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commit 25e97fe269225fb739af124be8e16e11c1c7460d
Author: Alexandre Mestiashvili <a...@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 <a...@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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