[med-svn] [subread] 09/10: Update arch_specific_flags patch, fix Makefile for sublong

[Alex Mestiashvili]

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malex-guest pushed a commit to branch master
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commit 25e97fe269225fb739af124be8e16e11c1c7460d
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Fri Nov 17 16:30:57 2017 +0100

    Update arch_specific_flags patch, fix Makefile for sublong
---
 debian/patches/arch_specific_flags.patch | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/debian/patches/arch_specific_flags.patch b/debian/patches/arch_specific_flags.patch
index 484b5b4..a7e6dc2 100644
--- a/debian/patches/arch_specific_flags.patch
+++ b/debian/patches/arch_specific_flags.patch
@@ -23,3 +23,19 @@ Author: Alex Mestiashvili <alex at biotec.tu-dresden.de>
  
  
  ALL_LIBS= core core-junction core-indel sambam-file sublog gene-algorithms hashtable input-files sorted-hashtable gene-value-index exon-algorithms HelperFunctions interval_merge long-hashtable core-bigtable seek-zlib
+--- subread.orig/src/longread-mapping/Makefile
++++ subread/src/longread-mapping/Makefile
+@@ -2,10 +2,10 @@
+ include make.version
+ 
+ OPT_LEVEL = 3
+-CCFLAGS = -mtune=core2 ${MACOS} -O${OPT_LEVEL} -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE  -D_FILE_OFFSET_BITS=64 -D SUBREAD_VERSION=\"${SUBREAD_VERSION}\"
+-LDFLAGS =  -lpthread -lz -lm -O${OPT_LEVEL} -DMAKE_FOR_EXON -D MAKE_STANDALONE # -DREPORT_ALL_THE_BEST
++CCFLAGS += -O${OPT_LEVEL} -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE  -D_FILE_OFFSET_BITS=64 -D SUBREAD_VERSION=\"${SUBREAD_VERSION}\"
++LDFLAGS +=  -lpthread -lz -lm -O${OPT_LEVEL} -DMAKE_FOR_EXON -D MAKE_STANDALONE # -DREPORT_ALL_THE_BEST
+ CC_EXEC = gcc
+-CC = ${CC_EXEC}  ${CCFLAGS}  -fmessage-length=0  -ggdb
++CC = ${CC_EXEC} ${CFLAGS} ${CPPFLAGS} ${CCFLAGS} -fmessage-length=0  -ggdb
+ 
+ ALL_LIBS=LRMsorted-hashtable LRMbase-index LRMchro-event LRMhelper seek-zlib LRMfile-io hashtable
+ 

-- 
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