diff -ur bfast-0.7.0a/bfast/Makefile.am bfast-0.7.0a.new/bfast/Makefile.am
--- bfast-0.7.0a/bfast/Makefile.am 2011-10-29 20:31:58.000000000 +0100
+++ bfast-0.7.0a.new/bfast/Makefile.am 2014-06-07 09:41:28.877188021 +0100
@@ -41,4 +41,4 @@
aflib.c aflib.h \
Main.c Main.h
-bfast_LDADD =
+bfast_LDADD = -lpthread
diff -ur bfast-0.7.0a/bfast/Makefile.in bfast-0.7.0a.new/bfast/Makefile.in
--- bfast-0.7.0a/bfast/Makefile.in 2011-10-29 20:32:58.000000000 +0100
+++ bfast-0.7.0a.new/bfast/Makefile.in 2014-06-07 09:42:05.084587000 +0100
@@ -100,7 +100,7 @@
INSTALL_PROGRAM = @INSTALL_PROGRAM@
INSTALL_SCRIPT = @INSTALL_SCRIPT@
INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-LDFLAGS = @LDFLAGS@
+LDFLAGS = @LDFLAGS@ -lpthread
LIBOBJS = @LIBOBJS@
LIBS = @LIBS@
LTLIBOBJS = @LTLIBOBJS@
@@ -204,7 +204,7 @@
aflib.c aflib.h \
Main.c Main.h
-bfast_LDADD =
+bfast_LDADD = -lpthread
all: all-am
.SUFFIXES:
diff -ur bfast-0.7.0a/butil/Makefile.am bfast-0.7.0a.new/butil/Makefile.am
--- bfast-0.7.0a/butil/Makefile.am 2010-11-13 07:15:28.000000000 +0000
+++ bfast-0.7.0a.new/butil/Makefile.am 2014-06-07 10:05:03.951552114 +0100
@@ -21,7 +21,7 @@
../bfast/AlignedEntry.c ../bfast/AlignedEntry.h \
balignmentscoredistribution.c balignmentscoredistribution.h
-balignmentscoredistribution_LDADD =
+balignmentscoredistribution_LDADD = -lpthread
balignsim_SOURCES = \
SimRead.c SimRead.h \
@@ -45,7 +45,7 @@
../bfast/AlignMatrix.c ../bfast/AlignMatrix.h \
balignsim.c balignsim.h
-balignsim_LDADD =
+balignsim_LDADD = -lpthread
bevalsim_SOURCES = \
../bfast/BError.c ../bfast/BError.h \
@@ -61,7 +61,7 @@
../bfast/AlignedEntry.c ../bfast/AlignedEntry.h \
bevalsim.c bevalsim.h
-bevalsim_LDADD =
+bevalsim_LDADD = -lpthread
bgeneratereads_SOURCES = \
../bfast/BError.c ../bfast/BError.h \
@@ -74,7 +74,7 @@
SimRead.c SimRead.h \
bgeneratereads.c bgeneratereads.h
-bgeneratereads_LDADD =
+bgeneratereads_LDADD = -lpthread
bindexdist_SOURCES = \
../bfast/BError.c ../bfast/BError.h \
@@ -87,7 +87,7 @@
../bfast/RGReads.c ../bfast/RGReads.h \
bindexdist.c bindexdist.h
-bindexdist_LDADD =
+bindexdist_LDADD = -lpthread
bindexhist_SOURCES = \
../bfast/BError.c ../bfast/BError.h \
@@ -100,7 +100,7 @@
../bfast/RGReads.c ../bfast/RGReads.h \
bindexhist.c bindexhist.h
-bindexhist_LDADD =
+bindexhist_LDADD = -lpthread
bmfmerge_SOURCES = \
../bfast/BError.c ../bfast/BError.h \
@@ -116,7 +116,7 @@
../bfast/aflib.c ../bfast/aflib.h \
bmfmerge.c
-bmfmerge_LDADD =
+bmfmerge_LDADD = -lpthread
brepeat_SOURCES = \
../bfast/BError.c ../bfast/BError.h \
@@ -128,7 +128,7 @@
../bfast/RGRanges.c ../bfast/RGRanges.h \
brepeat.c brepeat.h
-brepeat_LDADD =
+brepeat_LDADD = -lpthread
btestindexes_SOURCES = \
../bfast/RGMatch.c ../bfast/RGMatch.h \
@@ -140,4 +140,4 @@
../bfast/BLib.c ../bfast/BLib.h \
btestindexes.c btestindexes.h
-btestindexes_LDADD =
+btestindexes_LDADD = -lpthread
diff -ur bfast-0.7.0a/butil/Makefile.in bfast-0.7.0a.new/butil/Makefile.in
--- bfast-0.7.0a/butil/Makefile.in 2011-10-29 20:32:58.000000000 +0100
+++ bfast-0.7.0a.new/butil/Makefile.in 2014-06-07 09:37:32.296978731 +0100
@@ -170,7 +170,7 @@
INSTALL_PROGRAM = @INSTALL_PROGRAM@
INSTALL_SCRIPT = @INSTALL_SCRIPT@
INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-LDFLAGS = @LDFLAGS@
+LDFLAGS = @LDFLAGS@ -lpthread
LIBOBJS = @LIBOBJS@
LIBS = @LIBS@
LTLIBOBJS = @LTLIBOBJS@
diff -ur bfast-0.7.0a/scripts/Makefile.am bfast-0.7.0a.new/scripts/Makefile.am
--- bfast-0.7.0a/scripts/Makefile.am 2010-11-13 07:15:28.000000000 +0000
+++ bfast-0.7.0a.new/scripts/Makefile.am 2014-06-07 10:10:58.904244848 +0100
@@ -10,6 +10,6 @@
../bfast/aflib.c ../bfast/aflib.h \
solid2fastq.c
-solid2fastq_LDADD =
+solid2fastq_LDADD = -lpthread
dist_bin_SCRIPTS = bfast.resubmit.pl bfast.submit.pl ill2fastq.pl
diff -ur bfast-0.7.0a/scripts/Makefile.in bfast-0.7.0a.new/scripts/Makefile.in
--- bfast-0.7.0a/scripts/Makefile.in 2011-10-29 20:32:58.000000000 +0100
+++ bfast-0.7.0a.new/scripts/Makefile.in 2014-06-07 09:36:49.767986215 +0100
@@ -93,7 +93,7 @@
INSTALL_PROGRAM = @INSTALL_PROGRAM@
INSTALL_SCRIPT = @INSTALL_SCRIPT@
INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-LDFLAGS = @LDFLAGS@
+LDFLAGS = @LDFLAGS@ -lpthread
LIBOBJS = @LIBOBJS@
LIBS = @LIBS@
LTLIBOBJS = @LTLIBOBJS@
diff -ur bfast-0.7.0a/tests/Makefile.in bfast-0.7.0a.new/tests/Makefile.in
--- bfast-0.7.0a/tests/Makefile.in 2011-10-29 20:32:58.000000000 +0100
+++ bfast-0.7.0a.new/tests/Makefile.in 2014-06-07 09:42:37.481628272 +0100
@@ -72,7 +72,7 @@
INSTALL_PROGRAM = @INSTALL_PROGRAM@
INSTALL_SCRIPT = @INSTALL_SCRIPT@
INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-LDFLAGS = @LDFLAGS@
+LDFLAGS = @LDFLAGS@ -lpthread
LIBOBJS = @LIBOBJS@
LIBS = @LIBS@
LTLIBOBJS = @LTLIBOBJS@