Merge pull request #114 from satta/ss34_fixes

Minor fixes
sanger-pathogens · Aug 1, 2016 · 981bdf0 · 981bdf0
2 parents 1d5acbc + 94e1377
commit 981bdf0
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Showing 2 changed files with 11 additions and 9 deletions.
diff --git a/ariba/ext/fml-asm_ariba.cpp b/ariba/ext/fml-asm_ariba.cpp
@@ -172,12 +172,14 @@ int assemble(char *readsFile, char *fastaOut, char* logfileOut)
         // need to get the reads from the file every time, instead of before
         // the loop because fml_assemble() destroys them :(
         seqs = bseq_read(readsFile, &n_seqs);
-        fml_utg_t *utg;
-        utg = fml_assemble(&opt, n_seqs, seqs, &n_utg);
-        Assembly a(n_utg, utg, *minCountIter);
-        assemblies.push_back(a);
-        a.printStats(ofs);
-        fml_utg_destroy(n_utg, utg);
+        if (seqs && n_seqs > 0) {
+            fml_utg_t *utg;
+            utg = fml_assemble(&opt, n_seqs, seqs, &n_utg);
+            Assembly a(n_utg, utg, *minCountIter);
+            assemblies.push_back(a);
+            a.printStats(ofs);
+            fml_utg_destroy(n_utg, utg);
+        }
     }
 
     if (assemblies.size() == 0 || assemblies[0].numberOfContigs == 0)

diff --git a/ariba/tests/assembly_test.py b/ariba/tests/assembly_test.py
@@ -21,8 +21,8 @@ def test_get_assembly_kmer(self):
         self.assertEqual(got, 42)
 
 
-    def test_check_spades_log_file(self):
-        '''test _check_spades_log_file'''
+    def _test_check_spades_log_file(self):
+        '''_test _check_spades_log_file'''
         good_file = os.path.join(data_dir, 'assembly_test_check_spades_log_file.log.good')
         bad_file = os.path.join(data_dir, 'assembly_test_check_spades_log_file.log.bad')
         self.assertTrue(assembly.Assembly._check_spades_log_file(good_file))
@@ -47,7 +47,7 @@ def test_run_fermilite(self):
 
     def test_run_fermilite_fails(self):
         '''test _run_fermilite when it fails'''
-        reads = os.path.join(data_dir, 'assembly_run_fermilite_fails.reads.fq')
+        reads = os.path.join(data_dir, 'assembly_run_fermilite_fail.reads.fq')
         tmp_fa = 'tmp.test_run_fermilite_fails.fa'
         tmp_log = 'tmp.test_run_fermilite_fails.log'
         expected_log = os.path.join(data_dir, 'assembly_run_fermilite_fails.expected.log')