[med-svn] [Git][med-team/tantan][master] 7 commits: New upstream version 23

[Steffen Möller]

Steffen Möller pushed to branch master at Debian Med / tantan


Commits:
5d55a974 by Steffen Moeller at 2020-05-09T16:22:25+02:00
New upstream version 23
- - - - -
16c22f35 by Steffen Moeller at 2020-05-09T16:22:25+02:00
routine-update: New upstream version

- - - - -
ed054b35 by Steffen Moeller at 2020-05-09T16:22:25+02:00
Update upstream source from tag 'upstream/23'

Update to upstream version '23'
with Debian dir ab2da0808102878474128f6a9a49c83e80a41290
- - - - -
a5e5f2d4 by Steffen Moeller at 2020-05-09T16:22:27+02:00
routine-update: Add salsa-ci file

- - - - -
825225c7 by Steffen Moeller at 2020-05-09T16:22:27+02:00
routine-update: Rules-Requires-Root: no

- - - - -
f5f471a4 by Steffen Moeller at 2020-05-09T16:22:33+02:00
Use secure URI in Homepage field.

Fixes: lintian: homepage-field-uses-insecure-uri
See-also: https://lintian.debian.org/tags/homepage-field-uses-insecure-uri.html

- - - - -
81c7ecc3 by Steffen Moeller at 2020-05-09T16:22:50+02:00
routine-update: Ready to upload to unstable

- - - - -


6 changed files:

- ChangeLog.txt
- debian/changelog
- debian/control
- + debian/salsa-ci.yml
- src/tantan.cc
- src/version.hh


Changes:

=====================================
ChangeLog.txt
=====================================
@@ -1,8 +1,14 @@
+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] [tip]
+	[3523060bcfb9]
 
 	* src/tantan_repeat_finder.cc, src/tantan_repeat_finder.hh:
 	Make -f4 a bit faster


=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+tantan (23-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream version
+  * Add salsa-ci file (routine-update)
+  * Rules-Requires-Root: no (routine-update)
+  * Use secure URI in Homepage field.
+
+ -- Steffen Moeller <moeller at debian.org>  Sat, 09 May 2020 16:22:36 +0200
+
 tantan (22-2) unstable; urgency=medium
 
   * Add registry references (thanks Steffen Moeller).


=====================================
debian/control
=====================================
@@ -7,7 +7,8 @@ Build-Depends: debhelper-compat (= 12)
 Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/tantan
 Vcs-Git: https://salsa.debian.org/med-team/tantan.git
-Homepage: http://www.cbrc.jp/tantan/
+Homepage: https://www.cbrc.jp/tantan/
+Rules-Requires-Root: no
 
 Package: tantan
 Architecture: any


=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml


=====================================
src/tantan.cc
=====================================
@@ -274,6 +274,10 @@ struct Tantan {
     return seqPtr - seqBeg < maxRepeatOffset;
   }
 
+  int maxOffsetInTheSequence() {
+    return isNearSeqBeg() ? (seqPtr - seqBeg) : maxRepeatOffset;
+  }
+
   const uchar *seqFurthestBack() {
     return isNearSeqBeg() ? seqBeg : seqPtr - maxRepeatOffset;
   }
@@ -296,6 +300,50 @@ struct Tantan {
     }
   }
 
+  void calcForwardTransitionAndEmissionProbs() {
+    if (endGapProb > 0) {
+      calcForwardTransitionProbsWithGaps();
+      calcEmissionProbs();
+      return;
+    }
+
+    double b = backgroundProb;
+    double fromForeground = 0;
+    double *foregroundBeg = BEG(foregroundProbs);
+    const double *lrRow = likelihoodRatioMatrix[*seqPtr];
+    int maxOffset = maxOffsetInTheSequence();
+
+    for (int i = 0; i < maxOffset; ++i) {
+      double f = foregroundBeg[i];
+      fromForeground += f;
+      foregroundBeg[i] = (b * b2fProbs[i] + f * f2f0) * lrRow[seqPtr[-i-1]];
+    }
+
+    backgroundProb = b * b2b + fromForeground * f2b;
+  }
+
+  void calcEmissionAndBackwardTransitionProbs() {
+    if (endGapProb > 0) {
+      calcEmissionProbs();
+      calcBackwardTransitionProbsWithGaps();
+      return;
+    }
+
+    double toBackground = f2b * backgroundProb;
+    double toForeground = 0;
+    double *foregroundBeg = BEG(foregroundProbs);
+    const double *lrRow = likelihoodRatioMatrix[*seqPtr];
+    int maxOffset = maxOffsetInTheSequence();
+
+    for (int i = 0; i < maxOffset; ++i) {
+      double f = foregroundBeg[i] * lrRow[seqPtr[-i-1]];
+      toForeground += b2fProbs[i] * f;
+      foregroundBeg[i] = toBackground + f2f0 * f;
+    }
+
+    backgroundProb = b2b * backgroundProb + toForeground;
+  }
+
   void rescale(double scale) {
     backgroundProb *= scale;
     multiplyAll(foregroundProbs, scale);
@@ -322,8 +370,7 @@ struct Tantan {
     initializeForwardAlgorithm();
 
     while (seqPtr < seqEnd) {
-      calcForwardTransitionProbs();
-      calcEmissionProbs();
+      calcForwardTransitionAndEmissionProbs();
       rescaleForward();
       *letterProbs = static_cast<float>(backgroundProb);
       ++letterProbs;
@@ -343,8 +390,7 @@ struct Tantan {
       // a sequence:
       *letterProbs = 1 - static_cast<float>(nonRepeatProb);
       rescaleBackward();
-      calcEmissionProbs();
-      calcBackwardTransitionProbs();
+      calcEmissionAndBackwardTransitionProbs();
     }
 
     double z2 = backwardTotal();


=====================================
src/version.hh
=====================================
@@ -1 +1 @@
-"22"
+"23"



View it on GitLab: https://salsa.debian.org/med-team/tantan/-/compare/8cbd776d1dd4e18d0e674f321d8ea22923c693cf...81c7ecc308e3dbd31c15c89432160cdad28b0b1b

-- 
View it on GitLab: https://salsa.debian.org/med-team/tantan/-/compare/8cbd776d1dd4e18d0e674f321d8ea22923c693cf...81c7ecc308e3dbd31c15c89432160cdad28b0b1b
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