Move makeSAMRecord (from googlegenomics/gatk-tools-java) to ReadConverter

[davidadamsphd]

ReadConverter.makeRead takes a SamRecord and produces a model read. I think the reverse process should also live in this file (or at least near this file in this repo).

I'll do the PR if there is agreement on this change. (This change is a request from the GATK team at the Broad)

[deflaux]

@davidadamsphd If this is reusable code for both dataflow-java and gatk-tools-java, consider placing it in utils-java instead. I'm not familiar with the details though. @iliat What do you think?

[pgrosu]

There also seems to be some duplication between utils-java and ReadConverter as well. Below is basically the same code duplicated in both places:

ReadConverter.java from dataflow-java

ReadUtils.java in utils-java

It might help to have them in one place as Nicole suggested.

Have a great weekend everyone!
Paul

[davidadamsphd]

ping @iliat. @pgrosu, I'm happy to also move those too. @deflaux, what do you think?

[deflaux]

sounds great! Its always joyful to delete obsolete or redundant code :-)

[pgrosu]

@davidadamsphd Less is more ;)

Thanks,
~p