replacing uses of deprecated class SAMFileReader

[lbergelson]

Replacing all references to SAMFileReader, this is a long deprecated htsjdk class that's been replaced by SamReader.

[AmplabJenkins]

Can one of the admins verify this patch?

[fnothaft]

Awesome, thanks @lbergelson! I will take a look at this later today.

[fnothaft]

Jenkins, test this please.

[AmplabJenkins]

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1552/
Test PASSed.

[fnothaft]

This looks good to me, but there's a couple of small style nits (mostly import ordering stuff, we're picky). I'll clean those up. Thanks for making the upgrade pass @lbergelson!

[lbergelson]

Ah, sorry about the import stuff. My IDE did some automatic import shuffling I think.

[fnothaft]

Ah, sorry about the import stuff. My IDE did some automatic import shuffling I think.

Oh, no worries! It's a pretty small bit of cleanup.

[lbergelson]

I can do a quick fix up of them if you'd like, or if it's easier I'll leave it to you.

[fnothaft]

I can do a quick fix up of them if you'd like, or if it's easier I'll leave it to you.

No sweat; I've got it 75% done already.

[fnothaft]

I've cleaned up the little import nits in #1236. Thank you @lbergelson for the patches!

[lbergelson]

Thank you!