Bowtie is using outdated copy of gcc header file
Hi,
I realised that bowtie (verisons 1 and 2) are using an outdated copy of
the gcc internal header file cpuid.h. This seems to be originated from
amd64 architecture and results in the fact that bowtie fails to build on
other architectures. Debian tries to provide its packaged software on
several architectures and with the advent of amd64 there might be
applications also for non-amd64 architectures to take over sequencing
tasks.
I tried to build bowtie 1.0.1 with the following patch
--- a/Makefile
+++ b/Makefile
@@ -4,7 +4,7 @@
SEQAN_DIR = /usr/include/seqan
SEQAN_INC = -I $(SEQAN_DIR)
-INC = $(SEQAN_INC) -I third_party
+INC = $(SEQAN_INC)
CPP = g++
CXX = $(CPP)
CC = gcc
which compiled successfully. I wonder about your motivations to ship an
old copy of cpuid.h which in turn might mean that you are loosing
enhancements of newer gcc versions even on amd64. Did you applied any
specific patch in this header file and did you compared the result with
an up to date cpuid.h from gcc-4.9? Could you imagine that the patch
above has any negative effect on bowtie?
BTW, it would help if you would create some unit tests (possibly based
on the example indexes you are providing). This would help verifying
whether the code works as expected.
Kind regards and thanks for providing bowtie as free software
Andreas.
--
http://fam-tille.de
Reply to: