Add --output-orphaned option to split-paired-reads.py#1164
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This should fix #847, right? |
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@camillescott may I snarf this? |
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ping @camillescott |
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Taking it and making it my own. |
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LGTM |
…option Conflicts: scripts/split-paired-reads.py
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…option Conflicts: scripts/split-paired-reads.py
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Update - removed filename option with -0, since was ambiguous.
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Ready for review @mr-c @bocajnotnef @luizirber |
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Fixes #847. |
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Can you indent this to match your name?
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Why not use args.output_orphaned everywhere you check allow_orphans?
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On Tue, Aug 04, 2015 at 09:52:19AM -0700, Michael R. Crusoe wrote:
@@ -128,47 +131,48 @@ def main():
# Use default filename created above
fp_out2 = get_file_writer(open(out2, 'wb'), args.gzip, args.bzip)
put orphaned reads here, if -0!
- allow_orphans = False
Why not use
args.output_orphanedeverywhere you checkallow_orphans?
It's partly a leftover of some now-removed logic that permitted -0 without
a filename, but what made me keep it in was this code:
require_paired=not allow_orphans
which I think would be uglier and less clear if it was
not args.output_orphaned. What do you think?
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I'm okay with not args.output_orphaned
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On Tue, Aug 04, 2015 at 03:54:24PM -0700, Michael R. Crusoe wrote:
@@ -128,47 +131,48 @@ def main():
# Use default filename created above
fp_out2 = get_file_writer(open(out2, 'wb'), args.gzip, args.bzip)
put orphaned reads here, if -0!
- allow_orphans = False
I'm okay with
not args.output_orphaned
That doesn't address "here's my reasoning, what do you think" but I'll give
it a whirl ;)
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Otherwise, this LGTM |
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Add --output-orphaned option to split-paired-reads.py
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Great, thanks! |
Currently, so far as I can tell, there's no way to both split paired reads into .1 and .2 files while also outputting orphans to their own file without doing messy pipe stuff. This adds that feature to split-paired-reads.py with an extra command line option.