sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch


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Fixes missing tinythread.cpp when using TBB:

ebwt_search.cpp:(.text+0x91bb): undefined reference to `tthread::thread::join()'

--- bowtie-1.1.2/Makefile
+++ bowtie-1.1.2/Makefile
@@ -106,10 +106,7 @@
 endif
 
 OTHER_CPPS = ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp \
-             edit.cpp ebwt.cpp
-ifneq (1,$(WITH_TBB))
-	OTHER_CPPS += tinythread.cpp
-endif
+             edit.cpp ebwt.cpp tinythread.cpp
 
 SEARCH_CPPS = qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp \
               log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp \