[med-svn] [eagle] 03/06: Update changelogs

[Dylan Aïssi]

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

commit ee7d31ba9bae2b3d0cb87d085a1fc8fb9c22e349
Author: Dylan Aïssi <bob.dybian at gmail.com>
Date:   Fri Jan 12 22:58:29 2018 +0100

    Update changelogs
---
 debian/changelog          | 5 +++--
 debian/upstream.changelog | 9 +++++++++
 2 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 51abf0d..3b43b92 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,8 +1,9 @@
-bio-eagle (2.3.5-2) UNRELEASED; urgency=medium
+bio-eagle (2.4-1) UNRELEASED; urgency=medium
 
+  * New upstream release.
   * Restrict building architecture to x86, upstream supports only x86 arch.
 
- -- Dylan Aïssi <bob.dybian at gmail.com>  Sun, 05 Nov 2017 15:16:38 +0100
+ -- Dylan Aïssi <bob.dybian at gmail.com>  Fri, 12 Jan 2018 22:57:01 +0100
 
 bio-eagle (2.3.5-1) unstable; urgency=medium
 
diff --git a/debian/upstream.changelog b/debian/upstream.changelog
index 3559dac..98bdaca 100644
--- a/debian/upstream.changelog
+++ b/debian/upstream.changelog
@@ -1,5 +1,14 @@
 # Copy/Paste from https://data.broadinstitute.org/alkesgroup/Eagle/
 
+Version 2.4 (December 13, 2017):
+    Fixed bug that had allowed target/ref allele flips: allele-matching was only being checked when --allowRefAltSwap was specified. Also enforced requirement that --allowRefAltSwap only apply to SNPs (not indels).
+    Fixed bug causing a stack overflow for samples with very large numbers of missing genotypes (thanks to Laurent Francioli).
+    Added --pbwtOnly option that skips non-PBWT iterations in non-reference mode (automatically set when N>200K).
+    Added --keepMissingPloidyX option that keeps ploidy of missing VCF genotypes ('.' or './.') in chrX. (Because missing genotypes sometimes have incorrectly-coded ploidy, Eagle tries to guess the right ploidy by default.)
+    Added --vcfExclude option for ignoring a list of variants when phasing in ref-mode.
+    Allowed ‘chr’ prefixes in VCF chromosome names (to support hg38).
+    Improved error-checking of genetic maps.
+    Suppressed warnings about individuals with low heterozygosity when phasing chrX.
 Version 2.3.5 (August 2, 2017): Fixed minor bug causing Eagle to erroneously terminate with failed assertion in rare cases.
 Version 2.3.4 (June 5, 2017): Fixed bug causing incorrect imputation of missing genotypes prior to the first heterozygous site in each sample.
 Version 2.3.3 (May 25, 2017):

-- 
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