recal 2-step

[oabio...@gmail.com]

I was wondering if it would be possible to have bamutils recal process an input file in 2-real steps, for instance when given a recal file generated already. This could work when you have a stream into bamutils to read the file, and output a recal table, only to use it later on when you are again reading a stream. I am thinking of ways to use streams as much as possible in pipelines, so if we can separate the two steps, we can implement them separately, during the workflow. So does that make sense or not?

Thank you

[Mary Kate Wing]

Having the option to split recalibration into 2 steps is a good suggestion.  It is not currently implemented, but it should not be too hard to add.  I had been considering adding this option, but had not yet had the chance or need.  

If this is something you need, I could probably add it in the next few weeks.  

Mary Kate 

On Thu, Sep 29, 2016 at 11:35 AM, <oabio...@gmail.com> wrote:

I was wondering if it would be possible to have bamutils recal process an input file in 2-real steps, for instance when given a recal file generated already. This could work when you have a stream into bamutils to read the file, and output a recal table, only to use it later on when you are again reading a stream. I am thinking of ways to use streams as much as possible in pipelines, so if we can separate the two steps, we can implement them separately, during the workflow. So does that make sense or not?

Thank you

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