[med-svn] [kmer-tools] 04/07: Update patches to apply cleanly to new upstream SVN "release"

[Afif Elghraoui]

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afif-guest pushed a commit to branch master
in repository kmer-tools.

commit 536e4522d7fd21eeca1dcb8ba38df76c424758a6
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Thu May 21 23:27:30 2015 -0700

    Update patches to apply cleanly to new upstream SVN "release"
---
 debian/patches/kazlib.patch        |  4 ++--
 debian/patches/remove-kazlib.patch | 17 +++++++++++++++--
 2 files changed, 17 insertions(+), 4 deletions(-)

diff --git a/debian/patches/kazlib.patch b/debian/patches/kazlib.patch
index 6ca94a0..5815136 100644
--- a/debian/patches/kazlib.patch
+++ b/debian/patches/kazlib.patch
@@ -23,8 +23,8 @@
 +++ kmer-tools/configure.sh
 @@ -369,8 +369,8 @@
  CXXLD             := \${CXX}
- CCDEP		  := gcc -MM -MG
- CXXDEP	          := g++ -MM -MG
+ CCDEP             := \${CC} -MM -MG
+ CXXDEP	          := \${CXX} -MM -MG
 -CLIBS             += -lm -lbz2
 -CXXLIBS           += -lm -lbz2
 +CLIBS             += -lm -lbz2 -lkaz
diff --git a/debian/patches/remove-kazlib.patch b/debian/patches/remove-kazlib.patch
index 62a6a1f..060812e 100644
--- a/debian/patches/remove-kazlib.patch
+++ b/debian/patches/remove-kazlib.patch
@@ -2,8 +2,8 @@
 +++ kmer-tools/configure.sh
 @@ -369,8 +369,8 @@
  CXXLD             := \${CXX}
- CCDEP		  := gcc -MM -MG
- CXXDEP	          := g++ -MM -MG
+ CCDEP             := \${CC} -MM -MG
+ CXXDEP	          := \${CXX} -MM -MG
 -CLIBS             += -lm -lbz2 -lkaz
 -CXXLIBS           += -lm -lbz2 -lkaz
 +CLIBS             += -lm -lbz2
@@ -11,3 +11,16 @@
  PYTHON            := $PYTHON
  PYTHON_H          := $CFLAGS_PYTHON/Python.h
  CFLAGS_PYTHON     := -I$CFLAGS_PYTHON
+--- kmer-tools.orig/libutil/Make.include
++++ kmer-tools/libutil/Make.include
+@@ -2,9 +2,7 @@
+ 
+ $(eval $(call Include,$/mt19937ar/))
+ 
+-src    := $/bigQueue.C \
+-          $/bigQueue.H \
+-          $/bitOperations.h \
++src    := $/bitOperations.h \
+           $/bitPackedArray.C \
+           $/bitPackedArray.H \
+           $/bitPackedFile.C \

-- 
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