Added libgsl to build process and added Bonf corr to approx

configure.ac

@@ -146,11 +146,12 @@ AX_PTHREAD([
         AC_MSG_ERROR([No pthread support on this machine]))
 #AX_PTHREAD()
 
-
-# explicit libm check
+# if any of these sit in unusual places use
+# export LDFLAGS="-L$path" before calling configure
 AC_CHECK_LIB(m, log,, AC_MSG_ERROR([Could not find libm]))
 AC_CHECK_LIB(z, gzread,, AC_MSG_ERROR([Could not find libz]))
-
+AC_CHECK_LIB([gslcblas],[cblas_dgemm])
+AC_CHECK_LIB(gsl, gsl_cdf_poisson_P,, AC_MSG_WARN([libgsl not found. Not using fast approximation]))
 
 # http://www.gnu.org/software/automake/manual/html_node/Python.html
 AM_PATH_PYTHON([2.7])

src/lofreq/Makefile.am

@@ -41,4 +41,5 @@ LIBS_for_htslib = -lhts
 endif
 
 # note: order matters
-lofreq_LDADD = $(LIBS_for_htslib) ../cdflib90/libcdf.a -l:libgsl.a -lcblas -lm
+lofreq_LDADD = $(LIBS_for_htslib) ../cdflib90/libcdf.a
+# -l:libgsl.a -lm

src/lofreq/snpcaller.c

@@ -1102,17 +1102,22 @@ snpcaller(long double *snp_pvalues,
         goto free_and_exit;
     }
 
-    // Only approximate if sufficient data available
-    if (num_err_probs > 100) {
-        long double mu = 0;
-        for (int i = 0; i < num_err_probs; ++i) {
-            mu += err_probs[i];
-        }
-        const long double poibin_approximation = 1 - gsl_cdf_poisson_P(max_noncons_count - 1, mu);
-        if (poibin_approximation > sig_level + 0.05) {
-            goto free_and_exit;
-        }
-    }
+#ifdef HAVE_LIBGSL
+     #ifdef HAVE_LIBGSLCBLAS
+     // Only approximate if sufficient data available
+     if (num_err_probs > 100) {
+          long double mu = 0;
+          for (int i = 0; i < num_err_probs; ++i) {
+               mu += err_probs[i];
+          }
+          const long double poibin_approximation = 1 - gsl_cdf_poisson_P(max_noncons_count - 1, mu);
+          if (poibin_approximation * (double)bonf_factor > sig_level) {
+               goto free_and_exit;
+          }
+     }
+     #endif
+#endif
+
     probvec = poissbin(&pvalue, err_probs, num_err_probs,
                        max_noncons_count, bonf_factor, sig_level);