[med-svn] [plink1.9] 03/03: Update d/*

[Dylan Aïssi]

This is an automated email from the git hooks/post-receive script.

bob.dybian-guest pushed a commit to branch master
in repository plink1.9.

commit f0f0fe89ce231ebd4dd4dcfddc9fc8c7b1babbeb
Author: Dylan Aïssi <bob.dybian at gmail.com>
Date:   Fri Nov 3 00:02:03 2017 +0100

    Update d/*
---
 debian/changelog                        | 10 +++++++++-
 debian/control                          |  2 +-
 debian/patches/01.Fix_Makefile.patch    |  8 +++-----
 debian/upstream.docs/upstream.changelog | 11 ++++++++++-
 4 files changed, 23 insertions(+), 8 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 40edc7b..d6d2e39 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,11 @@
+plink1.9 (1.90~b4.9-171013-1) UNRELEASED; urgency=medium
+
+  * New upstream release.
+  * Bump Standards-Version: 4.1.1 (no changes needed).
+  * Remove trailing whitespace characters in d/changelog.
+
+ -- Dylan Aïssi <bob.dybian at gmail.com>  Thu, 02 Nov 2017 23:54:39 +0100
+
 plink1.9 (1.90~b4.7-170906-1) unstable; urgency=medium
 
   * New upstream release.
@@ -137,7 +145,7 @@ plink (1.07-2) unstable; urgency=low
   * debian/source/format: 3.0 (quilt)
   * debian/get-orig-source: Better chances to get a unique upstream
     tarball after repackaging
-  * debian/copyright: 
+  * debian/copyright:
     - Rewritten to match DEP5 and verified using
        cme fix dpkg-copyright
     - Fix FSF address
diff --git a/debian/control b/debian/control
index 3ffc86f..45733c6 100644
--- a/debian/control
+++ b/debian/control
@@ -8,7 +8,7 @@ Build-Depends: debhelper (>= 10),
                libatlas-base-dev,
                liblapack-dev,
                zlib1g-dev
-Standards-Version: 4.1.0
+Standards-Version: 4.1.1
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/plink1.9.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/plink1.9.git
 Homepage: https://www.cog-genomics.org/plink/1.9/
diff --git a/debian/patches/01.Fix_Makefile.patch b/debian/patches/01.Fix_Makefile.patch
index 6e7b9b8..88e6701 100644
--- a/debian/patches/01.Fix_Makefile.patch
+++ b/debian/patches/01.Fix_Makefile.patch
@@ -3,11 +3,9 @@ Description: Take into account the user-provided CPPFLAGS compiler flags.
 Last-Update: 2017-09-12
 Forwarded: TODO
 
-Index: plink1.9/Makefile
-===================================================================
---- plink1.9.orig/Makefile
-+++ plink1.9/Makefile
-@@ -96,7 +96,7 @@ clean:
+--- a/Makefile
++++ b/Makefile
+@@ -96,7 +96,7 @@
  # includes a C++ header and exposed functions will need to be declared with
  # extern "C".
  %.o: %.c
diff --git a/debian/upstream.docs/upstream.changelog b/debian/upstream.docs/upstream.changelog
index 3c1f534..3504eb3 100644
--- a/debian/upstream.docs/upstream.changelog
+++ b/debian/upstream.docs/upstream.changelog
@@ -1,6 +1,15 @@
 # Copy/Paste from https://www.cog-genomics.org/plink/1.9/
 
-15 Aug 2017: --lasso should now work properly when there are samples with all covariates present but the main phenotype missing.
+15 Oct 2017: A2 allele is now consistently reference on chr3 in our 1000 Genomes phase 1 downloads. As a general rule, you shouldn't expect to keep REF/ALT alleles straight with PLINK 1.x, but we tried to make A2 consistently reference in these files and still didn't quite succeed; sorry about that.
+(Why was this discovered now, more than 2.5 years after the fact? Because PLINK 2.0 now has a --ref-from-fa flag which can easily check for this type of error.)
+
+13 Oct: "--freq counts" no longer gives reversed results when alleles have been flipped from the initial .bim/.bed order. Fixed --logistic bug that could cause spurious NA results.
+
+12 Oct: --snps/--exclude-snps no longer always includes other variants at the same positions as the variant(s) you named.
+
+7 Oct: Fixed corner-case (two of the four haplotypes have no known observations) bug in --ld/--r2/--blocks/--clump's statistical phasing procedure. 32-bit build can now sort >2GB .bed files without crashing. --annotate and --gene-report now work with --allow-extra-chr.
+
+15 Aug: --lasso should now work properly when there are samples with all covariates present but the main phenotype missing.
 
 25 Jul: --lfile now works properly when the .map file has three columns.
 

-- 
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