Allow percent id on burst.

knights-lab · Sep 8, 2017 · 08b7d5f · 08b7d5f
1 parent 3e406c8
commit 08b7d5f
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/shogun/aligners/burst_aligner_best.py b/shogun/aligners/burst_aligner_best.py
@@ -24,7 +24,7 @@ def align(self, infile, outdir, align=True):
 
         #TODO: pie chart and coverage
         if align:
-            proc, out, err = burst_align_best(infile, self.outfile, self.database, accelerator=self.accelerator, shell=self.shell, threads=self.threads)
+            proc, out, err = burst_align_best(infile, self.outfile, self.database, accelerator=self.accelerator, shell=self.shell, threads=self.threads, percent_id=self.percent_id)
         else:
             proc, out, err = (None, None, None)
         if self.post_align:

diff --git a/shogun/wrappers/burst_wrapper.py b/shogun/wrappers/burst_wrapper.py
@@ -9,7 +9,7 @@
 from shogun.utils import run_command
 
 
-def burst_align_best(input_fp, output_fp, burst_db_prefix, accelerator=False, threads=1, shell=False):
+def burst_align_best(input_fp, output_fp, burst_db_prefix, accelerator=False, threads=1, shell=False, percent_id=.98):
     """
     :param input_fp:
     :param output_fp:
@@ -33,6 +33,7 @@ def burst_align_best(input_fp, output_fp, burst_db_prefix, accelerator=False, th
         '--threads', str(threads),
         '--mode', 'BEST',
         '--npenalize',
+        '--id', str(percent_id),
         '--forwardreverse'
     ]