[med-svn] [libseqlib] 01/03: fermi-light includes are in subdir fml

[Andreas Tille]

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tille pushed a commit to branch master
in repository libseqlib.

commit 714642f3c29a21f8db1c4b6b3c5138728cd64579
Author: Andreas Tille <tille at debian.org>
Date:   Fri Feb 3 15:32:41 2017 +0100

    fermi-light includes are in subdir fml
---
 debian/changelog                      | 13 -------------
 debian/patches/fml_include_path.patch | 15 +++++++++++++++
 2 files changed, 15 insertions(+), 13 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 89ddcf9..67bc496 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,18 +1,5 @@
 libseqlib (1.1.1-1) UNRELEASED; urgency=medium
 
   * Initial release (Closes: #???)
-  TODO:
-g++ -DHAVE_CONFIG_H -I. -I..  -I../ -I/usr/include/fml -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/build/libseqlib-1.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libseqlib_a-RefGenome.o `test -f 'RefGenome.cpp' || echo './'`RefGenome.cpp
-g++ -DHAVE_CONFIG_H -I. -I..  -I../ -I/usr/include/fml -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/build/libseqlib-1.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libseqlib_a-BamWriter.o `test -f 'BamWriter.cpp' || echo './'`BamWriter.cpp
-In file included from ../SeqLib/BamWalker.h:15:0,
-                 from BamWriter.cpp:1:
-../htslib/cram/cram.h:45:32: fatal error: cram/cram_samtools.h: No such file or directory
- #include "cram/cram_samtools.h"
-                                ^
-compilation terminated.
-Makefile:518: recipe for target 'libseqlib_a-BamWriter.o' failed
-make[4]: *** [libseqlib_a-BamWriter.o] Error 1
-make[4]: *** Waiting for unfinished jobs....
-
 
  -- Andreas Tille <tille at debian.org>  Fri, 27 Jan 2017 13:18:48 +0100
diff --git a/debian/patches/fml_include_path.patch b/debian/patches/fml_include_path.patch
index fe0a500..1116aa5 100644
--- a/debian/patches/fml_include_path.patch
+++ b/debian/patches/fml_include_path.patch
@@ -31,3 +31,18 @@ Description: Make sure header files will be found in /usr/include/fml
  
  libseqlib_a_SOURCES =   FastqReader.cpp BFC.cpp ReadFilter.cpp SeqPlot.cpp jsoncpp.cpp ssw_cpp.cpp ssw.c \
  			GenomicRegion.cpp RefGenome.cpp BamWriter.cpp BamReader.cpp \
+--- a/SeqLib/FermiAssembler.h
++++ b/SeqLib/FermiAssembler.h
+@@ -9,9 +9,9 @@
+ 
+ extern "C" 
+ {
+-#include "fermi-lite/htab.h"
+-#include "fermi-lite/fml.h"
+-#include "fermi-lite/bfc.h"
++#include <fml/htab.h>
++#include <fml.h>
++#include <fml/bfc.h>
+ }
+ 
+ namespace SeqLib {

-- 
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