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commit 5c511662a89faf1420067bf1d2c04e07101a74a8 Author: Roland Fehrenbacher <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> -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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/fasttree.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
