fixed coveralls

Author: walaj

.travis.scripts/coveralls.sh

@@ -19,7 +19,7 @@ then
     ## download the test data
     mkdir test_data
     cd test_data
-    wget -r -nH -nd -np -R index.html* https://data.broadinstitute.org/snowman/SeqLibTest/
+    wget -r -nH -nd -np -R index.html* https://data.broadinstitute.org/snowman/SeqLib/
     cd ..
 
     export LD_LIBRARY_PATH=${BOOST_ROOT}/lib:${LD_LIBRARY_PATH}

Makefile.in

@@ -285,7 +285,6 @@ pdfdir = @pdfdir@
 prefix = @prefix@
 program_transform_name = @program_transform_name@
 psdir = @psdir@
-runstatedir = @runstatedir@
 sbindir = @sbindir@
 sharedstatedir = @sharedstatedir@
 srcdir = @srcdir@

configure

@@ -703,7 +703,6 @@ infodir
 docdir
 oldincludedir
 includedir
-runstatedir
 localstatedir
 sharedstatedir
 sysconfdir
@@ -781,7 +780,6 @@ datadir='${datarootdir}'
 sysconfdir='${prefix}/etc'
 sharedstatedir='${prefix}/com'
 localstatedir='${prefix}/var'
-runstatedir='${localstatedir}/run'
 includedir='${prefix}/include'
 oldincludedir='/usr/include'
 docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
@@ -1034,15 +1032,6 @@ do
   | -silent | --silent | --silen | --sile | --sil)
     silent=yes ;;
 
-  -runstatedir | --runstatedir | --runstatedi | --runstated \
-  | --runstate | --runstat | --runsta | --runst | --runs \
-  | --run | --ru | --r)
-    ac_prev=runstatedir ;;
-  -runstatedir=* | --runstatedir=* | --runstatedi=* | --runstated=* \
-  | --runstate=* | --runstat=* | --runsta=* | --runst=* | --runs=* \
-  | --run=* | --ru=* | --r=*)
-    runstatedir=$ac_optarg ;;
-
   -sbindir | --sbindir | --sbindi | --sbind | --sbin | --sbi | --sb)
     ac_prev=sbindir ;;
   -sbindir=* | --sbindir=* | --sbindi=* | --sbind=* | --sbin=* \
@@ -1180,7 +1169,7 @@ fi
 for ac_var in	exec_prefix prefix bindir sbindir libexecdir datarootdir \
 		datadir sysconfdir sharedstatedir localstatedir includedir \
 		oldincludedir docdir infodir htmldir dvidir pdfdir psdir \
-		libdir localedir mandir runstatedir
+		libdir localedir mandir
 do
   eval ac_val=\$$ac_var
   # Remove trailing slashes.
@@ -1333,7 +1322,6 @@ Fine tuning of the installation directories:
   --sysconfdir=DIR        read-only single-machine data [PREFIX/etc]
   --sharedstatedir=DIR    modifiable architecture-independent data [PREFIX/com]
   --localstatedir=DIR     modifiable single-machine data [PREFIX/var]
-  --runstatedir=DIR       modifiable per-process data [LOCALSTATEDIR/run]
   --libdir=DIR            object code libraries [EPREFIX/lib]
   --includedir=DIR        C header files [PREFIX/include]
   --oldincludedir=DIR     C header files for non-gcc [/usr/include]

seq_test/Makefile.am

@@ -12,7 +12,7 @@ seq_test_LDADD = \
 	../htslib/libhts.a \
 	-lboost_unit_test_framework -lboost_system -lboost_timer -lboost_chrono
 
-seq_test_LDFLAGS = --coverage
+seq_test_LDFLAGS = --coverage -pthread
 
 seq_test_SOURCES = seq_test.cpp \
 	../src/BFC.cpp ../src/GenomicRegion.cpp \