[med-svn] [salmon] 01/02: add patch again

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository salmon.

commit cf2b88835e462879e446277c4429d9f1fdb3f16c
Author: Sascha Steinbiss <satta at debian.org>
Date:   Wed Sep 7 15:32:01 2016 +0000

    add patch again
---
 debian/patches/add_MEM_F_SELF_OVLP.patch | 23 +++++++++++++++++++++++
 debian/patches/series                    |  1 +
 2 files changed, 24 insertions(+)

diff --git a/debian/patches/add_MEM_F_SELF_OVLP.patch b/debian/patches/add_MEM_F_SELF_OVLP.patch
new file mode 100644
index 0000000..40dd0b7
--- /dev/null
+++ b/debian/patches/add_MEM_F_SELF_OVLP.patch
@@ -0,0 +1,23 @@
+Description: redefine MEM_F_SELF_OVLP
+ libbwa upstream has dropped MEM_F_SELF_OVLP in their commit 
+ 1247dc234668c1d7357fa6343222e9b5730e832d. This patch re-introduces this
+ definition to fix an FTBFS.
+Author: Sascha Steinbiss <sascha at steinbiss.name>
+--- a/src/SalmonQuantify.cpp
++++ b/src/SalmonQuantify.cpp
+@@ -56,6 +56,7 @@
+ #include "ksort.h"
+ #include "kvec.h"
+ #include "utils.h"
++#define MEM_F_SELF_OVLP 0x40
+ }
+ 
+ // Jellyfish 2 include
+@@ -125,6 +126,7 @@
+ #include "SalmonOpts.hpp"
+ //#include "TextBootstrapWriter.hpp"
+ 
++
+ /****** QUASI MAPPING DECLARATIONS *********/
+ using MateStatus = rapmap::utils::MateStatus;
+ using QuasiAlignment = rapmap::utils::QuasiAlignment;
diff --git a/debian/patches/series b/debian/patches/series
index f665fe7..c519d7b 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -6,3 +6,4 @@ use-system-pkg-config-tbb
 0008-Remove-salmon_core-lib.patch
 0009-Remove-FIND_PACKAGE-for-liblzma-and-libbz2.patch
 use_debian_packaged_rapmap.patch
+add_MEM_F_SELF_OVLP.patch

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