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correct indentation

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This commit is contained in:
Ignacio
2016-11-16 20:53:41 +01:00
committed by mvdbeek
parent 953ee32599
commit 5bb86a3b68
1 changed files with 8 additions and 9 deletions
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lib/galaxy/datatypes/converters/sam_to_bam.py
+8 -9
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@@ -20,17 +20,16 @@ def cleanup_before_exit( tmp_dir ):
if tmp_dir and os.path.exists( tmp_dir ):
shutil.rmtree( tmp_dir )
def getSamtoolsVersion():
cmd = 'samtools --version'
proc = subprocess.Popen( args=cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True )
stdout, stderr = proc.communicate()
if proc.returncode:
sys.stderr.write(stderr)
return None
sys.stderr.write(stderr)
return None
else:
return stdout.split("\n")[0].split()[-1]
return stdout.split("\n")[0].split()[-1]
def __main__():
@@ -66,11 +65,11 @@ def __main__():
sorted_stderr_filename = os.path.join( tmp_dir, 'sorted.stderr' )
sorting_prefix = os.path.join( tmp_dir, 'sorted_bam' )
# samtools changed sort command arguments (starting from version 1.3)
samtools_version = LooseVersion(getSamtoolsVersion())
if samtools_version < LooseVersion('1.3'):
cmd = 'samtools sort -o "%s" "%s" > "%s"' % ( unsorted_bam_filename, sorting_prefix, output_filename )
samtools_version = LooseVersion(getSamtoolsVersion())
if samtools_version < LooseVersion('1.3'):
cmd = 'samtools sort -o "%s" "%s" > "%s"' % ( unsorted_bam_filename, sorting_prefix, output_filename )
else:
cmd = 'samtools sort -T "%s" "%s" > "%s"' % ( sorting_prefix, unsorted_bam_filename, output_filename )
cmd = 'samtools sort -T "%s" "%s" > "%s"' % ( sorting_prefix, unsorted_bam_filename, output_filename )
proc = subprocess.Popen( args=cmd, stderr=open( sorted_stderr_filename, 'wb' ), shell=True, cwd=tmp_dir )
return_code = proc.wait()