+ double zInv = 1 / z;
initializeBackwardAlgorithm();
while (seqPtr > seqBeg) {
--seqPtr;
--letterProbs;
- double nonRepeatProb = *letterProbs * backgroundProb / z;
+ double nonRepeatProb = *letterProbs * backgroundProb * zInv;
// Convert nonRepeatProb to a float, so that it is more likely
// to be exactly 1 when it should be, e.g. for the 1st letter of
// a sequence:
View it on GitLab: https://salsa.debian.org/med-team/tantan/-/compare/ac7c941629892880851d18f0523f253473a594ad...2de79d6416bd7479bc3bd75f85efcbccb818032a
--
View it on GitLab: https://salsa.debian.org/med-team/tantan/-/compare/ac7c941629892880851d18f0523f253473a594ad...2de79d6416bd7479bc3bd75f85efcbccb818032a
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