Merge pull request #31 from martinghunt/master

Spades use untrusted-contigs
sanger-pathogens · Jul 14, 2015 · e6ee55c · e6ee55c
2 parents 8b5b95a + 21e18e4
commit e6ee55c
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Showing 4 changed files with 4 additions and 4 deletions.
diff --git a/ariba/cluster.py b/ariba/cluster.py
@@ -289,7 +289,7 @@ def _assemble_with_spades(self, unittest=False):
             '-o', self.assembler_dir,
             '-k', str(self.assembly_kmer),
             '--threads', str(self.threads),
-            '--trusted-contigs', self.gene_fa,
+            '--untrusted-contigs', self.gene_fa,
         ])
         if self.spades_other is not None:
             cmd += ' ' + self.spades_other

diff --git a/ariba/common.py b/ariba/common.py
@@ -1,7 +1,7 @@
 import sys
 import subprocess
 
-version = '0.4.0'
+version = '0.4.1'
 
 def syscall(cmd, allow_fail=False, verbose=False):
     if verbose:

diff --git a/ariba/faidx.py b/ariba/faidx.py
@@ -13,7 +13,7 @@ def write_fa_subset(seq_names, infile, outfile, samtools_exe='samtools', verbose
         common.syscall(' '.join([
             samtools_exe + ' faidx',
             infile,
-            name,
+            '"' + name + '"',
             '>>', outfile
         ]))
 
diff --git a/setup.py b/setup.py
@@ -7,7 +7,7 @@
 
 setup(
     name='ariba',
-    version='0.4.0',
+    version='0.4.1',
     description='ARIBA: Antibiotic Resistance Identification By Assembly',
     packages = find_packages(),
     author='Martin Hunt',