debian/changelog

+bio-eagle (2.4.1-1) UNRELEASED; urgency=medium
+
+  * New upstream release.
+  * Update my email address.
+
+ -- Dylan Aïssi <daissi@debian.org>  Sat, 24 Nov 2018 14:57:37 +0100
+
 bio-eagle (2.4-2) unstable; urgency=medium
 
   * Team upload

debian/control

 Source: bio-eagle
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
-Uploaders: Dylan Aïssi <bob.dybian@gmail.com>
+Uploaders: Dylan Aïssi <daissi@debian.org>
 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 11),

debian/patches/Makefile_config.patch

@@ -5,27 +5,34 @@ Forwarded: not-needed
 
 --- a/src/Makefile
 +++ b/src/Makefile
-@@ -5,14 +5,14 @@
+@@ -9,20 +9,20 @@
  
  ### modify these paths to local BLAS, Boost and htslib install directories
  LBLAS = -lopenblas # alternatively -llapack (just need sgemm_)
--BLAS_DIR = /opt/openblas/0.2.14/lib
--BOOST_INSTALL_DIR = /home/pl88/boost_1_58_0/install
--HTSLIB_DIR = /groups/price/poru/external_software/htslib/htslib-1.4
+-BLAS_DIR = /n/app/openblas/0.2.19/lib # or /n/groups/price/poru/external_software/openblas/0.2.14/lib (copied from Orchestra /opt/openblas/0.2.14/lib)
 +BLAS_DIR =
+ 
+-BOOST_INSTALL_DIR = /home/pl88/boost_1_58_0/install
 +BOOST_INSTALL_DIR =
+ # boost_1_58_0 was installed using GCC 4.8.5?
+ 
+-HTSLIB_DIR = /n/groups/price/poru/external_software/htslib/htslib-1.9
 +HTSLIB_DIR =
  ### NOTE: to reduce dependencies from htslib, configure htslib with: ./configure --disable-bz2 --disable-lzma --disable-plugins --disable-libcurl --disable-gcs --disable-s3
  
- ### these paths are used only for static linking
--ZLIB_STATIC_DIR = /opt/zlib-1.2.8/lib # probably unnecessary on most systems
+ ### only for static linking (unnecessary in a local install; probably unnecessary on most systems)
+-ZLIB_STATIC_DIR = /n/groups/price/poru/external_software/zlib/zlib-1.2.11
+-LIBSTDCXX_STATIC_DIR = /n/groups/price/poru/external_software/libstdc++/usr/lib/gcc/x86_64-redhat-linux/4.8.5/
++ZLIB_STATIC_DIR =
++LIBSTDCXX_STATIC_DIR =
+ 
+ ### only for linking=static, which is discouraged
 -GLIBC_STATIC_DIR = /home/pl88/glibc-static/usr/lib64
-+ZLIB_STATIC_DIR = # probably unnecessary on most systems
 +GLIBC_STATIC_DIR =
  
  
  ifeq ($(strip ${linking}),)
-@@ -31,7 +31,7 @@
+@@ -41,7 +41,7 @@
  	LFLAGS += -pg
  endif
  
@@ -34,7 +41,7 @@ Forwarded: not-needed
  LFLAGS += -fopenmp
  
  
-@@ -93,10 +93,10 @@
+@@ -102,10 +102,10 @@
  .PHONY: clean
  
  $T: ${OMAIN}

debian/upstream.changelog

 # Copy/Paste from https://data.broadinstitute.org/alkesgroup/Eagle/
 
+Version 2.4.1 (November 18, 2018):
+    Allowed --noImpMissing whenever input is provided in VCF format. (Previously, --noImpMissing was only allowed in reference mode when using 1 PBWT iteration.)
+    Fixed bug causing --bpStart and --bpEnd to be ignored when --chrom was not specified. (Now --chrom is required with --bpStart/--bpEnd.)
+    Added support for multithreaded HTSlib I/O (thanks to David Heise).
+    Improved error-checking.
 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).