Re: [galaxy-dev] Sam2interval.py bug
The read_name has been implemented as well. Thanks, K On Wed, Aug 24, 2011 at 1:15 PM, Kanwei Li wrote: > Hi Shaun, > > Thanks for reporting this, I have just committed the fix. I will let you > know if we add the read_name to the truncated output. > > -K > > > On Tue, Aug 2, 2011 at 6:54 AM, SHAUN WEBB wrote: > >> >> Hi, I've noticed a bug in sam2interval.py. >> >> There are a few indentation errors in the final lines of code. I think >> there should be an indent after: >> >>if not ref_name == '*': >> >> And this whole if statement should be included in the for loop above. >> >> >> Also, would you be able to add read_name to the truncated output (when not >> printing all fields). This makes downstream analysis a lot easier, e.g. >> looking at reads that map multiple times. >> >> Thanks >> Shaun Webb >> >> -- >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. >> >> >> __**_ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> >> http://lists.bx.psu.edu/ >> > > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Sam2interval.py bug
Hi Shaun, Thanks for reporting this, I have just committed the fix. I will let you know if we add the read_name to the truncated output. -K On Tue, Aug 2, 2011 at 6:54 AM, SHAUN WEBB wrote: > > Hi, I've noticed a bug in sam2interval.py. > > There are a few indentation errors in the final lines of code. I think > there should be an indent after: > >if not ref_name == '*': > > And this whole if statement should be included in the for loop above. > > > Also, would you be able to add read_name to the truncated output (when not > printing all fields). This makes downstream analysis a lot easier, e.g. > looking at reads that map multiple times. > > Thanks > Shaun Webb > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > > __**_ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Sam2interval.py bug
Hi, I've noticed a bug in sam2interval.py. There are a few indentation errors in the final lines of code. I think there should be an indent after: if not ref_name == '*': And this whole if statement should be included in the for loop above. Also, would you be able to add read_name to the truncated output (when not printing all fields). This makes downstream analysis a lot easier, e.g. looking at reads that map multiple times. Thanks Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
