[med-svn] [salmon] 01/01: fix FTBFS (#818397)

[Sascha Steinbiss]

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sascha-guest pushed a commit to branch master
in repository salmon.

commit 20d755ab4a9be989dc5c77938699f6bc48c5edee
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Tue Apr 5 21:30:10 2016 +0000

    fix FTBFS (#818397)
---
 debian/changelog                         |  8 ++++++++
 debian/patches/add_MEM_F_SELF_OVLP.patch | 15 +++++++++++++++
 debian/patches/series                    |  1 +
 3 files changed, 24 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 24f9d14..322f2d4 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,11 @@
+salmon (0.4.2+ds1-3) unstable; urgency=medium
+
+  * Team upload.
+  * Re-introduce bitmask for MEM_F_SELF_OVLP dropped by libbwa upstream.
+    Closes: #818397
+
+ -- Sascha Steinbiss <sascha at steinbiss.name>  Tue, 05 Apr 2016 21:20:56 +0000
+
 salmon (0.4.2+ds1-2) unstable; urgency=medium
 
   * Make build reproducible.
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..320fc13
--- /dev/null
+++ b/debian/patches/add_MEM_F_SELF_OVLP.patch
@@ -0,0 +1,15 @@
+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
+@@ -131,6 +131,7 @@
+ /******* STUFF THAT IS STATIC IN BWAMEM THAT WE NEED HERE --- Just re-define it *************/
+ #define intv_lt(a, b) ((a).info < (b).info)
+ KSORT_INIT(mem_intv, bwtintv_t, intv_lt)
++#define MEM_F_SELF_OVLP 0x40 
+ 
+ typedef struct {
+     bwtintv_v mem, mem1, *tmpv[2];
diff --git a/debian/patches/series b/debian/patches/series
index 94988cd..c4872e9 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -9,3 +9,4 @@ use-system-pkg-config-tbb
 0008-Remove-salmon_core-lib.patch
 0009-Remove-FIND_PACKAGE-for-liblzma-and-libbz2.patch
 reproducible-build
+add_MEM_F_SELF_OVLP.patch

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