Pysam 0.13 compatibility fix

[pkMyt1]

As you know, Pysam 0.13 is a code breaking update. There are some nice changes to the API that I wanted to use in my pipeline. The fix for Connor is in the def build_writer() function;

    hd = input_bam.header # rename the header variable in this line.
    header = hd.to_dict() # add this line

[cgates]

Thanks, pkMyt1 - I will have a look and see if we can extend support to 0.13. Are you currently blocked?

[pkMyt1]

What do you mean by “blocked?” I made the fix on my local copy an I am running it right now. If you need to maintain backwards compatibility my fix will not work. According to the lead pysam developer there are major API changes planned. Sent from Mail for Windows 10 From: Chris Gates Sent: Wednesday, January 10, 2018 10:39 AM To: umich-brcf-bioinf/Connor Cc: Dennis Simpson; Author Subject: Re: [umich-brcf-bioinf/Connor] Pysam 0.13 compatibility fix (#4) Thanks, pkMyt1 - I will have a look and see if we can extend support to 0.13. Are you currently blocked? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

[cgates]

I wanted to confirm you have a working solution and are not waiting on me. Yes, we need to maintain some backwards compatibility so I will see how tricky it will be to support both.
All is well. Thanks.