moving the code from picard to htsjdk

[lindenb]

Hi, I'm currently moving my code from picard1.100 to htsjdk. So far I cannot see how I should now map those 'old' classes:

• PicardException
• net.sf.samtools.cmdline.*

any hint ?
Thanks.

[nh13]

• PicardException was in net.sf.picard, so you can continue to use it if you want by including the picard API (https://github.com/broadinstitute/picard/). Otherwise I would recommend SAMException.
• net.sf.samtools.cmdline did not exist (see http://sourceforge.net/p/picard/code/HEAD/tree/trunk/src/java/net/sf/samtools/), perhaps you are thinking of net.sf.picard.cmdline

I think your main confusion was that picard was split into two: picard and htsjdk, with net.sf.picard.* staying in picard, while net.sf.samtools.* and org.* going into htsjdk, albeit with package names renamed. Some classes from net.sf.picard were moved into htsjdk.