Fix broken test, as part of #530.

cfe-lab · Jun 10, 2020 · d724084 · d724084
1 parent fed2058
commit d724084
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Showing 2 changed files with 3 additions and 48 deletions.
diff --git a/micall/tests/test_remap.py b/micall/tests/test_remap.py
@@ -1034,53 +1034,6 @@ def test_star_region(self):
         self.assertEqual(expected_remap_counts, self.remap_counts.getvalue())
         self.assertEqual(expected_seed_counts, seed_counts)
 
-    def test_unmapped_flag(self):
-        self.maxDiff = None
-        prelim_csv = StringIO("""\
-qname,flag,rname,pos,mapq,cigar,rnext,pnext,tlen,seq,qual
-example1,89,R1-seed,1,0,54M,=,1,0,\
-AAACCCTTTAAACCCTTTAAACCCTTTAAACCCTTTAAACCCTTTAAACCCTTT,\
-BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
-example2,89,R1-seed,1,0,54M,=,1,0,\
-AAAACCTTTAAAACCTTTAAAACCTTTAAAACCTTTAAAACCTTTAAAACCTTT,\
-BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
-example3,93,R1-seed,*,*,*,*,*,*,\
-AAAACCTTTAAAACCTTTAAAACCTTTAAAACCTTTAAAACCTTTAAAACCTTT,\
-BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
-""")
-        count_threshold = 2
-        expected_sam_file = """\
-@HD	VN:1.0	SO:unsorted
-@SQ	SN:R1-seed	LN:9
-@SQ	SN:R2-seed	LN:12
-@PG	ID:bowtie2	PN:bowtie2	VN:2.2.3	CL:""
-example1\t89\tR1-seed\t1\t0\t54M\t=\t1\t0\t\
-AAACCCTTTAAACCCTTTAAACCCTTTAAACCCTTTAAACCCTTTAAACCCTTT\t\
-BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
-example2\t89\tR1-seed\t1\t0\t54M\t=\t1\t0\t\
-AAAACCTTTAAAACCTTTAAAACCTTTAAAACCTTTAAAACCTTTAAAACCTTT\t\
-BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
-example3\t93\tR1-seed\t*\t*\t*\t*\t*\t*\t\
-AAAACCTTTAAAACCTTTAAAACCTTTAAAACCTTTAAAACCTTTAAAACCTTT\t\
-BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
-"""
-        expected_remap_counts = """\
-type,filtered_count,count
-prelim *,0,1
-prelim R1-seed,2,2
-"""
-        expected_seed_counts = {'R1-seed': 2}
-
-        seed_counts = convert_prelim(prelim_csv,
-                                     self.sam_file,
-                                     self.remap_counts_writer,
-                                     count_threshold,
-                                     self.projects)
-
-        self.assertEqual(expected_sam_file, self.sam_file.getvalue())
-        self.assertEqual(expected_remap_counts, self.remap_counts.getvalue())
-        self.assertEqual(expected_seed_counts, seed_counts)
-
     def test_best_in_group(self):
         self.maxDiff = None
         prelim_csv = StringIO("""\
@@ -1166,7 +1119,8 @@ def test_unmapped_read(self):
 """
         expected_remap_counts = """\
 type,filtered_count,count
-prelim R1-seed,1,2
+prelim *,0,1
+prelim R1-seed,1,1
 """
         expected_seed_counts = {}
 

diff --git a/micall_docker.py b/micall_docker.py
@@ -43,6 +43,7 @@
 logging.basicConfig(level=logging.INFO,
                     format='%(asctime)s[%(levelname)s]%(name)s.%(funcName)s(): %(message)s')
 logger = logging.getLogger('micall')
+# logging.getLogger('micall.core.trim_fastqs').setLevel(logging.DEBUG)
 
 
 class BSrequest: