Add -l 15 to fermilite assemblies

sanger-pathogens · Jul 28, 2016 · efc2b23 · efc2b23
1 parent c2d142a
commit efc2b23
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Showing 2 changed files with 5 additions and 4 deletions.
diff --git a/ariba/tests/cluster_test.py b/ariba/tests/cluster_test.py
@@ -184,12 +184,12 @@ def test_full_run_ok_presence_absence(self):
         c.run()
 
         expected = [
-            'presence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.scaffold.1\t158\t17.4\t1\tSNP\tp\tA10V\t1\tA10V\tNONSYN\t28\t28\tC\t83\t83\tT\t22\t.\t22\tpresence_absence1:1:0:A10V:.:Ref has wild, reads have variant so report\tGeneric description of presence_absence1',
-            'presence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.scaffold.1\t158\t17.4\t0\t.\tp\t.\t0\t.\tSYN\t53\t53\tT\t108\t108\tC\t32\t.\t32\t.\tGeneric description of presence_absence1',
+            'presence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.scaffold.1\t213\t15.0\t1\tSNP\tp\tA10V\t1\tA10V\tNONSYN\t28\t28\tC\t83\t83\tT\t22\t.\t22\tpresence_absence1:1:0:A10V:.:Ref has wild, reads have variant so report\tGeneric description of presence_absence1',
+            'presence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.scaffold.1\t213\t15.0\t0\t.\tp\t.\t0\t.\tSYN\t53\t53\tT\t108\t108\tC\t32\t.\t32\t.\tGeneric description of presence_absence1',
 
-            'presence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.scaffold.1\t158\t17.4\t1\tSNP\tp\tR3S\t0\t.\t.\t7\t9\tC;G;C\t62\t64\tC;G;C\t18;17;17\t.;.;.\t18;17;17\tpresence_absence1:1:0:R3S:.:Ref and assembly have wild type\tGeneric description of presence_absence1',
+            'presence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.scaffold.1\t213\t15.0\t1\tSNP\tp\tR3S\t0\t.\t.\t7\t9\tC;G;C\t62\t64\tC;G;C\t18;17;17\t.;.;.\t18;17;17\tpresence_absence1:1:0:R3S:.:Ref and assembly have wild type\tGeneric description of presence_absence1',
 
-            'presence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.scaffold.1\t158\t17.4\t1\tSNP\tp\tI5A\t1\t.\t.\t13\t15\tG;C;G\t68\t70\tG;C;G\t18;20;20\t.;.;.\t18;20;20\tpresence_absence1:1:0:I5A:.:Ref and reads have variant so report\tGeneric description of presence_absence1',
+            'presence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.scaffold.1\t213\t15.0\t1\tSNP\tp\tI5A\t1\t.\t.\t13\t15\tG;C;G\t68\t70\tG;C;G\t18;20;20\t.;.;.\t18;20;20\tpresence_absence1:1:0:I5A:.:Ref and reads have variant so report\tGeneric description of presence_absence1',
         ]
 
         self.assertEqual(expected, c.report_lines)

diff --git a/third_party/fermi-lite-0.1/fml-asm_ariba.cpp b/third_party/fermi-lite-0.1/fml-asm_ariba.cpp
@@ -143,6 +143,7 @@ int assemble(char *readsFile, char *fastaOut, char* logfileOut)
     bseq1_t *seqs;
     fml_opt_init(&opt);
     opt.max_cnt = 10000;
+    opt.min_asm_ovlp = 15;
     std::vector<unsigned short> minCounts;
     minCounts.push_back(4);
     minCounts.push_back(8);