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Forgot to import amplian

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1 parent f42121f commit b9c2a76b6210c80e9d64d82e24ee02aaa6d7e8c9 @ozagordi committed
Showing with 3 additions and 2 deletions.
  1. +3 −2 shorah.py
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5 shorah.py
@@ -78,6 +78,7 @@ def run_child(exe_name, arg_string):
import dec
import mm
import snv
+ import amplian
# parse command line
optparser = optparse.OptionParser()
@@ -125,8 +126,8 @@ def run_child(exe_name, arg_string):
if options.p:
# amplicon_mode, run only diri_sampler and snv.py
- amplian.main()
-
+ amplian.main(in_bam=options.b, in_fasta=options.f,
+ max_coverage=options.x, alpha=options.a)
if not os.path.exists('snv/SNV.txt'):
# 1. run dec.py
sholog.debug('running dec.py')

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