[med-svn] [ariba] 01/03: Imported Upstream version 2.2.4+ds
Sascha Steinbiss
satta at debian.org
Wed Aug 24 23:55:56 UTC 2016
This is an automated email from the git hooks/post-receive script.
satta pushed a commit to branch master
in repository ariba.
commit a05dfdecb78bd8a58a32742deab0867df1240358
Author: Sascha Steinbiss <satta at debian.org>
Date: Wed Aug 24 08:14:01 2016 +0000
Imported Upstream version 2.2.4+ds
---
ariba/reference_data.py | 2 +-
ariba/report.py | 48 +++-
ariba/report_filter.py | 4 +-
ariba/summary_cluster_variant.py | 10 +-
ariba/tests/cluster_test.py | 25 +-
...luster_full_run_smtls_known_snp_presabs_nonc.fa | 3 +
...uster_full_run_smtls_known_snp_presabs_nonc.tsv | 2 +
.../reads_1.fq | 296 +++++++++++++++++++++
.../reads_2.fq | 296 +++++++++++++++++++++
.../references.fa | 3 +
ariba/tests/reference_data_test.py | 4 +-
ariba/tests/report_filter_test.py | 3 +-
ariba/tests/summary_cluster_variant_test.py | 5 +-
setup.py | 4 +-
14 files changed, 676 insertions(+), 29 deletions(-)
diff --git a/ariba/reference_data.py b/ariba/reference_data.py
index a945a4a..2ddbac0 100644
--- a/ariba/reference_data.py
+++ b/ariba/reference_data.py
@@ -8,7 +8,7 @@ from ariba import sequence_metadata, cdhit
class Error (Exception): pass
-rename_sub_regex = re.compile(r'''[|()\[\];"':!@,-]''')
+rename_sub_regex = re.compile(r'''[^a-zA-Z0-9_.]''')
class ReferenceData:
diff --git a/ariba/report.py b/ariba/report.py
index 1884c9a..324124a 100644
--- a/ariba/report.py
+++ b/ariba/report.py
@@ -135,6 +135,7 @@ def _samtools_depths_at_known_snps_all_wild(sequence_meta, contig_name, cluster,
def _report_lines_for_one_contig(cluster, contig_name, ref_cov_per_contig, pymummer_variants):
lines = []
+ reported_known_vars = set()
contig_length = len(cluster.assembly.sequences[contig_name])
assert contig_length != 0
@@ -229,6 +230,7 @@ def _report_lines_for_one_contig(cluster, contig_name, ref_cov_per_contig, pymum
for matching_var in matching_vars_set:
if contributing_vars is None:
samtools_columns = _samtools_depths_at_known_snps_all_wild(matching_var, contig_name, cluster, pymummer_variants)
+ reported_known_vars.add(str(matching_var.variant))
variant_columns[3] = str(matching_var.variant)
if matching_var.has_variant(cluster.ref_sequence) == (ref_ctg_change is not None):
@@ -251,23 +253,41 @@ def _report_lines_for_one_contig(cluster, contig_name, ref_cov_per_contig, pymum
[matching_vars_column] + [free_text_column]
))
- for contig_name in remaining_samtools_variants:
+ if contig_name in remaining_samtools_variants:
for var_position in remaining_samtools_variants[contig_name]:
depths_tuple = cluster.samtools_vars.get_depths_at_position(contig_name, var_position)
+
if depths_tuple is not None:
- new_cols = [
- '0', # known_var column
- 'HET', # var_type
- '.', '.', '.', '.', '.', '.', '.', '.', # var_seq_type ... ref_nt
- str(var_position + 1), str(var_position + 1), # ctg_start, ctg_end
- depths_tuple[0], # ctg_nt
- str(depths_tuple[2]), # smtls_total_depth
- depths_tuple[1], # smtls_alt_nt
- str(depths_tuple[3]), # smtls_alt_depth
- '.',
- free_text_column,
- ]
- lines.append('\t'.join(common_first_columns + new_cols))
+ ref_coord, in_indel = None, None
+ if contig_name in cluster.assembly_compare.nucmer_hits:
+ for hit in cluster.assembly_compare.nucmer_hits[contig_name]:
+ if hit.qry_coords().distance_to_point(var_position) == 0:
+ ref_coord, in_indel = hit.ref_coords_from_qry_coord(var_position, pymummer_variants)
+ break
+
+ if ref_coord is None:
+ ref_coord = '.'
+ ref_nt = '.'
+ var_string = None
+ else:
+ ref_nt = cluster.ref_sequence[ref_coord]
+ var_string = depths_tuple[0] + str(ref_coord + 1) + depths_tuple[1]
+ ref_coord = str(ref_coord + 1)
+
+ if var_string not in reported_known_vars:
+ new_cols = [
+ '0', # known_var column
+ 'HET', # var_type
+ '.', '.', '.', var_string, '.', ref_coord, ref_coord, ref_nt, # var_seq_type ... ref_nt
+ str(var_position + 1), str(var_position + 1), # ctg_start, ctg_end
+ depths_tuple[0], # ctg_nt
+ str(depths_tuple[2]), # smtls_total_depth
+ depths_tuple[1], # smtls_alt_nt
+ str(depths_tuple[3]), # smtls_alt_depth
+ '.',
+ free_text_column,
+ ]
+ lines.append('\t'.join(common_first_columns + new_cols))
if len(lines) == 0:
lines.append('\t'.join(common_first_columns + ['.'] * (len(columns) - len(common_first_columns) - 1) + [free_text_column]))
diff --git a/ariba/report_filter.py b/ariba/report_filter.py
index 8748749..e2b147d 100644
--- a/ariba/report_filter.py
+++ b/ariba/report_filter.py
@@ -1,3 +1,4 @@
+import pprint
import pyfastaq
from ariba import report, flag
@@ -119,8 +120,7 @@ class ReportFilter:
def _report_dict_passes_essential_filters(self, report_dict):
return ReportFilter._flag_passes_filter(report_dict['flag'], self.exclude_flags) \
and report_dict['pc_ident'] >= self.min_pc_ident \
- and report_dict['ref_base_assembled'] >= self.min_ref_base_assembled \
- and report_dict['var_type'] != 'HET'
+ and report_dict['ref_base_assembled'] >= self.min_ref_base_assembled
def _filter_list_of_dicts(self, dicts_list):
diff --git a/ariba/summary_cluster_variant.py b/ariba/summary_cluster_variant.py
index fa9a867..d113b9b 100644
--- a/ariba/summary_cluster_variant.py
+++ b/ariba/summary_cluster_variant.py
@@ -33,7 +33,7 @@ class SummaryClusterVariant:
@classmethod
def _get_het_percent(cls, data_dict):
- if data_dict['gene'] == '1' or data_dict['ref_ctg_effect'] != 'SNP' or data_dict['smtls_alt_nt'] == '.' or ';' in data_dict['smtls_alt_nt'] or data_dict['smtls_alt_depth'] == 'ND':
+ if data_dict['gene'] == '1' or not (data_dict['ref_ctg_effect'] == 'SNP' or data_dict['var_type'] == 'HET') or data_dict['smtls_alt_nt'] == '.' or ';' in data_dict['smtls_alt_nt'] or data_dict['smtls_alt_depth'] == 'ND':
return None
else:
nucleotides = [data_dict['ctg_nt']] + data_dict['smtls_alt_nt'].split(',')
@@ -43,7 +43,13 @@ class SummaryClusterVariant:
raise Error('Mismatch in number of inferred nucleotides from ctg_nt, smtls_alt_nt, smtls_alt_depth columns. Cannot continue\n' + str(data_dict))
try:
- var_nucleotide = data_dict['known_var_change'][-1] if data_dict['known_var_change'] != '.' else data_dict['ref_ctg_change'][-1]
+ if data_dict['var_type'] == 'HET':
+ var_nucleotide = data_dict['smtls_alt_nt']
+ elif data_dict['known_var_change'] != '.':
+ var_nucleotide = data_dict['known_var_change'][-1]
+ else:
+ var_nucleotide = data_dict['ref_ctg_change'][-1]
+
if var_nucleotide == '.':
return None
depths = [int(x) for x in depths]
diff --git a/ariba/tests/cluster_test.py b/ariba/tests/cluster_test.py
index 352b74e..10b59ea 100644
--- a/ariba/tests/cluster_test.py
+++ b/ariba/tests/cluster_test.py
@@ -275,7 +275,7 @@ class TestCluster(unittest.TestCase):
c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=148, total_reads_bases=13320)
c.run()
expected = [
- 'ref_gene\t1\t0\t155\t148\tcluster_name\t96\t96\t100.0\tcluster_name.scaffold.1\t335\t39.8\t0\tHET\t.\t.\t.\t.\t.\t.\t.\t.\t137\t137\tG\t63\tA\t32,31\t.\tGeneric description of ref_gene'
+ 'ref_gene\t1\t0\t155\t148\tcluster_name\t96\t96\t100.0\tcluster_name.scaffold.1\t335\t39.8\t0\tHET\t.\t.\t.\tG18A\t.\t18\t18\tG\t137\t137\tG\t63\tA\t32,31\t.\tGeneric description of ref_gene'
]
self.assertEqual(expected, c.report_lines)
shutil.rmtree(tmpdir)
@@ -293,7 +293,7 @@ class TestCluster(unittest.TestCase):
c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=148, total_reads_bases=13320)
c.run()
expected = [
- 'ref_gene\t1\t1\t155\t148\tcluster_name\t96\t96\t100.0\tcluster_name.scaffold.1\t335\t39.8\t0\tHET\t.\t.\t.\t.\t.\t.\t.\t.\t137\t137\tG\t63\tA\t32,31\t.\tGeneric description of ref_gene'
+ 'ref_gene\t1\t1\t155\t148\tcluster_name\t96\t96\t100.0\tcluster_name.scaffold.1\t335\t39.8\t0\tHET\t.\t.\t.\tG18A\t.\t18\t18\tG\t137\t137\tG\t63\tA\t32,31\t.\tGeneric description of ref_gene'
]
self.assertEqual(expected, c.report_lines)
shutil.rmtree(tmpdir)
@@ -366,7 +366,23 @@ class TestCluster(unittest.TestCase):
c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=148, total_reads_bases=13320)
c.run()
expected = [
- 'ref_seq\t0\t0\t147\t148\tcluster_name\t96\t96\t100.0\tcluster_name.scaffold.1\t335\t39.8\t0\tHET\t.\t.\t.\t.\t.\t.\t.\t.\t137\t137\tG\t63\tA\t32,31\t.\tGeneric description of ref_seq'
+ 'ref_seq\t0\t0\t147\t148\tcluster_name\t96\t96\t100.0\tcluster_name.scaffold.1\t335\t39.8\t0\tHET\t.\t.\t.\tG18A\t.\t18\t18\tG\t137\t137\tG\t63\tA\t32,31\t.\tGeneric description of ref_seq'
+ ]
+ self.assertEqual(expected, c.report_lines)
+ shutil.rmtree(tmpdir)
+
+
+ def test_full_run_smtls_known_snp_presabs_nonc(self):
+ '''test complete run where samtools calls a snp in a presence/absence noncoding sequence at a known snp position'''
+ fasta_in = os.path.join(data_dir, 'cluster_full_run_smtls_known_snp_presabs_nonc.fa')
+ tsv_in = os.path.join(data_dir, 'cluster_full_run_smtls_known_snp_presabs_nonc.tsv')
+ refdata = reference_data.ReferenceData([fasta_in], [tsv_in])
+ tmpdir = 'tmp.cluster_test_full_run_smtls_known_snp_presabs_nonc'
+ shutil.copytree(os.path.join(data_dir, 'cluster_full_run_smtls_known_snp_presabs_nonc'), tmpdir)
+ c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=148, total_reads_bases=13320)
+ c.run()
+ expected = [
+ 'ref_seq\t0\t0\t147\t148\tcluster_name\t96\t96\t100.0\tcluster_name.scaffold.1\t335\t39.8\t1\tSNP\tn\tG18A\t0\t.\t.\t18\t18\tG\t137\t137\tG\t63\tA\t32,31\tref_seq:0:0:G18A:.:Description of G18A\tGeneric description of ref_seq'
]
self.assertEqual(expected, c.report_lines)
shutil.rmtree(tmpdir)
@@ -382,7 +398,7 @@ class TestCluster(unittest.TestCase):
c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=148, total_reads_bases=13320)
c.run()
expected = [
- 'ref_seq\t0\t1\t147\t148\tcluster_name\t96\t96\t100.0\tcluster_name.scaffold.1\t335\t39.8\t0\tHET\t.\t.\t.\t.\t.\t.\t.\t.\t137\t137\tG\t63\tA\t32,31\t.\tGeneric description of ref_seq'
+ 'ref_seq\t0\t1\t147\t148\tcluster_name\t96\t96\t100.0\tcluster_name.scaffold.1\t335\t39.8\t0\tHET\t.\t.\t.\tG18A\t.\t18\t18\tG\t137\t137\tG\t63\tA\t32,31\t.\tGeneric description of ref_seq'
]
self.assertEqual(expected, c.report_lines)
shutil.rmtree(tmpdir)
@@ -460,3 +476,4 @@ class TestCluster(unittest.TestCase):
]
self.assertEqual(expected, c.report_lines)
shutil.rmtree(tmpdir)
+
diff --git a/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.fa b/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.fa
new file mode 100644
index 0000000..a23e635
--- /dev/null
+++ b/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.fa
@@ -0,0 +1,3 @@
+>ref_seq
+ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCAT
+ATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
diff --git a/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.tsv b/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.tsv
new file mode 100644
index 0000000..b93ab7f
--- /dev/null
+++ b/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.tsv
@@ -0,0 +1,2 @@
+ref_seq 0 0 . . Generic description of ref_seq
+ref_seq 0 0 G18A . Description of G18A
diff --git a/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_1.fq b/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_1.fq
new file mode 100644
index 0000000..1d056e7
--- /dev/null
+++ b/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_1.fq
@@ -0,0 +1,296 @@
+ at ref_gene:1:147:247/1
+AGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGGCTGATACCCATAATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:2:89:186/1
+AATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:3:40:139/1
+CCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:4:113:213/1
+CGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:5:111:210/1
+AGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:6:29:129/1
+AGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:7:112:212/1
+GCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:8:45:145/1
+ATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:9:121:219/1
+ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:10:82:182/1
+ACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:11:96:196/1
+AATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:12:125:225/1
+ATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:13:114:215/1
+GTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:14:100:199/1
+AGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:15:90:188/1
+ATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:16:54:154/1
+ATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:17:110:210/1
+GAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:18:63:162/1
+TCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:19:83:183/1
+CAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:20:94:194/1
+GGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:21:65:164/1
+CTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:22:27:126/1
+CGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:23:39:141/1
+TCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:24:107:208/1
+CAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:25:72:170/1
+GCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:26:10:111/1
+TCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:27:55:155/1
+TTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:28:83:184/1
+CAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:29:11:110/1
+CGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:30:76:177/1
+CAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:31:77:176/1
+AGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:32:96:195/1
+AATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:33:19:118/1
+CAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:34:40:141/1
+CCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:35:68:167/1
+GTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:36:70:170/1
+TTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:37:94:194.dup.2/1
+GGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:38:27:127/1
+CGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:39:102:201/1
+TACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:40:131:231/1
+AAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:41:13:113/1
+GCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:42:82:182/1
+ACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:43:84:183/1
+AAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:44:118:218/1
+CCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:45:44:144/1
+CATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:46:92:189/1
+ATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:47:132:233/1
+AGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:48:45:143/1
+ATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:49:26:125/1
+TCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:50:87:185/1
+CTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:51:107:205/1
+CAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:52:47:147/1
+TCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:53:3:103/1
+CAGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:54:127:228/1
+CGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:55:69:169/1
+TTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:56:8:107/1
+CGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:57:51:149/1
+GTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:58:141:243/1
+CCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGGCTGATACCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:59:3:102/1
+CAGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:60:17:116/1
+GGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:61:21:120/1
+GGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:62:20:118/1
+AGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:63:4:105/1
+AGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:64:7:107/1
+ACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:65:127:227/1
+CGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:66:98:197/1
+TGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:67:116:216/1
+AGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:68:134:235/1
+CGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACACGGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:69:65:165/1
+CTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:70:81:179/1
+GACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:71:41:140/1
+CTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:72:2:100/1
+TCAGGACGTCGGCGCGGCAGGCATTCGAGTTAATCTTTCCTCCATTCACGTGATTTAGTTGTCCTTGTTTGCGACAGCTGACAAGCTAAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:73:83:184/1
+CAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGAACGCGCGAGCACCAACA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:74:66:164/1
+TTGTTTGCGACAGCTGACAAGCTAATATGGAATGAGTACGCCAAGAGCGTAGCCGATGGATCGCGAAGCGATAACCCATGAAGCGACCGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
diff --git a/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_2.fq b/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_2.fq
new file mode 100644
index 0000000..31885ad
--- /dev/null
+++ b/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_2.fq
@@ -0,0 +1,296 @@
+ at ref_gene:1:147:247/2
+TGTTTGCGTACATACCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:2:89:186/2
+TGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:3:40:139/2
+GTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:4:113:213/2
+TCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:5:111:210/2
+TGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:6:29:129/2
+TGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:7:112:212/2
+CATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:8:45:145/2
+TTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:9:121:219/2
+ACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:10:82:182/2
+TACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:11:96:196/2
+TTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:12:125:225/2
+GAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:13:114:215/2
+CCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:14:100:199/2
+TAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:15:90:188/2
+TCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:16:54:154/2
+CGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:17:110:210/2
+TGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:18:63:162/2
+TATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:19:83:183/2
+ATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:20:94:194/2
+CTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:21:65:164/2
+GATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:22:27:126/2
+TATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:23:39:141/2
+GGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:24:107:208/2
+GCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:25:72:170/2
+GTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:26:10:111/2
+CACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGATCCATCGGCTACGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:27:55:155/2
+ACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:28:83:184/2
+TATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:29:11:110/2
+ACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGATCCATCGGCTACGCTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:30:76:177/2
+CGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:31:77:176/2
+GGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:32:96:195/2
+TCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:33:19:118/2
+GCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGATCCATCGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:34:40:141/2
+GGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:35:68:167/2
+GGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:36:70:170/2
+GTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene:37:94:194.dup.2/2
+CTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:38:27:127/2
+TTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:39:102:201/2
+AATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:40:131:231/2
+GGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:41:13:113/2
+CCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:42:82:182/2
+TACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:43:84:183/2
+ATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:44:118:218/2
+CATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:45:44:144/2
+TATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:46:92:189/2
+CTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:47:132:233/2
+CCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:48:45:143/2
+ATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:49:26:125/2
+ATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:50:87:185/2
+GTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:51:107:205/2
+TAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:52:47:147/2
+AATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:53:3:103/2
+AATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:54:127:228/2
+TCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:55:69:169/2
+TAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:56:8:107/2
+CGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:57:51:149/2
+GAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:58:141:243/2
+TGCGTACATACCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:59:3:102/2
+ATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGCGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:60:17:116/2
+TTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:61:21:120/2
+ATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:62:20:118/2
+GCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:63:4:105/2
+CTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:64:7:107/2
+CGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:65:127:227/2
+CTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:66:98:197/2
+GTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:67:116:216/2
+TCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:68:134:235/2
+TACCGGGTCTGAGTTTACATCCTCATGGCATAGTAATAGTTCTCGTCTCTGTATACTGCGGTATTGTAGGAGATATAACTACGGATGAAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:69:65:165/2
+AGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:70:81:179/2
+TGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:71:41:140/2
+GGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:72:2:100/2
+GCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTTATCGCTTCGCGATCCATCGGCTACGCTCTTGGCGTACT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:73:83:184/2
+TATACTGCGGTATTGTAGGAGATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+ at ref_gene_with_snp:74:66:164/2
+GATATAACTACGGATGAAATTATGGGTATCAGCCGTGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
diff --git a/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/references.fa b/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/references.fa
new file mode 100644
index 0000000..a23e635
--- /dev/null
+++ b/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/references.fa
@@ -0,0 +1,3 @@
+>ref_seq
+ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCAT
+ATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
diff --git a/ariba/tests/reference_data_test.py b/ariba/tests/reference_data_test.py
index 9b12088..ae723b2 100644
--- a/ariba/tests/reference_data_test.py
+++ b/ariba/tests/reference_data_test.py
@@ -292,6 +292,7 @@ class TestReferenceData(unittest.TestCase):
"abc'5",
'abc"6',
'abc|7',
+ r'''zaphod<>/\b{}[]|!''',
}
got = reference_data.ReferenceData._seq_names_to_rename_dict(names)
expected = {
@@ -305,7 +306,8 @@ class TestReferenceData(unittest.TestCase):
"abc'5": 'abc_5',
'abc"6': 'abc_6',
'abc|7': 'abc_7',
- 'eggs,123': 'eggs_123'
+ 'eggs,123': 'eggs_123',
+ r'''zaphod<>/\b{}[]|!''': 'zaphod____b______',
}
self.assertEqual(expected, got)
diff --git a/ariba/tests/report_filter_test.py b/ariba/tests/report_filter_test.py
index f9d4bfc..63c94d8 100644
--- a/ariba/tests/report_filter_test.py
+++ b/ariba/tests/report_filter_test.py
@@ -278,7 +278,7 @@ class TestReportFilter(unittest.TestCase):
'ref1': {
'ref1.scaff1': [
{'flag': flag.Flag(27), 'pc_ident': 91.0, 'ref_base_assembled': 9, 'known_var': '1', 'has_known_var': '1', 'var_type': 'SNP'},
- {'flag': flag.Flag(27), 'pc_ident': 91.5, 'ref_base_assembled': 9, 'known_var': '1', 'has_known_var': '1', 'var_type': 'HET'},
+ {'flag': flag.Flag(27), 'pc_ident': 91.5, 'ref_base_assembled': 11, 'known_var': '1', 'has_known_var': '1', 'var_type': 'HET'},
{'flag': flag.Flag(27), 'pc_ident': 89.0, 'ref_base_assembled': 10, 'known_var': '1', 'has_known_var': '1', 'var_type': 'SNP'},
{'flag': flag.Flag(27), 'pc_ident': 90.0, 'ref_base_assembled': 11, 'known_var': '1', 'has_known_var': '0', 'var_type': 'SNP'},
{'flag': flag.Flag(27), 'pc_ident': 90.0, 'ref_base_assembled': 11, 'known_var': '1', 'has_known_var': '1', 'var_type': 'SNP'},
@@ -304,6 +304,7 @@ class TestReportFilter(unittest.TestCase):
expected = {
'ref1': {
'ref1.scaff1': [
+ {'flag': flag.Flag(27), 'pc_ident': 91.5, 'ref_base_assembled': 11, 'known_var': '1', 'has_known_var': '1', 'var_type': 'HET'},
{'flag': flag.Flag(27), 'pc_ident': 90.0, 'ref_base_assembled': 11, 'known_var': '1', 'has_known_var': '1', 'var_type': 'SNP'},
]
},
diff --git a/ariba/tests/summary_cluster_variant_test.py b/ariba/tests/summary_cluster_variant_test.py
index ec09942..24d2d1f 100644
--- a/ariba/tests/summary_cluster_variant_test.py
+++ b/ariba/tests/summary_cluster_variant_test.py
@@ -29,10 +29,11 @@ class TestSummaryClusterVariant(unittest.TestCase):
'ref1\t0\t0\t531\t78\tcluster1\t120\t100\t98.33\tctg_name\t279\t24.4\t1\tSNP\tn\tA14T\t1\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t17\t.\t17\tnon_coding1:0:0:A14T:id1:foo_bar\tspam eggs',
'ref1\t0\t0\t531\t78\tcluster1\t120\t100\t98.33\tctg_name\t279\t24.4\t1\tSNP\tn\tA42T\t1\tA42T\tSNP\t42\t42\tA\t84\t84\tT\t40\tA\t10,30\tnon_coding1:0:0:A42T:id1:foo_bar\tspam eggs',
'ref1\t0\t0\t531\t78\tcluster1\t120\t100\t98.33\tctg_name\t279\t24.4\t1\tSNP\tn\tA62T\t1\tA62T\tSNP\t62\t62\tA\t84\t84\tA\t40\tT\t10,30\tnon_coding1:0:0:A62T:id2:foo_bar\tspam eggs',
- 'ref1\t0\t0\t531\t78\tcluster1\t120\t100\t98.33\tctg_name\t279\t24.4\t1\tSNP\tn\tA82T\t1\tA82T\tSNP\t82\t82\tA\t84\t84\tA\t100\tT,G\t10,40,50\tnon_coding1:0:0:A82T:.:foo_bar\tspam eggs'
+ 'ref1\t0\t0\t531\t78\tcluster1\t120\t100\t98.33\tctg_name\t279\t24.4\t1\tSNP\tn\tA82T\t1\tA82T\tSNP\t82\t82\tA\t84\t84\tA\t100\tT,G\t10,40,50\tnon_coding1:0:0:A82T:.:foo_bar\tspam eggs',
+ 'ref1\t0\t0\t531\t78\tcluster1\t120\t100\t98.33\tctg_name\t279\t24.4\t0\tHET\t.\t.\t.\t.\t.\t.\t.\t.\t84\t84\tA\t50\tT\t40,10\t.\t.'
]
- expected = [None, 25.0, 75.0, 40.0]
+ expected = [None, 25.0, 75.0, 40.0, 20.0]
assert len(lines) == len(expected)
for i in range(len(lines)):
diff --git a/setup.py b/setup.py
index 4e8a837..3479118 100644
--- a/setup.py
+++ b/setup.py
@@ -51,7 +51,7 @@ fermilite_mod = Extension(
setup(
ext_modules=[minimap_mod, fermilite_mod],
name='ariba',
- version='2.2.3',
+ version='2.2.4',
description='ARIBA: Antibiotic Resistance Identification By Assembly',
packages = find_packages(),
package_data={'ariba': ['test_run_data/*']},
@@ -65,7 +65,7 @@ setup(
'dendropy >= 4.1.0',
'pyfastaq >= 3.12.0',
'pysam >= 0.8.1',
- 'pymummer>=0.6.1',
+ 'pymummer>=0.8.1',
],
license='GPLv3',
classifiers=[
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ariba.git
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