[med-svn] [Git][med-team/tantan][master] 10 commits: Fix fetch URL - tantan has moved to gitlab
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Wed Jun 2 20:09:07 BST 2021
Nilesh Patra pushed to branch master at Debian Med / tantan
Commits:
019ba9c1 by Nilesh Patra at 2021-06-03T00:19:46+05:30
Fix fetch URL - tantan has moved to gitlab
- - - - -
3505195e by Nilesh Patra at 2021-06-03T00:20:23+05:30
New upstream version 26
- - - - -
e4aecfdd by Nilesh Patra at 2021-06-03T00:20:24+05:30
Update upstream source from tag 'upstream/26'
Update to upstream version '26'
with Debian dir 0ad4e0ec8b77f5a2479b8e2c606798b1819a193f
- - - - -
360922e9 by Nilesh Patra at 2021-06-03T00:25:19+05:30
Refresh patch
- - - - -
7db04e4e by Nilesh Patra at 2021-06-03T00:26:56+05:30
Bump debhelper-compat version to 13
- - - - -
a8f55764 by Nilesh Patra at 2021-06-03T00:27:12+05:30
Declare compliance with policy 4.5.1
- - - - -
772d64f1 by Nilesh Patra at 2021-06-03T00:28:33+05:30
d/control: Fix homepage
- - - - -
bc5b9db5 by Nilesh Patra at 2021-06-03T00:32:10+05:30
d/copyright: Fix Source URL, migrate to https
- - - - -
d3b5a5e6 by Nilesh Patra at 2021-06-03T00:35:11+05:30
Update d/u/metadata
- - - - -
a5d2fc77 by Nilesh Patra at 2021-06-03T00:37:18+05:30
Interim changelog entry
- - - - -
18 changed files:
- + .gitattributes
- − ChangeLog.txt
- Makefile
- − README.html
- README.txt → README.rst
- debian/changelog
- debian/control
- debian/copyright
- debian/patches/buildflags.patch
- debian/upstream/metadata
- debian/watch
- src/LambdaCalculator.cc
- src/LambdaCalculator.hh
- src/Makefile
- + src/cbrc_linalg.cc
- + src/cbrc_linalg.hh
- src/mcf_tantan_options.cc
- − src/version.hh
Changes:
=====================================
.gitattributes
=====================================
@@ -0,0 +1 @@
+src/Makefile export-subst
=====================================
ChangeLog.txt deleted
=====================================
@@ -1,140 +0,0 @@
-2020-05-07 Martin C. Frith <Martin C. Frith>
-
- * src/tantan.cc:
- Make it faster
- [6b7981c6d602] [tip]
-
-2018-12-19 Martin C. Frith <Martin C. Frith>
-
- * src/tantan.cc:
- Make it faster
- [3523060bcfb9]
-
- * src/tantan_repeat_finder.cc, src/tantan_repeat_finder.hh:
- Make -f4 a bit faster
- [1fccdf6e21be]
-
- * README.txt, src/mcf_tantan_options.cc, src/mcf_tantan_options.hh,
- src/tantan_app.cc, src/tantan_repeat_finder.cc,
- src/tantan_repeat_finder.hh, test/hard.fa, test/tantan_test.out,
- test/tantan_test.sh:
- Add option to find straightforward tandem repeats
- [1bae60144712]
-
- * README.txt, src/mcf_tantan_options.cc, src/tantan.cc,
- src/tantan_app.cc:
- Tweak the help message
- [fc1ca32a72aa]
-
-2018-12-10 Martin C. Frith <Martin C. Frith>
-
- * README.txt, src/mcf_tantan_options.cc, src/mcf_tantan_options.hh,
- src/tantan_app.cc, test/tantan_test.out, test/tantan_test.sh:
- Add match score, mismatch cost options
- [2383404c795a]
-
- * src/tantan.cc:
- Refactor
- [d61af119db30]
-
- * src/tantan.cc:
- Refactor
- [81bdfe23217d]
-
- * src/CA_code/lambda_calculator.c, src/CA_code/lambda_calculator.h,
- src/CA_code/lubksb.c, src/CA_code/ludcmp.c, src/CA_code/nrutil.c,
- src/CA_code/nrutil.h, src/LambdaCalculator.cc,
- src/LambdaCalculator.hh, src/Makefile,
- src/mcf_score_matrix_probs.cc, src/mcf_score_matrix_probs.hh,
- src/tantan_app.cc:
- Use Konta-san's code for matrix lambda
- [fccc8e5e9c1b]
-
- * src/tantan.cc, src/tantan_app.cc, test/tantan_test.sh:
- Refactor
- [f9a9da99553d]
-
-2012-10-16 Martin C. Frith <Martin C. Frith>
-
- * README.txt:
- Expanded the documentation: installation & FAQ
- [946a951b1a06]
-
- * src/CA_code/nrutil.c:
- Just fixed a compiler warning
- [fa79ce69a581]
-
-2012-08-08 Martin C. Frith <Martin C. Frith>
-
- * Makefile:
- Avoid getting extra, unwanted files in the zip archive
- [d1d55af0e693]
-
- * test/tantan_test.sh:
- Made the test script less likely to use an unexpected version of
- tantan
- [894f9fc63c3e]
-
- * Makefile, README.txt:
- Added "make install", and HTML-ization of the README
- [674f2f7da185]
-
- * src/Makefile:
- Made the Makefile check the version number
- [ea0be7d72912]
-
- * README.txt:
- Converted the README to reStructuredText
- [25b631ab86b4]
-
- * src/Makefile:
- Generalized the Makefile
- [9c324ee14279]
-
-2011-07-07 Martin C. Frith <Martin C. Frith>
-
- * README.txt:
- Just changed the documentation a bit
- [2d6dfe34fe33]
-
-2011-03-22 Martin C. Frith <Martin C. Frith>
-
- * README.txt, src/mcf_tantan_options.cc, src/mcf_tantan_options.hh,
- src/tantan_app.cc:
- Added BED output option. Clarified the README (thanks: Joe Ryan).
- [db4af8e37a20]
-
-2011-01-07 Martin C. Frith <Martin C. Frith>
-
- * README.txt, src/mcf_fasta_sequence.cc, src/mcf_fasta_sequence.hh,
- test/panda.fastq, test/tantan_test.out, test/tantan_test.sh:
- Made tantan work on fastq format, and improved the README
- [e7d454a5982d]
-
-2010-11-16 Martin C. Frith <Martin C. Frith>
-
- * README.txt, src/Makefile, src/mcf_alphabet.cc, src/mcf_alphabet.hh,
- src/mcf_tantan_options.cc:
- Fixed compile error with g++ 4.0.1
- [97a2b94e5835]
-
-2010-10-13 Martin C. Frith <Martin C. Frith>
-
- * src/tantan_app.cc:
- Boost the version number to 1
- [c5a20b01a563]
-
- * COPYING.txt, README.txt, src/CA_code/lambda_calculator.c,
- src/CA_code/lambda_calculator.h, src/CA_code/lubksb.c,
- src/CA_code/ludcmp.c, src/CA_code/nrutil.c, src/CA_code/nrutil.h,
- src/Makefile, src/mcf_alphabet.cc, src/mcf_alphabet.hh,
- src/mcf_fasta_sequence.cc, src/mcf_fasta_sequence.hh,
- src/mcf_score_matrix.cc, src/mcf_score_matrix.hh,
- src/mcf_score_matrix_probs.cc, src/mcf_score_matrix_probs.hh,
- src/mcf_tantan_options.cc, src/mcf_tantan_options.hh,
- src/mcf_util.cc, src/mcf_util.hh, src/tantan.cc, src/tantan.hh,
- src/tantan_app.cc, test/atMask.mat, test/hg19_chrM.fa,
- test/tantan_test.out, test/tantan_test.sh, test/titin_human.fa:
- First commit
- [4f9b0ba31588]
-
=====================================
Makefile
=====================================
@@ -12,14 +12,5 @@ install: all
clean:
@cd src && ${MAKE} clean
-README.html: README.txt
- rst2html README.txt > README.html
-
-log:
- hg log --style changelog > ChangeLog.txt
-
-distdir = tantan-`hg id -n`
-dist: README.html log
- @cd src && ${MAKE} version.hh
- rsync -rC --exclude tantan src test Makefile *.txt README.html ${distdir}
- zip -qrm ${distdir} ${distdir}
+tag:
+ git tag -m "" `git rev-list HEAD^ | grep -c .`
=====================================
README.html deleted
=====================================
@@ -1,555 +0,0 @@
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-<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-<meta name="generator" content="Docutils 0.6: http://docutils.sourceforge.net/" />
-<title>tantan</title>
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-</style>
-</head>
-<body>
-<div class="document" id="tantan">
-<h1 class="title">tantan</h1>
-
-<div class="section" id="introduction">
-<h1>Introduction</h1>
-<p>tantan is a tool for masking simple regions (low complexity and
-short-period tandem repeats) in biological sequences.</p>
-<p>The aim of tantan is to prevent false predictions when searching for
-homologous regions between two sequences. Simple repeats often align
-strongly to each other, causing false homology predictions.</p>
-</div>
-<div class="section" id="setup">
-<h1>Setup</h1>
-<p>You need to have a C++ compiler. On Linux, you might need to install
-a package called "g++". On Mac, you might need to install
-command-line developer tools. On Windows, you might need to install
-Cygwin.</p>
-<p>Using the command line, go into the tantan directory. To compile it,
-type:</p>
-<pre class="literal-block">
-make
-</pre>
-<p>Optionally, copy tantan to a standard "bin" directory (using "sudo" to
-request administrator permissions):</p>
-<pre class="literal-block">
-sudo make install
-</pre>
-<p>Or copy it to your personal bin directory:</p>
-<pre class="literal-block">
-make install prefix=~
-</pre>
-<p>You might need to log out and back in for your computer to recognize
-the new program.</p>
-</div>
-<div class="section" id="normal-usage">
-<h1>Normal usage</h1>
-<ul>
-<li><p class="first">Suppose you have some nucleotide sequences (DNA or RNA) in a
-FASTA-format file called "ntseqs.fa". You can identify simple
-repeats like this:</p>
-<pre class="literal-block">
-tantan ntseqs.fa > masked.fa
-</pre>
-<p>This will create a new FASTA file called "masked.fa" that replaces
-all masked regions with lowercase letters. (tantan also works on
-FASTQ-format, though it does not use the quality data.)</p>
-</li>
-<li><p class="first">To mask proteins effectively, tantan needs to use different
-algorithm parameters than for nucleotides. You have to tell it when
-you have proteins, using the "-p" option:</p>
-<pre class="literal-block">
-tantan -p aaseqs.fa > masked.fa
-</pre>
-<p>If you omit "-p" and the sequences look proteinaceous, tantan will
-print a warning message.</p>
-</li>
-</ul>
-</div>
-<div class="section" id="advanced-usage">
-<h1>Advanced usage</h1>
-<ul>
-<li><p class="first">By default, tantan indicates repetitive regions with lowercase
-letters. You can make it replace repetitive letters with (say) "N"
-by using the "-x" option:</p>
-<pre class="literal-block">
-tantan -x N ntseqs.fa > masked.fa
-</pre>
-</li>
-<li><p class="first">By default, tantan does not preserve lowercase letters in the input
-sequences. You can tell it to preserve them by using the "-c"
-option. So the output will have the union of the lowercase in the
-input and the lowercase assigned by tantan:</p>
-<pre class="literal-block">
-tantan -c ntseqs.fa > masked.fa
-</pre>
-</li>
-<li><p class="first">tantan's masking rate is usually OK, but you can alter it by
-changing the "-r" parameter from its default value of 0.005. Higher
-values increase the amount of masking, and lower values decrease it.
-This increases the masking rate:</p>
-<pre class="literal-block">
-tantan -r 0.02 ntseqs.fa > masked.fa
-</pre>
-</li>
-<li><p class="first">Finally, to mask extremely AT-rich DNA, you should change tantan's
-scoring matrix. The "test" directory contains a matrix "atMask.mat"
-that works well for DNA with ~80% A+T, such as Plasmodium and
-Dictyostelium genomes. We recommend masking such DNA like this:</p>
-<pre class="literal-block">
-tantan -m atMask.mat -r 0.01 atrich.fa > masked.fa
-</pre>
-</li>
-</ul>
-<p>The preceding examples cover all of tantan's options that you should
-ever need.</p>
-</div>
-<div class="section" id="recommendations-for-homology-search">
-<h1>Recommendations for homology search</h1>
-<ol class="arabic simple">
-<li>Mask <em>both</em> (sets of) sequences.</li>
-<li>If for some reason you wish to mask only one (set of) sequence(s),
-increase "-r" to 0.02 (0.05 for AT-rich DNA).</li>
-<li>For DNA-versus-protein alignment, increase "-r" for the proteins to
-0.02. If for some reason you mask only one (set of) sequence(s),
-make sure it's the proteins.</li>
-<li>Some alignment tools exclude lowercase from their initial seeding
-phase, but treat lowercase identically to uppercase during their
-subsequent extension phase. Unfortunately, this does not reliably
-prevent false homology predictions. It is OK to re-align without
-masking after homology has been decided: FASTA and LAST can do
-this.</li>
-</ol>
-<p>For more information, please read the tantan publication (see below).</p>
-</div>
-<div class="section" id="faq">
-<h1>FAQ</h1>
-<div class="section" id="why-does-tantan-sometimes-mask-isolated-bases">
-<h2>Why does tantan sometimes mask isolated bases?</h2>
-<p>This happens when a region is borderline repetitive, and a single base
-creeps just over the threshold. Don't worry about it, it's not a
-problem (at least for tantan's aim of preventing false homology).</p>
-</div>
-<div class="section" id="does-tantan-mask-functional-sequence">
-<h2>Does tantan mask functional sequence?</h2>
-<p>Of course. Proteins and protein-coding exons can contain simple
-repeats. Repeats can be functional. If we want to avoid false
-homology we have to mask them. Remember that tantan merely lowercases
-repeats, so it's easy to lift the masking after determining homology.</p>
-</div>
-</div>
-<div class="section" id="options">
-<h1>Options</h1>
-<table class="docutils option-list" frame="void" rules="none">
-<col class="option" />
-<col class="description" />
-<tbody valign="top">
-<tr><td class="option-group">
-<kbd><span class="option">-p</span></kbd></td>
-<td>interpret the sequences as proteins</td></tr>
-<tr><td class="option-group">
-<kbd><span class="option">-x</span></kbd></td>
-<td>letter to use for masking, instead of lowercase</td></tr>
-<tr><td class="option-group">
-<kbd><span class="option">-c</span></kbd></td>
-<td>preserve uppercase/lowercase in non-masked regions</td></tr>
-<tr><td class="option-group">
-<kbd><span class="option">-m</span></kbd></td>
-<td>file for letter-pair score matrix</td></tr>
-<tr><td class="option-group">
-<kbd><span class="option">-r</span></kbd></td>
-<td>probability of a repeat starting per position</td></tr>
-<tr><td class="option-group">
-<kbd><span class="option">-e</span></kbd></td>
-<td>probability of a repeat ending per position</td></tr>
-<tr><td class="option-group">
-<kbd><span class="option">-w</span></kbd></td>
-<td>maximum tandem repeat period to consider</td></tr>
-<tr><td class="option-group">
-<kbd><span class="option">-d</span></kbd></td>
-<td>probability decay per period (period-(i+1) / period-i)</td></tr>
-<tr><td class="option-group">
-<kbd><span class="option">-i</span></kbd></td>
-<td>match score</td></tr>
-<tr><td class="option-group">
-<kbd><span class="option">-j</span></kbd></td>
-<td>mismatch cost</td></tr>
-<tr><td class="option-group">
-<kbd><span class="option">-a</span></kbd></td>
-<td>gap existence cost</td></tr>
-<tr><td class="option-group">
-<kbd><span class="option">-b</span></kbd></td>
-<td>gap extension cost</td></tr>
-<tr><td class="option-group">
-<kbd><span class="option">-s</span></kbd></td>
-<td>minimum repeat probability for masking</td></tr>
-<tr><td class="option-group">
-<kbd><span class="option">-n</span></kbd></td>
-<td>minimum copy number, affects -f4 only</td></tr>
-<tr><td class="option-group">
-<kbd><span class="option">-f</span></kbd></td>
-<td>output type: 0=masked sequence, 1=repeat probabilities,
-2=repeat counts, 3=BED, 4=tandem repeats</td></tr>
-<tr><td class="option-group">
-<kbd><span class="option">-h</span>, <span class="option">--help</span></kbd></td>
-<td>show help message, then exit</td></tr>
-<tr><td class="option-group">
-<kbd><span class="option">--version</span></kbd></td>
-<td>show version information, then exit</td></tr>
-</tbody>
-</table>
-</div>
-<div class="section" id="advanced-issues">
-<h1>Advanced issues</h1>
-<p>When tantan masks tandem repeats, it tends to leave the first
-(left-most) repeat unit unmasked. This sometimes allows us to find
-homologs we would otherwise miss:</p>
-<pre class="literal-block">
-TGCAAGCTA TTAGGCTTAGGTCAGTGC ttaagcttaggtcagtgc AACATA
-||| ||| | |||||||||||||||||| ||| |||||||||||||| ||| ||
-TGCTAGCAA TTAGGCTTAGGTCAGTGC ttaggcttaggtcagtgc AACGTA
-</pre>
-<p>However, there is a danger of non-equivalent repeat units being
-unmasked. This happens especially if we mask DNA on one strand but
-align it on the other strand:</p>
-<pre class="literal-block">
- TGCAAGCTA TTAGGCTTAGGTCAGTGC ttaagcttaggtcagtgc AACATA
- ||||||||||||||||||
-TGCTAGCAA ttaggcttaggtcagtgc TTAGGCTTAGGTCAGTGC AACGTA
-</pre>
-<p>(My thanks to Junko Tsuji and Paul Horton for finding these issues.)</p>
-</div>
-<div class="section" id="finding-straightforward-tandem-repeats">
-<h1>Finding straightforward tandem repeats</h1>
-<p>Option -f4 runs tantan in a different mode, where it finds
-straightforward tandem repeats only. (Technically, it uses a Viterbi
-algorithm instead of a Forward-Backward algorithm.) This is <em>not</em>
-recommended for avoiding false homologs! But it might be useful for
-studying tandem repeats. The output looks like this:</p>
-<pre class="literal-block">
-mySeq 14765 14780 6 2.5 GTCATG GTCATG,GTCATG,GTC
-mySeq 632362 632377 2 6 GC GC,GC,GC,GCt,GCT,GCT
-mySeq 1278353 1278369 3 6.5 TCA TCA,TCA,TCA,TC-,TC,TC,T
-mySeq 3616084 3616100 3 5.33333 TGG TGA,TGA,TGG,TGG,TGG,T
-</pre>
-<p>The first 3 columns show the start and end coordinates of the
-repetitive region, in <a class="reference external" href="https://genome.ucsc.edu/FAQ/FAQformat.html#format1">BED</a> format. Column
-4 shows the length of the repeating unit (which might vary due to
-insertions and deletions, so this column shows the most common
-length). Column 5 shows the number of repeat units. Column 6 shows
-the repeating unit (which again might vary, so this is just a
-representative). Column 7 shows the whole repeat: lowercase letters
-are insertions relative to the previous repeat unit, and dashes are
-deletions relative to the previous repeat unit.</p>
-</div>
-<div class="section" id="miscellaneous">
-<h1>Miscellaneous</h1>
-<p>tantan is distributed under the GNU General Public License, either
-version 3 of the License, or (at your option) any later version. For
-details, see COPYING.txt.</p>
-<p>If you use tantan in your research, please cite:
-"A new repeat-masking method enables specific detection of homologous
-sequences", MC Frith, Nucleic Acids Research 2011 39(4):e23.</p>
-<p>tantan's website is: <a class="reference external" href="http://www.cbrc.jp/tantan/">http://www.cbrc.jp/tantan/</a></p>
-<p>If you have any questions, comments, or problems concerning tantan,
-please email: tantan (ATmark) cbrc (dot) jp.</p>
-</div>
-</div>
-</body>
-</html>
=====================================
README.txt → README.rst
=====================================
@@ -208,8 +208,3 @@ details, see COPYING.txt.
If you use tantan in your research, please cite:
"A new repeat-masking method enables specific detection of homologous
sequences", MC Frith, Nucleic Acids Research 2011 39(4):e23.
-
-tantan's website is: http://www.cbrc.jp/tantan/
-
-If you have any questions, comments, or problems concerning tantan,
-please email: tantan (ATmark) cbrc (dot) jp.
=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+tantan (26-1) UNRELEASED; urgency=medium
+
+ * Team Upload.
+ * New upstream version 26
+ * d/watch: Fix fetch URL - tantan has moved to gitlab
+ * d/control:
+ + Fix homepage
+ + Bump debhelper-compat version to 13
+ + Declare compliance with policy 4.5.1
+ * d/copyright: Fix Source URL, migrate to https
+
+ -- Nilesh Patra <nilesh at debian.org> Thu, 03 Jun 2021 00:34:03 +0530
+
tantan (23-1) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -3,11 +3,11 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Sascha Steinbiss <satta at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper-compat (= 12)
-Standards-Version: 4.5.0
+Build-Depends: debhelper-compat (= 13)
+Standards-Version: 4.5.1
Vcs-Browser: https://salsa.debian.org/med-team/tantan
Vcs-Git: https://salsa.debian.org/med-team/tantan.git
-Homepage: https://www.cbrc.jp/tantan/
+Homepage: https://gitlab.com/mcfrith/tantan
Rules-Requires-Root: no
Package: tantan
=====================================
debian/copyright
=====================================
@@ -1,6 +1,6 @@
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: tantan
-Source: http://www.cbrc.jp/tantan/
+Source: https://gitlab.com/mcfrith/tantan
Files: *
Copyright: © 2010 Martin Frith <tantan at cbrc.jp>
@@ -25,7 +25,7 @@ License: GPL-3+
GNU General Public License for more details.
.
You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>.
+ along with this program. If not, see <https://www.gnu.org/licenses/>.
.
On Debian Systems you can find a copy of the text of GPL version 3
at /usr/share/common-licenses/GPL-3.
=====================================
debian/patches/buildflags.patch
=====================================
@@ -3,12 +3,9 @@ Description: add buildflags
Author: Sascha Steinbiss <sascha at steinbiss.name>
--- a/src/Makefile
+++ b/src/Makefile
-@@ -1,11 +1,14 @@
--CXXFLAGS = -O3 -Wall -W -Wcast-qual -Wswitch-enum -Wundef \
---Wcast-align -Wold-style-cast
-+#CXXFLAGS = -O3 -Wall -W -Wcast-qual -Wswitch-enum -Wundef \
-+#-Wcast-align -Wold-style-cast
- # -Wconversion
+@@ -1,9 +1,12 @@
+-CXXFLAGS = -O3 -Wall
++#CXXFLAGS = -O3 -Wall
all: tantan
=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,8 @@
+---
+Bug-Database: https://gitlab.com/mcfrith/tantan/issues
+Changelog: https://gitlab.com/mcfrith/tantan/tags
+Repository: https://gitlab.com/mcfrith/tantan.git
+Repository-Browse: https://gitlab.com/mcfrith/tantan
Reference:
Author: Frith, Martin C.
Title: >
=====================================
debian/watch
=====================================
@@ -1,2 +1,2 @@
-version=3
-http://cbrc3.cbrc.jp/~martin/tantan/tantan-([0-9]*).zip
+version=4
+ https://gitlab.com/mcfrith/tantan/-/tags?sort=updated_desc .*/archive/(\d\S+)/.*\.tar\.gz
=====================================
src/LambdaCalculator.cc
=====================================
@@ -1,186 +1,29 @@
// Copyright 2015 Yutaro Konta
#include "LambdaCalculator.hh"
-#include <vector>
+#include "cbrc_linalg.hh"
#include <cassert>
-#include <cstdio> // sprintf
-#include <cstdlib>
#include <cfloat>
#include <cmath>
+#include <numeric>
//#include <iostream>
using namespace std;
-static double roundToFewDigits(double x)
+static bool calculate_inv_sum(double **matrix, int alpha_size, double tau, double* inv_sum, double **tmpMat, double *tmpVec)
{
- // This rounding fixes some inaccuracies, e.g. for DNA with a simple
- // match/mismatch matrix it's likely to make all the probabilities
- // exactly 0.25, as they should be.
- char buffer[32];
- sprintf(buffer, "%g", x);
- return atof(buffer);
-}
-
-static double** makematrix(int m, int n, double val)
-{
- double** mat = new double* [m];
- for (int i=0; i<m; i++)
- {
- mat[i] = new double [n];
- for (int j=0; j<n; j++)
- mat[i][j] = val;
- }
- return mat;
-}
-
-static void deletematrix(double** a, int m)
-{
- for (int i=0; i<m; i++)
- delete[] a[i];
- delete[] a;
-}
-
-static double summatrix(double** a, int m, int n)
-{
- double s = 0;
- for (int i=0; i<m; i++)
- for (int j=0; j<n; j++)
- s += a[i][j];
- return s;
-}
-
-static int max_index(double** a, int n, int i)
-{
- double max = -DBL_MAX;
- int maxindex = -1;
-
- for (int j=i; j<n; j++)
- {
- if (fabs(a[j][i]) > max)
- {
- max = fabs(a[j][i]);
- maxindex = j;
- }
- }
- return maxindex;
-}
-
-static void swap_matrix(double** a, int i, int j)
-{
- double* v = a[i];
- a[i] = a[j];
- a[j] = v;
-}
-
-static void swap_vector(int* a, int i, int j)
-{
- int v = a[i];
- a[i] = a[j];
- a[j] = v;
-}
-
-static bool lu_pivoting(double** a, int* idx, int n)
-{
- int v;
-
- for (int i=0; i<n; i++)
- idx[i] = i;
-
- for (int i=0; i<n; i++)
- {
- v = max_index(a, n, i);
- assert(v >= 0);
- if (fabs(a[v][i]) < 1e-10)
- {
- return false; // singular matrix!
- }
-
- swap_matrix(a, i, v);
- swap_vector(idx, i, v);
-
- a[i][i] = 1.0/a[i][i];
- for (int j=i+1; j<n; j++)
- {
- a[j][i] = a[j][i] * a[i][i];
- for (int k=i+1; k<n; k++)
- a[j][k] = a[j][k] - a[j][i] * a[i][k];
- }
- }
- return true;
-}
-
-static void solvep(double **a, double *x, double *b, int n)
-{
- double *y = new double [n];
-
- for (int i=0; i<n; i++)
- {
- y[i] = b[i];
- for (int j=0; j<i; j++)
- y[i] -= a[i][j] * y[j];
- }
-
- for (int i=n-1; i>=0; i--)
- {
- x[i] = y[i];
- for (int j=i+1; j<n; j++)
- x[i] -= a[i][j] * x[j];
- x[i] *= a[i][i]; // needed because a[i][i] is inverted
- }
- delete[] y;
-}
-
-static void transpose(double **a, int n)
-{
- double v;
- for (int i=0; i<n; i++)
- {
- for (int j=0; j<i; j++)
- {
- v = a[i][j];
- a[i][j] = a[j][i];
- a[j][i] = v;
- }
- }
-}
-
-static bool invert(double **a, double **inv, int n)
-{
- int* idx = new int [n];
-
- double **e = makematrix(n,n,0);
-
- if(!lu_pivoting(a, idx, n))
- return false;
-
- for (int i=0; i<n; i++)
- e[idx[i]][i] = 1; // transposed
-
- delete[] idx;
-
- for (int i=0; i<n; i++)
- solvep(a, inv[i], e[i], n);
-
- deletematrix(e, n);
- transpose(inv, n); // transpose inv to make the inverted matrix of a
- return true;
-}
-
-static bool calculate_inv_sum(double **matrix, int alpha_size, double tau, double* inv_sum)
-{
- double **m = makematrix(alpha_size, alpha_size, 0);
- double **y = makematrix(alpha_size, alpha_size, 0);
-
for (int i=0; i<alpha_size; i++)
for (int j=0; j<alpha_size; j++)
- m[i][j] = exp(tau * matrix[i][j]);
+ tmpMat[i][j] = exp(tau * matrix[i][j]);
- if(!invert(m, y, alpha_size))
- return false;
+ std::fill_n(tmpVec, alpha_size, 1.0);
- *inv_sum = summatrix(y, alpha_size, alpha_size);
+ try {
+ cbrc::linalgSolve(tmpMat, tmpVec, alpha_size);
+ } catch(...) {
+ return false;
+ }
- deletematrix(m, alpha_size);
- deletematrix(y, alpha_size);
+ *inv_sum = std::accumulate(tmpVec, tmpVec + alpha_size, 0.0);
return true;
}
@@ -265,12 +108,21 @@ bool LambdaCalculator::binary_search(double** matrix, int alpha_size, double lb,
double r_sum=0;
int iter=0;
+ std::vector<double> tmpVals(alpha_size * alpha_size);
+ std::vector<double *> tmpPtrs(alpha_size);
+ for (int i = 0; i < alpha_size; ++i)
+ tmpPtrs[i] = &tmpVals[i * alpha_size];
+ double **tmpMat = &tmpPtrs[0];
+
+ double *tmpVec = &letprob2[0];
+
while (iter < maxiter && (l>=r || (l_sum < 1.0 && r_sum < 1.0) || (l_sum > 1.0 && r_sum > 1.0)))
{
l = lb + (ub - lb)*rand()/RAND_MAX;
r = lb + (ub - lb)*rand()/RAND_MAX;
- if (!calculate_inv_sum(matrix, alpha_size, l, &l_sum) || !calculate_inv_sum(matrix, alpha_size, r, &r_sum))
+ if (!calculate_inv_sum(matrix, alpha_size, l, &l_sum, tmpMat, tmpVec) ||
+ !calculate_inv_sum(matrix, alpha_size, r, &r_sum, tmpMat, tmpVec))
{
l = 0;
r = 0;
@@ -285,7 +137,7 @@ bool LambdaCalculator::binary_search(double** matrix, int alpha_size, double lb,
{
double mid = (l + r)/2.0;
double mid_sum;
- if (!calculate_inv_sum(matrix, alpha_size, mid, &mid_sum))
+ if (!calculate_inv_sum(matrix, alpha_size, mid, &mid_sum, tmpMat, tmpVec))
return false;
if (fabs(mid_sum) >= DBL_MAX)
@@ -309,7 +161,7 @@ bool LambdaCalculator::binary_search(double** matrix, int alpha_size, double lb,
if (fabs(l_sum - 1.0) < fabs(r_sum - 1.0))
{
- if (check_lambda(matrix, l, alpha_size, letprob1, letprob2))
+ if (check_lambda(matrix, l, alpha_size, letprob1, letprob2, tmpMat))
{
*lambda = l;
return true;
@@ -317,7 +169,7 @@ bool LambdaCalculator::binary_search(double** matrix, int alpha_size, double lb,
return false;
}
- if (check_lambda(matrix, r, alpha_size, letprob1, letprob2))
+ if (check_lambda(matrix, r, alpha_size, letprob1, letprob2, tmpMat))
{
*lambda = r;
return true;
@@ -346,63 +198,62 @@ double LambdaCalculator::calculate_lambda(double** matrix, int alpha_size, vecto
return lambda;
}
-bool LambdaCalculator::check_lambda(double** matrix, double lambda, int alpha_size, vector<double>& letprob1, vector<double>& letprob2)
+bool LambdaCalculator::check_lambda(double** matrix, double lambda, int alpha_size, vector<double>& letprob1, vector<double>& letprob2, double** tmpMat)
{
- double **m = makematrix(alpha_size, alpha_size, 0);
- double **y = makematrix(alpha_size, alpha_size, 0);
-
for (int i=0; i<alpha_size; i++)
for (int j=0; j<alpha_size; j++)
- m[i][j] = exp(lambda * matrix[i][j]);
+ tmpMat[i][j] = exp(lambda * matrix[i][j]);
- invert(m, y, alpha_size);
+ std::fill_n(&letprob2[0], alpha_size, 1.0);
+ cbrc::linalgSolve(tmpMat, &letprob2[0], alpha_size);
for (int i=0; i<alpha_size; i++)
{
- double p = 0;
- for (int j=0;j<alpha_size; j++)
- p += y[i][j];
+ double p = letprob2[i];
if (p < 0 || p > 1)
- {
- letprob2.clear();
- return false;
- }
- letprob2.push_back(roundToFewDigits(p));
+ return false;
+ letprob2[i] = roundToFewDigits(p);
}
+ for (int i=0; i<alpha_size; i++)
+ for (int j=0; j<alpha_size; j++)
+ tmpMat[i][j] = exp(lambda * matrix[j][i]);
+
+ std::fill_n(&letprob1[0], alpha_size, 1.0);
+ cbrc::linalgSolve(tmpMat, &letprob1[0], alpha_size);
+
for (int j=0; j<alpha_size; j++)
{
- double q = 0;
- for (int i=0; i<alpha_size; i++)
- q += y[i][j];
+ double q = letprob1[j];
if (q < 0 || q > 1)
- {
- letprob2.clear();
- letprob1.clear();
- return false;
- }
- letprob1.push_back(roundToFewDigits(q));
+ return false;
+ letprob1[j] = roundToFewDigits(q);
}
- deletematrix(m, alpha_size);
- deletematrix(y, alpha_size);
-
return true;
}
void LambdaCalculator::calculate(const const_int_ptr *matrix, int alphSize) {
assert(alphSize >= 0);
- setBad();
+ lambda_ = -1;
+ letterProbs1_.resize(alphSize);
+ letterProbs2_.resize(alphSize);
int maxiter = 1000;
int max_boundary_search_iter = 100;
double lb_ratio = 1e-6;
- double** mat = makematrix(alphSize, alphSize, 0);
+ std::vector<double> matVals(alphSize * alphSize);
+ std::vector<double *> matPtrs(alphSize);
+ for (int i = 0; i < alphSize; ++i)
+ matPtrs[i] = &matVals[i * alphSize];
+ double** mat = &matPtrs[0];
+
for (int i=0; i<alphSize; i++)
for (int j=0; j<alphSize; j++)
mat[i][j] = matrix[i][j];
+
+ // xxx srand ?
lambda_ = calculate_lambda(mat, alphSize, letterProbs1_, letterProbs2_, maxiter, max_boundary_search_iter, lb_ratio);
- deletematrix(mat, alphSize);
}
}
=====================================
src/LambdaCalculator.hh
=====================================
@@ -14,11 +14,23 @@
#define LAMBDA_CALCULATOR_HH
#include <vector>
+#include <stdio.h> // sprintf
+#include <stdlib.h> // atof
namespace cbrc{
typedef const int *const_int_ptr;
+inline double roundToFewDigits(double x)
+{
+ // This rounding fixes some inaccuracies, e.g. for DNA with a simple
+ // match/mismatch matrix it's likely to make all the probabilities
+ // exactly 0.25, as they should be.
+ char buffer[32];
+ sprintf(buffer, "%g", x);
+ return atof(buffer);
+}
+
class LambdaCalculator{
public:
LambdaCalculator() { setBad(); }
@@ -50,7 +62,7 @@ class LambdaCalculator{
bool find_ub(double **matrix, int alpha_size, double *ub);
bool binary_search(double** matrix, int alpha_size, double lb, double ub, std::vector<double>& letprob1, std::vector<double>& letprob2, double* lambda, int maxiter);
double calculate_lambda(double** matrix, int alpha_size, std::vector<double>& letprob1, std::vector<double>& letprob2, int maxiter, int max_boundary_search_iter, double lb_ratio);
- bool check_lambda(double** matrix, double lambda, int alpha_size, std::vector<double>& letprob1, std::vector<double>& letprob2);
+ bool check_lambda(double** matrix, double lambda, int alpha_size, std::vector<double>& letprob1, std::vector<double>& letprob2, double** tmpMat);
};
} // end namespace
=====================================
src/Makefile
=====================================
@@ -1,6 +1,4 @@
-CXXFLAGS = -O3 -Wall -W -Wcast-qual -Wswitch-enum -Wundef \
--Wcast-align -Wold-style-cast
-# -Wconversion
+CXXFLAGS = -O3 -Wall
all: tantan
@@ -10,11 +8,12 @@ tantan: *.cc *.hh version.hh Makefile
clean:
rm -f tantan
-VERSION = \"`hg id -n`\"
+VERSION1 = git describe --dirty
+VERSION2 = echo ' (HEAD -> main, tag: 26) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'
+
+VERSION = \"`test -e ../.git && $(VERSION1) || $(VERSION2)`\"
version.hh: FORCE
- if test -e ../.hg; \
- then echo $(VERSION) | cmp -s $@ - || echo $(VERSION) > $@ ; \
- fi
+ echo $(VERSION) | cmp -s $@ - || echo $(VERSION) > $@
FORCE:
=====================================
src/cbrc_linalg.cc
=====================================
@@ -0,0 +1,38 @@
+// Copyright 2013 Martin C. Frith
+
+#include "cbrc_linalg.hh"
+#include <algorithm>
+#include <cmath>
+#include <stdexcept>
+
+namespace cbrc {
+
+void linalgSolve(double **m, double *v, unsigned s) {
+ for (unsigned k = 0; k < s; ++k) {
+ // partial pivoting:
+ unsigned iMax = k;
+ for (unsigned i = k; i < s; ++i)
+ if (std::fabs(m[i][k]) > std::fabs(m[iMax][k]))
+ iMax = i;
+ if (iMax > k) {
+ std::swap_ranges(m[k], m[k] + s, m[iMax]);
+ std::swap(v[k], v[iMax]);
+ }
+
+ if (m[k][k] == 0.0)
+ throw std::runtime_error("singular matrix");
+
+ for (unsigned i = 0; i < s; ++i) {
+ if (i == k) continue;
+ double q = m[i][k] / m[k][k];
+ for (unsigned j = k; j < s; ++j)
+ m[i][j] -= q * m[k][j];
+ v[i] -= q * v[k];
+ }
+ }
+
+ for (unsigned k = 0; k < s; ++k)
+ v[k] /= m[k][k];
+}
+
+}
=====================================
src/cbrc_linalg.hh
=====================================
@@ -0,0 +1,27 @@
+// Copyright 2013 Martin C. Frith
+
+// This routine solves simultaneous linear equations, such as:
+//
+// m11 * x1 + m12 * x2 + m13 * x3 = v1
+// m21 * x1 + m22 * x2 + m23 * x3 = v2
+// m31 * x1 + m32 * x2 + m33 * x3 = v3
+//
+// We know m and v, and we wish to determine x.
+//
+// Input: m should be a matrix of size s*s, and v should be a vector
+// of length s.
+//
+// Output: the result is written into v. The calculation modifies m.
+//
+// If the matrix is singular, an error is thrown.
+
+#ifndef CBRC_LINALG_HH
+#define CBRC_LINALG_HH
+
+namespace cbrc {
+
+void linalgSolve(double **m, double *v, unsigned s);
+
+}
+
+#endif
=====================================
src/mcf_tantan_options.cc
=====================================
@@ -92,9 +92,6 @@ Options (default settings):\n\
+ stringify(outputType) + ")\n\
-h, --help show help message, then exit\n\
--version show version information, then exit\n\
-\n\
-Report bugs to: tantan at cbrc.jp\n\
-Home page: http://www.cbrc.jp/tantan/\n\
";
// -k for transition cost?
=====================================
src/version.hh deleted
=====================================
@@ -1 +0,0 @@
-"23"
View it on GitLab: https://salsa.debian.org/med-team/tantan/-/compare/81c7ecc308e3dbd31c15c89432160cdad28b0b1b...a5d2fc77e38695809581404e61810739313252bf
--
View it on GitLab: https://salsa.debian.org/med-team/tantan/-/compare/81c7ecc308e3dbd31c15c89432160cdad28b0b1b...a5d2fc77e38695809581404e61810739313252bf
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