[med-svn] [fasttree] 03/03: Remove increase-branch-length-precision.patch + update d/changelog

[Roland Fehrenbacher]

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rfehren-guest pushed a commit to branch master
in repository fasttree.

commit 5c511662a89faf1420067bf1d2c04e07101a74a8
Author: Roland Fehrenbacher <rf at q-leap.de>
Date:   Tue Mar 31 10:57:36 2015 +0000

    Remove increase-branch-length-precision.patch + update d/changelog
---
 debian/changelog                                   |  9 ++-
 .../patches/increase-branch-length-precision.patch | 65 ----------------------
 debian/patches/series                              |  1 -
 3 files changed, 7 insertions(+), 68 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index e3d60e3..f3c7674 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,11 +1,16 @@
-fasttree (2.1.7-3) UNRELEASED; urgency=medium
+fasttree (2.1.8-1) UNRELEASED; urgency=medium
 
+  [ Andreas Tille ]
   * Move debian/upstream to debian/upstream/metadata
   * cme fix dpkg-control
   * Priority: optional
   * d/rules: cleanup from cruft
 
- -- Andreas Tille <tille at debian.org>  Fri, 27 Mar 2015 13:34:20 +0100
+  [ Roland Fehrenbacher ]
+  * New upstream version 2.1.8
+  * Makes debian/patches/increase-branch-length-precision.patch obsolete
+
+ -- Roland Fehrenbacher <rf at q-leap.de>  Tue, 31 Mar 2015 10:54:39 +0000
 
 fasttree (2.1.7-2) unstable; urgency=low
 
diff --git a/debian/patches/increase-branch-length-precision.patch b/debian/patches/increase-branch-length-precision.patch
deleted file mode 100644
index 751447e..0000000
--- a/debian/patches/increase-branch-length-precision.patch
+++ /dev/null
@@ -1,65 +0,0 @@
-From 66d0f73b44065272ddefc71870156d35aad4df64 Mon Sep 17 00:00:00 2001
-From: Roland Fehrenbacher <rf at q-leap.de>
-Date: Tue, 24 Mar 2015 18:21:03 +0000
-Subject: [PATCH] Use double precision and increase branch length precision
-
-This is absolutely crucial to prevent flawed data analysis as
-described e.g. in
-http://darlinglab.org/blog/2015/03/23/not-so-fast-fasttree.html
----
- fasttree.c | 19 ++++++++++++++-----
- 1 file changed, 14 insertions(+), 5 deletions(-)
-
-diff --git a/fasttree.c b/fasttree.c
-index 12862e2..a8426ab 100644
---- a/fasttree.c
-+++ b/fasttree.c
-@@ -1,4 +1,10 @@
- /*
-+ * 2014/12/11 - Modifications to raise the precision of branch length
-+ *              estimation. This should accompany setting USE_DOUBLE.
-+ *              Search tolerances have been decreased to 1e-9 from 
-+ *              their original 1e-4.
-+ *
-+ * 
-  * FastTree -- inferring approximately-maximum-likelihood trees for large
-  * multiple sequence alignments.
-  *
-@@ -852,10 +858,13 @@ const double Log2 = 0.693147180559945;
-    were increased to prevent numerical problems in rare cases.
-    If compiled with -DUSE_DOUBLE then these minimums could be decreased.
- */
--const double MLMinBranchLengthTolerance = 1.0e-4; /* absolute tolerance for optimizing branch lengths */
-+const double MLMinBranchLengthTolerance = 1.0e-9; /* absolute tolerance for optimizing branch lengths */
- const double MLFTolBranchLength = 0.001; /* fractional tolerance for optimizing branch lengths */
--const double MLMinBranchLength = 5.0e-4;
--const double MLMinRelBranchLength = 2.5e-4; /* minimum of rate * length */
-+const double MLMinBranchLength = 5.0e-9;
-+const double MLMinRelBranchLength = 2.5e-9; /* minimum of rate * length */
-+
-+const double fPostTotalTolerance = 1.0e-20; /* mzd 2015/01/06, added as original assertion is violated when 
-+	                                           MLMMinBranchLengthTolerance is decreased to 1e-9. */
- 
- int mlAccuracy = 1;		/* Rounds of optimization of branch lengths; 1 means do 2nd round only if close */
- double closeLogLkLimit = 5.0;	/* If partial optimization of an NNI looks like it would decrease the log likelihood
-@@ -4962,7 +4971,7 @@ profile_t *PosteriorProfile(profile_t *p1, profile_t *p2,
-       double fPostTot = 0;
-       for (j = 0; j < 4; j++)
- 	fPostTot += fPost[j];
--      assert(fPostTot > 1e-10);
-+      assert(fPostTot > fPostTotalTolerance);
-       double fPostInv = 1.0/fPostTot;
- #if 0 /* SSE3 is slower */
-       vector_multiply_by(fPost, fPostInv, 4);
-@@ -5025,7 +5034,7 @@ profile_t *PosteriorProfile(profile_t *p1, profile_t *p2,
- 	fPost[j] = value >= 0 ? value : 0;
-       }
-       double fPostTot = vector_sum(fPost, 20);
--      assert(fPostTot > 1e-10);
-+      assert(fPostTot > fPostTotalTolerance);
-       double fPostInv = 1.0/fPostTot;
-       vector_multiply_by(/*IN/OUT*/fPost, fPostInv, 20);
-       int ch = -1;		/* the dominant character, if any */
--- 
-2.1.4
-
diff --git a/debian/patches/series b/debian/patches/series
index a317da9..5b1c0a4 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1 @@
 Makefile.patch
-increase-branch-length-precision.patch

-- 
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