replacing uses of deprecated class SAMFileReader #1235

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lbergelson commented Nov 2, 2016

Replacing all references to SAMFileReader, this is a long deprecated htsjdk class that's been replaced by SamReader.

removing usages of deprecated class SAMFileReader
this is necessary to be compatible with htsjdk 2.7.0+
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Can one of the admins verify this patch?

Can one of the admins verify this patch?

@lbergelson lbergelson referenced this pull request in broadinstitute/gatk Nov 2, 2016

Merged

Update htsjdk to 2.7.0 #2247

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

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fnothaft commented Nov 2, 2016

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

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Jenkins, test this please.

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fnothaft commented Nov 2, 2016

Jenkins, test this please.

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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.

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.

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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!

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fnothaft commented Nov 2, 2016

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!

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

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lbergelson commented Nov 2, 2016

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

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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.

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fnothaft commented Nov 2, 2016

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.

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

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lbergelson commented Nov 2, 2016

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

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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.

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fnothaft commented Nov 2, 2016

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.

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

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fnothaft commented Nov 2, 2016

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

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@lbergelson lbergelson deleted the lbergelson:lb_remove_SAMFileRader branch Nov 2, 2016

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Thank you!

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lbergelson commented Nov 2, 2016

Thank you!

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