Merge pull request #250 from dib-lab/all-seed-matches

Reporting all seed matches

kevlar/localize.py

@@ -107,7 +107,9 @@ def get_exact_matches(contigstream, bwaindexfile, seedsize=31):
     (seqid, startpos) for each exact match found.
     """
     kmers = unique_seed_string(contigstream, seedsize)
-    cmd = 'bwa mem -k {k} -T {k} {idx} -'.format(k=seedsize, idx=bwaindexfile)
+    cmd = 'bwa mem -k {k} -T {k} -a -c 5000 {idx} -'.format(
+        k=seedsize, idx=bwaindexfile
+    )
     cmdargs = cmd.split(' ')
     for seqid, pos in bwa_align(cmdargs, seqstring=kmers):
         yield seqid, pos

kevlar/tests/test_alac.py

@@ -147,11 +147,11 @@ def test_alac_bigpart():
     assert len(calls) == 3
 
 
-@pytest.mark.parametrize('cc,numrawcalls', [
-    ('26849', [3, 4, 5, 7]),  # Assembly deterministic on OS X, but not Linux
-    ('138713', [14]),
+@pytest.mark.parametrize('cc,numrawcalls,numfiltcalls', [
+    ('26849', 4, 2),
+    ('138713', 14, 1),
 ])
-def test_alac_inf_mate_dist(cc, numrawcalls):
+def test_alac_inf_mate_dist(cc, numrawcalls, numfiltcalls):
     readfile = data_file('inf-mate-dist/cc{}.augfastq.gz'.format(cc))
     refrfile = data_file('inf-mate-dist/cc{}.genome.fa.gz'.format(cc))
     readstream = kevlar.parse_augmented_fastx(kevlar.open(readfile, 'r'))
@@ -160,10 +160,9 @@ def test_alac_inf_mate_dist(cc, numrawcalls):
                               seedsize=51, fallback=True)
     calls = list(caller)
     print(*[c.vcf for c in calls], sep='\n', file=sys.stderr)
-    assert len(calls) in numrawcalls
+    assert len(calls) == numrawcalls
     filtcalls = [c for c in calls if c.filterstr == 'PASS']
-    print(*[c.vcf for c in filtcalls], sep='\n', file=sys.stderr)
-    assert len(filtcalls) == 1
+    assert len(filtcalls) == numfiltcalls
 
 
 def test_alac_no_mates():
@@ -175,16 +174,16 @@ def test_alac_no_mates():
                               seedsize=51, fallback=True)
     calls = list(caller)
     print(*[c.vcf for c in calls], sep='\n', file=sys.stderr)
-    assert len(calls) in [3, 4, 5, 7]
+    assert len(calls) == 4
     filtcalls = [c for c in calls if c.filterstr == 'PASS']
-    assert len(filtcalls) == 2
+    assert len(filtcalls) == 3
 
 
 @pytest.mark.parametrize('vcfposition,X,cigar', [
-    (40692, 10000, '30595D96M6I91M15137D'),
-    (40692, 1000, '37D96M6I91M44D'),
-    (40692, 0, '30595D96M6I91M132906D'),
-    (40692, None, '37D96M6I91M44D'),
+    (40692, 10000, '32713D96M6I91M15142D'),
+    (40692, 1000, '50D96M6I91M50D'),
+    (40692, 0, '32713D96M6I91M140025D'),
+    (40692, None, '50D96M6I91M50D'),
 ])
 def test_alac_maxdiff(vcfposition, X, cigar):
     pstream = kevlar.parse_partitioned_reads(

kevlar/tests/test_localize.py

@@ -163,9 +163,9 @@ def test_extract_regions_boundaries():
 @pytest.mark.parametrize('X,numtargets', [
     (100000, 1),
     (10000, 5),
-    (1000, 23),
+    (1000, 33),
     (0, 1),
-    (None, 23),
+    (None, 33),
 ])
 def test_maxdiff(X, numtargets):
     contigstream = kevlar.parse_augmented_fastx(