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Make additional files output by SamToFastq when using read groups be fastqsanger format instead of just fastq.

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This commit is contained in:
Daniel Blankenberg
2012-01-25 12:11:27 -05:00
parent 4e13241036
commit 5b8845fae6
1 changed files with 2 additions and 2 deletions
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tools/picard/picard_SamToFastq_wrapper.py
+2 -2
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@@ -80,13 +80,13 @@ def __main__():
shutil.move( os.path.join( tmp_dir, filename ), fastq_1_name )
fastq_1_name = None
else:
shutil.move( os.path.join( tmp_dir, filename ), os.path.join( options.new_files_path, 'primary_%s_%s - 1_visible_fastq' % ( file_id_1, filename[:-len( '_1.fastq' )] ) ) )
shutil.move( os.path.join( tmp_dir, filename ), os.path.join( options.new_files_path, 'primary_%s_%s - 1_visible_fastqsanger' % ( file_id_1, filename[:-len( '_1.fastq' )] ) ) )
elif filename.endswith( '_2.fastq' ):
if fastq_2_name:
shutil.move( os.path.join( tmp_dir, filename ), fastq_2_name )
fastq_2_name = None
else:
shutil.move( os.path.join( tmp_dir, filename ), os.path.join( options.new_files_path, 'primary_%s_%s - 2_visible_fastq' % ( file_id_2, filename[:-len( '_2.fastq' )] ) ) )
shutil.move( os.path.join( tmp_dir, filename ), os.path.join( options.new_files_path, 'primary_%s_%s - 2_visible_fastqsanger' % ( file_id_2, filename[:-len( '_2.fastq' )] ) ) )
cleanup_before_exit( tmp_dir )